Table_5_Efficacy of Fecal Sampling as a Gut Proxy in the Study of Chicken Gut Microbiota.xlsx

Despite the convenience and non-invasiveness of fecal sampling, the fecal microbiota does not fully represent that of the gastrointestinal (GI) tract, and the efficacy of fecal sampling to accurately represent the gut microbiota in birds is poorly understood. In this study, we aim to identify the efficacy of feces as a gut proxy in birds using chickens as a model. We collected 1,026 samples from 206 chickens, including duodenum, jejunum, ileum, cecum, and feces samples, for 16S rRNA amplicon sequencing analyses. In this study, the efficacy of feces as a gut proxy was partitioned to microbial community membership and community structure. Most taxa in the small intestine (84.11–87.28%) and ceca (99.39%) could be identified in feces. Microbial community membership was reflected with a gut anatomic feature, but community structure was not. Excluding shared microbes, the small intestine and ceca contributed 34.12 and 5.83% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria members in the ceca could be well mirrored by the observations in fecal samples (ρ = 0.54–0.71 and 0.71–0.78, respectively, P < 0.001). However, there were few significant correlations for each genus between feces and each of the four gut segments, and these correlations were not high (ρ = −0.2–0.4, P < 0.05) for most genera. Our results suggest that fecal microbial community has a good potential to identify most taxa in the chicken gut and could moderately mirror the microbial structure in the intestine at the microbial population level with phylum specificity. However, it should be interpreted with caution by using feces as a proxy to study associations for microbial structure at individual microorganism level.

尽管粪便采样兼具便捷性与非侵入性优势，但粪便菌群无法完全代表胃肠道（gastrointestinal tract, GI）菌群，且粪便采样能否准确反映鸟类肠道菌群的应用效能目前仍不明确。本研究以家鸡为模型，旨在明确粪便作为鸟类肠道替代样本的效能。我们从206只家鸡体内采集了1026份样本，涵盖十二指肠、空肠、回肠、盲肠及粪便样本，用于开展16S rRNA扩增子测序分析。本研究将粪便作为肠道替代样本的效能拆解为微生物群落组成与群落结构两个维度进行评估。小肠内的绝大多数分类群（84.11%~87.28%）与盲肠内的分类群（99.39%）均可在粪便样本中被检出。微生物群落组成可通过肠道解剖特征实现有效反映，但群落结构则无法通过粪便样本复刻。剔除共有微生物后，小肠与盲肠分别贡献了粪便总菌群成员的34.12%与5.83%。小肠内厚壁菌门（Firmicutes）菌群的组成，以及盲肠内放线菌门（Actinobacteria）、拟杆菌门（Bacteroidetes）、厚壁菌门与变形菌门（Proteobacteria）菌群的组成，均可通过粪便样本的检测结果得到较好的匹配（相关系数ρ=0.54~0.71与0.71~0.78，均P<0.001）。然而，粪便菌群与四个肠道节段各自的属水平微生物间仅存在少量显著相关性，且多数菌属的相关系数并不理想（ρ=-0.2~0.4，P<0.05）。本研究结果显示，粪便微生物组具备良好潜力，可用于识别家鸡肠道内的绝大多数分类群，且在微生物种群层面可适度反映具有门水平特异性的肠道菌群结构。但以粪便作为替代样本开展个体微生物水平的菌群结构关联研究时，仍需谨慎解读实验结果。