Abstract
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.
Highlights
Many studies have reported the important roles of gut microbiota in host metabolism and health in humans (Rosenbaum et al, 2015), other mammals (Shin et al, 2014), and birds (Brisbin et al, 2008)
The 16S rRNA gene-based sequencing from 206 chickens produced 62,193,309 reads, 58,959,487 of which remained after quality filtration
The cecal microbial community exhibited a distant relationship with the small intestine community, and the microbial community in feces showed an intermediate relationship between those of the ceca and small intestines
Summary
Many studies have reported the important roles of gut microbiota in host metabolism and health in humans (Rosenbaum et al, 2015), other mammals (Shin et al, 2014), and birds (Brisbin et al, 2008). The microbiota present in different GI segments have been investigated using traditional sequencing methods (Gong et al, 2007) or high-throughput sequencing techniques (Choi et al, 2014; Xiao et al, 2016). These studies had small sample sizes (N = 3–8), were primarily aimed at examining the spatial heterogeneity among different segments, and did not focus on the spatial microbiota relationships between feces and the GI tract
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