ABSTRACT
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.
IMPORTANCE Fecal sample is the important object used in gut microbial study, as the collection of feces is convenient and noninvasive. It is well known that the microbial community in fecal sample may not be fully representative of that in gastrointestinal tract (GI), but the extent to which the fecal sample reflect the microbiota in GI is not fully clear. Instead of focus on the variation of different sampling sites, this study demonstrated the spatial relationships of microbiota among duodenum, jejunum, ileum, cecum and feces and partitioned the efficacy of feces as a gut proxy to quantitatively identify the extent to which fecal samples are appropriately used in gut study. Enterotype concept was used to confirm the efficacy of feces as a gut proxy. This work gives insights and provide future directions regarding the usage of fecal samples in studies of the gut microbiome.