Riverine pollution influences the intraspecific variation in the gut microbiome of an invasive fish, (Linn., 1758).

Unlabelled: Humans are significantly impacting riverine systems worldwide, prompting us to investigate the effects of water pollution on the gut microbiome of (common carp). Using 16S rRNA gene sequencing, we compared the gut microbiomes of common carp from two sites along river Yamuna with different pollution levels. Water pollution significantly altered the fish gut microbiome structure and microbial composition. dominated in both sampling sites, while prevailed in polluted water samples, indicating sewage and fecal contamination. Less polluted samples exhibited and , negatively correlated with pollution levels. The polluted site had higher prevalence of potentially pathogenic and heavy metal-resistant bacteria, as well as microbial communities associated with wastewater treatment systems. Functional prediction highlighted the significant role of the gut microbiome in digestion and metabolism, with active enzymes for breaking down various organic substances. Biosynthetic pathways for leucine, valine, and isoleucine were present in both sites, known to be involved fish immunity. The host maintained a stable and diverse bacterial consortium, while microbial diversity became more specialized due to human activities, adapting to anthropogenic stress and selection pressures.

Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03747-0.