LAUSR

Abstract This study analyzed the pond, gut region and fish species influences on the gut bacterial communities in three Indian major carps (IMCs), rohu (Labeo rohita), catla (Catla catla) and mrigal (Cirrhinus mrigala), using high-throughput sequencing. Foregut and hindgut communities from IMCs cohabiting in three polyculture ponds were investigated. The communities of all three IMC's were dominated by Proteobacteria (accounting for 15–40% of sequence reads), Firmicutes (16–21%), Actinobacteria (18–34%), and Bacteroidetes (6–19%). Catla presented a significantly higher abundance of Proteobacteria (40.4%) and Fusobacteria (1.8%) than mrigal (14.6% and 0.46%, respectively) and rohu (24.4% and 0.42%, respectively). Catla also contained the lowest relative abundance of Bacteroidetes (5.9% vs. 17.7% for mrigal and 18.7% for rohu). At deeper levels the relative abundances of a number of OTUs differed between the species. Despite this, a core microbiota were observed. Comparing the presence/absence of OTUs (unweighted distances), all beta diversity parameters (PERMANOVA, ANOSIM, distance-based redundancy analysis and delta) revealed significant differences in the three factors studied: gut region, fish species and ponds. These results suggested that gut microbiome might have resulted from niche partitioning and selective pressures that could be species-specific.