title: 16S rRNA gene-based analysis of mucosa-associated bacterial community and phylogeny in the chicken gastrointestinal tracts: from crops to ceca.
abstract: Mucosa-associated microbiota from different regions of the gastrointestinal (GI) tract of adult broilers was studied by analysis of 16S rRNA gene sequences. The microbiota mainly comprised Gram-positive bacteria along the GI tract. Fifty-one operational taxonomic units (OTUs) (from 98 clones) were detected in the ceca, as compared with 13 OTUs (from 49 clones) in the crops, 11 OTUs (from 51 clones) in the gizzard, 14 OTUs (from 52 clones) in the duodenum, 12 OTUs (from 50 clones) in the jejunum and nine OTUs (from 50 clones) in the ileum. Ceca were dominantly occupied by clostridia-related sequences (40%) with other abundant sequences being related to Faecalibacterium prausnitzii (14%), Escherichia coli (11%), lactobacilli (7%) and Ruminococcus (6%). Lactobacilli were predominant in the upper GI tract and had the highest diversity in the crop. Both Lactobacillus aviarius and Lactobacillus salivarius were the predominant species among lactobacilli. Candidatus division Arthromitus was also abundant in the jejunum and ileum.
authors.affiliation: Food Research Program, Agriculture and Agri-Food Canada, Guelph, ON, Canada. gongj@agr.gc.ca
authors.forename: Jianhua
authors.initials: J
authors.lastname: Gong
authors.forename: Weiduo
authors.initials: W
authors.lastname: Si
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Forster
authors.forename: Ruilin
authors.initials: R
authors.lastname: Huang
authors.forename: Hai
authors.initials: H
authors.lastname: Yu
authors.forename: Yulong
authors.initials: Y
authors.lastname: Yin
authors.forename: Chengbo
authors.initials: C
authors.lastname: Yang
authors.forename: Yanming
authors.initials: Y
authors.lastname: Han
mesh_terms: D000818:Animals; D001419:Bacteria / Q000235:genetics* / Q000254:growth & development*; D002645:Chickens / Q000382:microbiology*; D003013:Clostridium / Q000235:genetics / Q000254:growth & development; D004926:Escherichia coli / Q000235:genetics / Q000254:growth & development; D041981:Gastrointestinal Tract / Q000382:microbiology*; D007413:Intestinal Mucosa / Q000382:microbiology*; D007778:Lactobacillus / Q000235:genetics / Q000254:growth & development; D010802:Phylogeny; D019936:Probiotics / Q000494:pharmacology; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D045857:Ruminococcus / Q000235:genetics / Q000254:growth & development
chemical_list: D012336:RNA, Ribosomal, 16S