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.

Abalone is an economically important mollusk, whose slow growth has impeded the recovery of its wild populations and development of aquaculture. The three-way cross hybrid abalone ((Haliotis discus hannai♀ × H. fulgens♂)♀ × H. gigantea♂, DF × SS) demonstrated notable diversity in growth traits across the population with genetic differentiation, offering a model for exploring the molecular mechanisms of abalone growth. In this study, a total of 89 SNPs and 97 candidate genes were identified to be associated with growth-related traits of abalone using whole-genome resequencing and a genome-wide association study (GWAS) analysis. Then, ten overlap genes were found among these candidate genes by combining the results of GWAS and comparative transcriptomic analyses between the large individuals (L group) and small individuals (S group) of DF × SS. These overlap genes include up-regulated genes (fabG) and down-regulated genes (HMCN1, TLR3, ITIH3) between the L and the S groups, which are thought to function in growth in other organisms. The biological functions of these candidate genes in abalone still have to be confirmed, but they have improved our understanding of the molecular mechanisms behind abalone growth traits and provided molecular markers for abalone breeding programs.