Unveiling the Gut and Flesh Microbiome Signature and Diversity of the Bangladesh National Fish Hilsa (Tenualosa ilisha)

Abstract

Abstract Fish microbiome science is progressing fast, but it is mostly restricted to farmed or laboratory fish species compared to natural or marine fish populations. The aim of this study was to unveil the gut and flesh microbiome signature and diversity of the anadromous fish, Tenualosa ilisha (hilsa), the national fish of Bangladesh. We analysed 18 samples including 15 gut (intestinal contents) and three flesh samples from 18 individual hilsa fishes collected from three major habitats (e.g., freshwater, brackish water and marine water) of hilsa in Bangladesh through 16S rRNA (V3 – V4 region) gene sequencing-based metagenomics. A total of 325 operational taxonomic units (OTUs) including 67 and 258 in flesh and gut samples, respectively were identified. The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our findings revealed substantial taxonomic variability between sample categories (i.e., gut and flesh; p = 0.0127; Kruskal Wallis test), and habitats (freshwater, brackish water, and marine water; (p = 0.007; Kruskal Wallis test) of the hilsa fishes, indicated by their higher degree of shared microbiota. Of the identified genera, Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, Hafnia etc. were the major bacterial genera detected in hilsa fish. Importantly, we detected six genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella seem to be specific to the hilsa fishes. Our data provided evidence for the existence of both unique and shared bacteriomes with probiotics potentials in the gut and flesh of hilsa fishes, which might be taken into consideration for undertaking future microbiome study in this economically important fish species.