Supplementary Material for: Developmental Dynamic Analysis of the Excreted Microbiome of Chickens Using Next-Generation Sequencing

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.

禽肉污染在很大程度上可归因于生产过程中鸡粪便的存在。供人类食用的生鲜鸡肉产品中常检出粪便污染。本研究的核心研究内容为采用下一代测序技术（next-generation sequencing）对鸡粪便微生物群落开展定量分析。本研究从30只肉鸡的两个生长时间点（发育第1天和第35天）采集粪便样本，对每份样本提取的16S核糖体RNA（16S rRNA）进行454焦磷酸测序（454 pyrosequencing），并通过多种自动化生物信息学分析流程探究微生物种群动态变化。在5周的生长周期内，鸡粪便微生物群落的属水平多样性呈上升趋势。尽管多样性有所提升，但每份粪便样本中仅存在少量占比超过80%的优势细菌类群，绝大多数类群为样本特有，仅少数类群可在不同样本间共享。属水平的种群分析结果显示，微生物多样性随肉鸡的生长发育逐渐升高。对占比超过1%的高丰度微生物进行分类学与系统发育分析后，清晰发现厚壁菌门（Firmicutes）与变形菌门（Proteobacteria）等类群间存在极高的序列相似性。上述结果表明，鸡粪便微生物组是一个动态系统，其种群结构具有分化特征，且仅包含数量极为有限的高等分类单元。