Metagenomic insights into microbial community, antibiotic resistance genes and virulence factor in Saryu river water, India

River convergences are an important ecosystem to investigate their microbial community and functional profile. Enormous application of trace elements and antibiotics, release in the environment, causing pollution and selective pressure which facilitated the proliferation and dissemination of resistance genes for antibiotics metals and biocides in bacterial communities. Therefore, we aimed to elucidate the occurrence of resistance genes and virulence factors among the microbial community of Saryu river water, leveraging high-throughput metagenomics coupled with bioinformatic analyses. The identified highly dominant ARGs types were rifampin, tetracycline, macrolide, polymyxin, rifampicin multidrug/efflux. The ARGs such as rpoB2, Txr , adeF , tetB(P) and acrB were found to be abundant in Saryu river water. Among the detected MRGs subtypes namely ruvB and arsB were the most abundant in water. Further, identified resistance against biocides were ethidium bromide, triclosan, sodium dodecyl sulphate etc. Among the virulence factors, tufa, htpB (adherence), Gmd (Immune-modulation), cheD (Motility), clpV1 (effector-delivery-system) were found to be highly prevalent. Taxonomic classification revealed that Cyanobateriota followed by Pseudomonadota (Proteobacteria), Bacteriodota were dominant phyla in river water. Microcystis was the most dominant genera, followed by Desulfomicrobium , Dechloromonas . The present study depicts that an antibiotics and metals are the major source for developing resistance against genes and dissemination in bacteria dwelling in the environment. Metagenomic exploration plays a pivotal role in deciphering riverine ecosystems and offers valuable insights into the mitigation of pollution and the dissemination of resistance genes. Monitoring microbial diversity can aid in identifying various prokaryotes, pathogens, and pollutants, including dyes and their associated resistance genes.