Comparative Analysis of the Intestinal Microbiota of Wild Mangrove Mudcrabs, Scylla serrata and S. olivacea Employing 16S rRNA High Throughput Sequencing

Mud crabs of the genus Scylla (Scylla serrata and S. olivacea) are important species for aquaculture diversification in India. The current scientific focus is to understand the microbiome of S. serrata and S. olivacea from the same habitat to know the similarity or difference due to host phylogeny to enable species-specific interventions for seed production and farming practices. Intestinal microbiota strongly influence the overall physiological processes of aquatic organisms. This study investigates the gut bacterial composition of two economically important mud crab species (S. serrata and S. olivacea), employing 16S rRNA high-throughput sequencing. The α-diversity indices of S. serrata showed increased richness compared to S. olivacea. The β-diversity indices showed strong clustering based on the host phylogeny. Detected bacteria in S. serrata were classified into 31 phyla leading to 564 genera. In S. olivacea, the detected bacteria were classified into 26 phyla leading to 405 genera. The dominant phyla in the gut of S. serrata were Firmicutes, Proteobacteria, Fusobacteriota, and Bacteroidota, while the dominant phyla in S. olivacea belonged to Firmicutes, Campylobacterota, Fusobacteriota, and Proteobacteria. The dominant genus was represented by ZOR0006, Hypnocyclicus, Candidatus_Bacilloplasma, Psychrilyobacter, and Vibrionaceae unclassified in S. serrata, and in addition to these, Halarcobacter was dominant in S. olivacea. The analysis showed that the gut microbiota of S. serrata and S. olivacea varied significantly, though they inhabited the same environment, indicating the role of host species in shaping the gut microbiota.