Cooperative Associations Between Fishes and Bacteria: The Influence of Different Ocean Fishes on the Gut Microbiota Composition

Gut microbial communities perform a multitude of physiological functions for their hosts; however, the drivers and distribution patterns of microbiota in wild animals remain largely underexplored. Our understanding of how these microbial communities are structured across hosts in natural environments—especially within a single host species remains limited. Here, we characterized the gut microbial communities of four species of ocean fish using 16S rRNA high-throughput sequencing to investigate the structural and functional features of these microbial communities across different fish species. By comparing the gut microbiota compositions of blue sharks (Prionace glauca), bigeye tuna (Thunnus obesus), sickle pomfret (Taractichthys steindachneri), and mackerel (Scomber japonicus), we identified several microbial taxa—including Photobacterium, Pelomonas, Ralstonia, and Rhodococcus—that were consistently detected across all samples, indicating they likely constitute a “common microbiota”. However, the relative abundances of these taxa varied significantly among species, with Photobacterium exhibiting the highest diversity. Blue sharks and bigeye tuna harbored relatively few dominant microbial species, but the abundance of these dominant bacteria was remarkably high, and inter-individual differences in microbial composition were pronounced. In contrast, mackerel and sickle pomfret contained a greater variety of dominant genera, each with low relative abundance, and inter-individual differences within the same species were minimal. Functionally, metabolic pathways, biosynthesis of secondary metabolites, and microbial metabolism represent the predominant functional categories of the intestinal microbiota in marine fish, with only minor interspecific differences observed. In contrast, biosynthesis of amino acids, ABC transporters, and two-component systems are the key functional pathways that exhibit significant variations across different fish species. Collectively, these findings reveal differences in gut microbial stability among different fish hosts. Such variations may be associated with the hosts’ energy utilization needs, and changes in the gut microbiota play a critical role in shaping the diverse survival strategies of these fish species.