Khafipour et al 2016 effects of grain feeding on microbiota in the digestive tract of cattle animal

Published April 5, 2016

Effects of grain feeding on microbiota in the digestive tract of cattle E. Khafipour,*† S. Li,* H.M. Tun,* H. Derakhshani,* S. Moossavi,† and J.C. Plaizier* * Department of Animal Science, University of Manitoba, Winnipeg, MB, Canada † Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada

Implications • Culture-independent high-throughput sequencing methodologies have recently provided comprehensive insights into microbial communities in the digestive tract of cattle.

• Although the composition and the functionality of the microbiota in the digestive tract of cattle are considered robust, high-grain feeding reduces the richness, diversity, and functionality of these microbiota, and thereby affects animal health and production.

• Cattle vary in their susceptibility to these adverse effects of highgrain feeding.

• Adverse effects of high-grain feeding to cattle can be attenuated, but not prevented, by the use of supplements, such as buffers, yeasts, yeast culture products, direct-fed microbials, and probiotics, as well as by microbiota engineering.

Key words: 16S rRNA gene sequencing, high-grain feeding, hindgut, metagenomics, microbiome, rumen

Introduction In recent years, the potential for milk production of dairy cows has increased substantially throughout the world. In order for these cows to meet their potential, high-energy diets must be fed. This is most often achieved by feeding more concentrates, especially grain, and less forages.

However, these diets can adversely affect the microbiota of the digestive tract, affecting both the composition and functionality of microbiota, and potentially lead to colonization of opportunistic pathogens (Russell and Rychlik, 2001; Plaizier et al., 2008; Krause et al., 2013). Cows rely on their symbiosis with the micobiota in their rumen and intestines, as these microbiotas allow cows to digest fiber, convert non-protein nitrogen into protein, synthesize vitamins, and break down toxic compounds in digesta (NRC, 2001; Russell and Rychlik, 2001; Krause et al., 2013).

Hence, adverse conditions for gut microbiota affect the health, production, and welfare of cows. Until recently, the technology was not available to comprehensively monitor the composition and functionality of microbiota, as many microorganisms cannot be cultured, and quantitative PCR techniques do not target all microorganisms. Recent advances in sequencing technologies offer rapid low-cost molecular-based methodologies that can investigate microbial communities as a whole (Krause et al., 2013). © Khafipour, Li, Tun, Derakhshani, Moossavi, and Plaizier. doi:10.2527/af.2016-0018

These new techniques are either based on high-throughput sequencing of hypervariable regions of highly conserved and universal 16S rRNA genes for bacterial and archaeal communities (Woese and Fox, 1977; Pace et al., 1985), 18S or the internal transcribed spacer (ITS) regions of rRNA genes for fungal and protozoal communities (Firkins and Yu, 2015), or massive shotgun sequencing of total DNA (metagenomics) or RNA (metatranscriptomics) from microbial communities (Desai et al., 2012).

These methodologies can be used to determine changes in the microbial community composition and function under high-grain feeding and identify strategies to reduce the impact of high-grain diets on the microbiota of the digestive tract of high-yielding dairy cows, and, therefore, prevent poor gut health.

Microbiota in the Ruminant Digestive Tract The digestive tract of ruminants is an immunologically active organ system, which is constantly exposed to a multitude of endogenous and exogenous stimuli. The gastrointestinal (GI) tract is also home to a complex and diverse ecosystem of microbes known as the microbiota or microbiome.

The number of bacterial species present in the GI tract of ruminants varies depending on the diet, feeding strategy, and geographical location and has been estimated to be more than 5,000 (Henderson et al., 2015). It is important to note that when we describe the microbiome using omics methodologies, where microorganisms are not directly observed/assessed, we often use “operational taxonomic units” (OTUs) instead of “species.” In this context, a unique OTU is defined as a cluster of sequence reads with a given similarity that is expected to be assigned to a taxonomical level; for instance, sequences with 97% similarity are expected to approximately correspond to species.

Different ecological measures, such as richness, abundance, evenness, and diversity, are used to describe and compare microbiotas among animals and across treatments (Caporaso et al., 2010; Gotelli and Colwell, 2010). Whereas richness refers to the number of different OTUs that are present in a given community, evenness and diversity also take into account the abundances of these OTUs Gut microorganisms differ in their functionality and their ability to use fractions of the substrate resources in the digestive tract (Levine and D’antonio, 1999; Henderson et al., 2015). Hence, a high microbiota richness, evenness, and diversity is considered beneficial, as this enhances the stability of the microbiota, especially during nutritional challenge conditions, and allows it to use limiting resources more efficiently (Russell and Rychlik, 2001; Ley et al., 2006b). A decrease in richness and diversity has been reported in humans with Crohn’s disease (Dicksved et al., 2008; Walker et al., 2011) and type 1 and type 2 diabetes (Giongo et al., 2011). In ruminants, a number of metabolic disorders, such as subacute and acute ruminal acidosis,

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are associated with a reduction in the diversity of rumen and hindgut bacteria (Khafipour et al., 2009b; Azad et al., 2015; Plaizier et al., 2016). That being said, the richness of microbiota has been reported to increase under some intestinal and extra-intestinal inflammation and infections, such as bacterial vaginosis (Ling et al., 2010) and helminthic parasitosis (Lee et al., 2014).

Therefore, diversity and richness indices may hold potential for use as biomarkers for determining the animal's state of health or disease.

Digesta in the digestive tract contain commensal and pathogenic microorganisms and food residues, which impose a continuous immunologic challenge to the host animal (Russell and Rychlik, 2001). An appropriate immunological response, including an immunological response to the content of digesta, requires the capability to distinguish pathogens from commensals as well as “tolerance” to the commensal microbiota (Russell and Rychlik, 2001; Malon et al., 2015).

Significant differences in terms of the composition and the diversity of the normal microbiota exist between the stomach (abomasum) and small intestine and between the foregut (reticulum, rumen, and omasum) and the hindgut (cecum and colon). A relatively lower number and fewer species of bacteria reside in the stomach and the upper small intestine (duodenum and jejunum) due to the specific characteristics of digesta in the foregut and hindgut, including acidity, and the propulsive motion of the region (Russell and Rychlik, 2001; Penner et al., 2014). On the other hand, the foregut and the hindgut are habitat to diverse and densely populated microbiota, composed of bacteria, archaea, fungi, protozoa, and viruses that enable fermentation of digesta (Russell and Rychlik, 2001; Krause et al., 2013; Henderson et al., 2015). The diversity of the rumen microbiome is comparable to that of the cecum and colon when high forage diets are fed, but not when high grain diets are fed (Russell and Rychlik, 2001; Khafipour et al., 2011; Krause et al., 2013). Apart from diversity, the composition of foregut microbiome is different from that of the hindgut with more acid-tolerant bacteria present in the foregut compared with the hindgut (Khafipour et al., 2011). Overall, the bacterial concentration both in the foregut and hindgut of cows reaches 1012–1014 cells/ml of digesta (Krause et al., 2013).

The mammalian intestinal tract is colonized by microbes following birth, and the gut microbiota reach a stable state in a period of time that varies from a couple of months to a couple of years, depending on the host species (Jami et al., 2013; Yáñez-Ruiz et al., 2015). It is now known that both host genetics and environmental exposures, such as the method of birth, diet, and medication use, impact the pattern of initial colonization of the digestive tract, which contributes to the health/disease status of the host (Li et al., 2012; Munyaka et al., 2014; Yáñez-Ruiz et al., 2015).

The role of the gut microbiome in intestinal and extra-intestinal diseases is emerging (Russell and Rychlik, 2001; Krause et al., 2013). The gut microbiome has been shown to impact host physiology, metabolism, and immune function and confer indirect (immune-mediated) and direct resistance against enteric pathogens. Disruption of the gut microbiome or dysbiosis—which is referred to as an abnormal balance of beneficial and protective versus opportunistic members of microbiota—has been linked to a growing number of chronic conditions in humans, such as obesity, insulin resistance, and inflammatory bowel diseases (Brown et al., 2012). In ruminants, the majority of metabolic disorders that occur around early to midlactation, such as acute and subacute ruminal acidosis, milk fat depression, and bloat, are associated with a disturbed rumen microbiome composition and function (Khafipour et al., 2009b; Azad et al., 2015; Plaizier et al., 2016). Dysbiosis of the gut microbiome impacts the profile of metabolites and compounds produced by the microbiota (Plaizier et al., 2008; Plaizier et al., 2012; Saleem et al., 2012). These molecules influence the metabolic and immunological capacities of the host both within and outside of the gut, e.g., through the enterohepatic pathway or gut-brain axis (Collins and Bercik, 2009; Lyte, 2014). Neuroactive chemicals produced by the gut microbiota have been shown to influence hormonal responses of the brain via the gut-brain axis, resulting in an altered hormonal profile (Holzer and Farzi, 2014; Lyte, 2014). This not only impacts the diversity and behavior of the microbiome in the digestive tract, but can also potentially influence the microbiomes of other body sites, such as the vaginal tract and mammary system, resulting in initiation or progression of infectious diseases, e.g., mastitis (Derakhshani et al., 2016). As such, the gut microbiome can be considered the largest endocrine organ in the body (Lyte, 2014).

Effects of High-Grain Diets on the Physiological Conditions in the Foregut and Hindgut of Cattle

Anaerobic culturing facility (source: © 2016 khafipourmicrobiomelaboratory.com).

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The substitution of forages with grain in cattle diets increases the starch content of digesta and the proportion of the dietary dry matter that is fermented in the foregut and the hindgut (Plaizier et al., 2008; Plaizier et al., 2012). This increases the production of organic acids, such as volatile fatty acids and lactic acid, in the rumen. Consequently, these acids accumulate, as the capacity of the rumen mucosa to absorb these acids is limited. Accumulation of these acids decreases the pH and increase the osmolality of the digesta in the rumen (Plaizier et al., 2008; Plaizier et al., 2012; Mao et al., 2013). Cows on a high-grain diet will also chew less than cows on a forage-based diet. Chewing stimulates the production of saliva, which acts as a buffer for digesta in the rumen. Hence, lowering the forage content of the diet will also lower the pH of the rumen (Plaizier et al., 2008). Feeding high-grain diets, therefore, may lead to subacute ruminal acidosis (SARA), a metabolic disorder characterized by a reversible rumen pH depression for extended periods each day (Plaizier et al., 2008; Plaizier et al., 2012).

Metabolomic research (Ametaj et al., 2010; Saleem et al., 2012) has shown that increased grain feeding increases the concentrations of a large

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number of metabolites in rumen digesta, including glucose, maltose, uracil, xanthine, ethanol, phenylacetate, methylamines, phenylacetylglycine, nicotinate, glycerol, fumarate, putrescine, ethanolamine, and several short-chain fatty acids, and disrupts the amino acid profile. While many of these metabolites are substrates for beneficial microorganisms and can be utilized by the cow, some are toxic and inflammatory. Large increases in grain in the diet of cattle have also been shown to increase the content of bacterial endotoxins, such as lipopolysaccharides (LPS) in the digesta of the rumen and hindgut (Plaizier et al., 2008, Plaizier et al., 2012; Saleem et al., 2012; Plaizier et al., 2014).

In summary, excessive grain feeding can benefit some microorganisms by providing more substrate and specific niches, but it can be detrimental to microorganisms that rely on fiber and are sensitive to a low pH of digesta or any of the gut metabolites and compounds whose concentrations are increased by grain feeding.

Effects of High-Grain Diets on the Microbiota in the Foregut and Hindgut of Cattle As mentioned earlier, culture-independent, high-throughput sequencing methodologies allow for the determination of richness and diversity of the entire microbiota. More importantly, the functional capacity of the microbiome can be characterized, and compositional changes that result in significant change in the function of the community can be determined. Many studies have shown that feeding high-grain diets to cattle reduces the richness, evenness, and diversity of the microbiota of the foregut, hindgut, and feces (Khafipour et al., 2009b; Fernando et al., 2010; Mao et al., 2013; Petri et al., 2012; Li et al., 2016); hence, transforming these microbiotas into a less functional state (Levine and D’antonio, 1999). However, the magnitudes of these effects vary among studies and among cows within experiments (Khafipour et al., 2009b; Petri et al., 2012; Plaizier et al., 2016). These variations are, in part, due to host–microbiota coevolution throughout the course of life that results in codifferentiation or codiversification of host–microbiota in an individualized manner (Zaneveld et al., 2008). As a result, the susceptibility of cows to these reductions, and the resilience of the microbiota to the dietary changes differs. That being said, some of the conflicting and inconsistent results among studies may be caused by other factors, such as variations in the inclusion rate and the type of grain; differences between experimental approaches, including those used for microbiota characterization, such as DNA extraction methodology, standardization of amount of DNA for sequencing, and the choice of primers used (universal bacterial primers vs. target-specific primers; or different choices of hypervariable regions of 16S rRNA gene); and the small scale of these studies.

The gram-negative Bacteroidetes and the gram-positive Firmicutes are the most abundant phyla in digesta of the foregut and hindgut of cattle. Together, they represent between 76.0 and 96.1% of bacteria in these digesta (Khafipour et al., 2009b; Mao et al., 2013; Petri et al., 2012; Plaizier et al., 2016). Mao et al. (2013) and Li et al. (2012), reported that excessive grain feeding increased the relative abundance of Firmicutes and decreased that of Bacteroidetes, and, thereby, increased the Firmicutes to Bacteroidetes ratio. Limited studies, however, (e.g., Fernando et al., 2010), reported the opposite. A recent study (El Kaoutari et al., 2013) examined the carbohydratedigestive capacity of a simplified mini-microbiome. The authors reported that members of phylum Bateroidetes had higher mean glycoside hydrolases (GHs) and polysaccharide lyases (PLs) genes per genome as well as signal peptide-containing GHs and PLs compared with the members of the

phylum Firmicutes or any other bacterial phyla in the GI tract. The authors further suggested that members of phylum Bacteroidetes are the primary degraders of complex polysaccharides in the plant cell wall due to a greater range of GHs and PLs in this phylum. As cattle rely on these enzymes for efficient degradation and digestion of fiber, an increase in the Firmicutes to Bacteroidetes ratio in the digesta is undesirable. A recent survey of the rumen and foregut microbial communities of 742 samples collected from 32 species across 35 countries from different geographical regions (Henderson et al., 2015) reported that the most relatively abundant taxa within the rumen microbiota were the genera Prevotella (phylum Bateroidetes) followed by Butyrivibrio and Ruminococcus (both from phylum Firmicutes). The data also indicated that the order Bacteroidales (phylum Bateroidetes), which includes species encoding a broad range of plant polysaccharide-degrading capabilities, as well as the family Ruminococcaceae (phylum Firmicutes) were the most relatively abundant taxa in all forage-fed animals. In cattle, genus Fibrobacter (gram-negative phylum Fibrobacteres), which includes cellulose degraders, was abundant in forage-fed cattle, and its proportion declined in concentrate-fed animals. In concentrate-fed animals, members of the genus Prevotella (phylum Bateroidetes) and family Succinivibrionaceae, which are major producers of propionate and the propionate-precursor succinate, were more abundant.

When cattle are fed high amount of grains, the relative abundances of the members of the phyla Bacteroidetes and Fibrobacter in the microbial communities in the digestive tract decline, allowing Firmicutes and other opportunistic phyla, such as gram-negative Proteobacteria, to proliferate faster per unit of time resulting in an increase in the proportions of Firmicutes and Proteobacteria (Russell, 2007; Khafipour et al., 2009b).

Under SARA conditions, the decline in the proportions of Bacteroidetes and Fibrobacteres in the community in the rumen is severe, resulting in a dysbiotic community with loss of function (Khafipour et al., 2009b).

Members of phylum Proteobacteria have diverse metabolic functions (Russell and Rychlik, 2001; Khafipour et al., 2011) and together with the phylum Bacteroidetes and Fibrobacteres are the major contributors to the free LPS pool in the rumen and hindgut digesta. These endotoxins are part of the outer membrane of the gram-negative bacterial cell wall, which in their free form acts as an immunogenic compound (Hurley, 1995). They are extensively shed during the logarithmicand stationary phases of bacterial growth and also released following cell disintegration and lysis (Hurley, 1995; Plaizier et al., 2012). Previous reports indicate that the LPS content of the rumen

Source: anon, via Wikimedia Commons.

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and hindgut digesta increases during high-grain feeding. This is in part due to release of LPS during the logarithmic growth phase, which results in a higher absolute number of gram-negative bacteria in the rumen and hindgut (Plaizier et al., 2008; Plaizier et al., 2012). This increase, however, might not necessarily translate into a higher proportion of these bacteria in the community. In particular, Mao et al. (2010) and Li et al. (2013) reported that large increases in grain feeding increased the abundance of Proteobacteria, whereas Khafipour et al. (2009b) and Plaizier et al. (2016) did not observe this effect.

Feeding high-grain diets also decreases the populations of ciliate protozoa (Hristov et al., 2001; Khafipour et al., 2009b; Plaizier et al., 2016). This can aggravate the impact of these diets as protozoa contribute to the stability of rumen conditions by storing starch granules (Russell and Rychlik, 2001).

It appears that diet is the main factor in shaping the rumen microbiome (Henderson et al., 2015) and the composition of the core members of this community is relatively stable in adult animals (Petri et al., 2012).

In rumen digesta, Prevotella is the most abundant genus of Bacteroidetes, and Ruminococcus is the most abundant genus of Firmicutes (Petri et al., 2012; Mao et al., 2013; Plaizier et al., 2016). However, this does not hold true for hindgut digesta, where higher bacterial diversity is observed (Plaizier et al., 2016). Seemingly, grain feeding is in general associated with increases in the relative abundances of Prevotella, Sharpea, Ruminococcus, Shuttleworthia, Bifidobacterium, Atopobium Pseudobutyrivibrio, Selenomonas, and Megasphaera and reductions in Treponoma, Anaeroplasma, Papilibacter, Acinetobacter and Lentisphaera, although the results highly depend on the level of grain feeding (Petri et al., 2012; Mao et al., 2013; Plaizier et al., 2016).

Studies on the abundances of individual species of bacteria have mainly been conducted using real-time quantitative PCR (qPCR), as highthroughput sequencing of the 16S rRNA gene does not have sufficient resolution for targeting bacteria at the species level. Studies employing qPCR showed that large increases in grain feeding increased the abundances of Selenomonas ruminantium, Streptococcus bovis, and Prevotella bryantii while decreasing the abundances of Butyrivibrio fibrisolvens and Fibrobacter succinogenes in rumen digesta (Fernando et al., 2010). Plaizier et

al. (2016) observed that excessive grain feeding increased the abundances of Prevotella albensis, Prevotella bryantii, and Selenomonas runiantium.

These authors also found that grain feeding increased the abundances of Prevotella albensis, Prevotella bryantii,and Selenomonas ruminantium in cecal digesta. The authors, however, did not observe an effect of grain feeding on fibrolytic bacteria, which might be due to analyses of liquid digesta in the rumen only. Fibrolytic bacteria are more associated with the solid than with the liquid digesta fraction (Petri et al., 2012). Hence, reductions in the abundances of these bacteria may not be evident when only liquid digesta is analyzed. Petri et al. (2012) also reported that higher grain feeding increased the proportion of Selenomonas ruminantiumand decreased that of Fibrobacter succigenes in rumen digesta.

Increases in grain feeding that did not result in severe rumen acidosis have also been associated with increases in the abundance of Megasphaera elsdenii, a lactic acid utilizer (Khafipour et al., 2009b; Fernando et al., 2010; Petri et al., 2012).

Large increases in grain feeding can also affect populations of opportunistic and pathogenic bacteria. High-grain feeding has been associated with increases in populations of pathogenic Escherichia coli and Clostridium perfringens in the rumen and hindgut (Russell and Rychlik, 2001; Khafipour et al., 2009b; Khafipour et al., 2011; Plaizier et al., 2016). These increases appear to be limited when the increased grain feeding does not result in severe rumen and hindgut acidosis (Khafipour et al., 2009b).

These results show that, as long as no severe ruminal acidosis is induced, large increases in grain feeding affect the abundances of some, but not all, amylolytic and fibrolytic bacterial species, and that these effects vary among studies. These changes reflect the alterations of the dietary content of grain and fiber and do not indicate that irreversible dysbiosis occurs.

Microorganisms in the digestive tract of ruminants are competitive, and functionality is shared by a variety of microbial species that are taxonomically different (Russell and Rychlik, 2001; Firkins and Yu, 2015).

This enhances the stability and robustness of the composition and the functionality of the microbiota in the digestive tract but also infers that because of redundancy in bacterial functions, changes in the composition

PCR and qPCR systems (source: Š 2016 khafipourmicrobiomelaboratory.com).

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Animal Frontiers

of microbiota may not be reflective of changes in the functionality of microbiota. To assess the changes in functionality, functional metagenomics and metatranscriptomics, and possibly proteomics and metabolomics, analyses are required (Firkins and Yu, 2015).

Solutions We believe that a healthy rumen and hindgut is characterized by a) a high richness, evenness, diversity, stability, and activity of their microbiomes; b) the presence of healthy digesta that have desirable ranges in acidity, ammonia, osmolality, redox potential, antimicrobial peptides, and antigen-specific IgA while avoiding the formation of toxins or colonization by pathogens; and c) the health of the epithelia of the digestive tract, which has adequate capacity to absorb, transport, and metabolize nutrients and have a strong barrier function that prevents the passage of toxins and pathogens from the digestive tract into the blood and lymph circulations.

In that context, high and excessive grain feeding in cattle can reduce the diversity and functionality of the microbiomes and the metabolomes and jeopardize the health of digesta and epithelia. The impact of excessive grain feeding depends on many factors, including the characteristics of the grains, forages, and animals. Grains vary in how fast they are digested and fermented in the rumen, which depends on the type of grain and the processing (Plaizier et al., 2008). Forages vary in their buffering capacity, due to a multitude of factors, including their coarseness and protein content (Plaizier et al., 2008). Cows also vary in their susceptibility to nutritional disorders caused by high grain feeding, such as how fast they absorb acids produced during fermentation, their feeding and sorting behavior, and the composition and metabolic capacity of the microbiota in their digestive tract (Plaizier et al., 2008; Khafipour et al., 2009a; Plaizier et al., 2012). The National Research Council (NRC, 2001) recommends that when the dietary contents of neutral detergent fiber from forages and total neutral detergent fiber exceed 19 and 25% of the dietary dry matter, respectively, the dietary content of non-fiber carbohydrates, including sugars and starch, can be as high as 44% of the dietary dry matter. When the dietary contents of neutral deter-

gent fiber from forages and total neutral detergent fiber do not exceed 16 and 31% of the dietary dry matter, respectively, NRC (2001) recommends not including more than 38% of the dietary dry matter as non-fiber carbohydrates. These recommendations are, most likely, too general.

Feeding high-grain diets to high-yielding cows is difficult to avoid, as high-forage diets do not contain sufficient energy, and only a small portion of the grain in the diet can be replaced with fat (NRC, 2001). Also, cows have been selected to produce high milk yields, and they will attempt to produce these yields, even at the cost of other functions and the energy reserves of their body. As a result, several feed supplements are available to attenuate the adverse effects high-grain feeding (NRC, 2001). These include natural supplements such as buffers, yeasts, yeast culture products, direct-fed microbials, and probiotics. Buffers, such as sodium bicarbonate, are routinely included in the diets of dairy cows and feedlot cattle (NRC, 2001). Yeast and yeast culture products, especially those derived from Saccharomyces cerevisiae, have shown promise in stabilizing the conditions in the foregut and hindgut of cattle (Al Ibrahim et al., 2012; Chiquette et al., 2015; Li et al., 2016). Direct-fed microbials, such as Enterococcus faecium and Lactococcus lactis, ionophores, and polyphenols, have also shown such promise (De Nardi et al., 2014; Golder et al., 2014; Chiquette et al., 2015). However, the effectiveness of these supplements varies among studies. Reasons for these variations may include that the mechanisms through which these supplements attenuate the impact of high-grain feeding are not fully understood and that, as a result, the most effective doses of these supplements have not yet been fully established. The new techniques available for a comprehensive assessment of the microbiota and their functionality will be a great aid in obtaining this knowledge.

One method to restore “healthy” microbiota in the digestive tract is microbiota ecosystem engineering that aims to manipulate the microbial composition and function. In human medicine, fecal microbiota transplant (FMT)—which consists of infusing stool obtained from a healthy donor into the intestine of a recipient with a disturbed microbiota to re-establish normal population—is a FDA-approved therapeutic option for pseudomembranous colitis in recent years (Van den Abbeele et al., 2013). Fecal microbiota transplants are currently also investigated for treatment of other diseases of the intestinal tract and extraintestinal conditions, such as metabolic syndrome, diabetes, and obesity (Van den Abbeele et al., 2013).

While the results of FMT studies are very promising, there are concerns for potential transmission of infections from the donors to the recipients.

This has led gut microbiologists to take a reductionist approach and create synthetic multi-species microbial communities that while preventing pathogen transmission, allow standardized treatment regimen, and consider inter-individual genetics and microbiome differences. It is conceivable that gut microbiota engineering will also become a practical tool to attenuate reductions in gut health that result from high-grain feeding in ruminants, and to prevent and treat infectious diseases and improve the health and production efficiency of food-producing animals.

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Animal Frontiers

About the Authors Dr. Ehsan Khafipour is an Assistant Professor in the Department of Animal Science and Department of Medical Microbiology, University of Manitoba, Canada. Khafipour’s lab uses cutting-edge sequencing technologies, coupled with bioinformatics, and statistical and mathematical approaches to link the composition, function, and dynamics of microbiomes in the gut, vaginal tract, and mammary system with individuals’ diet, lifestyle factors, and health/disease status. He is using this approach to move from the current "one-size fits all" recommendations for prevention and treatment of metabolic disorders toward precision farming and personalized nutrition and medicine. Khafipour is currently involved in disease-health research with human and swine as well as dairy and beef cattle.

Correspondence: Ehsan.Khafipour@umanitoba.ca Dr. Shucong Li is a Research Associate in the Department of Animal Science at the University of Manitoba, Canada. He has published 31 peer-reviewed articles to date, and his research program focuses on 1) metabolism diseases affecting the productivity and welfare of dairy cows; and 2)the role of bovine digestive microbiome in dairy cow health and disease.

Dr. Hein Min Tun is a postdoctoral fellow in the Department of Animal Science, University of Manitoba. He obtained his DVM from the University of Veterinary Science, Myanmar; M.Sc. in Veterinary Public Health from Chulalongkorn University, Thailand; and Ph.D. in molecular biology from the University of Hong Kong, Hong Kong. He is undertaking cutting-edge technologies, such as microbial genomics and metagenomics to study the interactions between the gastrointestinal microbiome and diet in humans and food-producing animals and their role in health and disease. A significant focus of his research is on manipulating diet and microbiome toward improving production performance, mitigation of methane emission, and reducing metabolic disorders in ruminants, especially in dairy cattle.

Saleem, F., B.N. Ametaj, S. Bouatra, R. Mandal, Q. Zebeli, S.M. Dunn, and D.S. Wishart. 2012. A metabolomics approach to uncover the effects of grain diets on rumen health in dairy cows. J. Dairy Sci. 95(11):6606–6623. doi:10.3168/ jds.2012-5403.

Van den Abbeele, P., W. Verstraete, S. El Aidy, A. Geirnaert, and T. Van de Wiele.

2013. Prebiotics, faecal transplants and microbial network units to stimulate biodiversity of the human gut microbiome. Microb. Biotechnol. 6(4):335–340. doi:10.1111/1751-7915.12049.

Walker, A.W., J.D. Sanderson, C. Churcher, G.C. Parkes, B.N. Hudspith, N. Rayment, et al. 2011. High-throughput clone library analysis of the mucosa-as-

Dr. Hooman Derakhshani obtained his DVM from the University of Tehran, Iran and his M.Sc. in animal science from The University of Queensland, Australia. He is currently a Ph.D. student at the University of Manitoba, Canada. His Ph.D. project is focused on exploring cross-sectional and temporal profiles of mammary microbiome and mycobiome in dairy cattle and their associations with host genotype and udder health. Derakhshani has contributed to two peer-reviewed papers as the first author, three papers as the co-author, and more than 15 scientific abstracts submitted and presented at various national and international conferences.

Dr. Shirin Moossavi obtained her Medical Doctorate from Tehran University of Medical Sciences, Iran, and her M.Sc. in genetic manipulation and molecular biology from the University of Sussex, UK. She is currently a Ph.D. student in the Department of Medical Microbiology, University of Manitoba, Canada and a Research Fellow at the Digestive Disease Research Institute, Tehran, Iran. Moossavi’s Ph.D. research is focused on the association between milk microbiota and childhood asthma and allergy as well as interactions of lifestyle factors and gut microbiota on development of metabolic disorders. Her interest extends into clinical application of gut microbiota ecosystem engineering as a modifiable biomarker for early diagnosis, prognosis, and monitoring response to therapy as well as metabolic interventions in the context of precision medicine.

Dr. Kees Plaizier is Professor in Dairy Nutrition and Management at the University of Manitoba, in Winnipeg, Canada. His current research program focuses on the enhancing health and nutrient utilization of dairy cows, as well as environmental sustainability of dairy farms, and the evaluation of novel feeds for cattle. He has authored or co-authored more than 80 manuscripts in scientific journals and numerous conference abstracts, articles, extension materials, and technical reports. Since January 2014, Plaizier has been Editor-in-Chief of the Canadian Journal of Animal Science. At the University of Manitoba, he teaches dairy cattle production and ruminant nutrition at the diploma, degree, and graduate levels.

Correspondence: Kees.Plaizier@umanitoba.ca sociated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol. 11:7. doi:10.1186/1471-2180-11-7.

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Front. Microbiol. 6:1133. doi:10.3389/fmicb.2015.01133.

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