title: The gastrointestinal tract microbiota of the Japanese quail, Coturnix japonica.
abstract: Microbiota in the gastrointestinal tract (GIT) plays an essential role in the health and well-being of the host. With the exception of chickens, this area has been poorly studied within birds. The avian GIT harbours unique microbial communities. Birds require rapid energy bursts to enable energy-intensive flying. The passage time of feed through the avian GIT is only 2-3.5 h, and thus requires the presence of microbiota that is extremely efficient in energy extraction. This investigation has used high-throughput 16S rRNA gene sequencing to explore the GIT microbiota of the flighted bird, the Japanese quail (Coturnix japonica). We are reporting, for the first time, the diversity of bacterial phylotypes inhabiting all major sections of the quail GIT including mouth, esophagus, crop, proventriculus, gizzard, duodenum, ileum, cecum, large intestine and feces. Nine phyla of bacteria were found in the quail GIT; however, their distribution varied significantly between GIT sections. Cecal microbiota was the most highly differentiated from all the other communities and showed highest richness at an OTU level but lowest richness at all other taxonomic levels being comprised of only 15 of total 57 families in the quail GIT. Differences were observed in the presence and absence of specific phylotypes between sexes in most sections.
authors.affiliation: Institute of Future Farming, Central Queensland University, Bruce Highway, Building 6 Room 2.33, Rockhampton, QLD, 4702, Australia.|Poultry Cooperative Research Centre, University of New England Armidale, Armidale, NSW, 2351, Australia.
authors.forename: Ngare
authors.initials: N
authors.lastname: Wilkinson
authors.affiliation: Poultry Cooperative Research Centre, University of New England Armidale, Armidale, NSW, 2351, Australia.|South Australian Research and Development Institute, Pig and Poultry Production Institute, Roseworthy, South Australia, 5371, Australia.|School of Animal and Veterinary Sciences Roseworthy, The University of Adelaide, Adelaide, South Australia, 5371, Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Hughes
authors.affiliation: Institute of Future Farming, Central Queensland University, Bruce Highway, Building 6 Room 2.33, Rockhampton, QLD, 4702, Australia.
authors.forename: William J
authors.initials: WJ
authors.lastname: Aspden
authors.affiliation: Institute of Future Farming, Central Queensland University, Bruce Highway, Building 6 Room 2.33, Rockhampton, QLD, 4702, Australia.|Poultry Cooperative Research Centre, University of New England Armidale, Armidale, NSW, 2351, Australia.
authors.forename: James
authors.initials: J
authors.lastname: Chapman
authors.affiliation: Poultry Cooperative Research Centre, University of New England Armidale, Armidale, NSW, 2351, Australia.|School of Applied Sciences and Health Innovations Research Institute (HIRi), RMIT University, Bundoora, VIC, 3083, Australia.|Department of Microbiology, Monash University, Clayton, VIC, 3800, Australia.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Moore
authors.affiliation: Institute of Future Farming, Central Queensland University, Bruce Highway, Building 6 Room 2.33, Rockhampton, QLD, 4702, Australia. D.Stanley@cqu.edu.au.|Poultry Cooperative Research Centre, University of New England Armidale, Armidale, NSW, 2351, Australia. D.Stanley@cqu.edu.au.
authors.forename: Dragana
authors.initials: D
authors.lastname: Stanley
mesh_terms: D000818:Animals; D003370:Coturnix / Q000382:microbiology*; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D000069196:Gastrointestinal Microbiome; D041981:Gastrointestinal Tract / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: Diversity; Intestinal; Japanese quail; Microbiota