Core Microbiota and Differentially Abundant Taxa Vary with Swimming Performance, but Overall Microbial Communities and Functional Profiles Are Generally Consistent in Fish Hindguts

The fish gut microbiome, consisting of bacteria, viruses and fungi, play important roles in maintaining overall health, development, and metabolic functions. Extensive research explores how diet and environment affect the gut microbiome, but there is a limited understanding as to how the gut microbiome affects fish swimming performance. We analyzed 16S rRNA sequencing data from hindgut samples of Southern California fish characterized by swim performance, comparing hindgut microbial diversity, core microbiota, differentially abundant taxa and predicted MetaCyc functional pathways in slow- and fast- swimming fish. We found that overall microbial richness, diversity, and community structure were consistent across swim performance groups. However, slow-swimming fish retained a distinct set of unique core microbial taxa. Meiothermus and Geobacillus appeared as differentially abundant in the slow-swimming group, and phytate degradation I and phycourobilin biosynthesis predicted by MetaCyc functional analysis differed between swim groups, suggesting functional differences in slow- and fast-swimming fish. However, contributions to predicted energy metabolic pathways were distributed across many families, suggesting there are no single microbial drivers of these functional shifts. This research can serve as a framework for investigating other factors that may influence fish swim performance, such as trophic ecology, which is a likely explanation for unique core microbiome taxa observed in slow-swimming groups, despite the absence of differences in richness, evenness, and community composition. This work has potential applications in improving aquaculture and conservation of endangered fish species.