High-throughput sequencing reveals significant diversity in the gut microbiomes of humpback (Chanodichthys dabryi) and crucian carp (Carassius carassius

Abstract

While the fish gut microbiome composition is important to fish health, studies of the gut microbiome of fish lag behind those of terrestrial vertebrates. Whether the microbial communities in an aquatic habitat affect the gut microbiomes of resident fish is unclear. This study investigates and compares the composition of bacterial communities in the gut of crucian carp and humpback and in the water of their habitat using high-throughput sequencing of two hypervariable regions (V3 and V4) of the 16S rRNA gene. We identified 2058 operational taxonomic units (OTUs) in the humpback, 2551 OTUs in crucian carp, and 1760 OTUs in their habitat water. 218 OTUs were common to all three bacterial communities. Linear discriminant analysis revealed multiple species that differed significantly in abundance between the communities. This study aims to improve our understanding of the influence of the aquatic habitat on fish–microbe relationships.