Core microbiomes found in habitats with sandy bottom substratum are the most phylogenetically diverse among trophic level three ray-finned fish midgut samples

Fish gut microbiomes play an indispensable role in regulating fish growth, behavior and immune health, yet little is known about the environmental factors that influence its composition. We investigated how habitat substrata affects the midgut microbiome in carnivorous ray-finned fish, hypothesizing that fish from similar substrata have similar midgut microbial compositions. Using alpha diversity metrics, midgut samples demonstrate the highest variety and abundance of microbial species compared to other body sampling sites. Midgut samples from fish found in habitats with kelp forest, sandy bottom and rocky reef substrata exhibit distinct core microbiomes, only sharing one common core species: Pseudoalteromonas sp. In addition, we characterized the relative and total abundance of midgut samples at a phylum level and identified Proteobacteria, followed by Bacteroidetes and Firmicutes, to be the most dominant phyla in the core midgut microbiota. The midgut microbiomes from fish living in habitats with sandy bottom substratum are characterized by the key indicator species Synechococcus sp. CC9902 and Psychromonas sp. Overall, this study demonstrates that the fish gut microbiome is associated with the fish’s habitat, with the key species identified providing the foundation in understanding the major phyla associated with carnivorous fish microbiota. We hope to extend this knowledge into developing probiotics to promote fish digestive and immune health, as well as technology to monitor fish populations.