title: Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing.
abstract: Poultry contamination can be largely attributed to the presence of chicken feces during the production process. Fecal contamination is often found in raw chicken products sold for human consumption. Quantitative analysis of the fecal microbial community of chickens using next-generation sequencing techniques is the focus of this study. Fecal samples were collected from 30 broiler chickens at two time points: days 1 and 35 of development. 454 pyrosequencing was conducted on 16S rRNA extracted from each sample, and microbial population dynamics were investigated using various automated bioinformatics pipelines. Diversity of the microbial community at the genus level increased during the 5-week growth period. Despite this growth, only a few dominant bacteria groups (over 80%) were identified in each fecal sample, with most groups being unique and only a few were shared between samples. Population analysis at the genus level showed that microbial diversity increased with chicken growth and development. Classification and phylogenetic analysis of highly represented microbes (over 1%) clearly showed high levels of sequence similarity between groups such as Firmicutes and Proteobacteria. These results suggest that the chicken fecal excreted microbiome is a dynamic system with a differentiated population structure that harbors a highly restricted number of higher taxa.
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, Korea.
authors.forename: Sooyeon
authors.initials: S
authors.lastname: Lim
authors.forename: SooHyun
authors.initials: S
authors.lastname: Cho
authors.forename: Kelsey
authors.initials: K
authors.lastname: Caetano-Anolles
authors.forename: Seok Geun
authors.initials: SG
authors.lastname: Jeong
authors.forename: Mi Hwa
authors.initials: MH
authors.lastname: Oh
authors.forename: Beom Young
authors.initials: BY
authors.lastname: Park
authors.forename: Hyun Jung
authors.initials: HJ
authors.lastname: Kim
authors.forename: Seoae
authors.initials: S
authors.lastname: Cho
authors.forename: Sang Ho
authors.initials: SH
authors.lastname: Choi
authors.forename: Sangryeol
authors.initials: S
authors.lastname: Ryu
authors.forename: Ju-Hoon
authors.initials: JH
authors.lastname: Lee
authors.forename: Heebal
authors.initials: H
authors.lastname: Kim
authors.forename: Jun Sang
authors.initials: JS
authors.lastname: Ham
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D002645:Chickens / Q000254:growth & development / Q000382:microbiology*; D005243:Feces / Q000382:microbiology*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D064307:Microbiota; D008969:Molecular Sequence Data; D010802:Phylogeny