Environmental factors shape the intestinal microbiota and function of Manila clam Ruditapes philippinarum

Intestinal microbiota of aquatic animals is closely associated with the environment, influencing their health, immune defense, and environmental adaptability. To understand the relationships among the Manila clam (Ruditapes philippinarum) intestinal microbiota, the bacterial communities in their habitats, and environmental factors, as well as the characteristics and potential functions of the intestinal microbiota. This study systematically analyzed the bacterial communities in the clam intestines, seawater, and sediment samples from two typical habitats using 16S rRNA gene (V3-V4) sequencing. The results revealed significant differences in bacterial community composition among the intestines, seawater and sediment, with pronounced regional variations also evident within the same sample type. The clams gut microbiota in Fuqing was predominantly composed of Alphaproteobacteria, Gammaproteobacteria, Bacteroidota, Bacillota, and Cyanobacteria. In Putian, Cyanobacteria comprised an exceptionally high proportion. However, Bacillota, Bacteroidota, and Actinomycetota showed similar relative abundances in both regions, indicating a potential “core bacterial community”. Regarding the α-diversity of gut microbiota, although no significant differences were observed between clam samples from the two regions, their diversity was significantly lower than that of the sediment bacterial communities. The intestinal bacterial communities exhibited high similarity to the aquatic bacterial communities in terms of richness, diversity, and dominant species abundance, and it shares most of the ASVs with the sediment, suggesting that environmental microorganisms may serve as the primary source of the clam intestinal microbiota. Environmental drivers of bacterial communities differed regionally. In Fuqing, bacterial communities were associated with temperature, DO, pH, and salinity, and exhibited broader niche widths; in Putian, they were mainly influenced by nutrients, showing narrower niches. Compared to bacterial networks in the environment, the interactions among members within the gut bacterial communities of clams display modularity, indicative of functional specialization. The composition and functions of the intestinal microbiota of clams vary significantly in different environments, which may be a manifestation of their ecological adaptability. The composition and function of clam intestinal microbiota varied with environment, reflecting their ecological adaptability. These findings provide a scientific theoretical basis for water quality regulation and disease prevention in aquatic animal farming operations.