| Summary: | Host-associated microbiota play important roles in the nutrition, immune system, and health of fish. However, the composition, diversity, and function of microbiota associated with certain niches in fish bodies and fish habitats remain to be elucidated. In the present study, 16S sequencing was carried out to compare microbial communities found in the gills and guts in two filter-feeding fish (Hypophthalmichthys molitrix and Hypophthalmichthys nobilis) and to determine the influence of sediment and water on fish microbiota in an unfed aquaculture system. Results revealed significant variations in the water, sediment, gill, and gut microbial communities of the two filter-feeding fish in terms of composition, core taxa, diversity, and predictive function. Microbial diversity was significantly higher in the habitat samples (water and sediment) than in the fish host samples (gill and gut) and was significantly higher in the gills than in the gut. Both body niche (i.e., gill vs gut) and host species significantly impacted the fish-associated microbiota, but permutational multivariate analysis of variance (PERMANOVA) and cluster analysis of core taxa indicated that the effect of body niche outweighed that of the host species in influencing the microbial community. Host microbial communities were more similar to the water microbiota than the sediment microbiota. Source tracking analysis further confirmed that water had a greater contribution than sediment to the fish microbiota, consistent with their upper water-layer habitats. The gill and gut possessed unique core microbiota and predictive functions in comparison to the surrounding environment. These findings should improve our understanding of the composition, diversity, and function of aquatic host microbiota and their associations with habitat.
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