Distinct Structuring Mechanisms of Extrinsic and Intrinsic Factors on the Wild Marine Fish Gut Microbiome

The fish gut microbiome (GM) plays a critical role in nutrient absorption, immune homeostasis, and host physiology. Although shaped by extrinsic and intrinsic factors, the distinct mechanisms driving GM structure (e.g., whether through shifts in microbial abundance or changes in phylogenetic community composition) remain unclear. In this study, we characterized the GM of 21 wild marine fish species using 16S rRNA amplicon sequencing and examined how season, trophic level, and fish species differentially structure GM. Season and trophic level were primarily associated with shifts in microbial abundance, whereas fish species showed phylogenetic similarity among GMs, as evidenced by the phylogenetic clustering of fish species-core amplicon sequence variants (ASVs). This suggests that host-specific filtering drives the phylogenetic structure of GM within fish species. In addition, the predicted functional pathway profiles were stratified by season. Collectively, our findings reveal that extrinsic and intrinsic factors differentially structure fish GM through distinct processes.