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Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota

By Wei Yan, Jiangxia Zheng, Chaoliang Wen, Congliang Ji, Dexiang Zhang, Yonghua Chen, Congjiao Sun, Ning Yang

Posted 04 May 2018
bioRxiv DOI: 10.1101/313577 (published DOI: 10.3389/fmicb.2019.02126)

Despite the convenience and noninvasiveness 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. Using chickens as a model, we collected 1,026 samples from 206 animals, including duodenum, jejunum, ileum, cecum and feces samples. Most taxa in the small intestine (94.10-94.82%) and ceca (99.57%) 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 26.69 and 2.36% of the total fecal members, respectively. The composition of Firmicutes members in the small intestine and that of Actinobacteria, Bacteroidetes and Proteobacteria members in ceca could mirrored that observed in fecal samples well (ρ = 0.68-0.79 and 0.66-0.79, respectively, P < 0.05). Enterotype-like clustering was performed in GI tract and all sites were clustered into 2 or 3 enterotype-like clusters. Feces from different clusters reflected the GI microbiota with different efficacies, giving a new insight into observing efficacy of feces as a gut proxy. Our results provide evidences that the good potential of feces to identify most taxa in chicken guts, but microbial structure analyses using feces as a proxy for gut should be interpreted with caution.

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