Peter scott moore microbiota in gut health copie

The importance of gut microbiota to gut health Robert Moore Research Professor of Biotechnology Host-­‐Microbe Interac8ons Laboratory RMIT University, Melbourne, Australia

BACTERIA

§ A dominant, but often hidden, kingdom of life § Estimated to be at least 10 million species § Estimated to be 5 x 1030 bacterial cells on earth

Bacteria help digest food The gastrointes8nal tract harbours a large collec8on of microbes

Gut Microbiota

Bacteria provide enzyma8c ac8vi8es lacking in the host, helps digest otherwise inaccessible nutrients

Produces essen8al micronutrients such as bio8n and vitamin K

Microbiota – definition • All the microbes in a par8cular environment/niche • Typically a complex, dynamic popula8on • Bacteria, Archaea, Pro8sts, Fungi, Viruses

Human Microbiota § We may carry up to 10 times more bacterial cells than human cells. § Each of us carries 1,000’s of different sorts of bacteria § Each part of our body carries a distinctive microbiota

The “Metaorganism” Concept § Microbiota has co-­‐evolved with host § Highly adapted, mutualis8c rela8onship § Host has about 20,000 genes § Microbiota has 100’s of 1000’s of unique genes § The microbiota greatly extends the “biochemical poten8al” of the host § Microbiota can be regarded as another “organ”

Microbiota + Host = “Metaorganism”

Animal/Human Microbiota § Composition is influenced by diet, age, environment § Method of birth influences composition § Composition can have a profound influence on health

Microbiota impacts on diverse functions FUNCTION • Diges;on/Nutri;on

• Gut func;on

mobilisa8on of inaccessible nutrients supply of micronutrients (e.g. bio8n, vitK) organic acid produc8on

gut development preven8on of pathogen colonisa8on energy supply

• Immune system

• Gut/Brain axis

immune development self/non-­‐self recogni8on

neural ac8vity endocrine ac8vity

Microbiota impacts on diverse functions DYSFUNCTION • Diges;on/Nutri;on

• Gut func;on

• Immune system

• Gut/Brain axis

obesity food allergies

irritable bowel syndrome pathogen infec8on (e.g. C. difficile coli8s)

asthma diabetes

anxiety depression au8sm

Diverse influence of microbiota § Renewal of gut epithelial cells, gut barrier integrity § Breakdown of toxins § Bile acid metabolism → endocrine ac8vity § S8mulates immune system development § Affects the nervous system / brain § Metabolic disease resistance/suscep8bility e.g. diabetes § Key role in leanness/obesity § Influences cancer development

Microbiota and gut health in poultry • A role in produc8vity level and performance variability — mobilisa8on of inaccessible nutrients — absorp8on, storage, energy harvest — organic acid produc8on → host energy produc8on — produces micronutrients, e.g. Bio8n and Vitamin K • Compe88ve exclusion of pathogens • Important in forma8on of the immune system • A role in disease suscep8bility & progression • Modifies the “quality” of excreta & compos8ng

Fibre and SCFAs help the immune system Cell receptors

Microbiota Short Chain FaLy Acids

Signal transduc;on

Fibre Immune system modula;on

Analysis of microbiota composi;on Sample (e.g. caecal content)

Extract total DNA

PCR amplify species specific 16S ribosomal RNA genes

High throughput sequencing of PCR products (10,000 -­‐ 100,000 sequences per sample)

Analysis to define species composi8on of samples (High performance computer, sobware, interpreta8on, etc.)

Composi;on analysis of microbiota Phylogene8c analysis Phylum, Class, Order, Family, Genus, Species

e.g. Firmicutes, Bacilli, Lactobacillales, Lactobacillaceae, Lactobacillus, L. salivarius

Compare and contrast across samples

Sta8s8cal tools to find significant differences across samples

Visualiza8on tools to explore and present data

Structure of 16S rRNA • The 16S gene is present in all bacteria.

• It has conserved regions which allow the design of general PCR amplifica8on primers.

• The variable regions differ in each bacterial species – allowing determina8on of the species from which each sequence is derived

16S rRNA gene amplifica;on Whole microflora DNA – complex mixture of chromosomal DNA from all bacteria present

= variable = conserved

PCR amplifica8on

= PCR primer

DNA Sequencing

Visualizing microbiota composition data

OTU238 OTU36

100 90

OTU16 OTU102 OTU67 OTU4 OTU133 OTU179 OTU85

80 70 60

14 2 3 4 5 5 7 12

50 40

18

30 20 10 0

Pie Charts and Stacked Column Graphs

30

Basic visualiza;on of microbiota profiles

Pie Charts

Sample 2 Bacteroides Clostridium Lactobacillus Bacillus Enterococcus Fusobacterium Heliobacillus Bifidobacterium

Sample 1

Stretococcus

Sample 3

Microbiota differences across 3 replicate trials

Visualising microbiota differences across replicate trials Red – Trail 1 birds Blue – Trial 2 birds Black dots – OTUs

OTUs are approximately equivalent to species.

OTUs unique to Trial 2

OTUs shared between trials

OTUs unique to Trial 1

Could do a similar analysis to compare across treatment groups within a single trial.