Spatial region of habitat drives fish gut microbial diversity, composition, and functionality

Abstract

The gut microbiome in fish aids in nutrient distribution by mediating the breakdown of food, nutrient absorption, energy homeostasis and waste excretion. The composition of the gut microbiome is largely influenced by the location of the fish as prey consumption and nutrient availability differs from the coast to the open and deep ocean regions. However, there are limited large-scale studies exploring how the gut microbiome differs across ocean regions, and the functional involvement of the microbiome from an inferred metagenomic perspective. Using a dataset of 101 fish species, we investigated the effects of spatial region habitat on the internal and external fish microbiome. We found that spatial region is a driver of internal organ, but not external organ diversity. Only open ocean internal samples contain a core microbiome of six taxa, including representatives from the genera: Synechococcus CC9902, Psychromonas, Acinetobacter, and Sva0081 Sediment Group. We also identified differing abundances of metabolic pathways between the samples, including pathways involved in xenobiotic detoxification, glycosaminoglycan degradation, ABC transporters, and the renin-angiotensin system. Our findings demonstrate that spatial region is a driver of fish gut microbial diversity, composition, and functionality.