{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T05:17:40Z","timestamp":1787894260734,"version":"build-2784847793"},"reference-count":105,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>Riverine sediments serve as critical reservoirs of microbial diversity and functional genes, reflecting both natural ecological processes and anthropogenic impacts. In the present study, we employed a shotgun metagenomic approach to investigate microbial community composition, antimicrobial resistance (AMR) genes, and virulence factors in sediments collected from three environmentally distinct locations of the Yamuna River near Agra, India, representing BSA, TGY, and YEA. The sediment DNA was subjected to high-throughput Illumina sequencing, followed by quality control, assembly, and open reading frame prediction. Taxonomic classification and diversity analyses were performed using MEGAN6 and R-based statistical tools, while AMR genes were identified from predicted metagenomic proteins using the Resistance Gene Identifier (RGI) against the CARD database, with high-confidence perfect and strict hits retained; ARGs were interpreted independently of species-level host assignment. Virulence factors were assessed through presence\u2013absence profiling of functionally relevant gene categories. The results revealed pronounced spatial heterogeneity in microbial communities, with increasing taxonomic diversity, functional complexity, and evenness from BSA to TGY and YEA. TGY and YEA composite samples showed greater observed representation of high-confidence AMR gene predictions spanning multiple drug classes and resistance mechanisms, alongside a diverse repertoire of virulence-associated genes linked to motility, adhesion, and secretion systems. In contrast, the BSA site harbored a comparatively simpler resistome and virulome. Overall, this study highlights Yamuna River sediments as important reservoirs of resistance and virulence determinants and underscores the need for long-term genomic surveillance to inform risk assessment, pollution control, and sustainable river management strategies.<\/jats:p>","DOI":"10.3389\/fmicb.2026.1938385","type":"journal-article","created":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T04:30:44Z","timestamp":1787891444000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Metagenomic insights into antibiotic resistance genes and virulence factors in sediments of river Yamuna"],"prefix":"10.3389","volume":"17","author":[{"given":"Ajaya Kumar","family":"Rout","sequence":"first","affiliation":[{"name":"College of Fisheries (Datia), Rani Lakshmi Bai Central Agricultural University","place":["Jhansi, India"]},{"name":"ICAR-Central Inland Fisheries Research Institute","place":["Barrackpore, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Partha Sarathi","family":"Tripathy","sequence":"additional","affiliation":[{"name":"College of Fisheries (Datia), Rani Lakshmi Bai Central Agricultural University","place":["Jhansi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sujata","family":"Dey","sequence":"additional","affiliation":[{"name":"ICAR-Central Inland Fisheries Research Institute","place":["Barrackpore, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neelesh","family":"Kumar","sequence":"additional","affiliation":[{"name":"College of Fisheries (Datia), Rani Lakshmi Bai Central Agricultural University","place":["Jhansi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ganesh","family":"Kumar","sequence":"additional","affiliation":[{"name":"College of Fisheries (Datia), Rani Lakshmi Bai Central Agricultural University","place":["Jhansi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pranaya Kumar","family":"Parida","sequence":"additional","affiliation":[{"name":"ICAR-Central Inland Fisheries Research Institute","place":["Barrackpore, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ashutosh","family":"Singh","sequence":"additional","affiliation":[{"name":"College of Agriculture, Rani Lakshmi Bai Central Agricultural University","place":["Jhansi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Budheswar","family":"Dehury","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education","place":["Manipal, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pramod Kumar","family":"Pandey","sequence":"additional","affiliation":[{"name":"College of Fisheries (Datia), Rani Lakshmi Bai Central Agricultural University","place":["Jhansi, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bijay Kumar","family":"Behera","sequence":"additional","affiliation":[{"name":"ICAR-Central Inland Fisheries Research Institute","place":["Barrackpore, India"]},{"name":"National Fisheries Development Board, Department of Fisheries, Government of India","place":["Hyderabad, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,8,28]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"8490","DOI":"10.4081\/jbr.2020.8490","article-title":"Tetracycline resistant genes as bioindicators of water pollution.","volume":"93","author":"Abdelall","year":"2020","journal-title":"J. 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