Analysis of Bacterial Community Diversity in the Intestine and Habitat of the Whitmania pigra

The intestinal microbiota serves as a critical mediator of digestive efficiency, nutrient assimilation, and host-pathogen interactions in aquatic organisms. To systematically investigate microbial community dynamics within integrated aquaculture environments, we conducted a comparative analysis of bacterial assemblages across three distinct ecological niches in a pond aquosystem: the intestinal tract of Whitmania pigra, benthic sediment, and water column. The results demonstrated significant variations in both the structure and diversity of bacterial communities among W. pigra intestines, sediment, and water. Sediment samples exhibited the highest richness and diversity, which decreased markedly in water samples and were lowest in intestinal samples (P < 0.05). In the intestines of W. pigra, the predominant phyla included Firmicutes (36.45%), Proteobacteria (30.59%), and Bacteroidota (20.93%). By contrast, sediment was dominated by Proteobacteria (34.90%) and Bacteroidota (17.41%), while aquaculture water was characterized by Proteobacteria (42.08%), Bacteroidota (19.49%), Cyanobacteria (16.86%), and Actinobacteriota (14.66%). At the genus level, Aeromonas (24.67%), Cetobacterium (8.56%), and Epulopiscium (8.29%) were prevalent in the intestines, whereas unclassified_Bacteroidales (2.66%) and Hydrogenophaga (1.02%) were notable in sediment. In aquaculture water, Planktothrix_NIVA_CYA_15 (10.81%) and Flavobacterium (10.60%) were the dominant genera. Compared with water samples, intestinal bacterial communities showed greater similarity to those in sediment. Traceability analysis further indicated that 41.14% of the intestinal bacterial communities originated from sediment, while 27.35% were derived from water. Functional comparisons among the three habitats revealed numerous significant differences. Overall, bacterial communities in W. pigra intestines, sediment habitats, and aquaculture water exhibited significant differences but were closely interconnected, providing valuable insights for further resea