Abstract
The composition of the fish microbiome plays key roles in immune response and host protection. Investigations into factors modulating the fish microbiome have key implications in understanding the vertebrate microbiome given the large number of fish species. Previous studies have identified strong effects of fish species and habitat on various fish body site microbiomes. However, the contribution of fish morphology to taxonomic and functional diversity of the microbiome has not been extensively characterized. In studies on terrestrial animals, effects of morphological variables on the microbiome have revealed strong effects, with the species-area relationship shown to correlate increased microbiome diversity with increased organism size. In this study, we aimed to determine if morphological variables describing fish species located in Southern California correlate with changes in microbiome taxonomy across body sites. Here we investigate the microbiome of four different body sites, gill, skin, midgut, and hindgut, using 16S rRNA sequencing collected from 101 fish species off the coast of Southern California. Initial analysis of alpha and beta diversity revealed the primary driver of microbiome diversity differences to be, not a morphological variable, but the method by which fish were caught. Subsequent core microbiome, differential abundance, and indicator taxa analysis revealed that the effects of catch method are body site-specific and drive differences in microbial composition at the ASV level. These findings reveal a novel confounding variable in fish microbiome studies, potentially informing updated best practices and study designs for fish microbiome sampling. Future directions include establishing causality of the method of catch either through direct impacts on microbial composition of collected samples or biasing the taxonomic profile of sampled fish.