Chapter outline: Animal Gut Microbiomes

Animal Gut Microbiomes--Marchesi

Focus on livestock and companion animals

Introduction

Focus and benefits of studying animal gut microbiota:

·     Comparison with other animals and humans – relating to phylogeny and dietary differences

·     Understanding and improving feed conversion and nutrition (diet)

·     Controlling methane production in ruminants

·     Understanding enteric disease (infection > imbalance)

·     Public Health Microbiology (carriage of zoonotic agents)

·     Novel pathogen discovery (bacterial and viral?)

·     Impact of antibiotics, vaccines, etc

·     Sample sizes (number of replicates) can be much larger than human studies

Sampling considerations

·     Faecal samples are readily available but exposure to air means they may not be completely representative of communities in the gut.

·     Individual gut sections and/or luminal contents can be sampled during post-mortem examinations or via surgical fistulations – different regions will harbour different microbial communities and will have different physicochemical conditions.

·     Methods for selective recovery of planktonic and adherent microbial communities from digesta.

Detection of specific microorganisms of interest (e.g. enteric pathogens)

·     Bacteria (e.g. Salmonella, Campylobacter, etc)

·     Viruses and bacteriophage

·     Protozoa

·     Archaea

·     Yeasts and Fungi

Microbial community analysis

·     Nucleic acid extraction methods

·     Metagenome shotgun sequencing (including library construction and screening)

·     Targeted amplicon sequencing (e.g. 16S, Fungal ITS, AMR genes, etc)

·     RNA extraction, enrichment and analysis methods

·     Data analysis and interpretation

Metabolism of the gut microbiome

·     Methanogenesis and other hydrogen sinks in the GI tract

·     Role of hydrogen consuming organisms in the rumen

·     Microbial groups which utilise hydrogen

·     Approaches and methods for characterisation of the different functional groups

·     Biotransformation and biodegradation of phytochemicals (that toxify and detoxify)

·     Significance of microorganisms that metabolise phytochemicals.

Metaproteomics

·     Extraction methods

    Analysis