Research to go psa (rs)

Research to Go – Production Systems Animals

A summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Table of Contents Effect of targeted selective treatment at lambing on Haemonchus burdens on Ontario sheep farms with anthelmintic resistance................................................................................................................................. 0 Evaluating Genetic and Epigenetic Regulation of the Bovine Immune System to Improve Dairy Health and Wellbeing ...................................................................................................................................................... 2 Identifying pigs with disease resistance robustness that can be fed low cost reduced animal-protein diets without compromising health and performance.......................................................................................... 4 Genome-wide identification of genetic defects in innate disease resistance genes of swine ..................... 7 Antibody responses and modulation of fecal bacterial shedding during subclinical Johne’s disease in calves........................................................................................................................................................... 10 Uncovering new applications for probiotics and their mode of action in dairy cow production systems . 12 Responsible antibiotic use on Ontario dairy farms – approaches, outcomes and attitudes ...................... 15 Immune response of chickens for enhanced protection against viral infections ....................................... 17 Optimizing Lighting for Precision Broiler Breeder Feeding ......................................................................... 20 Validation of a new LED light bulb designed for the egg-laying industry ................................................... 22 Expansion and validation of genetic marker set for boar taint ................................................................. 24 Better control of Bacterial Cold Water Disease in farmed rainbow trout by the development of an effective Flavobacterium psychrophilum vaccine ...................................................................................... 26 Stimulating innate immune responses to prevent bacterial pneumonia in cattle ..................................... 28 Can horses modulate their mechanical interaction with the ground surface to mitigate potentially harmful properties of the surface? ............................................................................................................. 30 Reducing dietary protein costs while maximizing milk production in dairy cows ...................................... 33 Understanding and controlling necrotic enteritis in broiler chickens ........................................................ 36 Toward commersialization of a novel fermented product for enhancing intestine development and productivity of early-weaned pigs .............................................................................................................. 38 Nitrogen (N) nutrition for growing pigs, to increase flexibility in feed formulation, reduce N losses into the environment and improve gut health .................................................................................................. 40 Precision feeding of gestating sows using electronic sow feeders to reduce environmental impact and feed costs, while improving sow welfare and productivity ........................................................................ 43 Controlled fermentation and steeping to enhance the feeding value of co-products for pigs .................. 46 Patterns of nitrogen retention and nutrient utilization efficiency in gestating and lactating sows........... 48 Combating infertility in mares .................................................................................................................... 50 Prevalence of Enteric Disease Agents in Ontario Commercial Rabbits: Zoonotic Potential and Impact on Animal Health ............................................................................................................................................. 53

The design and analysis of experiments and observational studies on infectious disease spread in the livestock industries. .................................................................................................................................... 56 Complex mathematical and statistical modelling of between-farm disease transmission in the Ontario swine industry. ............................................................................................................................................ 59 Characterizing Streptococcus suis from clinical cases and healthy-carrier pigs ......................................... 62 Molecular pedigree analysis for the establishment of an elite rainbow trout broodstock with maximal growth and spawn-timing performance ..................................................................................................... 65 Enhancing the efficacy of poultry vaccines using innate immune adjuvants ............................................. 68 Probiotics for enhanced poultry health ...................................................................................................... 70 Best Management Practices for Control of Nuisance Flies in Poultry Production ..................................... 73 Genomic applications in the feedlot to improve beef quality and efficiency............................................. 76 Investigation of the prevalence of heart lesions in market hogs that die in-transit and testing for a genetic association...................................................................................................................................... 78 The effects of alternative feeding strategies for broiler breeders ............................................................. 80 Influence of rearing and housing of parent stock on offspring's phenotype in layer strains ..................... 83 Strategies for early identification and prevention/treatment approaches to metabolic disease in dairy cows ............................................................................................................................................................ 86 Improving cow health and enhancing nutritional quality of milk through knowledge of dairy cow behaviour .................................................................................................................................................... 88 Meeting the growing demand for Ontario Water Buffalo meat and milk products through the use of reproductive biotechnology........................................................................................................................ 91 Within-herd dynamics of influenza in nursery herds and effective methods for elimination ................... 93 Development of risk-based and consequence-based approaches to surveillance in swine populations using PRRS virus as a model ........................................................................................................................ 95

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Effect of targeted selective treatment at lambing on Haemonchus burdens on Ontario sheep farms with anthelmintic resistance UofG2011-1068

Funding Program

Production Systems Animals sheep, parasites, anthelmintic resistance, closantel Andrew Peregrine University of Guelph 01/05/2012 End Date

OMAFRA - U of G Research

30/04/2015

Abstract Haemonchus contortus is increasingly being recognised as a significant constraint to sheep production on pasture in Ontario. Recent work in the province has demonstrated a high prevalence of resistance in this parasite to the two most commonly used anthelmintics in sheep, i.e. resistance to ivermectin and fenbendazole has been demonstrated on >90% of tested farms. Improved control strategies are therefore urgently required. This project will define the parameters that influence the infectivity of H. contortus on pasture and thus help enhance control programs for the parasite. In addition, via a proof of concept study, the ability of closantel (a narrow-spectrum anthelmintic with activity against H. contortus, not previously used in Canada) to control drug-resistant H. contortus infections will be assessed; two treatment strategies for ewes at lambing will be evaluated. The resultant data should help generate novel strategies for controlling drug-resistant infections and for reducing anthelmintic use on sheep farms, thus contributing to more prudent use of anthelmintics in Ontario flocks. The data may also assist in the approval of a new anthelmintic for use in sheep in Canada.

Objectives 1. To determine the influence of temperature and humidity on the rate of development of H. contortus eggs to the infective larval stage and associations with anthelmintic resistance.

2. To determine the efficacy of closantel against H. contortus infections that are resistant to ivermectin and fenbendazole.

3. To generate preliminary information on whether selective treatment of ewes with closantel at lambing controls H. contortus on farms as effectively as whole flock treatment at lambing.

0 For more information, please visit www.uoguelph.ca/research/PSA

Benefits The work will benefit the sheep industry because it will: 1. Generate information on environmental parameters that influence the rate of development of H. contortus from egg to the infective stage on pasture on Ontario sheep farms with anthelmintic resistance.

This will help producers and veterinarians rationalise control programs for this parasite.

2. Generate information on the efficacy of closantel against drug-resistant H. contortus. With the support of Elanco Animal Health (the manufacturer of closantel), this may result in the approval of an anthelmintic for controlling parasite infections that are resistant to ivermectin and/or fenbendazole.

3. Generate information on the extent to which selective treatment with closantel at lambing can be used to control anthelmintic-resistant H. contortus infections and haemonchosis on farms. Information on the impact of selective treatment at lambing is also applicable to other anthelmintics when administered in the same manner at lambing, when parasites are drug susceptible. As indicated in the literature review, such treatment protocols should slow the development of anthelmintic resistance. They should also reduce anthelmintic drug costs for farms.

4. Help reduce losses due to gastrointestinal parasitism, thereby improving farm productivity, profitability and animal welfare.

Co-Funder List • • • • •

Ontario Sheep Marketing Agency Elanco Animal Health University of Guelph Ontario Sheep Marketing Agency NSERC-CRD

Team Member 1. Dr. John VanLeeuwen Collaborators 2. Mr. Jacob Avula

Non-UofG Faculty/Research Scientist

University of Guelph Technician

3. Dr. Andria Jones-Bitton University of Guelph UofG Faculty (On Campus) 4. Dr. Paula Menzies

University of Guelph Collaborating Researcher

5. Dr. Trisha Westers

Collaborators

UofG Graduate Student

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Evaluating Genetic and Epigenetic Regulation of the Bovine Immune System to Improve Dairy Health and Wellbeing UofG2012-1294

Funding Program

OMAFRA - U of G Research

Production Systems Animals Immunogenetics, Epigenetics, Dairy Health, Immunity Bonnie Mallard University of Guelph 30/05/2013 End Date 31/05/2016

Abstract The immune system is designed to control infectious disease and individuals with robust and appropriate immune responses have health advantages. At the University of Guelph, researchers have developed a patented test system to identify animals with a balanced and enhanced or "High Immune Response" (HIR).

HIR dairy cattle have been shown to be at lower risk of diseases, including mastitis, the mostly costly disease of dairy cows. HIR animals are expected to be healthier, shed less pathogenic organisms and require less therapeutic intervention, including antibiotics, thereby improving milk and meat quality. The next critical steps to improve understanding of the HIR technology is to perform genome-wide association studies to determine potential genetic markers associated with the various IR phenotypes. Further, this study will determine differences in key immunological mechanisms, including innate mechanisms, as well as epigenetic influences on these immune traits. Finally, it is also relevant to evaluate potential value added milk quality effects of HIR cows, such as bioactive peptides, to establish any added human health benefits of milk from HIR cows. Results of this study are expected to provide novel insight into the potential inclusion of immune response traits in genetic selection indices to improve inherent animal health.

Objectives Main Goal: Evaluate the genetic and epigenetic regulation of the bovine immune system by obtaining the immune response (IR) phenotypes and genotypes of ~ 850 Holstein dairy cows/year that are part of the National Health Project. To tackle genomic and health aspects of the project we will work with the Canadian Dairy Network (CDN) as they co-ordinate genomic testing of 10,000 cows (known as the ten thousand cow project). This is intended to improve disease resistance by expanding our understanding of immunological and genetic mechanisms associated with high, average and low immune responder phenotypes. This is also expected to extend the use of the High Immune Response technology into novel applications, such as healthful dairy foods and genomic evaluations for immune response traits.

2 For more information, please visit www.uoguelph.ca/research/PSA

Cows will be classified as High, Average or Low immune responders and associations with disease investigated.

Benefits Animal Production Systems: This research on genetic and epigenetic regulation of the bovine immune system in the context of high and low immune responder dairy cows is expected to produce animal health benefits via improved understanding of bovine immunity and disease resistance. In addition, genetic technology advances are anticipated by integrating genomic information on immune response into existing genomic profiles on dairy cattle. The genome-wide association study described here also is expected to identify additional genetic markers associated with improved animal health.

Dairy producers will gain by having healthier animals with reduced disease occurrence and severity. This will providing savings on disease costs, milk loss and treatment costs.

Canadian breeding companies, such as the Semex Alliance, will gain by being able to market bull semen nationally and internationally from high immune responders with superior health attributes. Using genomic approaches to do this gives additional cost savings and accuracy to the selection of healthier animals.

The High Immune Response technology is a patented University of Guelph method to identify livestock with genetically superior health attributes. Improved understanding of the mechanisms of action associated with improved immune response using this method is likely to lead to additional applications for the technology that will benefit agri-food business.

Co-Funder List •

Canadian Dairy Network

Team Member 1. Ms. Marlene Paibomesai

University of Guelph

Graduate Student

2. Mrs. Lauraine Wagter-Lesperance UoG

Graduate Student

3. Ms. Kelly Flemming

University of Guelph

Graduate Student

4. Dr. Mehdi emam

University of Guelph

Graduate Student

5. Dr. David Kelton

University of Guelph (internal) UofG Other

6. Dr. Filippo Miglior

University of Guelph

UofG Adjunct Faculty

7. Prof. Bonnie Mallard

University of Guelph

UofG Faculty (On Campus)

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Identifying pigs with disease resistance robustness that can be fed low cost reduced animal-protein diets without compromising health and performance UofG2013-1472

Funding Program

Production Systems Animals genetics, swine, health, nutrition Brandon Lillie University of Guelph 19/05/2014 End Date

OMAFRA - U of G Research

31/01/2018

Abstract Our experimental studies at the Arkell swine unit have shown that lower cost reduced animal-protein diets can be fed to nursery pigs without any negative impact on subsequent performance up to market weight as long as pigs do not become diseased. We have also identified several pig genotypes that are associated with growth rate and infectious disease resistance. We propose to investigate the application of lower animalprotein feed under various farm conditions, and to see if pigs with genotypes associated with infectious disease resistance perform better under these diets/conditions. Approximately thirteen hundreds pigs will be selected at farrowing on twelve farms. At weaning, pigs will be assigned to either a reduced animalprotein or a conventional nursery feed. The pigs will be weighed repeatedly between birth and marketing.

Blood and fecal samples will also be collected. Pigs will be monitored for occurrence of clinical and subclinical diseases, and genotyped for single nucleotide polymorphisms (SNPs) in innate disease resistance genes. This study will shed light on practical aspects of reduced animal-protein feeding under commercial conditions. It will also identify pigs that are genetically resistant against infectious diseases, and thus can be fed with lower animal-protein feed with no compromised health.

Objectives The overall objective is to evaluate the application of lower cost reduced animal-protein diets in nursery pigs under varied farm conditions and to investigate whether pigs with infectious disease resistance genotypes and robust immune responses can be fed with those diets with no consequent compromised health and growth performance.

The specific objectives: 1) To investigate whether nursery pigs fed with a lower cost reduced animal-protein under farm condition will be able to express compensatory growth during the grower-finisher phase, with no impact on days-tomarket and carcass quality

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2) To identify pig genotypes associated with immune function (cytokine response) and resistance to clinical and subclinical infectious diseases 3) To identify pig genotypes that relate to growth performance and carcass quality under commercial conditions 4) To investigate whether pigs with genotypes for robust immune response that are fed with lower cost reduced animal-protein rations will have satisfactory growth up to marketing Benefits This research will explore interactive effects of reduced animal-protein nursery diets and pig genotype on productivity and ability to deal with disease challenges up to market weight, under commercial conditions.

Previous work under controlled conditions showed that, when not faced with a disease challenge, nursery pigs can be fed a relatively inexpensive reduced animal-protein diet, and although they initially grow slowly, pigs undergo compensatory growth during the grower-finisher phase, without impacting days to market and carcass value. This results in major savings in feed costs of more than $2.50 per pig. For the swine industry to take advantage of these savings we need to improve the animal’s robustness as far as its ability to deal with environmental stressors such as infectious diseases. We have identified several single nucleotide polymorphisms (SNPs) and other biomarkers of pig growth and immune function that may be associated with disease susceptibility, but their relevance needs to be tested under different commercial environments.

It may be possible to select for animals that are more resistant to disease challenges and as a result can be fed with lower-cost reduced animal-protein rations without significant risk of having significant disease due to infections with microbial agents. If disease challenge is low, savings could be realized by using reduced animal-protein starter diets. Presence of disease or environmental stresses might make that strategy unworkable, but enhanced management and/or selection of more disease resistant animals may make it possible to overcome health challenges without using antibiotics or other expensive disease control measures. The benefits include production efficiencies for the producer as far as reduced feed costs and reduced economic losses to infectious disease. In addition, reductions in infectious disease occurrence and/or severity should improve animal welfare and reduce the requirement and use of antimicrobial therapeutics and thus reducing antimicrobial resistance associated with animal production. These result in an improved societal image of the swine industry thus strengthening that sector of the agriculture economy as well as having food safety-pork quality benefits.

Co-Funder List • • • • •

Ontario Pork Swine Innovation Pork: Canadian Swine Research and Development Cluster Canadian Centre for Swine Improvement Inc. Alliance Genetic Canada NSERC Collaborative Research and Development Grant

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Team Member 1. Dr. Kees de Lange

University of Guelph (internal)

UofG Faculty (On Campus) UofG Faculty (On Campus)

2. Dr. Robert Friendship University of Guelph 3. Dr. Brian Sullivan

Canadian Centre for Swine Improvement Non-UofG Collaborator

4. Dr. Mohsen Jafarikia

Canadian Centre for Swine Improvement Non-UofG Collaborator Non-UofG Collaborator

5. Mr. Dave Vandenbroek University of Guelph

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Genome-wide identification of genetic defects in innate disease resistance genes of swine UofG2011-1075

Funding Program

Production Systems Animals innate disease resistance, genetics, pigs Brandon Lillie University of Guelph 01/06/2012 End Date

OMAFRA - U of G Research

31/05/2015

Abstract Infectious diseases remain one of the most common and significant causes of production and economic losses in the swine industry despite extensive ongoing research characterizing the pathogens involved and investigating ways to prevent or ameliorate the impact of infections. It is a multifactorial problem, with various genetic and environmental influences. Currently, there are few genetic markers to assist selection for better disease resistance and growth performance. Within a herd, poor performing pigs may carry genetic defects in essential liver proteins involved in innate disease resistance that could contribute negatively to polygenic production traits. We previously identified genetic defects in several innate immune proteins that are more frequent in pigs with infectious diseases and some that decrease hepatic expression of these proteins. This project will utilize a genome wide approach to identify genetic defects that decrease constitutive hepatic expression of genes involved in innate disease resistance in pigs. The impact of identified genetic defects will be investigated, both on disease resistance and overall production. These results will generate candidates for genetic selection to increase innate disease resistance to common infectious pathogens of swine. This will result in a stronger Ontario pork industry, increased overall animal welfare and decreased antimicrobial use.

Objectives Main Goal: Identify genetic differences responsible for reduced production of innate immune factors required for resistance to common infectious diseases. Previously, we identified a small set of single nucleotide polymorphisms (SNPs) in innate immune proteins by investigating one gene at a time. Some of these SNPs are strongly associated with increased frequency of infectious diseases and some major infectious pathogens of pigs. Newly available porcine gene expression microarray technology and the recently-released porcine genome now allow us to use this successful discovery strategy in a genome-wide approach to identifying other genetic markers that are strongly associated with impaired disease resistance in pigs.

Objectives: 1)Identify novel gene polymorphisms that reduce the production of innate immune plasma proteins of pigs.

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2)Determine which of these variants are most associated with common production-limiting diseases of pigs.

3)Determine the impact of these polymorphisms on production under various farm practices.

Benefits Identifying genetic defects in innate immune genes should lead to the development of novel genetic markers for use in selection panels along with traditional parameters used in the pork industry. This could lead to the development of genetic lines with increased innate disease resistance thus increasing the value and competitiveness of Ontario breeding stock. For domestic producers, this should decrease production costs associated with impaired growth performance due to subclinical disease and loss of pigs to overt pathogen-associated disease and decrease costs associated with therapeutic antibiotic use while increasing overall animal welfare.

In addition to the economic benefits to the swine industry, Ontario and the rest of Canada would benefit from healthier pork production and superior animal breeding. Further, antimicrobial resistance is a significant problem in human medicine as well as in veterinary medicine. By increasing innate disease resistance, there would be a reduced requirement for antimicrobial use in swine production which would help reduce the overall levels of antibiotic resistance, particularly resistance associated with antibiotic use in livestock. These gene expression studies likely will provide a strategy by which researchers could also identify genetic alterations associated with other production traits. For example, the approach could be used to reveal genetically impaired expression in particular tissues of interest (e.g. intestine, lung, muscle, uterus, lymphoid) that could be further investigated in later studies and/or in collaboration with other researchers interested in genetics of disease resistance or production.

Finally, these studies are part of a larger research program examining the mechanisms of genetic regulation of innate immunity and disease resistance in animals. This project will also help characterize the molecular pathways involved in innate disease resistance. The way the liver switches from nutrient assimilation and growth to the synthesis and secretion of numerous defense proteins during stress of weaning and disease may provide better management strategies of pigs during periods of increased vulnerability to disease. In addition, further information about the way gene splice variation or inhibitory RNA regulate and/or impair functional activity of innate defense proteins might be relevant to variation in levels of other proteins.

Co-Funder List • • • • • •

Ontario Pork NSERC Ontario Veterinary College NSERC NSERC Canadian Centre for Swine Improvement Inc.

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Team Member 1. Dr. M. Anthony Hayes

University of Guelph

Collaborating Researcher

2. Dr. James Squires

University of Guelph

Collaborating Researcher

Dr. Jutta Hammermueller

University of Guelph

Technician

4. Dr. Heindrich Snyman

University of Guelph

Graduate Student

5. Dr. Mohsen Jafarikia

Canadian Centre for Swine Improvement

Industry Collaborator

6. Dr. Brian Sullivan

Canadian Centre for Swine Improvement

Industry Collaborator

7. Dr. Tim Blackwell

Ontario Ministry of Agriculture, Food and Rural Affairs

Collaborating Specialist

8. Dr. John Harding

University of Saskatchewan

University Researcher

3.

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Antibody responses and modulation of fecal bacterial shedding during subclinical Johne’s disease in calves UofG2011-1077

Funding Program

OMAFRA - U of G Research

Production Systems Animals paratuberculosis, johne's disease, bovine, immunology Brandon Plattner University of Guelph 15/06/2012 End Date 14/06/2015

Abstract Johne’s disease (JD) is an important intestinal disease of ruminants caused by the bacteria Mycobacterium avium subspecies paratuberculosis (Map). Treatment is ineffective and JD is invariably fatal after a lengthy subclinical period. Control programs aim to detect infections by measuring serum antibodies or bacteria shed in feces, and infected cattle are culled to reduce transmission. Early detection is thus crucial to disease control. The onset of fecal shedding precedes clinical disease by months/years, so failure to identify animals early is a major obstacle to control. Serum antibody and fecal shedding are prominent during late JD; however little is known regarding subclinical infection. We will characterize antibodies generated during subclinical JD to identify potential targets for improved early diagnostic tests. We will also determine how monensin influences fecal shedding and JD progression. This work will enhance disease control by earlier diagnosis or by reducing fecal shedding and limiting Map transmission potential.

Objectives 1: To characterize Map-specific serum antibody responses during subclinical intestinal JD, and to compare to serum antibodies in cows with naturally occurring JD. We will experimentally infect calves with Ontario clinical bovine Map strain (gc86, Dr Mutharia). We will characterize Map-specific serum antibodies from infected calves and compare temporally with development and progression of intestinal lesions.

Furthermore, we will compare antibody profiles of experimentally infected calves with those of naturally infected field clinical cases (identification of field cases supported by DFO grant to Dr Kelton).

2: To understand the in vivo effects of monensin during enteric Map infection. We will determine how administration of monensin during subclinical intestinal Map infection affects tissue colonization by Map and proliferation of Map within the intestine during early enteric infection. In addition, we will evaluate how monensin affects the frequency, persistence and magnitude of fecal Map shedding in calves with subclinical JD.

10 For more information, please visit www.uoguelph.ca/research/PSA

Benefits The current JD control program in Ontario and throughout the world focuses on strategies to limit Map transmission, and this is accomplished primarily through identification and culling of high-titre cows (HTC’s) from herds. HTC’s are generally considered to be in the late subclinical phase of the infection and they show no signs of clinical disease such as weight loss or diarrhea. It is currently unknown what percent of HTC’s eventually progress to clinical JD. Anecdotal data however suggests that fecal shedding of live Map by HTC’s has either already begun or will soon commence and this represents a significant source of infectious material and therefore elevates risk of Map transmission to susceptible herdmates. Though the highest level of fecal Map shedding occurs during clinical phases of this disease, it is generally thought that intermittent fecal shedding is initiated during early subclinical infection prior to development of abundant Map-specific antibodies in serum of infected animals.

Targeted investigation of subclinical enteric Map infection outlined in this proposal will lead to enhanced understanding of the pathophysiology and immunology of this devastating disease. Furthermore, our data is expected to significantly contribute to JD control and management strategies in Ontario in several specific areas. For the first objective, characterization of Map-specific serum antibody responses during early subclinical enteric Map infection will allow progress in our understanding of how these antibodies influence pathogen clearance, persistent latency and disease progression. In addition, characterization of Map-specific antibodies during subclinical intestinal infection is likely to result in discovery of unique antibody profiles with potential use as targets of novel and rapid immuno-assays capable of earlier JD diagnosis in infected animals. The second objective of this project seeks to understand how the ionophore monensin sodium affects Map growth and therefore Map-induced lesion progression or regression within the bovine intestinal tract. The proposal is collectively designed to improve the ability of veterinary diagnosticians and Ontario dairymen to manage JD in herds through development of improved diagnostic or therapeutic techniques to limit JD progression and/or transmission of live Map to susceptible herdmates.

Co-Funder List • •

Elanco Animal Health University of Guelph

Team Member 1. Dr. David Kelton University of Guelph (internal) Collaborating Researcher 2. Dr. Todd Duffield University of Guelph

Collaborating Researcher

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Uncovering new applications for probiotics and their mode of action in dairy cow production systems UofG2011-1088

Funding Program

Production Systems Animals dairy cattle probiotics rumen health Brian McBride University of Guelph 01/05/2012 End Date

OMAFRA - U of G Research

30/04/2015

Abstract The aim of the proposed research project is to determine whether supplementing probiotics to dairy cattle can improve health and performance. Two experiments will be conducted to test the effects of new strains of probiotics during 1) the periparturient period and during 2) the onset of ruminal acidosis. Feed intake and milk production responses will be measured in concert with blood metabolites and indicators of inflammation to assess improvements to health due to supplementation of probiotics. Furthermore, changes in the entire microbiome will be measured using metagenomic techniques (pyrosequencing).

Finally, the effect of supplementing probiotics on the health and barrier function of the rumen epithelium will be assessed via microscopy and the expression of inflammatory and cell tight junctions genes.

Collectively, the proposed research will be the most comprehensive examination of the effects of probiotics in dairy cattle and potentially lead to new applications for probiotics and improve performance in dairy production.

Objectives The four main objectives for this proposed research project are as follows: 1. To characterize the mode of action of commonly used probiotics to serve as a platform for the development of new technologies that can serve as replacements for antibiotics in dairy and ruminant production systems 2. To uncover biomarkers of metabolic status and inflammation in the rumen and blood during the transition period and during the onset of ruminal acidosis that are influenced by supplementation of probiotics 3. To determine how feeding probiotics during the transition period and the onset of ruminal acidosis changes rumen microbial populations 4. To determine how feeding probiotics during the transition period and the onset of ruminal acidosis alters rumen epithelial inflammation and barrier function

12 For more information, please visit www.uoguelph.ca/research/PSA

Benefits Key benefits of this research project include the following: 1. Finding alternatives to antibiotic-ionophores will benefit the dairy industry as a whole as consumer acceptance of dairy products and production practices will be improved. All the results from our research will serve as a platform for future probiotic research in ruminants.

2. The findings from this research will lead to the development of novel and safe nutritional technologies to enhance performance and health during the transition period and during ruminal acidosis. It has been estimated that a transition cow problem equates to a loss of $300-600 per lactation in North American production systems (Wallace et al., 1996). With regard to ruminal acidosis, it has been estimated to occur in 20% of North American lactating dairy cattle and equates to a loss of $400 per lactation (Plaizier et al., 2008). All findings from this research will be reported in the public domain; therefore, technologies developed from this research will be able to be implemented by all producers to improve production efficiency.

3. The understanding gained from this research may lead to the development of new probiotic products, ultimately creating new employment opportunities in sales and manufacturing in Canada.

4. This project encompasses the training of three postdoctoral fellows and two PhD students. These young professionals will learn cutting-edge techniques in metagenomics and molecular physiology, providing them with unique skills they will be able to apply in their future careers in agriculture.

5. This project will foster collaborations within the University of Guelph and OMAFRA. In addition, external collaboration will be developed with leaders in the field of immunology and gut health, (Dr. Matt Koci, North Carolina State University) and rumen microbiology (Dr. Andre-Denis Wright, University of Vermont).

6. The grant-in-aid provided by our private partners (AB Vista and Chs. Hansen) allows for the development of intellectual property that will ultimately be transferred to the University of Guelph. All results will be in the public domain and will serve as a platform for future probiotic research.

Plaizier, J.C., et al 2008. Vet.J. 176:21-31.

Wallace, R.L., et al 1996. J.DairySci. 79(Suppl.1):205.

Co-Funder List • • •

NSERC Chr. Hansen AB Mauri

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Team Member 1.

Collaborators

Collaborating Researcher

2.

Collaborators

Collaborating Researcher

3. Dr. Todd Duffield

University of Guelph

Collaborating Researcher

4. Dr. Tom Wright

Ontario Ministry of Agriculture, Food and Rural Affairs

Advisory

5. Dr. Ousama AlZahal

University of Guelph

Post Doctorate Fellow

6. Dr. Michael Steele

University of Guelph

Post Doctorate Fellow

Mr. Louis Dionissopoulos

University of Guelph

Graduate Student

8. Mr. Anne Laarman

University of Guelph

Graduate Student

9.

Collaborators

University Researcher

7.

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Responsible antibiotic use on Ontario dairy farms – approaches, outcomes and attitudes UofG2013-1622

Funding Program

OMAFRA - U of G Research

Production Systems Animals,Emergency Management dairy cattle antibiotics attitudes outcomes David Kelton University of Guelph 01/05/2014 End Date 30/04/2017

Abstract The recent Ontario Medical Association white paper entitled ‘When antibiotics stop working’ has brought the use of antibiotics in animal agriculture under scrutiny. Mastitis is the most costly disease of dairy cattle, and also the target for the greatest antibiotic use on dairy farms. The implementation of the Canadian Quality Milk (CQM) program has brought some standardization to recording of antibiotic use on dairy farms.

While producers are subject to CQM audits as part of the provincial inspection program administered by Dairy Farmers of Ontario, there has not been a formal evaluation of the quality or quantity of the treatment records, the outcomes associated with mastitis treatment and antibiotic use, nor the attitudes of dairy farmers towards treatment recording or outcome assessment. The objectives of this study are to address these issues and to identify differences in approaches and attitudes among three distinct groups, tie-stall farms, free-stall parlour milked farms and farms utilizing robotic milking, to identify common and unique challenges. The outcomes of this work will contribute to the development of more effective strategies for treatment outcome assessment with the ultimate goal of decreasing the inappropriate use of antibiotics through the evaluation and elimination of ineffective treatment protocols.

Objectives The goal is to increase understanding of the rationale, quantity and quality of antibiotic use for mastitis treatment and develop novel approaches to promote treatment and outcome recording in support of prudent antimicrobial use.

1. To use CQM treatment records to describe antibiotic use for the treatment of mastitis on Ontario dairy farms in terms of numbers and types of treatments, and compare use in tie-stall, free-stall parlour and freestall robot milked herds.

2. To determine how often, and from what source, pathogen is used in selecting a protocol, and verify that treatment is appropriate for the pathogen.

3. To determine how often outcomes (success/failure) of treatment are recorded, and in their absence, use existing SCC and retreatment data to estimate success.

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4. To investigate barriers to treatment and outcome recording to develop strategies that will support improved outcome assessment for more appropriate and prudent use of antibiotics.

Benefits The benefits from this research will accrue to the dairy producer community, the veterinary community and the public under both the Production Systems Animal and Emergency Management themes.

Under Production Systems Animal this work will address the first Animal Health Priority (“Develop alternative methods that effectively and economically reduce the risk of infectious disease”) by critically evaluating the mastitis treatment protocols that are in place on all Ontario dairy farms. Control of infectious disease is best accomplished by prevention of infection and rapid elimination of infection if it does occur. If we find that these protocols are effective, then we will be confident that what we are doing is in fact effectively controlling mastitis risk with the prudent and responsible use of antibiotics. If we find that some of the protocols are ineffective, we can then move to addressing the deficiencies, why they occur and if necessary developing alternative methods for mastitis treatment and control, including increasing the focus on new and innovative prevention strategies and diagnostic technologies. Outcome assessment of treatment protocols is lacking in most animal and human therapeutic plans, and this work will move the dairy industry forward in the routine implementation of outcome assessment. By investigating the degree to which treatment outcome is assessed on Ontario dairy farms, identifying barriers to effective outcome assessment and then developing strategies to promote it, this work will increase the efficacy of mastitis treatment as well as potentially reducing the amount of antibiotic used in protocols that are deemed to be not effective.

The proposed studies will also address the second Animal Health priority, Animal Welfare, in that mastitis is known to cause pain, and thus prompt and effective treatment of clinical mastitis is an important strategy to mitigate pain in lactating dairy cows. By identifying ineffective treatment protocols, and either modifying or replacing them with more effective protocols, improved dairy cattle welfare will be achieved.

Co-Funder List • •

Dairy Farmers of Ontario CanWest DHI

Team Member 1. Dr. Ann Godkin

Ontario Ministry of Agriculture, Food and Rural Affairs UofG Adjunct Faculty

2. Dr. Kerry Lissemore University of Guelph

UofG Faculty (On Campus)

3. Dr. Jason Coe

University of Guelph

UofG Faculty (On Campus)

4. Dr. David Leger

Laboratory for Foodborne Zoonoses, PHAC, DST

Non-UofG Advisory

16

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Immune response of chickens for enhanced protection against viral infections UofG2012-1349

Funding Program

Production Systems Animals poultry, enhanced immune response, viruses Eva Nagy University of Guelph 01/07/2013 End Date

OMAFRA - U of G Research

30/06/2016

Abstract The poultry industry is a key contributor to Ontario’s agriculture, and of Canada, since Ontario is the largest producer and processor of chickens in the country with 35% of total production. The Canadian poultry industry contributes over $3 billion in farm gate receipts annually. The socio-economic benefits of the sector to the economy total over $11 billion. Chicken is the number one meat choice of Canadians, with a yearly 31.8 kg/person consumption. However, the high production comes with increased pressure from infectious diseases negatively impacting this industry.

This project focuses on poultry health with the goal of maintaining the superior health status of chickens which in turn will increase production efficiency (hence profitability of the industry) and provide a safer food source for human consumption. We will study the immune response of chickens to important viral infections, focusing now on fowl adenovirus and Marek’s disease virus, in order to enhance immunity conferred by vaccines and to reduce clinical disease. By improving our understanding of the factors contributing to the development and function of a strong immune system, the proposed studies will provide a framework for enhancement of disease resistance in Ontario’s poultry flocks and tailored novel vaccine design.

Objectives The overall objective of this study is to identify viral components/elements that impact the immune response of chickens (both innate and adaptive) to avian viruses; this knowledge is critical for the rational use vaccines.

The specific objectives of the work are: 1. To determine the role of the mucosal immune response to fowl adenoviruses (FAdVs) for enhanced protection 2. To study the cellular immune response to FAdVs 3. To determine the immune response to genetically engineered, novel FAdV vaccines

17 For more information, please visit www.uoguelph.ca/research/PSA

4. To identify immunological mediators of vaccine-conferred protection against Marek’s disease 5. To develop and employ novel strategies for delivery of immune system molecules to chickens to enhance their protection against Marek’s disease Benefits The value of the province’s poultry and egg processing sector is in excess of $ 1.6 billion per year. However, infectious diseases have significant impacts on the viability and profitability of the poultry industry.

Economic losses can be attributed to massive use of prophylactics and therapeutics, increased mortality/condemnation, diminished production, food safety concerns, and possible embargos. These problems are compounded by the occurrence of vaccine breakdowns and emergence of new viruses/diseases we have not seen before and the emergence of more virulent strains of indigenous pathogens. For example highly virulent strains of Marek’s disease virus against which the currently available vaccines are not effective have emerged; and inclusion body hepatitis (IBH; caused by fowl adenoviruses) is a very significant problem to the broiler industry. By improving our understanding of the factors contributing to the development and functioning of a strong immune system, the proposed studies will provide a framework for enhancement of disease resistance in Ontario’s poultry flocks and tailored, novel vaccine design.

Moreover the proposed research has a significant discovery impact as well since there is a lack of understanding of immunology against the targeted viruses.

The direct beneficiaries of our proposed research are the animals themselves, the poultry producers, vaccine manufacturers, and, in terms of contributing to affordable, safe and good quality food, the Ontario public.

This proposal will provide training in the area of molecular virology/immunology, vaccine design, animal experimentation and the trainees will use state of the art methodologies. Our approaches are highly innovative and our work combines aspects of basic and applied research. Moreover the knowledge gained can be applied to other species, even to human medicine.

Co-Funder List • • • •

NSERC NSERC Poultry Industry Council Canadian Poultry Res Council (CPRC)

18

Team Member 1. Dr. Shayan Sharif

University of Guelph

University Researcher

2. Mrs. Betty-Anne McBey

University of Guelph

Technician

3. Mr. Li Deng

University of Guelph

Graduate Student

4. Mr. Bryan Griffin

University of Guelph

Graduate Student

5. Dr. Csaba Varga

Ontario Ministry of Agriculture, Food and Rural Affairs

Advisory

6. Dr. Robert Kozak

University of Guelph

University Researcher

7. Dr. Lloyd Weber

Collaborators

Non-UofG Collaborator

8. Dr. Douglas Hodgins

University of Guelph

UofG Research Associate

9. Ms. Neda Barjesteh

University of Guelph

UofG Graduate Student

Ms. New student to be hired (new University of Guelph student)

UofG Graduate Student

10.

19

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Optimizing Lighting for Precision Broiler Breeder Feeding UofG2013-1668

Funding Program

Production Systems Animals Broiler breeders, feeding, lighting, management Gregoy Bedecarrats University of Guelph 01/09/2014 End Date

OMAFRA - U of G Research

31/03/2017

Abstract Poultry detect light via photoreceptors in the retina, pineal gland and hypothalamus. The retina regulates behaviors (including feeding) while the hypothalamus controls homeostatic and physiological processes (including reproduction). As each organ responds differently to wavelengths and intensities, it should be possible to adjust lighting programs to specifically promote precision feeding in pullets and reproduction in adults. This collaborative project between Drs. Bedecarrats and Zuidhof is unique as it combines two critical levels of expertise (precision feeding and spectrum lighting). The Precision Broiler Breeder Feeding System (PBBFS) automatically allocates feed for individual birds within a group-housed flock to precisely match realtime body weight measurements. The expected result is a highly uniform flock that will respond uniformly to photostimulation. To be cost effective, the PBBFS needs to be utilized by birds beyond the standard 8h photoperiod used to raise pullets. Thus, the objectives of the proposed research are to provide enough light for broiler breeder pullets to access the PBBFS 24 hours a day without triggering early sexual maturation. To that end, the effects and/or combination of light wavelength will be maximize to optimize proper utilization of the PBBFS in pullets without decreasing, and possibly improving, egg production in adults.

Objectives The overall objectives of the proposed research are to determine the best wavelength combinations to provide enough light for broiler breeder pullets to access feed from a Precision Broiler Breeder Feeding Station without triggering early sexual maturation and, to determine the best light combination/sequence to maximize and sustain the subsequent egg production in adults.

Specific Objectives: 1) To determine the effects of illuminating bell feeders with supplemental LED lights on reproduction and activity levels (sleep/wake patterns, aggression) in broiler breeder pullets – and to select the least photostimulatory wavelength.

2) To determine the optimum spectrum of the main lighting system during rearing of pullets and the subsequent photostimulation of adults.

20 For more information, please visit www.uoguelph.ca/research/PSA

3) To determine the effect of daytime rearing and photostimulation spectra, photoperiod and female body weight on reproductive success of precision-fed broiler breeders.

Benefits The Precision Broiler Breeder Feeding System feeds one bird at a time, sequentially. By evaluating bird body weight (BW) in real time, and feeding birds that are less than the target BW, this system allows to achieve very high flock BW uniformity. Metabolic stability associated with maintaining a consistent positive energy balance is key to improving reproductive performances. At target BW, hens produce more eggs and have higher fertility and roosters complete more matings. The net result is higher chick production per hen.

Optimizing and validating the precision feeding system directly addresses priority: 2-a: reducing feed cost per unit output by providing nutrients more frequently, increasing chick production and, identifying and implementing favorable treatments to reduce residual maintenance requirements.

2-b, c and d: precision feeding is a management decision making tool which measures BW in real-time and decides whether or not to feed individual animals to effectively express individuals maximum reproductive performance potential to maximize production.

Current management practices in the industry involve restricting birds' access to feed to prevent obesity, a condition responsible for poor reproductive performances. However, restricted feeding implies competition between birds for resources, which results in frustration, leading to aggression and injuries (a major welfare concern). Thus, allowing all birds to access feed for longer period of times based on their individual metabolic need will allow foraging throughout the day, as opposed to the current paradigm of mass competition for feed once per day or once every second day. This will reduce stress, frustration and aggression, addressing priority 4-a (investigate housing environments and management practices that meet health and welfare needs).

To date, the Precision Broiler Breeder Feeding System was shown to be effective under small scale experimental settings. However, to be economically viable, more birds need to access individual stations.

Our goal is to design the best lighting paradigm (combination of wavelength and photoperiod) that will allow prolong access to the station, especially during pullets rearing. This will result in more birds fed per station thus significantly reducing the cost of use, and promoting its adoption by the hatching egg industry (primary beneficiary).

Co-Funder List • • • •

Canadian Poultry Research Council Aviagen Thies Electrical Distributing Inc. Agriculture Funding Consortium (ALMA)

Team Member 1. Prof. Martin Zuidhof University of Alberta Non-UofG Faculty/Research Scientist

21

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Validation of a new LED light bulb designed for the egg-laying industry UofG2011-1161

Funding Program

OMAFRA - U of G Research

Production Systems Animals,Product Development and Enhancement through Value Chains Poultry, Lighting, Layers, LED, Energy Gregoy Bedecarrats University of Guelph 07/05/2012 End Date 01/05/2015

Abstract With the upcoming ban on inefficient light sources, there is a sense of urgency within the poultry industry to switch to efficient systems. Despite the multiple alternatives currently available, a well defined and studied system specifically addressing the requirements of egg-laying birds is lacking. Recently, we have shown that light from the red spectrum is critical to stimulate the reproductive axis. Based on these results, we designed a LED light bulb that delivers 60% red light. Furthermore, this bulb was manufactured to withstand harsh barn environment and can be dimmed without any loss of spectral output. This proposal aims at first testing our bulb theoretical efficiency and resiliency in an environment that mimics industrial setting and, compare its use versus standard incandescent and compact fluorescent lights. We anticipate that this light will result in higher egg production while minimizing energy consumption thus allowing producers to increase revenue while reducing environmental footprint. This will be then confirmed by testing our light system in a real commercial egg farm.

Objectives The specific objectives are: Production systems 1) Ensure that our light system triggers a rapid sexual maturation (age at first egg) 2) Ensure that our light system allows for prolonged peak egg production (total egg production) 3) Verify that any increase in production does not negatively impact egg quality 4) Ensure that our light system does not result in health and welfare concerns 5) Verify that data obtained on a small research scale can be transferred and replicated in a large commercial operation Product development 1) Compare the energy consumption of our system with other available light sources (compact fluorescent, incandescent) to confirm its efficiency

22 For more information, please visit www.uoguelph.ca/research/PSA

2) Test the resiliency and reliability of our light system (longevity of the bulbs in a barn environment) 3) Using AGVIRO's proprietary software, analyze the economical impact of using our light system 4) Determine the economical impact of our system in a real farm Benefits The cost associated with lighting accounts in average for over 20% of the electricity usage in egg-layer barns.

As of 2012, inefficient light bulbs will be phased out of the market and although various alternatives are available to producers, most bulbs are not designed for egg-production and are thus not optimum. We recently designed a new LED bulb based on recent research and anticipate it will be the best light source to induce high egg production while minimizing energy consumption. Thus, primary beneficiaries will be producers who will benefit from increased productivity with reduced production costs. This will be confirmed by testing our lights in a large commercial egg-laying operation. The barn to be used holds 40,000 hens and uses 250 light bulbs. Based on preliminary results, we anticipate 3-5% increase in egg production combined with a 90% reduction in energy consumption.

Co-Funder List • • • • • •

Poultry Industry Council Thies Electrical Distribution Co Dykstra's poultry farm NSERC NSERC CPRC/AAFC Poultry Cluster 2

Team Member 1. Dr. Tina Widowski University of Guelph Collaborating Researcher 2.

Collaborators

Industry Collaborator

3.

Collaborators

Industry Collaborator

23

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Expansion and validation of genetic marker set for boar taint UofG2011-1050

Funding Program

OMAFRA - U of G Research

Product Development and Enhancement through Value Chains,Production Systems Animals genetic markers, boar taint James Squires University of Guelph 01/05/2012 End Date 01/05/2105

Abstract Male pigs are currently castrated to prevent boar taint, but this negatively affects feed efficiency, lean yield and animal welfare. Our objective is to complete the work to develop a genetic solution for boar taint, using SNP genetic markers in candidate genes for boar taint. Application of our current marker set to produce pigs that are homozygous for the favourable SNP alleles would decrease fat skatole levels by 20-53% and fat androstenone would decrease by 26-61%, depending on the genetic line. More research is needed to develop additional SNP markers to expand our marker set and provide a more complete genetic solution for boar taint. We are currently working with The Canadian Centre for Swine Improvement and provincial breeding organizations in Ontario, Quebec and Alberta to validate these markers in the major Canadian swine breeds. This project provides a unique opportunity to immediately validate any new markers we can discover, thereby producing a more complete marker set. The ultimate goal is to identify the causative mutations in a handful of the most important genes, and then use these markers in breeding programs to develop lines of pigs that are free of boar taint but otherwise grow as normal boars.

Objectives The objective of this work is to expand our current marker set to identify low boar taint pigs. This larger set of markers will be included in our ongoing validation work to provide a more complete genetic solution to the problem of boar taint. The specific objectives are: 1. Investigate sequences of additional porcine candidate genes for boar taint to identify single nucleotide polymorphism (SNP) markers.

2. Genotype animals with known boar taint phenotype for each of the SNP markers 3. Conduct association analysis to determine the effectiveness of the expanded marker set to predict boar taint

24 For more information, please visit www.uoguelph.ca/research/PSA

4. Investigate whether any potential negative effects on production or reproduction are associated with any of the markers.

5. Develop lines of pigs with reduced boar taint using our expanded marker set.

Benefits The pork industry in Ontario and Canada will benefit by anticipating the emerging problem of preventing boar taint without castration. Animal welfare concerns about castration have led to legislation banning castration in several EU countries and a total ban on castration throughout the EU is planned for 2018. The Canadian pork industry can now anticipate that consumer trends in Canada will soon follow what is happening in Europe. Using our innovative genetic marker technology to produce lines of pigs that are low in boar taint, the markets for Canadian pork will improve as consumers will find this product more appealing than pork produced using traditional methods involving surgical castration. Pig breeders will benefit since worldwide markets for Canadian swine genetics will likely increase. Not castrating will also improve the environmental impact of pork production. The amount of inputs required (feed, labour, medication) will be reduced and the output of nitrogen and phosphorous in the manure will be decreased. The control of skatole production will also reduce the odour of swine manure, which will reduce one of the major complaints against swine production systems. Thus, both pork producers and consumers will benefit.

Processors and consumers will also benefit from the decreased fat content and improved quality of pork products from intact males.

Co-Funder List •

Alliance Genetic Canada

Team Member 1. Prof. Flavio Schenkel University of Guelph

Collaborating Researcher

2. Ms. Yanping Lou

University of Guelph

Technician

3. Dr. Brian Sullivan

Canadian Centre for Swine Improvement Industry Collaborator

25

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Better control of Bacterial Cold Water Disease in farmed rainbow trout by the development of an effective Flavobacterium psychrophilum vaccine UofG2012-1341

Funding Program

Production Systems Animals vaccine, genome, reverse vaccinology Janet MacInnes University of Guelph 01/06/2013 End Date

OMAFRA - U of G Research

31/05/2015

Abstract Bacterial Coldwater Disease(BCWD)caused by the Gram negative bacterium Flavobacterium psychrophilum, is a very costly disease in salmonid aquaculture around the world and the leading cause of mortality in farmed rainbow trout in Ontario. No commercial vaccine is currently available to prevent BCWD, and the disease is primarily managed through heavy antimicrobial application. Little is known about the virulence factors of, or appropriate vaccine targets for, this organism. The situation is further complicated by the fact that there are multiple genotypes and biotypes of F. psychrophilum in Ontario. Studies are currently underway to develop an effective vaccine for BCWD based on a small number of cold-induced gene products, but it is likely that additional gene products would be very helpful. To have a better chance of developing of an effective vaccine against F. psychrophilum we propose to analyze the genomes of 7 Ontario F. psychrophilum strains. From this genome information, genes encoding proteins that should be good vaccine antigens will be identified and the proteins will be expressed in E. coli. The antigenicity of these recombinant proteins and their ability to provide protection against challenge with a virulent strain of F. psychrophilum will be evaluated.

Objectives The main objective of this work is to develop an effective Flavobacterium psychrophilum vaccine.

To do this we need to first: 1. evaluate available genome sequence information, close gaps,and do comparisons to identify conserved genes 2. among the conserved genes,identify good vaccine targets Once this ground work is completed, we will then:

26 For more information, please visit www.uoguelph.ca/research/PSA

3. clone and express 10 candidate vaccine antigens 4. evaluate the antigenicity of vaccine antigens by immunoblotting and ELISA 5. test antigenicity of 6, and protective efficacy of 3 vaccine antigens as part of a current NSERC Strategic Program project Benefits In the short to medium term, the proposed work should benefit Ontario fish farmers. According to the Fisheries and Oceans Canada report CA-10-02-001, "Bacterial Cold Water Disease caused Flavobacterium psychrophilum is the most important production-limiting disease for Ontario Rainbow Trout farmers".

Losses can result from direct mortality and vertebral and other deformities that decrease the market value of fish that survive the infection as well as from the increased cost of managing and monitoring sick fish. No commercial vaccine is currently available to prevent BCWD so the disease is primarily managed with antibiotics. Given the decreasing sensitivity of F. psychrophilum isolates to antibiotics in recent years and growing concern about antibiotic usage in the environment, there is an increasing need for a good vaccine.

The proposed experiments are designed to rapidly identify antigens that would be the basis of a safe and effective vaccine for BCWD. In addition to lessening the costs associated with morbidity and mortality, an effective BCWD vaccine would reduce the need for treatment and consequently decrease the release of antibiotics in the environment.

Information obtained in this study should also be useful in understanding how this organism causes disease and help us in the design of molecular tools to track outbreaks in the field. Importantly, these studies should contribute more generally to our understanding of how fish mount an effective immune response and to the adjuvant potential of FliC. In addition to specific benefits that might be accrued from an effective BCWD vaccine, the technology used in this study should be readily transferable to the control of other bacterial pathogens of fish (and indeed, other species). Finally, these studies will help in the development of the bioinformatics and recombinant vaccinology skills of University of Guelph researchers--important areas where we are currently lagging.

Co-Funder List •

NSERC

Team Member 1. Mr. Glenn Soltes University of Guelph Technician 2. Dr. John Lumsden University of Guelph UofG Other

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Stimulating innate immune responses to prevent bacterial pneumonia in cattle UofG2013-1488

Funding Program

Production Systems Animals Beef, Respiratory disease, Prevention, Immunity Jeff Caswell University of Guelph 21/05/2014 End Date

OMAFRA - U of G Research

30/04/2017

Abstract Bovine respiratory disease is an important cause of economic loss for the beef industry, a major reason for preventative and therapeutic use of antibiotics, and a welfare issue. Antimicrobial peptides are small proteins that calves produce in their airways, which naturally defend the lung against infection. Although these peptides kill the bacteria that cause pneumonia in cattle, this response fails during stress and viral infection. This is a reason that stressed and virus-infected calves develop bacterial pneumonia. Stimulating the synthesis of these "natural antibiotics" to effectively prevent disease and thereby restore immunity is a novel strategy to prevent bacterial pneumonia in feedlot cattle.

We will identify the molecular signalling pathway that best stimulates calves to produce more antimicrobial peptide, and test the effect in cattle. These findings are expected to identify methods that stimulate calves to produce more antimicrobial peptide, evaluate the effect on disease resistance, and lead to drug candidates that enhance these responses. This development would reduce the occurrence of pneumonia in beef cattle, lessen the reliance on antibiotics for prevention, and improve the welfare of stressed, diseaseprone calves. These findings would be of interest to beef producers and veterinarians, pharmaceutical companies, and consumers of beef.

Objectives 1. Identify how to most effectively stimulate antimicrobial peptide expression in healthy calves, and how corticosteroids and viral infections impair this response 2. Characterize the relationship between stress, levels of antimicrobial peptide in nasal cavity and lung, bacterial populations in nasal cavity, and disease outcome 3. Determine whether enhancement of antimicrobial peptide expression affects development of bacterial pneumonia, as a new approach to disease prevention Benefits This project addresses the priorities of: "Develop alternative methods that effectively and economically reduce the risk of infectious disease" and "Improve understanding of animal immunity (including innate

28 For more information, please visit www.uoguelph.ca/research/PSA

immunity)".

Bovine respiratory disease is the most frequent and economically important disease causing production loss in Ontario beef production. The disease is also the major reason for preventative use of antibiotics in beef production and a welfare issue from disease-related suffering. The research develops improved methods to prevent this disease; specifically by stimulating innate immune responses in beef cattle during specific times of disease risk. Success would provide the following benefits: a. Show that stimulating innate immune responses is an effective method for prevention of bacterial pneumonia. b. Establish a system and experimental approach for testing immunostimulants. c. Test already-available specific candidate drugs that can be immediately used, or those that can be developed in the medium term, as immunostimulants to prevent pneumonia in cattle.

Benefits to beef producers involved in backgrounding and finishing operations would include reduced production costs by preventing pneumonia, which causes death losses, treatment costs of drugs and personnel, reduced feed conversion, and reduced carcass quality. These benefits reflect the main focus of the work—development of a practical method to stimulate immunity. A second outcome is improved knowledge of how nasal defences protect the lung against bacterial infection, and of how to best stimulate immunity in the nasal cavity and lung. Thus, shorter term benefits include improved understanding of how stressed calves develop pneumonia, and knowledge of how nasal immunity prevents bacterial infection in the lung.

Benefits to the industry as a whole would include improved consumer perception of Ontario beef by reducing the need for preventative use of antibiotics in beef production. Benefits to the industry would also include improved cattle welfare by reducing disease-associated suffering.

The present work is targeted to respiratory disease of feedlot beef cattle, but success could be similarly applied to prevention of respiratory disease in dairy and veal calves and in swine production, as well as mastitis and endometritis in recently calved dairy cows.

Co-Funder List • • • • •

Beef Producers of Ontario (OCA) Zoetis Canada (formerly Pfizer Animal Health) NSERC Discovery Grant NSERC Engage Grants program CONACYT: Mexican National Council for Science and Technology

Team Member Non-UofG Faculty/Research Scientist

1. Dr. Raksha Tiwari

Collaborators

2. Ms. Mary Ellen Clark

University of Guelph UofG Technician

3. Dr. Khaled Taha Abdelaziz University of Guelph UofG Research Associate 4. Dr. Sofia Rosales Martinez University of Guelph UofG Graduate Student

29

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Can horses modulate their mechanical interaction with the ground surface to mitigate potentially harmful properties of the surface?

UofG2013-1636

Funding Program

Production Systems Animals horse; locomotion; footings; "risk mitigation"; Jeff Thomason University of Guelph 27/05/2014 End Date

OMAFRA - U of G Research

27/11/2015

Abstract Many injuries to competitive equine athletes may be attributed to mechanical failure of bones, joints, tendons, etc., and a significant percentage of horses show chronic injuries (10-25%, depending on athletic discipline). In the showjumping discipline, the surfaces (footings) on which the horses perform are known to represent risk factors for injury. In addition to issues of health and welfare, injuries are expensive for animals that are worth up to $3 million, because of their ability to perform, and which have training/upkeep costs of up to $50,000 annually. We are among a handful of research groups worldwide to have begun the process of characterizing the effects of variation of surface properties (hardness, stiffness, etc.) on limb loading. We have assembled an international team with the Objective of quantifying the ability of individual horses to modulate their response to surfaces of varying type. We wish to see if the horses can mitigate the effects of differences in properties among surfaces by subtly altering how they move and place their feet on each one. The Aim is to provide public information to horse owners and footing developers on changes on horse activities and footings properties to enhance performance while reducing injuries.

Objectives Objective 1: We will seek a definitive answer to a 2-part question: Can performance horses (A) modify the way their feet make contact with underlying footings to (B) mitigate potentially harmful effects owing to the properties of those footings? part A should be answered conclusively; Part B will require interpretation as to which results are indicative of the potential for harm.

Objective 2: To provide horse owners with information on the relative contribution of horse and surface to risks for injury. How the horse's actions either contribute to or mitigate the potential for injury is rarely acknowledged, and has not been studied in this context.

Objective 3: Footings providers know how to manipulate the properties of surfaces, but essentially do it

30 For more information, please visit www.uoguelph.ca/research/PSA

empirically (by trial and error). We will provide evidence for them, on property combinations that that require minimal accommodation by the horse, which they can apply to footing design.

Benefits While the horse is not a production animal per se, the value of the horse industry to the Provincial economy is unquestionable: $2.6B annually (Wilton and Caldwell, OMAFRA Report on the Provincial Equine Industry, 2009). Province-wide, the expenditure for EACH service in the following list falls in the range of $100M to $400M per annum: boarding, bedding, feed, transport, farriery, veterinary care, and maintenance and repair of infrastructure. The horse is, therefore, invaluable to the rural economy of Ontario (and was a major factor in maintaining cash flow through that economy in the aftermath of the 2008 financial slump). Thirty-seven percent of the owners/riders surveyed reported participating in hunter-jumping (Wilton and Caldwell 2009), so the sector addressed by this proposal is economically significant in itself.

Lameness ranks with colic and respiratory issues as the three main health impediments to horses. All riding/jumping horses experience bouts of lameness during their careers, and as many as 20% experience chronic low-grade limb pain that hampers performance. A goal of this proposal is to help a shift in emphasis from curing lameness to preventing lameness, by virtue of data that will aid others in beneficially manipulating the horses’ ‘working’ environment. If successful, application of the results will come with associated shifts in costs of care. Any savings to the equine industry is likely to be reinvested, given the popularity of the horse, enabling that industry to become more economically efficient (by reducing the wastage associated with treating lameness). While the focus is on factors affecting lameness in performance horses (i.e., the surfaces that they are ridden and jumped on), the results will be applicable to surfaces used for other disciplines (e.g., racing). In summary, the beneficiaries will be all of the rural sectors who depend on horses for some of their income, and, of course, the horses themselves.

Co-Funder List • • • •

Footing First LLC Centenary College General Blacksmithing (Mr. Paul Martin) NSERC

31

Team Member 1. Dr Katrina Merkies

University of Guelph UofG Faculty (On Campus)

2. Dr. Kelly Munz

Collaborators

Non-UofG Collaborator

3. Prof. Michael Peterson Collaborators

Non-UofG Collaborator

4. Dr. Christie Mahaffey Collaborators

Non-UofG Technician

5. Mr. Warren Bignell

University of Guelph UofG Technician

6. Mr. William Sears

University of Guelph UofG Other

7. Ms. Cristin McCarty

University of Guelph UofG Research Associate

8. Ms. TBA TBA

University of Guelph UofG Graduate Student

32

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Reducing dietary protein costs while maximizing milk production in dairy cows UofG2013-1746

Funding Program

Production Systems Animals protein efficiency, dairy cow John Cant University of Guelph 02/09/2014 End Date

OMAFRA - U of G Research

01/09/2017

Abstract In typical dairy cow diets in Ontario, protein supplements make up approximately 21% of the diet's dry matter but approximately 38% of its cost. Thus, strategies to reduce inclusion level of protein supplements without affecting lactation performance will increase profitability of the enterprise. Amino acids absorbed into the bloodstream of a cow are partitioned into milk protein, body protein, or hepatic degradation. We propose to use glucose and branched-chain amino acid supplementaton to direct absorbed amino acids into milk protein, similar to a nutritional supplement for protein replenishment in elite human athletes. One experiment will use i.v. infusions of nutrients into cows to establish targets for formulating practical diets that will be tested in a second experiment. The infusions will be glucose and 2 levels of branched-chain amino acids on top of a low, 12%-protein diet, in comparison to a typical 16%-protein diet. The results will be used to design diets of 14 and 12% protein that maximize milk protein yields to the benefit of farmers, nutritionists and milk consumers.

Objectives If partitioning of metabolizable protein into degradation and body protein could be reduced to as low as 10% of daily MP supply, then diets of 12% crude protein could be fed to cows without compromising performance (Dijkstra et al., 2013). Our main objectives are: 1) to maximize milk protein and other solids yields from cows fed diets of 12% crude protein using a combination of carbohydrate and BCAA supplementation, and 2) to compare performance and milk revenue return over feed costs from optimized low- and moderateprotein diets.

Benefits The goal is to find diet formulations that will maximize milk revenue return over feed cost for diets of 12% and 14% crude protein. Beneficiaries will be: Dairy farmers - for having an increased return on investment. In a typical, Ontarion, corn/alfalfa-silage based

33 For more information, please visit www.uoguelph.ca/research/PSA

diet of 18% CP, 2.34 kg/d of CP intake comes from protein supplements at a cost of $2.44/d. The supplementary protein thus costs $2.44/2.34 kg = $1.04/kg, at current feed prices. If CP content of the diet could be dropped to 13%, CP intake from supplements would become 1.11 kg/d, and farmers could pay up to $2.44/1.11 kg = $2.20/kg supplemental protein and still come out ahead. Thus, even if the cost of supplemental protein were twice as much per kilogram on the modified diets, profitability would increase.

To be sure of the economic gain from switching to low-protein diets, we will calculate return over feed costs for the diets tested in our performance trial.

Feed formulators - for having additional strategies to maintain milk protein yields, and to reduce nitrogen losses on client herds Nutrition researchers - for having new information on how diet manipulations influence milk component yields. If regulation of mRNA translation is responsible for the effects of diet on milk protein yield, then study of translational regulation will open up new opportunities to use feed ingredients more judiciously for managing milk protein yields.

Milk consumers - for knowing that environmental effects of dairy farming are minimized through research.

The FAO (2004) has pointed out that growing demand for animal proteins throughout the world is putting a strain on the global supply of protein to feed livestock. Consumers are concerned about the safety of animal feeds and the environmental impact of animal production practices. To retain consumer confidence in animal products, a greater transparency in animal production systems was called for. Efforts such as ours to reduce the environmental impact of dairying in Ontario demonstrate responsible stewardship that will be rewarded by improved markets for dairy products.

Co-Funder List • • • •

Nutreco Canada Inc NSERC Canada canadian dairy commission Alberta Livestock and Meat Agency

34

Team Member UofG Faculty (On Campus)

1. Vern Osborne

University of Guelph

2. Dr. Tom Wright

Ontario Ministry of Agriculture, Food and Rural OMAF and MRA Staff Affairs Non-UofG Collaborator

3. Dr. John Doelman Collaborators 4.

Dr. Helene Lapierre

AAFC

Non-UofG Faculty/Research Scientist

5.

Ms. Richelle Curtis

University of Guelph

UofG Graduate Student

6.

Dr. Lorraine Doepel

University of Calgary

Non-UofG Faculty/Research Scientist

35

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Understanding and controlling necrotic enteritis in broiler chickens UofG2012-1347

Funding Program

Production Systems Animals Necrotic enteritis, chickens, vaccine development John Prescott University of Guelph 03/06/2013 End Date

OMAFRA - U of G Research

30/06/2016

Abstract To develop an attenuated C. perfringens strain for oral administration in the prevention of necrotic enteritis (NE), we will take four interlinked approaches: 1. Optimization of an oral whole cell vaccine schedule by using an infection-immunization approach using a virulent NE isolate; 2. Selection of target genes through transcriptomic analysis of C. perfringens genes; 3. Strain CP1 will be attenuated by mutation of gene targets.

Selection of genes will be based on transcriptomic analysis, on virulence genes already identified by genome sequencing and DNA microarray analysis, on selected “essential” metabolic or regulatory genes, and a combination. Attenuation of single deletion mutants will be determined by the severity of NE produced experimentally; single gene deletion strains showing attenuation will be selected as candidates for further gene deletion, and the additive or synergistic effect of the second deletion on attenuation will again be assessed. The anticipated attenuated strain will contain 2 or 3 gene deletions that will impair their ability to persist in the intestine but that will still express important immunogenic proteins. 4. Candidate attenuated strains will be assessed for immunogenicity using a vaccine dosage schedule based on Part 1 of the study.

Objectives To develop an attenuated C. perfringens strain for oral administration in the prevention of necrotic enteritis.

The approach will have four interlinked sub-objectives: 1. Optimization of an oral whole cell vaccine schedule by using an infection-immunization approach using a virulent NE isolate.

2. Selection of target genes through transcriptomic analysis of C. perfringens genes to confirm or identify critical genes for targeted deletion.

3. Attenuation of strain CP1 by mutation of gene targets. Selection of genes to be deleted will be based on transcriptomic analysis, on virulence genes already identified by genome sequencing and DNA microarray analysis, and on selected “essential” metabolic or regulatory genes. The anticipated final attenuated strain will contain gene mutations that will impair their ability to persist but that will express important immunogenic proteins.

36 For more information, please visit www.uoguelph.ca/research/PSA

4. Candidate attenuated strains will be assessed for immunogenicity using a vaccine dosage schedule based on Objective 1 of the study.

Benefits Necrotic enteritis of broiler chickens has been identified as a $2 billion disease globally. This is because of the cost of prevention by use of antimicrobial drugs, since this is an infection which, like coccidiosis, severely limits the intensive production of broilers if it is not controlled. The other cost of the disease is the reduced production associated with "subclinical" infection and intestinal damage without producing the full blown disease. Antibiotic resistance is an incrasingly recognized problem in the causative agent, Clostridium perfringens, so that there may be more subclincial diease than is currently recognized. As routine use of antibitoics in animal produciton comes under increasing public and regulatory scrutiny, because of the general problem of the emergence of antibiotic resistance, we need to find alterantive ways to control this infection. The benefits of finding alternatives would accrue to several constituencies: 1. Broiler farmers, by reducing antibiotic costs, by reducing problems associated with resistance, and by removing the need to use antibiotics in broiler production; 2. The chicken industry generally by addressing the need to reduce antibiotic use; 3. Society in general, by potentially reducing the burden of antibiotic use and the adverse criticism of modern agriculture.

Co-Funder List • •

Canadian Poultry Research Council-AAFC Cluster II funding NSERC

Team Member Collaborating Specialist

1. Dr. Valeria Parreira

University of Guelph

2. Mr. Dion Lepp

AAFC Guelph Food Research Centre Advisory

3. Dr. Joshua Gong

Agriculture and Agri-Food Canada

Advisory

4. Dr. Spiridoula Athanasiadou Collaborators

University Researcher

5. Dr. Yanlong Pei

Technician

University of Guelph

37

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Toward commersialization of a novel fermented product for enhancing intestine development and productivity of early-weaned pigs UofG2012-1280

Funding Program

Production Systems Animals early weaned pig, intestine, Julang Li University of Guelph 01/01/2014 End Date

OMAFRA - U of G Research

30/09/2016

Abstract Digestive upsets and the associated growth reductions of newly weaned pigs is a key concern in pig management. Developing an intestinal development enhancing-diet may help to optimize pig performance at this critical stage. We have generated epidermal growth factor (EGF) expressing Lactococcus lactis (L. lactis) via a bio-engineering approach. Our recent study showed that oral dosing of the fermentation product of L. lactis (after removal of the genetically modified bacteria) increased intestinal development and growth of early-weaned pig. To further this technology to commercial application, we intend to characterize the fermentation product, optimize procedures to ensure that the purified product is GMO free, examine stability during feed processing, and establish a dose-response relationship in newly-weaned piglets. It is anticipated that the end product will offer a novel line of feed additives for commercial pork production, minimize post-weaning growth lag and reduce reliance on using of antibiotic and expensive animal proteins in pig diets.

Objectives With the support from Ontario Pork and OMAFRA, we have previous generated EGF expressing L. lactis, and demonstrated that feeding the EGF containing fermentation product from this genetically modified L. lactis enhanced early weaned piglet growth and feed to gain conversion ratio. The overall aim of the proposed study is, in collaboration with our industry partner, to further characterize the fermentation product, meet the product registration requirements, and make the technology available to the pork industry. Specifically we will further analyze the functional properties of the fermentation product, demonstrate that the purified product is GMO free, examine it stability during feed processing, and establish a dose-response relationship in newly-weaned piglets.

Benefits Building upon our success on the first phase (generation of the EGF-producing L. lactis and preliminary mouse trial), and the second phase (production scale test in pig), which both supported by Ontario Pork,

38 For more information, please visit www.uoguelph.ca/research/PSA

OMAFRA, and NSERC, the proposed study is the third phase of our project to further the research to commercial application. The end product is a GMO-free fermentation product containing recombinant proteins that are beneficial to animal intestine development and growth performance. Feedback from relevant regulatory agent is that the registration of this product should be comparable to that of modified microbial producing enzymes that are currently being used in feed, suggesting the feasibility of registration of the product. Successful completion of the project will benefit the Ontario Pork industry by providing a novel means for improving gut health and development in newly-weaned pigs, and thus to improve animal productivity and welfare. Our previous animal trial shown that EGF- L. lactis was as efficient as animal plasma in enhancing piglet performance, demonstrating the potential to reduce usage of expensive feed animal source proteins. Moreover, given EGF's dual roles in enhancing the development and integrity of intestine, as well as innate immuno-defence (stimulation of antimicriobial peptide production), EGF containing fermented product may act as a non-antibiotic growth promoter. It may thus eliminate the reliance on in-feed antibiotics and in-feed animal plasma source proteins. In addition, pork from antibioticfree, animal plasma-free feed fed pig will offer additional value to Ontario Pork producer by make them in a unique position to be able to provide this attractive line of pork product addressing consumer concerns and food safety.

Co-Funder List • • • •

Grand Valley Fortifiers Ontario Pork NSERC AB Vista

Team Member 1. Dr. Kees de Lange University of Guelph (internal)

Collaborating Specialist

2. Ms. Evanna Huynh University of Guelph

Graduate Student

3. Ms. Julia Zhu

Technician Technician

4. Mr. Doug Wey

University of Guelph

5. Mr. Ron Lackey

Ontario Ministry of Agriculture, Food and Rural Affairs OMAFRA Staff

39

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Nitrogen (N) nutrition for growing pigs, to increase flexibility in feed formulation, reduce N losses into the environment and improve gut health UofG2013-1587

Funding Program

Production Systems Animals growing pigs, nitrogen, compensatory growth Kees de Lange University of Guelph 01/08/2014 End Date

OMAFRA - U of G Research

01/08/2016

Abstract Protein (amino acids, AA; nitrogen, N) is the second most expensive nutrient in pig diets. Effective protein nutrition is critical to optimize utilization of dietary energy, the single largest cost in pork production. With increased availability of crystalline AA, usage of conventional protein sources in pigs diets can be reduced, requirements for a large number of essential AA for optimal growth performance can be met simultaneously, and dietary supply of N may limit body protein (lean tissue) gain. The latter will negatively affect growth performance, feed efficiency and carcass quality of pigs. While dietary requirements for essential AA have been reasonably well defined, this is not the case for dietary N requirements needed for endogenous synthesis of non-essential AA by the pig for muscle deposition (protein and lean gain). The findings generated by this project will yield critical information on the efficiency of using different N sources for endogenous synthesis of non-essential AA and the compensatory growth response which occurs following a period of AA intake restriction. This will allow for the development of cost-effective feeding strategies to optimize pig productivity while minimizing N losses into the environment, accomplished in part through more effective application of updated decision support systems.

Objectives The overall aim of the proposed research is to better understand N utilization in non-ruminant animals, and more accurately define the response of growing pigs to dietary N and AA intake. Specific objectives are: 1) to determine the efficiency of using different dietary sources of N for body protein gain in pigs fed diets that are deficient in non-essential AA N, 2) to define the pig’s N requirements for maximum feed and N utilization efficiency, 3) to explore the dynamics of body protein gain during and following a period of feeding growing pigs below dietary N and AA requirements, and

40 For more information, please visit www.uoguelph.ca/research/PSA

4) to establish the impact of feeding nursery or growing pigs below requirements for N and AA during the energy intake dependent phase of body protein gain on growth performance up to market weight, carcass quality, and pig robustness (resistance to disease).

Benefits The main benefits are reduced feeding costs and N losses into the environment, and improved gut health in young pigs.

Improved understanding of protein (AA and N) utilization in growing pigs provides opportunity to optimize animal performance and profits, while lowering N excretion to reduce environmental impact. This research will provide the basis for factorial estimation of dynamic changes in daily N requirements and in the rate and composition of body weight gain following a period of AA intake restriction, which is critical for precision feeding pigs of varying genotypes that are managed under diverse environmental conditions (NRC, 2012).

The proposed research will contribute to further development of decision support systems, such as the NRC (2012) nutrient requirement models and the PorkMaster growth simulation model, which are available for use in Canada.

Dietary protein contributes to about 30% of diet costs and impacts utilization of dietary energy, which contributes to about 65% of diet costs. The current high cost of soybean meal (Can$615/MT vs. $1.70/kg for Lysine.HCl) provide an extra incentive to replace protein with crystalline AA, for which N requirements or the maximum inclusion level of crystalline lysine.HCl present constraints (see Literature review). Increasing the maximum lysine.HCl inclusion level from 3.5 to 4.0 kg/MT will reduce the cost of a typical grower diet by 1.5% and dietary N content by 1.7%. A reduction in feed costs by $1 per pig (about 1%) represents about $5,000,000 per year savings for the Ontario pork industry. Our recent research found that feed costs for pigs up to market weight could be reduced by more than 2% by capitalizing on compensatory growth induced by feeding less expensive protein sources to starter pigs (i.e. dietary nutrient levels were not altered). Based on NRC (2012), a 1.5 % reduction in N intake will reduce N losses into the environment by 2.5%.

Improved gut health of young pigs will reduce reliance on antibiotics, which addresses the public’s concern about food safety. Perceived improvements in pork safety will stimulate local and international demand for Canadian pork, contributing to increased revenues to pork producers and increased international trade.

Co-Funder List • • •

Ontario Pork Evonik Industries AG Wallenstein Feed & Supply Ltd.

41

Team Member 1. Dr. Ira Mandell

University of Guelph UofG Faculty (On Campus)

2. Mr. Wilfredo Mansilla University of Guelph UofG Graduate Student 3. Dr. Seema Hooda

University of Guelph UofG Post Doc Fellow

42

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Precision feeding of gestating sows using electronic sow feeders to reduce environmental impact and feed costs, while improving sow welfare and productivity UofG2013-1722

Funding Program

Production Systems Animals gestating sows, electronic feeding, performance Kees de Lange University of Guelph 01/08/2014 End Date

OMAFRA - U of G Research

31/12/2016

Abstract For optimum sow reproductive performance feed intake during gestation should be restricted. This is generally achieved by housing and feeding sows in individual stalls, which is an animal welfare concern.

Among the alternatives that are available to feed group-housed sow individually is the use of computer controlled electronic sow feeders (ESF). State-of-the-art ESFs will be installed at the Arkell research station, that include load cells to weigh sows at each visit and with the capacity to deliver up to 4 different diets, and their blends. Studies will be conducted to quantify costs and benefits, estimate nutrient losses into the environment and examine the effects on sow welfare and long-term reproductive performance, based on closely meeting the nutrient requirements of individual sows. A conventional feeding program using one diet and a constant feeding level throughout gestation will serve as control. Observations will be obtained on 100 sows per treatment across at least 3 parities over a two-year period. For a subsample of sows the effect of gestating sow feeding program on the quality of piglets will be evaluated as well, based on growth performance and carcass quality.

Objectives The overall aim of the proposed research is to explore the benefits of closely meeting the changing nutrient requirements of individual sows during gestation and across parities, in a group housing system and using computer controlled electronic sow feeders.

Specific objectives are to determine the effect of meeting the estimated nutrient requirements of individual (parity 1, 2 or 3) sows on: 1) sow welfare and reproductive performance: sow behaviour, injuries and health, litter size at birth, mean and average piglet weight at birth and weaning, sow feed intake and body weight changes during lactation, weaning to breeding interval, subsequent litter size, 2) quality of offspring: robustness (susceptibility to a pathogen challenge), growth performance, feed efficiency and carcass quality, and

43 For more information, please visit www.uoguelph.ca/research/PSA

3) estimated nitrogen, phosphorus and carbon balance during gestation and lactation and margin over feed costs.

Benefits Potential benefits include improved sow welfare, reduced feeding costs, reduced nutrient losses into the environment, and possibly improved sow reproductive performance and quality of newborn piglets.

Given the public concerns about housing and feeding sows individually in gestation stalls, alternative systems for managing gestating sows need to be explored. A promising alternative is the use of computer controlled electronic sow feeders (ESFs) for group housed sows. The latest versions of ESFs have been designed to minimize injuries and aggression among sows, minimize technical failures, and reduce efforts required to properly train sows.

ESFs can accommodate the unique energy and nutrient requirements of individual sows, as determined by sow body weight, parity, anticipated litter size, targeted maternal body weight gain, activity level and the thermal environment (e.g. NRC, 2012). By closely meeting the nutrient requirements of individual sows, feeding costs and nutrient losses into the environment can be reduced. Moehn and Ball (2012) estimated a reduction in feed costs of 10$ per sow per year by feeding close to requirements. Using the NRC (2012) swine nutrient requirements model and based on mass balance calculations it can be estimated that replacing one gestating diet, with two diets in a phase feeding program (changing diets at day 90 of gestation) nitrogen and phosphorus losses into the environment can be reduced by about 10%. By closely monitoring sow body weight and back fat changes adjustment to sow feeding management may be made in real time.

Accommodating the changing nutrient requirements during gestation and across parities is likely to benefit lifelong sow reproductive performance and piglet quality. In particular during late gestation nutrient needs increase quickly, to support rapidly increasing growth of the developing fetuses (Moehn and Ball, 2012; NRC, 2012). Failure to meet these requirements will force sows to mobilize body energy and nutrient stores, inducing a negative body nutrient balance even before the onset of lactation, likely impacting both the quality of piglets at birth (birth weight, number and type of muscle fibers, body energy reserves, robustness of the immune system) and subsequent reproductive performance.

Co-Funder List • • •

Ontario Pork / GrowingForward 2 Canarm BSM AgriProducts Farm.com

44

Team Member 1. Dr. Robert Friendship University of Guelph

UofG Faculty (On Campus)

2. Mr. Curtiss Littlejohn AAFC

Non-UofG Collaborator

3. Mr. Tim Thalen

UofG Technician

University of Guelph

4. Dr. Stephanie Torrey AAFC Guelph Food Research Centre UofG Adjunct Faculty 5. Dr. Ira Mandell

University of Guelph

UofG Faculty (On Campus)

6. Mr. Graham Dyer

Collaborators

Non-UofG Collaborator

45

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Controlled fermentation and steeping to enhance the feeding value of co-products for pigs UofG2012-1420

Funding Program

Production Systems Animals pigs, co-products, feeding value, energy Kees de Lange University of Guelph 03/06/2013 End Date

OMAFRA - U of G Research

31/05/2016

Abstract Starches and oils from grains and oilseeds are used increasingly for human food and biofuel production, elevating feeding costs of pigs. Viable pork production will rely increasingly on efficient usage of high fiber and protein co-products, such as corn distillers grains (DDGS), wheat shorts (WS) and soybean meal (SBM).

Usage of these co-products in pig diets is constrained, especially for young pigs, by low digestibility of fiber fractions, the negative impact of fiber on digestibility of other nutrients, and presence of anti-nutritional factors such as allergenic proteins in SBM. In preliminary studies in our laboratory we have been able to increase the nutritional value of DDGS by pre-treating with microbial inoculants and enzymes in swine liquid feeding systems. However, results have not been consistent. In vitro studies are proposed to evaluate alternative microbial inoculants and exogenous enzymes to improve the feeding value of co-products. In vivo digestibility, nutrient retention and performance studies are proposed to assess the feeding value of pre-treated DDGS, WS and SBM, and to better characterize the environmental footprint associated with feeding co-products to pigs. Achieving even a modest 1% improvement in feed cost would represent savings of over $5,000,000 per year for the Ontario pork industry.

Objectives It is hypothesized that through the strategic use of microorganisms and enzymes - some of which are currently used in soybean fermentation processing for human foods - SBM, WS and DDGS fermentation can be optimized to generate partly fermented products with improved nutritional values for pigs. These novel products will offer effective means to reduce feed costs, reducing the need for expensive grains and animal proteins in pig diets, while addressing public food safety concerns regarding animal protein use in pig feed.

The overall objective of the present study is to establish novel fermentation procedures to provide the pork industry pretreated SBM, WS and DDGS with increased digestibility, nutrient value, and decreased content of allergenic proteins and other dietary anti-nutritional factors for the pork industry. Optimal fermentation procedures will be established using in vitro studies, which will be evaluated in pig performance studies using both liquid and dry feeding systems.

46 For more information, please visit www.uoguelph.ca/research/PSA

Benefits This project will yield optimized pre-treatments of high fiber and high protein co-products from the food and biofuel industries to increase their nutritional values for pigs. Initially these benefits will be quantified with liquid fed pigs, based on the rationale that pre-treatment with enzymes and microbial inoculants is more effective in liquid feeding than dry feeding systems. During the latter stages of the project, benefits will be explored in dry feeding systems as well. It is estimated that approximately 25% of growing-finishing pigs in Ontario are raised on liquid feeding systems. Improved and better understanding of the nutritional value of feed ingredients (available energy from digestible energy yielding nutrients, available amino acids and phosphorus contents, decreased anti-nutritional activity, impact on gut health and development in young pigs) will allow more effective use of locally available co-products in pig diets, reducing feeding cost and reducing reliance on cereal grains and costly animal protein in pig diets. The latter also addresses the public food safety concerns about using animal proteins in pig diets. A modest 1% improvement in feed costs, through improvements in feed efficiency or use of less expensive ingredients, represents a savings of over $5,000,000 per year for the Ontario Pork industry. The impact of feeding co-products on nutrient retention in pigs will be determined, based on a mass balance (serial slaughter) approach. These observations will contribute to the further development of a systems approach to improve the prediction of feeding values of pig feed ingredients (based on digestibility of energy yielding nutrients, amino acids and phosphorus) and to accurately estimate the environmental footprint of pork production. These concepts were introduced in NRC (2012), and are becoming increasingly relevant when using co-products in pig diets.

Co-Funder List • •

Swine Innovation Pork AB Vista

Team Member 1. Dr. Julang Li

University of Guelph

University Researcher

2. Dr. Ira Mandell

University of Guelph

University Researcher

3. Ms. Melissa Wiseman

University of Guelph

Graduate Student

4. Mr. Ron Lackey

Ontario Ministry of Agriculture, Food and Rural Affairs Advisory

5. Ms. Julia Zhu

University of Guelph

Technician

6. Mr. Doug Wey

University of Guelph

Technician Graduate Student

7. Ms. Samansha Medeiros University of Guelph

47

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Patterns of nitrogen retention and nutrient utilization efficiency in gestating and lactating sows UofG2011-1029

Funding Program

Production Systems Animals sows, amino acid requirements, energy Kees de Lange University of Guelph 01/05/2012 End Date

OMAFRA - U of G Research

30/04/2015

Abstract Optimizing reproductive performance while minimizing diet cost and nutrient excretion are important components of sustainable pork production. In nitrogen balance studies we will establish the pattern of whole body N retention during gestation at different levels of energy intake and across different parities in sows. In addition, studies are proposed to evaluate the impact of feeding varying amounts of dietary protein but equivalent essential amino acids during lactation on whole body nitrogen excretion (including milk nitrogen output), milk protein yield, mammary amino acid utilization efficiency for milk production and piglet performance. In this manner key determinants of amino acid requirements of the reproductive sow are quantified. The resulting patterns of nitrogen retention, excretion and efficiency of amino acid utilization will provide necessary data with which to validate factorially-derived nutrient requirements in the reproductive sow and complement empirical amino acid requirement studies.

Objectives The overall aim of the proposed research is to explore the main determinants of AA and energy requirements of reproducing sows. This will provide the necessary background information to assess the impact of sow nutritional regimens - during gestation and lactation, and across multiple parities - on sow longevity, reproductive performance, and environmental contamination. Specific objectives are to (1) assess the pattern of whole body N retention in pregnant sows across multiple parities and at 2 levels of energy intake, and (2) determine the effect of reduced excessive dietary protein intake in lactating sows on N balance (including milk N output), milk protein yield, mammary AA utilization efficiency for milk production, and piglet performance. Additional observations will be made to explore mechanisms of amino acid utilization and regulation of energy status in sows and their offspring.

Benefits The proposed research will benefit Ontario pork producers and the environment. Understanding nitrogen balance patterns during gestation and lactation allows opportunity to formulate sow diets to optimize reproductive and piglet performance while minimizing N excretion and reducing the impact of pig

48 For more information, please visit www.uoguelph.ca/research/PSA

production on the environment. These studies will provide the basis for the factorial estimation of changes in daily amino acid requirements during gestation and across parities, at various levels of energy intake.

Moreover, effects of energy intake during gestation on the sow's energy status and physiological state of piglets at birth will be assessed. The proposed studies will provide insight on the negative effects of excessive protein intake and imbalanced dietary AA profiles on lactating sow and litter performance and nutrient losses into the environment.

Co-Funder List • • • •

Ontario Pork Natural Sciences and Engineering Research Council of Canada de Heus Voeders B.V. Ajinomoto

Team Member 1. Prof. Nathalie Trottier Collaborators

Non-UofG Faculty/Research Scientist

2. Dr. Crystal Levesque University of Guelph Non-UofG Faculty/Research Scientist 3. Ms. Lee-Anne Huber University of Guelph Graduate Student 4. Mr. Doug Wey

University of Guelph Technician

5. Mr. Greg Simpson

OMAFRA

Advisory

49

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Combating infertility in mares UofG2012-1412

Funding Program

Production Systems Animals Mares, infertility, pregnancy loss, ultrasonography Keith Betteridge University of Guelph 09/05/2013 End Date

OMAFRA - U of G Research

09/05/2016

Abstract Helping mares conceive, and reducing embryonic loss, require (a) an understanding of pregnancy establishment and (b) diagnostic and therapeutic methods. Our research covers both requirements but this proposal focuses on the second: first, by investigating the use of colour-Doppler ultrasonography for diagnosing impending pregnancy failure; second, by developing novel proteomic methods for assessing uterine health suitable for application to barren mares. The proteomic approach arises from developments in “shotgun� mass spectrometry for identifying and quantifying large numbers of proteins in biological samples. We hypothesize that adaptive innate immune responses to uterine infections or mucosal degeneration result in the secretion of proteins that harm the conceptus and terminate early pregnancy. To test this, we have analyzed uterine flushes, endometrial biopsies and conceptuses to characterize secreted protein profiles of mares during normal and failing (prostaglandin-treated) pregnancies. Harmful proteins that are markedly reduced during normal pregnancy are potential biomarkers of poor endometrial health and targets for therapeutic interventions. We will now establish analogous profiles in non-pregnant mares, both cyclic and barren with endometritis, for comparison with those from pregnancies. Diagnostic potential will be assessed using gene expression microarrays, quantitative RT-PCR and immunohistochemistry, resulting in complementary deliverables of ultrasonographic and proteomic diagnostic methods.

Objectives 1. To define protein profiles of equine uterine secretions of non-pregnant mares during the estrous cycle and prolonged luteal phases, and compare these with profiles from the same mares while normally pregnant or during prostaglandin-induced pregnancy failure.

2. To establish uterine flush protein profiles of barren mares with endometritis for comparison with those of normal mares in order to define a subset of potential biomarkers that correlate with poor pregnancy health.

3. To test the hypothesis that, from Day 18 of gestation, failing pregnancies involve compromise of the developing circulatory system in the conceptus and in the local endometrium of the mare that can be detected by colour-Doppler ultrasonography.

50 For more information, please visit www.uoguelph.ca/research/PSA

Benefits The equine industry contributes $19 billion/year to the Canadian economy and supports over 154,000 jobs.

Of the national herd (~ 1 million horses) ~22% are in Ontario. The Ontario horse-racing industry alone (using ~13% of the province’s horses) has been credited with $2 billion of recurrent expenditures in 2010 dollars, and is responsible for over 31,400 fulltime (and another 30,000 part-time) Ontario jobs. In the estimate of Econometric Research Ltd, it is among the top four subsectors contributing activities to the rural economy (along with dairy products, fruit and vegetables, soybeans and corn). Efficient reproduction (timely breeding and foaling) is vital to horse production in Ontario. Reproductive failures incur non-productive husbandry expenses for mares that fail to become or remain pregnant ($175/day for a Standardbred, $190/day for a Thoroughbred, $50/day for a farm horse), in addition to the non-productive capital losses and breeding and veterinary expenses. Improved mechanism-based methods for the assessment of uterine health, and for treatment of the underlying adverse effects on the developing embryo, would significantly offset some of these losses. Advances in analytical genetic technology are greatly improving our ability to define the composition of body fluids and identify novel molecular mediators or markers of disease processes. We are using protein mass spectrometry to characterize the composition of uterine secretions obtained by uterine lavage (flushing) and are defining changes that occur during the normal ovulation cycle and early pregnancy.

This work has lead to a mechanistic hypothesis to explain why the equine pregnancy is especially vulnerable to failure in early pregnancy, so we are well positioned to evaluate and correct impaired uterine health in barren mares. Our novel approach towards the development of ultrasonographic and molecular diagnostic methods, and the measurement of uterine levels of harmful inflammation-related proteins produced in barren mares are expected to provide veterinarians with new and less invasive management approaches to these problems. Horse breeders will improve the efficiency of production with fewer barren seasons.

Nutritionists will have new end-points for assessing the effects of diet on fertility, especially important in the context of understanding the “developmental origins of health and disease”.

Co-Funder List • •

NSERC Equine Guelph

51

Team Member 1. Dr. M. Anthony Hayes

University of Guelph UofG Emeritus

2. Dr. James I. Raeside

Collaborators

3. Dr. Brandon Lillie

University of Guelph UofG Faculty (On Campus)

4. Dr. Rudolf O. Waelchli

University of Guelph UofG Research Associate

5. Ms. Heather L. Christie

University of Guelph UofG Technician

UofG Emeritus

6. Dr. Krishnaswamy Narayanan University of Guelph UofG Post Doc Fellow 7. Ms. Bette Anne Quinn

University of Guelph UofG Technician

8. Dr. Eduardo Gastal

Collaborators

9. Tracey Chenier

University of Guelph UofG Faculty (On Campus)

10. Dr. Patrick Hearn

Collaborators

Non-UofG Collaborator

Non-UofG Advisory

52

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Prevalence of Enteric Disease Agents in Ontario Commercial Rabbits: Zoonotic Potential and Impact on Animal Health UofG2011-1205

Funding Program

OMAFRA - U of G Research

Production Systems Animals,Emergency Management rabbit, enteric disease, prevalence, risk Patricia V. Turner University of Guelph 01/05/2012 End Date 30/04/2015

Abstract The Ontario commercial rabbit industry produces an important alternative source of meat, and Ontario farms represent 32% of Canadian operations. Production losses from birth to weaning range up to 36%, largely from infectious enteric and respiratory diseases, and >60% of operations concurrently raise other food animal species, often in the same barns. There are few biosecurity practices in place within the industry and disease control efforts are made more challenging by industry practices including lairage prior to slaughter, transportation of live animals between provinces and to the U.S. for slaughter, and frequent sharing/sale of breeding stock. Further, off-label antimicrobial use for growth promotion and disease control is common. Preliminary industry disease surveys have identified pathogenic bacteria that may be infectious to humans and other agricultural species. In addition, newly emerging potentially zoonotic viruses have been identified in U.S. commercial rabbitries. This project will evaluate prevalence of common and emerging enteric disease agents (bacterial, parasitic, and viral), antimicrobial resistance, and potential risk to humans and other agricultural species. Our goals are to identity potential human and animal risks, improve production practices and human safety, and improve overall animal well-being Objectives a) to survey the Ontario commercial rabbit industry for prevalence of viral, bacterial, and parasitic enteric disease agents from clinically healthy and affected rabbits. We will examine two age groups at two different times of the year; b) to survey the Ontario commercial rabbit industry by questionnaire regarding on-farm euthanasia and deadstock disposal practices, antimicrobial use, and other livestock handling and management practices; c) to characterize isolated pathogenic bacteria and evaluate for anti-microbial resistance and cross-species infection potential;

53 For more information, please visit www.uoguelph.ca/research/PSA

d) to develop and validate specific rabbit hepatitis E and astrovirus PCR assays for rapid, high throughput screening of rabbit tissue/fecal samples; e) to characterize and compare the fecal microbiome from rabbits to evaluate changes in microbial shedding and resistance patterns; and f) to disseminate information to producers to enhance herd productivity, animal health and well-being, and human health and safety Benefits The beneficiaries of this project will be commercial rabbit producers, processors, retailers, feed suppliers, and consumers. Rabbit meat production has been steadily growing in Ontario but is still significantly short of current domestic demand, largely because of infectious disease with resultant loss of animals from birth to market. Consumers purchase rabbit meat as a white meat ‘alternative’; however, off-label and uncontrolled antimicrobial and coccidiostat use are widespread for growth promotion and disease control, and residue testing is minimal. As part of this project, we will be surveying producers for information about antimicrobial use. We will also be evaluating how the rabbit gastrointestinal microbiome changes with antimicrobial use.

Understanding disease prevalence and methods of transmission will enable producers to alter practices to eliminate disease, significantly increasing production efficiency. This will also help to eliminate infections in other co-housed livestock species, which may be susceptible to the same organisms. Evaluation of antimicrobial sensitivity and resistance is expected to provide a more reasoned approach to the use of feed additives, providing greater consumer confidence in this product.

We have had initial discussions with producers at OMAFRA-organized seminars regarding decision-making for euthanizing cull rabbits on-farm. This remains a contentious topic within the industry. Producers do not wish to prolong animal suffering intentionally; however, there are few readily available approved methods that can be used by producers. Based on clinical and gross post mortem evaluations of live submissions to the Animal Health Laboratory, many producers need to develop earlier endpoints for removing sick animals from their herds. A secondary objective for the on-farm visits and survey detailed in this proposal is to heighten producer awareness about this issue. We hope to develop practical decision-trees and training protocols for humanely killing cull rabbits to enhance overall animal well-being.

Finally, there is interest by CFIA and National Farm Animal Care Council in developing a national code of practice for the Canadian commercial rabbit industry. Development has been hampered by a lack of organization, interest and awareness of issues facing the industry. We believe that this project will help to define industry standards for production practices.

54

Co-Funder List • • • • • • • • •

Dr. Patrick Boerlin Dr. Scott Weese Dr. Patricia Turner Ontario Rabbit (Ontario Livestock Alliance) Floradale Feeds, Inc B&W Feed & Seed, Ltd Animal Health Laboratory Public Health Agency of Canada OVC Dean's Office

Team Member 1. Dr. Scott Weese

University of Guelph

University Researcher

2. Dr. Richard Reid-Smith

Laboratory for Foodborne Zoonoses, PHAC, DST

Collaborating Specialist

3. Dr. Marina Brash

Collaborators

UofG Faculty (On Campus)

4. Mr. Brian Tapscott

Ontario Ministry of Agriculture, Food and Rural Affairs

Collaborating Researcher

University of Guelph

Technician

6. Mrs. Jennifer Haley

Ontario Goat

Industry Collaborator

7. Dr. Scott McEwen

University of Guelph

University Researcher

8. Dr. Patrick Boerlin

University of Guelph

University Researcher

5.

Dr. Jutta Hammermueller

55

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

The design and analysis of experiments and observational studies on infectious disease spread in the livestock industries.

UofG2011-1010

Funding Program

OMAFRA - U of G Research

Emergency Management,Production Systems Animals infectious disease modelling; Bayesian statistics Rob Deardon University of Guelph 01/09/2012 End Date 31/08/2015

Abstract To control agricultural infectious diseases, it is vital to understand how they spread through populations and what factors lead to infection. Statistical models, preferably derived from high-quality observed data, such as the individual-level models (ILMs) of Deardon et al (2010), can aid greatly in such understanding. These ILMs can be spatial, contact network-based, and/or include numerous risk factors/covariates besides. They can also facilitate the design of experiments/observational studies for identifying key characteristics of disease systems.

The two overriding objectives of this project are concerned with: 1) Study Design – we plan to use ILM-based simulation studies to determine how best to design populationlevel and herd-level studies in which the aim is to understand underlying infection dynamics of disease systems; 2) Model Development – we plan to extend ILMs to enable the farm-level modelling of systems in which: a) there are multiple diseases/strains that can interact with each other; b) the time-varying infectiousness of individual farms is a key characteristic of the disease system in question, and can also depend upon individual-level covariates such as the number of animals on the farm; c) there is only partial information, and thus uncertainty, about underlying contact network structure.

Objectives 1. Develop an understanding about how best to design within-herd studies to extract maximum information about within-herd disease dynamics. (Theme 2) 2. Develop an understanding about how best to design population-level studies to extract maximum

56 For more information, please visit www.uoguelph.ca/research/PSA

information about between farm/barn disease dynamics. (Theme 2) 3. Develop multivariate infectious disease models to enable the analysis of multiple diseases/multiple-strain disease at the farm level. (Theme 1) 4. Assess how uncertainty about potentially covariate-dependent time-varying infectiousness of individual farms can be best incorporated into analysis of epidemic data. (Theme 1) 5. Assess how uncertainty/partial information about underlying contact networks can be best incorporated into analysis of epidemic data. (Theme 1) Benefits Successfully implemented, the objectives of this project would make the analysis of infectious disease data, and subsequent development of control strategies for a wide range of epidemic and endemic, animal, crop and human diseases, much easier and faster to do than is currently the case. The model development described would also mean that we could have greater confidence in resulting models of disease-spread than would currently be the case. This would be vital in an emergency outbreak (e.g. foot-and-mouth disease), wherein an epidemic, of perhaps an emergent disease, has just begun and the best control methods are not obvious. In such a situation (with quality, informative data), it would be possible to fit ILMs to data from the epidemic as it has so far proceeded, and simulate from the resulting model to study the effect of various control methods (e.g. vaccination programs). Similarly, in a disease-endemic situation (e.g. porcine reproductive and respiratory syndrome (PRRS) in the Ontario swine industry) such models can be used to understand disease dynamics and, thus, help to improve control, and risk-based surveillance systems, of both known, and emergent, strains of the disease. Such models and techniques could also help with understanding the dynamics, and thus control, of pest infestations (e.g. emerald ash borer in Ontario) and crop diseases (e.g. citrus canker). Also, simulation studies to develop control methods can incorporate cost-benefit analyses.

The obvious benefit to the agri-food industries would be an increased ability to control and detect diseases and pests, and thus an increase in yield and economic efficiency. For example, the Royal Society reported that the foot-and-mouth outbreak of 2001 cost ÂŁ3.1 billion to the UK agricultural and the food sectors.

Obvious public health benefits would also accrue in the case of zoonoses (e.g. swine or avian influenza).

Additionally, successful disease control, facilitated by data-driven modelling, would help to minimize public fears that can lead to sales-loss in an outbreak situation.

Finally, this project would result in the training of three PhD students in areas including infectious disease epidemiology, mathematical and statistical modelling, Bayesian inference, and computational statistics.

57

Co-Funder List • • • • •

NSERC NSERC Canadian Swine Health Board Canadian Swine Health Board Poultry Industry Council

Team Member 1. Dr. Michele Guerin

University of Guelph

University Researcher

2. Dr. Zvonimir Poljak

University of Guelph

University Researcher

3. Dr. Pui Sze Kwong

University of Guelph

Post Doctorate Fellow

4. Dr. Bruce McNab

Ontario Ministry of Agriculture, Food and Rural Affairs Advisory

5. Mr. Rajat Malik

University of Guelph

UofG Graduate Student UofG Graduate Student

6. Ms. Lin Zhang University of Guelph

UofG Graduate Student

8. Mr. Razvan Romenscu University of Guelph

UofG Graduate Student

9. Ms. Carolyn Augusta University of Guelph

UofG Graduate Student

7. Ms. Nadia Bifolchi

58

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Complex mathematical and statistical modelling of between-farm disease transmission in the Ontario swine industry.

UofG2013-1471

Funding Program

OMAFRA - U of G Research

Emergency Management,Production Systems Animals swine; infectious diseases; agent-based modelling Rob Deardon University of Guelph 01/07/2014 End Date 30/06/2017

Abstract Farm-level disease transmission models, preferably based on high-quality data, can aid greatly in understanding how diseases spread. They can also facilitate the design of disease control/surveillance strategies for controlling/monitoring disease.

Highly complex models can be constructed that mimic many different possible mechanisms of disease transmission and population dynamics (e.g. spatial-, trade-, animal movement- and/or supplier-based networks). However, data we collect from such systems are usually incomplete; e.g. infection times and/or animal movement data may contain measurement error and/or be only partially observed. Approximate Bayesian computation (ABC) techniques can be used to fit such complex models to only partially observed data, without the substantial computational burden of a full data-augmented Bayesian approach.

Here we propose to develop realistic, complex regional-level animal-movement-based disease transmission models for Ontario swine, testing the plausibility of control and surveillance methods for diseases such as PRRS, PED and influenza. Simultaneously, we will use simulation studies to implement, develop and test ABC methods for fitting disease transmission models to data that might be collected in practice. Finally, the complex Ontario swine models above will be fitted to observed data (e.g. from Niagara region PRRS projects) using ABC methods, and then, risk-based surveillance & control strategies developed.

Objectives O1) Develop complex agent-based meta-population models (AMBs) of Ontario swine industry and disease propagation through such systems (Theme 2).

O2) Test regional-level control/surveillance strategies for diseases such as PRRS and influenza in Ontario swine. (Theme 2).

59 For more information, please visit www.uoguelph.ca/research/PSA

O3) Develop and implement sequential approximate Bayesian computational (S-ABC) methods that can be used to fit complex individual-level/agent-based models (ILM/ABM) to observed disease data. (Theme 1).

O4) Validate S-ABC approach via spatial/network ILM-based simulation studies (Theme 1).

O5) Apply S-ABC/ABM approaches to real data to gain insights into how to control PRRS (and other diseases such as PED, pending data availability) in Ontario swine industry. (Themes 1 & 2).

O6) Apply S-ABC/ABM approaches to real data to gain insights into how to carry out risk-based surveillance for PRRS (and other diseases such as PED, pending data availability) in Ontario swine industry. (Themes 1 & 2).

Benefits Traditional methods of fitting infectious disease models to data (e.g. data-augmented MCMC) are often impracticably slow and cumbersome to implement in the typical situation where data is only partially observed (e.g. due to reporting delays, under-reporting, unobserved infection times/networks, etc). The implementation of this theme's objectives would enable such analyses, and subsequent development of disease control and surveillance strategies, to be much more easily and speedily carried out than is currently the case. Further, the use of robust statistical methods for data-fitting/-testing these complex models would facilitate far greater confidence in determining what conclusions can be reasonably drawn from them than typically possible currently.

This would be vital in an emergency outbreak (e.g. FMD or PED), wherein an epidemic, of perhaps an emergent disease, has just begun and the best control methods are not obvious. In such a situation, it would be possible to fit disease models to data on an epidemic as it has so far proceeded, and simulate from the resulting model to study the effect of various control methods (e.g. vaccination programs). Such models and techniques could also help with understanding the dynamics, and thus control, of pest infestations (e.g. emerald ash borer in Ontario) and crop diseases (e.g. citrus canker). Also, simulation studies to develop control methods can incorporate cost-benefit analyses. Further, simulation from models can be used to develop effective risk-based surveillance systems.

The obvious benefits to the agri-food industries would be an increased ability to control and monitor diseases and pests, and thus an increase in yield and economic efficiency. For example, the Royal Society reported that the foot-and-mouth outbreak of 2001 cost ÂŁ3.1 billion to the UK agricultural and the food sectors. Obvious public health benefits would also accrue in the case of zoonoses (e.g. swine or avian influenza). Additionally, successful disease control, facilitated by data-driven modelling, would help to minimize public fears that can lead to sales-loss in an outbreak situation.

Finally, this project would result in the training of a PhD student in areas including infectious disease epidemiology, mathematical and statistical modelling, (approximate) Bayesian and computational statistics, and the swine industry.

60

Co-Funder List • • •

Swine Innovation Porc NSERC NSERC - TBR

Team Member 1. Dr. Zvonimir Poljak University of Guelph UofG Faculty (On Campus) 2. Dr. Jane Carpenter Collaborators

Non-UofG Advisory

3. Dr. Pui Sze Kwong University of Guelph UofG Post Doc Fellow

61

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Characterizing Streptococcus suis from clinical cases and healthy-carrier pigs UofG2013-1497

Funding Program

OMAFRA - U of G Research

Production Systems Animals,Emergency Management S.suis,swine,serotype,virulence factors, antimicrobial resistance Robert Friendship University of Guelph 16/06/2014 End Date 28/04/2017

Abstract Losses due to diseases caused by Streptococcus suis are economically significant, and yet S. suis is commonly present on tonsils and in the respiratory tract of healthy pigs with no clinical effects. The serotypes and strains of S. suis vary in their ability to cause disease, and virulence factors (VFs) of S. suis are poorly understood. Likewise, outbreaks of S. suis disease tend to be triggered by complex environmental, management, and host factors which are not well understood.

The objectives of this study are: to investigate the distribution of S. suis serotypes, virulence factors, and antimicrobial resistance (AMR) profiles from clinical cases and healthy-carrier pigs; to determine the ability of a new multiplex PCR to identify S. suis serotypes; to investigate risk factors and treatment measures used on Ontario farms.

Nasal and tonsil swabs from healthy pigs and samples from clinical cases on 50 Ontario farms will be cultured for S. suis. Isolates from clinical cases across Ontario will also be included in the study. The isolates will be serotyped and tested for VFs and AMR. Furthermore, a survey will be conducted to examine on-farm risk factors, treatment-control strategies, and economic impact of S. suis infections on the study farms.

Objectives The overall objective is to investigate characteristics of Streptococcus suis isolated from clinical and healthycarrier pigs, as well as investigate risk factors associated with disease outbreaks and control measures commonly employed.

The specific objectives: 1)To determine the differences between S. suis isolates from clinical cases and isolates from healthy pigs including antimicrobial resistance patterns, virulence factors and serotypes (to improve our therapeutic approach and how we select strains for autogenous vaccines)

62 For more information, please visit www.uoguelph.ca/research/PSA

2)To investigate the agreement between coagglutination method and multiplex PCR for serotyping S. suis (to improve our diagnostic abilities in investigating outbreaks of disease) 3)To determine management and environmental conditions associated with outbreaks of streptococcal disease and to document the common approaches used to control an outbreak including therapeutics and management changes (in order find better methods of preventing and controlling S. suis diseases and reducing antibiotic use) Benefits Pork producers, veterinarians and the general public stand to benefit from the increased knowledge gained from this research regarding the prevalence of various strains and serotypes of Streptococcus suis isolated from healthy pigs and clinical cases. One priority that this research addresses is to “develop alternative methods that effectively and economically reduce the risk of infectious disease”. We will attempt to identify virulence factors and other characteristics to allow better differentiation of S. suis into pathogenic and nonpathogenic strains. Hopefully this will improve diagnostics and ensure more appropriate isolates are included in the creation of autogenous vaccines. Identifying antimicrobial resistance patterns will help producers and veterinarians make wise choices regarding treatment.

A second priority is to “investigate housing environments and management practices that meet health and welfare needs” and this project will attempt to identify the environmental or management indicators as well as the host factors that are associated with S. suis disease outbreaks”. This information should help veterinarians in developing preventive strategies that do not necessarily rely on antibiotics. Preventing disease through environmental and housing changes and host immunity can potentially result in major economic savings for the producer through reduced mortality and improved growth performance.

Other priorities that are met by this study include “worker safety” in that S. suis is a potential zoonotic pathogen, and “maximize profits” because streptococcal diseases are a major cause of pig mortality on many farms. One other benefit of this study is the development of a new, efficient and less expensive method for serotyping S. suis isolates in pigs and this should benefit diagnostic labs as well as those companies producing vaccines.

In summary the benefits resulting from this work include a better understanding of S. suis infection, including diagnostic techniques and strategies to control this economically important swine pathogen and potential human pathogen.

Co-Funder List • • •

Swine Innovation Porc Ontario Pork Mitacs- Accelerate

63

Team Member 1. Prof. Janet MacInnes University of Guelph UofG Faculty (On Campus) 2. Dr. Abdolvahab Farzan University of Guelph UofG Research Associate 3. Dr. Durda Slavic

University of Guelph UofG Other

4. Dr. Jackie Gallant

University of Guelph Non-UofG Collaborator

5. Mr. Glenn Soltes

University of Guelph UofG Technician

6. Dr. Shivani Ojha

University of Guelph UofG Post Doc Fellow

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Molecular pedigree analysis for the establishment of an elite rainbow trout broodstock with maximal growth and spawn-timing performance UofG2011-1141

Funding Program

Production Systems Animals pedigree analysis; growth; spawn-timing; Roy Danzmann University of Guelph 01/06/2012 End Date

OMAFRA - U of G Research

QTL 01/05/2015

Abstract Selection programs for aquaculture species in Canada are relatively underdeveloped at the current time.

While certain nations sponsor government-based research into the improvement of commercial stocks (e.g., China, Iceland, Denmark, Norway, Sweden and the United States) no such program exists in Canada. The major commercial strain of rainbow trout in Canada (i.e., LYNDON strain) is located in Ontario, and fish within this strain have recently been selected to achieve spawning on almost an entire circannual cycle.

Growth improvement in this strain has however lagged as a result of this single intensive selection goal. The current research is directed at identifying broodstock within the ‘tail-ends’ of the LYNDON strain spawning cycle that have superior growth alleles. Once identified, these broodstock will form the nucleus for an innovative quantitative genetic selection program aimed at maximizing growth performance and production efficiency while maintaining the current broad spawning distribution.

Objectives Within the past 5 years LYNDON Fish Hatcheries has launched a vigorous stock enhancement program to increase their female broodstock numbers from a starting base of approximately 600 fish to a target of 3000 fish in the 2012/13 breeding season. During this time period, the priority goal was to achieve year-round egg production, and growth enhancement, although important, was not the major target of selection. As such, many of the newly added female family lines were not selected for superior growth. The goal of the current research is to identify individual broodstock across the entire LYNDON strain spawning cycle that possess the best growth genotypes. This will be achieved using a combination of molecular genetic pedigree analysis and quantitative genetic evaluation methods. The marketable product for the industry will be superior growing progeny from selected broodstock.

Benefits

65 For more information, please visit www.uoguelph.ca/research/PSA

The research will enhance the PRODUCTION SYSTEM of Ontario rainbow trout aquaculture by increasing production efficiency through: a) benchmarking growth and spawning performance in the LYNDON strain; and b) selecting superior genetic resources that maximize growth efficiency. It will improve genetic technologies by: a) determining genetic relationships among superior broodstock and establishing a pedigree for use in advanced genetic evaluation; b) using known QTL regions to enhance selection for growth and spawning time; c) incorporating new growth traits into genetic evaluation; and d) providing baseline data on the genetic variability existing in the major Canadian farmed rainbow trout strain.

Growth of rainbow trout at Ontario’s aqua-cage facilities is variable dependent on the time of year production lots have been obtained from broodstock hatcheries. Ontario’s rainbow trout are known to have variable growth rates dependent upon seasonal spawning times. Fall spawning fish are superior in growth compared to winter/spring spawning fish. This research will improve the growth performance of progeny derived from sping/winter spawning fish in the largest egg-producing hatchery strain in Ontario (i.e., LYNDON strain). This will increase the profitability of aqua-cage growers in Ontario by reducing the time they need to rear winter/spring lots of fish to market size. This will increase their profit margins by reducing their total feed costs for production, thus minimizing excess food wastage to produce fish of comparable size with ‘slower-growing’ genetic backgrounds. Thus, there are eco-advantages to rearing faster growing more food efficient fish, as food wastage will be minimized.

The establishment of a genotyping database for the LYNDON strain will also predicate the first steps towards international establishment of ISO certification as a ‘genetically-characterized’ strain. This would enhance and accelerate future research directives aimed at other trait improvement studies such as disease resistance development, delay of maturation improvement, continued year-round egg production improvement etc. All of these research objectives would help improve Ontario’s fish-farming industry by providing a stable year-round production of fingerlings, that have maximal growth efficiency, along within continued enhancement of other growth improvement traits, and consumer assurance of quality with regard to genetic standards established for the strain.

Co-Funder List • •

Lyndon Fish Hatcheries Inc NSERC

Team Member

66

1. Dr. Stephen Miller University of Guelph Collaborating Researcher 2. Dr. Cheryl Quinton University of Guelph Post Doctorate Fellow 3. Ms. Xia Yue

University of Guelph Technician

4. Mr. Clarke Rieck

Collaborators

Industry Collaborator

5.

Collaborators

Industry Collaborator

6. Ms. Anne Easton

University of Guelph Technician

67

Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Enhancing the efficacy of poultry vaccines using innate immune adjuvants UofG2011-1220

Funding Program

Production Systems Animals avian influenza, immunity, vaccination, Shayan Sharif University of Guelph 02/07/2012 End Date

OMAFRA - U of G Research

03/07/2015

Abstract Vaccination is an integral part of poultry production in Ontario. Despite the widespread use of vaccines for maintenance of poultry health, vaccination is not able to eliminate the risk of pathogen transmission to other flocks or, in the case of zoonotic pathogens, to humans. Moreover, it has been shown that some routinely used vaccines in poultry, such as Marek’s disease (MD) vaccine, might have led to heightened virulence of the pathogen. We propose to investigate ways to enhance vaccine-conferred immunity against MD and avian influenza (AI), two diseases with significant impact on the poultry industry. We will examine a series of microbial products, pathogen-associated molecular patterns (PAMPs), to identify compounds with superior immune enhancing capabilities. We will use these novel compounds to enhance efficacy of vaccines against MD and AI. Special emphasis will be placed on developing formulations that could disrupt replication and transmission of the above viruses.

Objectives The overall objective of this study is to develop novel immunological compounds for inclusion in poultry vaccines. The specific aims are to: 1- screen various PAMPs for their immunostimulatory activities, 2evaluate efficacy of PAMPs for enhancement of immunity conferred by MD vaccines leading to reduced virus transmission, 3- investigate the utility of PAMPs to enhance immunogenicity of AIV vaccines and protection elicited by these vaccines.

Benefits Chickens raised in Ontario receive a significant number of vaccines in their lifetime. However, most of the currently available vaccines are not able to disrupt transmission of pathogens from vaccinated to nonvaccinated flocks or perhaps to humans (e.g. avian influenza vaccines) and some vaccines may drive the pathogen towards enhanced virulence (Marek’s disease vaccines). In addition, breakdown of vaccineconferred immunity is a problem, leaving the vaccinated flocks susceptible to occurrence of disease. In the proposed research, we aim to identify potent and robust immune enhancers that could potentiate protective efficacy of vaccines in a safe and cost-effective manner.

68 For more information, please visit www.uoguelph.ca/research/PSA

Co-Funder List • • •

Poultry Industry Council CPRC and Agriculture and Agri-Food Canada NSERC

Team Member 1. Dr. Douglas Hodgins University of Guelph

Post Doctorate Fellow

2. Mr. Michael St. Paul University of Guelph

Graduate Student

3. Dr. Jennifer Brisbin University of Guelph

Post Doctorate Fellow

4. Dr. Neda Barjesteh University of Guelph

Graduate Student

5. Dr. Csaba Varga

Ontario Ministry of Agriculture, Food and Rural Affairs Collaborating Specialist Industry Collaborator

6. Dr. Cynthia Philippe OMAFRA

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Probiotics for enhanced poultry health UofG2013-1650

Funding Program

Production Systems Animals Chickens, probiotics, Lactobacilli, immunity, health Shayan Sharif University of Guelph 01/12/2014 End Date

OMAFRA - U of G Research

30/11/2017

Abstract In poultry production, interest in probiotics stems from their use as alternatives to antibiotic growth promoters and as a strategy for control of intestinal colonization with enteric microbes that cause foodborne illness in humans, such as Salmonella and Campylobacter. Probiotic bacteria can also promote general health and enhance immunity against disease causing microbes. However, a limited number of probiotic products are available with proven immune enhancing capabilities. We have previously investigated commensal lactobacilli for their immunomodulatory activities and have developed a formulation with the ability to enhance immune responses and reduce Salmonella burden in chickens. The proposed studies are designed to further develop this formulation into a commercial probiotic for chickens that can enhance production, reduce colonization with food-borne pathogens and enhance immune competence. To this end we will evaluate this probiotic formulation to determine its safety, optimal route of administration, effects on growth and feed efficiency, and immune responsiveness. Finally, we intend to test this formulation in settings similar to commercial poultry operations.

Objectives The long-term objective of this research is to develop cost-effective commercial probiotic formulations for chickens that can enhance production, reduce colonization with food-borne pathogens and enhance immune competence.

The short-term objectives are: The long-term objective of this research is to develop cost-effective commercial probiotic formulations for chickens that can enhance production, reduce colonization with food-borne pathogens and enhance immune competence. The short-term objectives are: 1- To verify the safety of all members of the selected cocktail of lactobacilli to ensure their suitability for use as a commercial probiotic product, 2- To investigate the optimal delivery route and dosing of the selected cocktail of lactobacilli, 3- To assess whether probiotics containing lactobacilli administered via the selected (objective 2) delivery route(s) and dose(s) influence growth performance and vaccine efficacy under field conditions.

70 For more information, please visit www.uoguelph.ca/research/PSA

Benefits Antimicrobial growth promotants have been used for several decades in poultry and swine production.

However, the spread of antibiotic resistance threatens human health and has caused great concerns over the use of dietary antibiotics in livestock, including poultry. Therefore, recommendations to restrict dietary antibiotics have recently been proposed to Health Canada. In addition, the poultry industry in Canada has identified gut health, antibiotic replacement and mode of action of alternative products as one of its priority areas. Over the last decade, our group has conducted extensive research on basic mechanisms of probiotic bacteria interactions with the host as well as applied aspects of development of efficacious probiotic formulations. We have now developed a formulation of several lactobacilli, which has shown very promising results in proof of concept studies. We now plan to extend our previous research and further test its efficacy in experimental and commercial settings. Overall, there are two main perceived benefits of the proposed studies to the Ontario poultry industry: Directly, by developing efficacious probiotics that possess enhance production and immune competence as well as the ability to reduce food-borne pathogen carriage in chickens; indirectly, by the training of highly qualified individuals who would serve Canadian academic, diagnostic, and industrial institutions in the future. In terms of direct economic return, based on the amount of the annual chicken meat production in Canada and cost-benefit analysis of probiotic use (~$0.01 lower cost of production/kg body weight), a very conservative estimate predicts that the use of this formulation would reduce the cost of chicken meat production in Canada by ~$12 million/year. This does not include the reduction in costs associated with control of food-borne pathogens. From the pure academic point of view, this research will shed light on some of the basic mechanisms of immune system interactions with commensal microbes. This is of great interest to immunologists and microbiologists, because it can elucidate why the host immune system can tolerate these microbes. This knowledge may then be used for other applications that involve suppressing immune responses. Also, this research will lead to development of novel methods for disease control.

Co-Funder List • •

Canadian Poultry Research Council NSERC

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Team Member 1. Dr. Jennifer Brisbin

University of Guelph

UofG Post Doc Fellow

2. Dr. Douglas Hodgins

University of Guelph

UofG Post Doc Fellow

3. Dr. Neda Barjesteh

University of Guelph

UofG Graduate Student

4. Dr. Tamiru Alkie

University of Guelph

UofG Post Doc Fellow

5. Dr. Bahram Shojadoost University of Guelph

UofG Post Doc Fellow

6. Mr. Albert Dam

Ontario Ministry of Agriculture, Food and Rural Affairs OMAFRA Staff

7. Ms. TBA TBA

University of Guelph

UofG Graduate Student

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Best Management Practices for Control of Nuisance Flies in Poultry Production UofG2013-1426

Funding Program

Production Systems Animals house flies, IPM, control, poultry Simon Lachance University of Guelph 14/01/2013 End Date

OMAFRA - U of G Research

01/05/2015

Abstract The project will assess the efficacy of integrated pest management (IPM) programs and methods for the control of nuisance and disease transmitting pest flies in duck production. Flies can compromise the health and well-being of poultry animals, as well as of workers and neighboring residents.

Innovative, simple, safe and economically sound technologies will be evaluated and developed for Ontario poultry producers, to provide recommendations within a best management program. Methods implemented and tested in poultry barn will include biological control agents (parasitic wasps, predatory beetles), bio-insecticides formulated in baits, natural products, mechanical methods, synthetic insecticides and environmental manipulation to decrease the suitability of barns to fly breeding. All life stages of the flies will be targeted, with the objective of diminishing fly populations before they reach adulthood (the nuisance stage) and find their way out of the barn and settle at neighboring residences of businesses. Muscovy duck production, the cause of several recent complaints by neighbours, will be the main target. The effect of the methods on animal health and biodiversity of insects in manure will be also measured, as well as the economic and environmental benefits.

Objectives Develop a best management program for controlling filth flies in duck production, using a sustainable combination of practical methods that are economically feasible for producers and that target all life stages of the fly cycle.

Specific objectives are to evaluate: a) Predator and parasitoid performance in dry duck manure (hister beetles, parasitic wasps); b) Baited insecticides, synthetic and natural, and their use as a curative method at the end of duck production cycle to limit fly dispersal; c) The suitability of solid manure for fly breeding; d) Management techniques rendering the manure less suitable for fly breeding (drier manure through air flow, acidification), and to increased opportunity for parasitization; e) The impact of methods on biodiversity of beneficial insects in duck litter;

73 For more information, please visit www.uoguelph.ca/research/PSA

f) Dispersal of house flies from source farm, outdoor sampling methods and antibiotic resistance level of bacteria collected from flies; g) The economic costs of pest management practices Benefits Innovative, simple, safe and economically sound technologies will be evaluated and developed for all poultry producers, to provide recommendations for a best management practices program. Promising methods implemented and tested in duck barn will include biological control agents (parasitic wasps, predatory beetles), bio-insecticides formulated in baits and natural products, mechanical methods, synthetic insecticides and environmental manipulation to decrease the suitability of barns to fly breeding. All life stages of the flies will be targeted, with the objective of diminishing fly populations before they reach adulthood (the nuisance stage) and before they disperse and potentially cause public health issues. The effect of the methods on animal health and biodiversity of insects in manure will measured, as well as the economic and environmental benefits.

Because of the financial costs, health, food safety and environmental concerns over the use of synthetic insecticides, efforts will be made to identify and develop reduced-risk strategies for the control of fly numbers. More information and technology transfer on various beneficial insects, fungi, bacteria, and physical and cultural methods that may assist in the control of filth flies will be transferred to producers. The methods evaluated and tested will provide new tools in the management of pests for conventional and organic poultry producers, ultimately resulting in economic gains.

The lessons learned from the trials using ducks as the test production will be easily transferable to other poultry commodities. With more evaluated tools accessible to the Ontario poultry industry, farmers will have the ability to manage fly populations, decrease neighbor tensions, and decrease wash out times between flocks, while protecting food safety, bird health and workers.

Co-Funder List • •

Town of Lincoln Wine Council of Ontario

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Team Member University of Guelph

UofG Faculty (On Campus)

2. Mr. Hugh Fraser

OMAFRA

OMAFRA Staff

3. Mr. Albert Dam

Ontario Ministry of Agriculture, Food and Rural Affairs

OMAFRA Staff

4. Mr. Dan Ward

OMAFRA

OMAFRA Staff

5. Mr. Michael Short

Collaborators

Non-UofG Collaborator

6. Ms. Justine Shiell

University of Guelph

UofG Graduate Student

1.

Dr. Cynthia ScottDupree

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Genomic applications in the feedlot to improve beef quality and efficiency UofG2011-1212

Funding Program

Production Systems Animals Residual Feed Intake, Selection, DNA Stephen Miller University of Guelph 01/01/2013 End Date

OMAFRA - U of G Research

31/12/2016

Abstract Canadian beef producers have a tremendous opportunity to meet the increasing global demand for high quality animal protein products. However, high feed costs and inconsistent quality remain significant challenges. Research has been underway towards addressing these challenges through the use of DNA panels to allow animals to be selected and specifically managed according to DNA profile to increase production efficiency. This proposal will allocate weaned calves based on their DNA profile for efficiency and quality to different nutritional management scenarios and investigate the optimum placement of these calves on a nutritional management regimen to optimize value. This project will demonstrate and evaluate this technology to enable industry adoption.

Objectives This project will demonstrate to producers a practical application of using a DNA panel that predicts genetic differences in feed efficiency (RFI) and beef tenderness. Demonstrated will be the differences in efficiency and tenderness that can be expected with the employment of these technologies. Cattle ranking high and low on these DNA panels will be fed under different common production systems employing different feeding strategies such as high grain, or increased roughage. Management effects tested include the use of implants and beta agonists in the feeding program. The optimum use of the management strategies, in combination with the animals genetic potential for efficiency and quality will be determined so producers can best match animals and management scenario to meet consumer demand for a quality product while improving efficiency and reducing impact on the environment.

Benefits This research will develop methods for the adoption of genomic technologies for the improvement of feed efficiency and beef quality which will benefit many sectors of the beef industry. The Canadian consumer will benefit from a beef product with more desirable beef tenderness, produced more efficiently, offering better value. The processing and retail sectors will be able to further develop branded products to meet the demand for more tender beef. Feedlot operators will feed cattle more efficiently, realizing a savings in feed

76 For more information, please visit www.uoguelph.ca/research/PSA

costs. Cow-calf and seedstock breeders will have increased demand for cattle with desirable genomic profiles.

Co-Funder List • • • •

Canadian Simmental Association Beef Improvement Opportunities Genome Canada Genome Canada

Team Member 1. Dr. Ira Mandell

University of Guelph

UofG Faculty (On Campus)

2.

Collaborators

Industry Collaborator

3. Mr. Tim Caldwell

University of Guelph

Technician

4. Dr. Graham Plastow Collaborators

Non-UofG Faculty/Research Scientist

5. Dr. John Crowley

Collaborators

Non-UofG Faculty/Research Scientist

Collaborators

Non-UofG Advisory

Ontario Ministry of Agriculture, Food and Rural Affairs

Collaborating Specialist

University of Guelph

University Researcher

9. Ms. Narges Zare

University of Guelph

Graduate Student

10. Mr. Duc Lu

University of Guelph

Non-UofG Collaborator

6.

Mr. Tom LynchStaunton

7. Mr. Brian Pogue

8.

Dr. Gordon Vander Voort

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Investigation of the prevalence of heart lesions in market hogs that die in-transit and testing for a genetic association UofG2013-1547

Funding Program

Production Systems Animals In-transit losses, heart lesions, genetics Terri O'Sullivan University of Guelph 02/06/2014 End Date

OMAFRA - U of G Research

02/06/2016

Abstract An "in-transit" loss is a phrase used to describe hogs that perish after leaving the farm but before arriving at the abattoir. The number of pigs that die in-transit increases during the summer months in Canada and as such the cause of death has been attributed to heat stress. An initial pilot study conducted by members of the research team determined that the majority of hogs that died in-transit to an abattoir had cardiac abnormalities. These cardiac lesions were comparable to Hypertrophic Cardiomyopathy (HCM), a genetic heart disease recognized in humans, dogs, and cats. The goals of this research are to determine if there are genetic differences between pigs with HCM-like hearts and normal hearts; to determine the prevalence of HCM-like lesions in pigs from farms experiencing different rates of in-transit losses; and to conduct an onfarm risk assessment of potential management practices contributing to in-transit losses. The project will involve the gross and histological examination of hearts from hogs that die in-transit to an abattoir and compare them to normal hearts. Gene mapping and comparison will be conducted on affected and normal hearts. This research has the potential to improve animal welfare and our understanding of in-transit losses.

Objectives The objectives of the project are to determine: 1. the prevalence of heart failure as the cause of death in market hogs during transport to a federally inspected abattoir, 2. if there are any on-farm handling/management risk factors associated with in-transit losses in hog farms that experience low, medium, and high in-transit losses attributed to heart lesions, 3. if there are genetic differences between market hogs with Hypertrophic Cardiomyopathy(HCM)-like lesions and hogs with normal hearts, 4. if genes associated with HCM in swine are similar to genes associated with HCM in people, dogs, or cats.

78 For more information, please visit www.uoguelph.ca/research/PSA

Benefits The Ontario and Canadian swine industry will directly benefit from the results of this work by being the first to work towards identification of a potential genetic association with Hypertrophic Cardiomyophathy (HCM).

This work will also guide future research towards eliminating any HCM-associated genes through testing and selective breeding programs. By eliminating HCM from the swine population, animal welfare and economic sustainability will be improved. The elimination of the HCM gene(s) from commercial swine has the potential to greatly reduce in-transit losses and thereby demonstrate that animal care and handling during shipping is appropriate. The use of genetic testing in swine has previously been used successfully to eliminate the halothane gene which caused Porcine Stress Syndrome.

In-transit losses in market hogs is a global issue. Reducing or eliminating in-transit losses would provide an economic benefit for the Canadian swine industry over competitors.

Co-Funder List •

Ontario Pork

Team Member 1.

Dr. Robert Friendship

University of Guelph

UofG Faculty (On Campus)

2.

Dr. Tony Van Dreumel

University of Guelph

UofG Adjunct Faculty UofG Adjunct Faculty

3. Dr. Max Rothchild Collaborators

4. Dr. David Alves

5.

Ms. Kathy Zurbrigg

Ontario Ministry of Agriculture and Food and Ministry of Rural Affairs (OMAF and MRA)

UofG Adjunct Faculty

OMAFRA

UofG Graduate Student

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

The effects of alternative feeding strategies for broiler breeders UofG2013-1782

Funding Program

Production Systems Animals Poultry; Welfare; Production; Broiler Breeder Tina Widowski University of Guelph 02/06/2014 End Date

OMAFRA - U of G Research

31/05/2017

Abstract Broiler breeder feed management is an important welfare and economic issue for the poultry industry. In order to limit problems such as obesity, lameness, and ascites, and maintain adequate reproductive capabilities, broiler breeders are feed restricted throughout their production, most severely during the rearing phase, and often exhibit signs of chronic hunger. In Canada, most producers restrict breeders with the use of a non-daily feeding schedule, a practice that is banned in some countries because of its purported insult to welfare. Yet, there has been little empirical data on the welfare implications of such practices, and none in terms of production data in commercial conditions. In this project, we propose to investigate the use of non-daily feeding schedules for female broiler breeders (who comprise up to 90% of the breeding flock) during rearing, in conjunction with promising alternative diets incorporating fibrous bulking agents and appetite suppressants. The effects of these feeding strategies on growth, behaviour, stress physiology, egg production and hatchability, gastrointestinal morphology, and Salmonella colonization will be studied in experimental and simulated commercial conditions to make science-based recommendations to the poultry industry.

Objectives The objective of this project is to develop a better understanding of the effects of alternative feeding strategies on broiler breeder production, behaviour, and physiology. To accomplish this, we plan a series of experiments to answer both fundamental and applied research questions. The objectives for the experiments are: 1) To compare the behavioural and physiological signs of stress and hunger as broiler breeders transition onto and off of different feeding regimens 2) To determine the effect of different feeding strategies on the welfare and productivity of broiler breeders under simulated commercial conditions throughout production 3) To determine the effect of the alternative ingredients on gastrointestinal morphology, and Salmonella prevalence

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This proposal covers the first 3 years of a 5-year project, with the overall objective to investigate the welfare and production implications of alternative feeding strategies on the welfare and production of broiler breeders and their progeny.

Benefits This project directly addresses Animal Health and Welfare (High Priority) through the investigation of management practices (feeding strategies) that meet health and welfare needs This project is related to Production Efficiency (High Priority) in terms of feed production methods that maintain healthy body weights This project is related to Animal Health (High Priority) as alternative feeding regimens may effectively reduce bacterial colonization and increase nutrient absorption An informal survey by the Canadian Hatching Egg Producers (CHEP) found that the vast majority of producers utilize non-daily feeding strategies for broiler breeders, yet there is no empirical data on the welfare implications of this standard practice.

This project will directly benefit the 245 broiler breeder producers in Canada, a third of which are in Ontario.

The Ontario producers supply 38% of the eggs that produce the nation’s more than 650 million broiler chicks annually. Both welfare and flock body weight uniformity are of utmost importance to the industry, and this project will address ways to improve welfare while maintaining uniformity.

Feed restriction in broiler breeders is a major welfare issue for the poultry industry. The CHEP and the Canadian Poultry Research Council have identified feed restriction as a priority research area, and we have worked directly with CHEP and the Ontario Broiler Hatching Egg and Chick Commission in the development of this highly relevant project.

Feed restriction has been identified as a Priority Welfare Issue (PWI) by the combined Code Development Committee and Scientists Committee for the Canadian Code of Practice for the Care and Handling of Poultry (Chickens, Breeders and Turkeys) (National Farm Animal Care Council). During its review of the scientific literature, the Scientists Committee identified broiler breeder feed restriction as a topic with significant gaps in knowledge and forwarded the recommendation for further research. A European Union panel of scientists also identified feed restriction as an area lacking in research. In 2012, the Canadian Poultry Research Council, as representative of the poultry industry, identified poultry welfare as a ‘High Priority’ research area, and broiler breeder feed restriction as a recommended area of research.

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Co-Funder List • • • •

CPRC CHEP NSERC CRD PIC/Livestock Research Innovation Corporation

Team Member 1. Dr. Stephanie Torrey

AAFC Guelph Food Research Centre UofG Adjunct Faculty

2. Dr. Alexandra Harlander University of Guelph

UofG Faculty (On Campus)

3. Dr. James Squires

UofG Faculty (On Campus)

University of Guelph

4. Dr. Victoria Sandilands Collaborators

Non-UofG Collaborator

5. Dr. Henry Classen

University of Saskatchewan

Non-UofG Collaborator

6. Dr. Michele Guerin

University of Guelph

UofG Faculty (On Campus)

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Influence of rearing and housing of parent stock on offspring's phenotype in layer strains UofG2012-1396

Funding Program

Production Systems Animals hen, behaviour, stress, strain, epigenetics Tina Widowski University of Guelph 01/06/2013 End Date

OMAFRA - U of G Research

31/05/2016

Abstract Because of retailers’ requirements and customer expectations regarding the welfare of hens, many Canadian egg producers are adopting enriched and cage-free systems for laying hens. The economic success and bird welfare in these systems requires that the hens are calm, that they adapt well to change and novelty and that they have few behaviour problems. Although it is well established that strain affects flightiness of hens and their tendency to feather peck, there is also a growing body of evidence for epigenetic transfer of behavioural traits to offspring through changes in egg composition when parents are stressed. In a series of studies using commercial hybrids, traditional purebred lines of laying hens and Commercial grandparent stock, we will investigate how housing or acute or chronic stressors affects the characteristics and composition of their eggs and the behavior, stress response and gene expression of their offspring. We also will determine whether offspring behaviour differs with age of breeder flock and whether some genotypes are more sensitive to these effects than others. Our results will be extremely valuable for informing best practices for breeder flocks in order to enhance the welfare of laying hen chicks destined for alternative systems.

Objectives The overall objective is to investigate the transfer of behavioural traits and stress susceptibility from laying hens to their offspring through changes in egg composition and epigenetic mechanisms. We also will determine whether offspring behaviour differs with age of breeder flock and whether some genotypes are more sensitive to these effects than others.

Specific objectives: 1. To determine effects of rearing experience and adult housing system on behaviour, stress reactivity and patterns of gene expression of their offspring.

2. To determine any differences among strains and age of parent flock of commercial hybrids and traditional

83 For more information, please visit www.uoguelph.ca/research/PSA

lines of laying hens in the effects of stressors on behaviour, stress reactivity and patterns gene expression patterns of their offspring.

3. To determine the effect of housing and age of parent flock in two strains of commercial grandparent breeder flocks on behaviour, stress reactivity and patterns of gene expression in their Benefits Over the next decade, the Canadian Egg Industry will face a number of challenges as concern for the welfare of laying hens is changing the ways that eggs are produced and marketed around the world. In addition to legislated changes in the EU and USA, a growing number of Canadian food retailers, manufacturers and consumers now require that eggs be produced in alternative housing systems, and they want assurances about how hens are cared for. A major challenge for producers will be adoption of appropriate housing systems and management techniques for laying hens that not only address ethical concerns around highdensity housing systems, but that also ensure that the industry keep production costs in line and deliver safe, high quality product with minimal impact on the environment. Cage-free systems can incur the highest costs of production as well as poor welfare, particularly when birds have difficulty adapting to the housing system. Behaviour problems in hens in cage-free and enriched housing result lost product, poorer feed efficiency and higher mortality rates. Therefore, identifying best management practices for hens in alternative housing systems is important for both economics and animal welfare.

In 2009, egg farms in Canada generated $588.6 million in total farm cash receipts. Since Ontario egg producers account for 40% of total egg production in Canada, changes in requirements for hen housing will significantly impact the Ontario Agri-Food sector. Many egg producers in Canada are looking to adopt new housing systems for their hens. This research is important for maintaining a viable egg industry during this period of change Co-Funder List • • • • • •

Egg Farmers of Canada Poultry Industry Council LH Gray and Sons Limited Egg Farmers of Ontario Lohmann Teirzucht Canada Canadian Poultry Res Council (CPRC)

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Team Member 1. Dr. Alexandra Harlander University of Guelph

University Researcher

2. Dr. James Squires

University of Guelph

UofG Faculty (On Campus)

3. Dr. Niel Karrow

University of Guelph

UofG Faculty (On Campus)

4. Bas Rodenburg

Wageningen University Non-UofG Collaborator

5. Dr. Gregoy Bedecarrats Collaborators

UofG Faculty (On Campus)

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Strategies for early identification and prevention/treatment approaches to metabolic disease in dairy cows UofG2012-1287

Funding Program

Production Systems Animals ketosis hypocalcemia transition cow treatment Todd Duffield University of Guelph 04/06/2013 End Date

OMAFRA - U of G Research

30/04/2016

Abstract Metabolic disease in the transition period is recognized as one of the major impediments to maximized health, production and profitablility in dairy cows. The two most common and important metabolic problems are hypocalcemia and hyperketonemia, commonly referred to as milk fever and ketosis. These diseases occur at both the clinical and subclinical levels and may affect up to 70% of dairy cows. Cows incurring these conditions are at increased risk of other clinical disease including displaced abomasum and metritis, produce less milk, are more likely to be culled and are less likely to conceive.

Previous research has validated postcalving tests, defined thresholds for metabolic disease and measured disease incidence and impact. More directed research is required to evaluate precalving detection and both treatment and prevention methods. Recently we have discovered that a cowside ketone test is accurate at identifying precalving cows with elevated ketones. Early treatment of these cows may prevent postpartum metabolic disease. Calcium treatment at calving is common on some farms, but little research exists to support and validate its use. Several ketosis treatments exist but until recently there is a paucity of good data to support their use. This study will focus on metabolic disease treatment.

Objectives The following four objectives will be assessed during the length of this project: 1. Measure utility of early detection of disease using commercial rumen temperature boluses 2. Evaluate the efficacy of propylene glycol oral drench at calving in dairy cows for prevention of disease in cows identified at risk of ketosis precalving 3. Evaluate the efficacy of a new calcium solution for mitigation of hypocalcemia associated production losses 4. Assess the utility of adding glucogenic steroids to combined therapy of ketosis with propylene glycol.

The results from these studies will inform both veterinarians and farm managers on methods of early

86 For more information, please visit www.uoguelph.ca/research/PSA

detection and treatment of two of the most common and costly diseases of dairy cows. This research will answer questions on the utility of specific ketosis treatments for their long term benefits.

Benefits This research will benefit producers, veterinarians, dairy advisors and dairy researchers. This research will provide information on multiple aspects of transition cow problems. First, early identification of cows with problems may be possible with indwelling rumen temperature probes. Information on this potential tool and its utility will be provided to all industry partners. Secondly, identification of cows with elevated ketones precalving and efficacy of treatment will be evaluated. If successful, this information program can be implemented by farmers, and also employed by veterinarians and dairy advisors to monitor success of the close-up dry cow program.

The clinical trial on calcium treatment at calving will provide an estimate of hypocalcemia prevalence in Ontario dairy herds and measure efficacy of treatment. This information will be useful to all industry partners. The clinical trials testing ketosis treatments will be primarily useful to veterinarians for refinement of ketosis treatment protocols. However, dairy producers need this information for on-farm treatment decisions. This is especially important if current treatments such as steroids and dextrose therapy prove to be harmful.

Co-Funder List • • • •

Vetoquinol Canada Inc Dairy Cheq Bayer Animal Health Dairy Farmers of Ontario

Team Member 1. Dr. Stephen LeBlanc

University of Guelph University Researcher

2. Dr. Brian McBride

University of Guelph Advisory

3. Dr. Cynthia Miltenburg University of Guelph Graduate Student 4. Dr. Elise Tatone

University of Guelph UofG Graduate Student

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Improving cow health and enhancing nutritional quality of milk through knowledge of dairy cow behaviour UofG2013-1469

Funding Program

Production Systems Animals behaviour, rumination, milk quality, welfare Trevor DeVries University of Guelph 01/06/2014 End Date

OMAFRA - U of G Research

31/05/2016

Abstract There is growing empirical evidence to suggest that the behavioural patterns of dairy cows play a significant role in cow productivity, health, and welfare, and milk quality. Specifically, rumination and diet selection (sorting) behaviour may be linked to subclinical disease in early lactation. The overall objective of this research is to understand the associations of rumination, health, diet selection, and nutritional quality of milk of cows in early lactation. A study will be conducted on commercial dairy farms to determine if rumination behaviour (collected using a commercially available precision technology) can be used to identify cows at risk for subclinical illness and to determine the association of rumination behaviour and nutritional quality of milk. In a second, controlled study we will study how diet selection in early lactation relates to cow health and nutritional quality of milk and if health and nutritional quality of milk are improved when cows are fed a ration in early lactation that stimulates rumination and discourages feed sorting. From these results, improvements in health and welfare of dairy cows, in addition to milk nutritional quality, will not only allow Ontario dairy producers to be more profitable, but also increase consumer confidence in this agricultural sector.

Objectives The overall objective is to understand the associations of rumination, health, diet selection, and nutritional quality of milk of cows in early lactation.

Our specific objectives are to determine: 1) If rumination behaviour can be used to identify cows at risk for subclinical illness.

2) Associations of rumination behaviour and nutritional quality of milk.

3) How diet selection in early lactation relates to cow health and nutritional quality of milk.

4) If health and nutritional quality of milk are improved when cows are fed a ration in early lactation that maintain intake, stimulates rumination, and discourages feed sorting.

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We predict that early lactation cows with reduced rumination activity are at higher risk of subclinical illness.

We also predict that increased rumination activity, in particular as result of consuming a ration that is difficult to sort, will be related to production of less undesirable CLA in milk in early lactation cows.

Benefits This research will create new empirical knowledge addressing all four high-priority research areas for OMAF and MRA Production Systems Research Theme, including animal health, animal welfare, production efficiency, and product quality improvement. Specifically, we will investigate a precision technology tool (rumination behaviour) for monitoring and early detection of subclinical metabolic disorders, as well as identify nutritional strategies to prevent such disorders. The potential economic impact of this is large; particularly given that subclinical disorders, including ketosis and ruminal acidosis, impact a significant portion of dairy cows. These illnesses contribute to lower milk production, increased risk of other disease, reduced reproductive performance, as well as decreased efficiency of feed conversion. Thus, any reductions in the incidence of these illnesses will have a direct effect on increasing producer profitability, particularly in a supply-managed system such as that under which Ontario producers operate. Reduced and early detection of disease contribute directly to improved cow welfare. In addition, this research may also identify a behaviour (rumination) that may be used to measure and benchmark cow welfare. Finally, this research will also target the production of milk that is lower in less undesirable fatty acids, thus, enhance the nutritional quality of this food product. As this research will be conducted under local conditions, the results will be directly applicable to Ontario dairy producers. In all, this research not only has economic benefits to dairy producers, but also societal benefits. Nutritional quality of food products remains a primary factor influencing food choices by consumers. Further, the health and welfare of animals, especially those used in food production, is an area of increasing social concern. This concern is also beginning to affect choices by consumers of the products of animal agriculture. Thus, this research will not only contribute to production of a healthful food product for the consumer, but also satisfy consumers’ interest in purchasing products obtained from animals that have been raised in a humane manner. Thus, this research will help increase consumer confidence in consumption of milk products, helping maintain a strong Ontario dairy sector.

Co-Funder List • • • • •

Dairy Farmers of Canada NSERC Eastgen AAFC Brian McBride

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Team Member 1. Dr. Stephen LeBlanc University of Guelph UofG Faculty (On Campus) 2. Dr. Brian McBride

University of Guelph UofG Faculty (On Campus)

3. Dr. Todd Duffield

University of Guelph UofG Faculty (On Campus)

4. Ms. Emily Kaufman University of Guelph UofG Graduate Student

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Meeting the growing demand for Ontario Water Buffalo meat and milk products through the use of reproductive biotechnology UofG2012-1322

Funding Program

Production Systems Animals water buffalo, reproduction, fertility, seasonality, William Allan King University of Guelph 01/06/2013 End Date

OMAFRA - U of G Research

31/05/2016

Abstract Changing demographics in Ontario has led to a surge in demand for water buffalo (buffalo) products such as milk, cheese and meat, due to distinct qualities unavailable in other milk or meat sources. Hence, buffalo are being introduced into Ontario as an alternative livestock species to provide a local impetus to this growing market potential. However, this demand cannot be met due to the low number of animals in production and poor yield per lactation. The long-term solution is the genetic improvement of local buffalo however, the long, expensive quarantine periods for importation of high producing animals is problematic; reliance on imported animals is unsustainable. As proven in dairy cattle, rapid advances in propagating superior breeding and production animals can be obtained through reproductive technologies such as artificial insemination and embryo transfer. Adaptation of dairy cattle technologies to buffalo is in its infancy due to unique buffalo anatomy and physiology and therefore refinement is required before wide spread application. This research aims to investigate endocrine parameters associated with ovarian function, cyclicity and seasonality as well as establish and validate specific reproductive technologies for the production and transfer of embryos as a precursor to establishing Multiple Ovulation Embryo Transfer breeding systems.

Objectives Reproductive technologies initially developed for genetic improvement of cattle have been applied to buffalo, however, with much lower efficiency and success. Buffalo and cattle differ in a number of anatomical, physiological and behavioral aspects including seasonality that complicates the application of established cattle technologies to buffalo. The overall objectives are to develop effective reproductive techniques for buffalo reared under Ontario climate and management conditions. We will: • determine the impact of season on estrus cycle, follicular growth and conception • establish and validate protocols for ovarian stimulation and fixed-time insemination in and out of breeding season • evaluate quality of oocytes and embryos derived by ovarian stimulation in and out of breeding season

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These studies will provide much needed basic information on the seasonality of the buffalo breeding and fertility to identify appropriate protocols for estrous synchronization and ovulation to ensure calving and milk production through out the entire year.

Benefits There is a large and growing market potential for buffalo milk, cheese and meat products, that encompasses the local restaurant trade and individual households, notably those with Italian and South East Asian heritage. This market has traditionally been met with dairy cow substitutes and imported goods. The demand for local products, particularly fresh milk and cheeses has stimulated development of local artisanal buffalo cheese manufacturing and retail. Further more, being able to label the buffalo milk and meat products as “local food” holds an additional appeal for restaurant and specialty product consumers.

The industry is in its infancy and is being developed by a few farmers, cheese producers and milk suppliers. It is struggling to establish itself and to become sustainable and economically viable. The local and North American market potential is large and as the most sought after cheeses are fresh (eg mozzarella and ricotta) with a very short shelf-life a consistent supply of fresh milk is required. In addition there are a number of local spinoff economic opportunities. These include farm-gate sales of breeding stock, farmlabour employment opportunities and specialized construction such as milking facilities tailored to suit buffalo. At this stage in the development of the industry the most pressing need is to get enough animals on the ground to be able to begin a systematic program of genetic improvement. This can be achieved with minimal input in the form of development of appropriate reproductive technologies and training in their usage. Therefore investment at this stage of the industry will have cost-effective long-term benefits.

Co-Funder List • • •

Federal Economic Development Agency Ontario Water Buffalo (OWB) co Canada Research Chairs

Team Member 1. Pavneesh Madan

University of Guelph University Researcher

2. Dr. Gabriella Mastromonaco University of Guelph UofG Adjunct Faculty 3. Dr. Lesley Gonzalez

University of Guelph Graduate Student

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title Submission number Theme(s) Key words Lead Applicant Organization Start Date

Within-herd dynamics of influenza in nursery herds and effective methods for elimination UofG2013-1491

Funding Program

Production Systems Animals influenza, control, epidemiology, Zvonimir Poljak University of Guelph 04/06/2014 End Date

OMAFRA - U of G Research

03/06/2015

Abstract With multiple viral subtypes and variants affecting swine populations, influenza is becoming a more complex infection; and increasingly difficult to manage. It has recently been hypothesized that influenza virus could also be an important contributor to the development of other important diseases such as streptococcal meningitis in nursery pigs. Therefore, a current and detailed insight into the epidemiology of influenza infection in swine populations is needed. The overall objective of the proposed study is to evaluate patterns of influenza virus circulation in nursery pigs sourced from multiple sow herds. Seventy-five animals will be included in a longitudinal study over 7 weeks. Animals will be uniquely identified and blood sampled three times. In addition, weekly swabbing will be performed; treatments and mortality will be recorded daily.

Serum will be tested for the presence of influenza antibodies and swabs will be tested for influenza virus using MDCK cells. A limited number of positive samples will be plaque-purified, sequenced for three genes (hemagglutinin, neuranamidase, matrix), and analyzed for variability between animals, sources and sampling occasions. From this data, stochastic mathematical model of influenza transmission will be developed to assess effective ways of influenza control, and whether this control could influence Streptococcus suis circulation.

Objectives Objectives 1. To determine whether pigs in the nursery phase between 3 and 10 weeks of age can be repeatedly infected with influenza virus under field conditions.

2. To determine whether there is important genetic differences among viruses that circulate in a nursery barn with multiple sow sources over a period of time or at the same time.

3. To determine to what degree influenza positivity is associated with clinical disease due to Streptococcus suis.

4. To determine the most optimal scenario of influenza elimination from clinical and economical standpoints.

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Benefits First, this research will further elucidate epidemiology of influenza viruses in multi-source nursery herds.

This is important because we currently do not understand the degree of variability in influenza viruses in populations that are mixed from different sources. It is logical to expect that such populations represent a "breeding ground" for new recombinant viruses, but it is not clear whether such populations will regularly produce new recombinants or will just maintain one variant that emerges and is considered as the dominant virus. If the latter is the case, then the degree of variability of the dominant virus is unknown. All this has practical implications as it could influence the choice of vaccine and the entire vaccination strategy.

Secondly, the research will also address whether influenza viruses can repeatedly infect the same animal at different times. Knowledge about influenza viruses suggests that repeated infections with the same virus should not be common. However, swine practitioners frequently argue that there are two waves of influenza circulation in many pig populations, particularly in growing pigs. Certainly, this has been a common finding in this specific study herd. Recent publications/presentations indicate that pigs could be infected repeatedly and this could have large implications for infection control. Thirdly, it was recently suggested that the cells pre-infected with influenza virus showed a bacterial adhesion level that was increased 100 times in comparison to normal cells. The authors argued that influenza infection may facilitate the passage of Streptococcus suis from the respiratory tract into the bloodstream with subsequent bacteremia and septicemia. If this is correct, then influenza virus plays an important role in the pathogenesis of another important swine disease. Finally, data in this study will inform the development of a mathematical model of influenza control. Such model could then be used in order to assess efficacy of strategies under this or similar conditions, but before their field application or concurrently with them. By studying pigs from this system, we will aim to help management of this disease in this system, and in similar ones.

Co-Funder List • • • •

Southwest veterinary Services NSERC Swine Innovation Porc Ontario Veterinary College

Team Member 1. Dr. Robert Friendship University of Guelph UofG Faculty (On Campus) 2. Dr. Eva Nagy

University of Guelph UofG Faculty (On Campus)

3. Dr. Greg Wideman

Collaborators

Non-UofG Collaborator

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Research-to-Go

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Summary of current research funded by the Ministry of Agriculture, Food, and Rural Affairs-University of Guelph Partnership

Project Title

Submission number Theme(s) Key words Lead Applicant Organization Start Date

Development of risk-based and consequence-based approaches to surveillance in swine populations using PRRS virus as a model UofG2011-1031

Funding Program

OMAFRA - U of G Research

Emergency Management,Production Systems Animals Surveillance, PRRSV, disease-control, scenario-trees Zvonimir Poljak University of Guelph 03/09/2012 End Date 04/09/2015

Abstract Regional approach to control and elimination of porcine reproductive and respiratory syndrome virus (PRRSV) has recently grown in North America with respect to number of regions included, and their geographical distribution. One of the most critical issues in these projects is how to perform surveillance in the control zones. A targeted approach has a good potential to increase efficiency of surveillance, but no clear, scientifically-sound recommendations on how to do that are currently available. Our goal is to estimate "surveillance system sensitivity" and other measures of accuracy of alternative approaches to surveillance under two conditions: (1)after completion of elimination, 2)during regional control and elimination. Data for this project will be coming from the Niagara PRRSV project, and will be ultimately analyzed using stochastic scenario trees, and mathematical models. Although addressing endemic disease, the approach and expertise will be developed that could be used for substantiation of disease freedom, when resources need to be optimized; and after possible incursion of exotic diseases, when surveillance resources must be prioritized.

Objectives 1. To summarize epidemiological, biosecurity and diagnostic data from ongoing PRRS ARC&E projects in Ontario with specific purpose of informing design of targeted surveillance activities for PRRSV infection. By extension this information could also be used for design of surveillance for pathogens with similar transmission characteristics as PRRSV (ie. transmission through direct contacts via animal movement, indirect through mechanical vectors, fomites and vehicles, aerosol, and semen).

2. To estimate surveillance sensitivity, and other important parameters, of different approaches towards substantiation of freedom from PRRSV infection AFTER the elimination has been completed in PRRS ARC&E. 3. To estimate surveillance sensitivity, and other important parameters, of different approaches for ongoing surveillance of PRRSV infection in PRRS ARC&E project DURING the process of elimination.

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Benefits Ontario livestock populations have been free from foreign animal diseases for extended periods of time.

Consequently, the most practical approach to build capacity in emergency management is through developing expertise that could be used equivalently in control of endemic diseases and after incursion of an exotic disease. In both scenarios, the rationale is that for efficiency we need to focus on premises with the highest risk. This will be of help to government and industry. Developing risk-based approaches using PRRSV as a model has obvious benefits because of the strong involvement of producers and veterinarians, data availability, and clear needs.

Co-Funder List • •

Ontario Swine Health Advisory Board (OSHAB) NSERC

Team Member 1. Dr. Jane Carpenter

Collaborators

Industry Collaborator

2. Dr. Rob Deardon

University of Guelph

Collaborating Researcher

3. Dr. Pui Sze Kwong

University of Guelph

Post Doctorate Fellow

4. Dr. Robert Friendship University of Guelph

University Researcher

5. Dr. Janet Alsop

Ontario Ministry of Agriculture, Food and Rural Affairs Advisory

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For more information on these projects (including results) and many more please visit: www.uoguelph.ca/ktt/searchRP and www.uoguelph.ca/research/PSA

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