Low Trophic Level Mixed Carnivore Diets Increase Taxonomic Diversity but may Reduce Functional Diversity in the Fish Midgut Microbiome

Abstract

Understanding the composition of the fish gut microbiome is pivotal for comprehending its ecological role, function, and overall health, informing aquatic ecosystem management and conservation. While previous research has demonstrated that diet drives microbial diversity differences within the fish gut, the specific relationship between diet and the gut microbiome composition within fish of different trophic levels, and how diet mediates specific metabolic processes within the fish gut, remains understudied. To this end, a dataset of 101 different fish species was used to elucidate patterns of microbial diversity within the gut microbiome across different diets. Aligning with previous findings, our results demonstrate that the midgut contains the greatest microbial diversity. Contrary to prevailing trends observed in mammalian hosts, our results reveal that low trophic level mixed carnivores exhibit the greatest degree of microbial diversity compared to other diets. Our investigation of taxonomic and functional differences within low trophic mixed carnivores illuminated a significant taxonomic difference between the midgut microbiome of low trophic level mixed carnivores and that of other diets, while revealing limited functional differences: an upregulation of the reductive acetyl CoA pathway and a downregulation of peptidoglycan biosynthesis pathways. These unexpected findings necessitate further investigation into the factors influencing microbial diversity within the fish gut and highlights the complexity of dietary interactions within aquatic environments. The present study contributes valuable insight into the intricate dynamics of the fish gut microbiome, further implicating diet as a determinant of microbial diversity in marine ecosystems, and emphasizing its implications in aquaculture feeding practices.