Gut Bacterial Diversity of the Migratory Hilsa Shad Tenualosa ilisha (Hamilton, 1822) From Different Habitats in Bangladesh

ABSTRACT The present study was conducted to determine the distinct gut bacteriome diversity and composition in Hilsa Shad ( Tenualosa ilisha) , a biologically, nutritionally and economically significant species, across different habitats using next‐generation sequencing. Through amplicon sequencing of the 16S rRNA gene (V3–V4 regions), diverse bacterial taxa and their distribution within the gut microbiota of hilsa from three habitats, including freshwater, brackish water, and marine water in Bangladesh, were identified. The study identified 1809 operational taxonomic units across 42 bacterial phyla, 89 classes, 203 orders, 312 families and 570 genera. Hilsa gut microbiota showed significant habitat‐specific variation, with marine samples exhibiting higher Shannon diversity and greater Chao1 and ACE richness than freshwater and brackish samples. Simpson diversity did not differ significantly among habitats, indicating that habitat primarily influenced microbial richness rather than overall evenness. Freshwater hilsa gut microbiota was dominated by the genera Aeromonas , Lactococcus , Photobacterium , Clostridium , Burkholderia , Bacillus , Chryseobacterium and Cetobacterium . In contrast, marine and brackish water hilsa guts were dominated by Acinetobacter, Psychrobacter , Bacillus , Lactococcus , Photobacterium , Exiguobacterium and Pseudomonas , with Vibrio relatively abundant in the brackish water population. Notably, potential beneficial bacteria were more abundant than potential pathogenic bacteria in all sample types ( p < 0.05). PICRUSt2‐based functional prediction indicated habitat‐associated variation in microbial metabolic potential, with differences in predicted pathways related to carbohydrate metabolism, amino acid and nucleotide biosynthesis, vitamin and cofactor metabolism, sulphur metabolism and bacterial cell wall biosynthesis. Species co‐occurrence network analysis further revealed predominantly positive microbial associations and identified several highly connected taxa, suggesting cooperative microbial interactions that may contribute to community stability. Collectively, these findings suggest that habitat‐associated differences in the gut microbiota may influence nutrient metabolism and support host adaptation during migration, while providing a valuable foundation for future studies investigating host–microbiome interactions and the ecological functions of the hilsa gut microbiome.