Microbiota Structure and Functional Variation Across Intestinal Segments of Spinibarbus caldwelli

Spinibarbus caldwelli is an important commercial aquaculture species in China. To investigate gut microbiota composition, inter-species interactions, and their correlation with intestinal function across different gut segments, we analyzed 18 gut samples from six wild S. caldwelli individuals collected from the Yuanhe River. The V4–V5 hypervariable regions of the 16S rRNA gene were high-throughput sequenced, resulting in 1557 operational taxonomic units. The microbiota across gut segments exhibited homogeneity, with greater similarity between the foregut and hindgut than between either of these and the midgut. The foregut and hindgut microbiota had significantly higher richness and diversity than the midgut microbiota. Pseudomonas was the most abundant genus. Cetobacterium and Microbacterium were significantly more prevalent in the midgut than in the hindgut, whereas Bacillus and Cupriavidus were significantly less abundant in the midgut than in the other gut segments. Network analysis revealed that cooperative interactions among gut microbes outweighed competitive interactions. Functional prediction indicated that the microbial metabolic patterns of the foregut and hindgut were more similar to each other than either was to the midgut, and the different metabolic pathways were mainly concentrated in the metabolism and environmental information processing. These findings suggest that the spatial heterogeneity of S. caldwelli gut microbiota is closely associated with physiological functions of gut segments.