title: Extensive microbial and functional diversity within the chicken cecal microbiome.
abstract: Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the largely unexplored complex microbial community that inhabits the chicken gut, including the ceca. We have carried out deep microbial community profiling of the microbiota in twenty cecal samples via 16S rRNA gene sequences and an in-depth metagenomics analysis of a single cecal microbiota. We recovered 699 phylotypes, over half of which appear to represent previously unknown species. We obtained 648,251 environmental gene tags (EGTs), the majority of which represent new species. These were binned into over two-dozen draft genomes, which included Campylobacter jejuni and Helicobacter pullorum. We found numerous polysaccharide- and oligosaccharide-degrading enzymes encoding within the metagenome, some of which appeared to be part of polysaccharide utilization systems with genetic evidence for the co-ordination of polysaccharide degradation with sugar transport and utilization. The cecal metagenome encodes several fermentation pathways leading to the production of short-chain fatty acids, including some with novel features. We found a dozen uptake hydrogenases encoded in the metagenome and speculate that these provide major hydrogen sinks within this microbial community and might explain the high abundance of several genera within this microbiome, including Campylobacter, Helicobacter and Megamonas.
authors.affiliation: Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Sergeant
authors.affiliation: Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom.
authors.forename: Chrystala
authors.initials: C
authors.lastname: Constantinidou
authors.affiliation: School of Clinical Veterinary Science, Bristol, United Kingdom.
authors.forename: Tristan A
authors.initials: TA
authors.lastname: Cogan
authors.affiliation: AB Vista Feed Ingredients, Marlborough, United Kingdom.
authors.forename: Michael R
authors.initials: MR
authors.lastname: Bedford
authors.affiliation: Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom.
authors.forename: Charles W
authors.initials: CW
authors.lastname: Penn
authors.affiliation: Division of Microbiology and Infection, Warwick Medical School, University of Warwick, Coventry, United Kingdom.
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Pallen
mesh_terms: D000818:Animals; D044822:Biodiversity; D002432:Cecum / Q000382:microbiology*; D002645:Chickens / Q000382:microbiology*; D006859:Hydrogen / Q000378:metabolism; D064307:Microbiota
chemical_list: D006859:Hydrogen