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Decoding the chicken gastrointestinal microbiome

Authors: Burrows, PB.; Godoy-Santos, F.; Lawther, K.; Richmond, A.; Corcionivoschi, N.; Huws, SA.;

Decoding the chicken gastrointestinal microbiome

Abstract

Abstract Metataxonomic studies have underpinned a vast understanding of microbial communities residing within livestock gastrointestinal tracts, albeit studies have often not been combined to provide a global census. Consequently, in this study we characterised the overall and common ‘core’ chicken microbiota across the gastrointestinal tract (GIT), whilst assessing the effects of GIT location, bird breed, age and geographical location on the GIT resident microbes using metataxonomic data compiled from studies completed across the world. Specifically, bacterial 16S ribosomal DNA sequences from GIT samples associated with various breeds, differing in age, diet, GIT (caecum, faeces, ileum and jejunum) and geographical location were obtained from the Short Read Archive and analysed using the MGnify pipeline. Metataxonomic profiles produced across the 602 datasets illustrated the presence of 3 phyla, 25 families and 30 genera, of which core genera (defined by presence in over 90% of datasets) belonged to Lactobacillus, Faecalibacterium, Butyricicoccus, Eisenbergiella, Subdoligranulum, Oscillibacter, Clostridium & Blautia. PERMANOVA analysis also showed that GIT location, bird breed, age and geographical location all had a significant effect on GIT microbial diversity. On a genus level, Faecalibacterium was most abundant in the caeca, Lactobacillus was most abundant in the faeces, ileum and jejunum, with the data showing that the caeca and faeces were most diverse. AIL F8 progeny, Ross 308 and Cobb 500 breeds GIT bacteria were dominated by Lactobacillus, and Eisenbergiella, Megamonas and Bacteroides were most abundant amongst Sasso-T451A and Tibetan chicken breeds. Microbial communities within each GIT region develop with age, from a Lactobacillus and Streptococcus dominated community during the earlier stages of growth, towards a Faecalibacterium, Eisenbergiella, Bacteroides, Megamonas, and Lactobacillus dominated community during the later stages of life. Geographical locations, and thus environmental effectors, also impacted upon gastrointestinal tract microbiota, with Canadian and European datasets being dominated by Lactobacillus, whilst UK and Chinese datasets were dominated by Eisenbergiella and Bacteroides respectively. This study aids in defining what ‘normal’ is within poultry gastrointestinal tract microbiota globally, which is imperative to enhancing the microbiome for productive and environmental improvements.

Country
United Kingdom
Keywords

DNA, Bacterial, 570, broiler, Microbiology, diversity, Feces, RNA, Ribosomal, 16S, microbiota, Animals, Gut, /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being; name=SDG 3 - Good Health and Well-being, Phylogeny, metataxonomy, Bacteria, Broiler, GIT sites, Microbiota, Research, Sequence Analysis, DNA, QR1-502, name=SDG 3 - Good Health and Well-being, Gastrointestinal Microbiome, Gastrointestinal Tract, Metataxonomy, /dk/atira/pure/sustainabledevelopmentgoals/good_health_and_well_being, gut, 16S rRNA gene, Chickens, core microbiome

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citations
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
2
Average
Average
Average
Green
gold