Gastrointestinal (GI) microbiota is one of the most complicated microbial ecosystems and is vital in regulating biological processes associated with nutrient absorption and homeostatic maintenance. Although several efforts have been achieved in characterizing bacterial communities across gut regions, the variation of non-bacterial communities across GI tracts is still largely unexplored. To address this, we investigated microbial biogeography throughout the whole GI tracts of Ujimqin sheep (Ovis aries) by amplicon sequencing which targeted bacteria, fungi, and archaea. The results indicated that the community structures of all three domains were significantly distinguished according to GI tracts (stomach, small intestine, and large intestine), and a more strong and efficient species interaction was detected in small intestine based on cross-domain network analysis. Moreover, a between-domain difference in microbial assembly mechanism of among-GI regions was revealed here, wherein bacterial community is dominantly governed by variable selection (explaining ~62% of taxa turnover), while fungal and archaeal communities mainly governed by homogenizing dispersal (explaining ~49% and 60% of the turnover, respectively). Overall, these data highlight the GI section- and domain-dependence of GI microbial structure and assembly mechanism, suggesting that multi-domain should be explicitly considered when evaluating the influences of GI selection on gut microbial communities.
© 2021 Society for Applied Microbiology and John Wiley & Sons Ltd.