{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,1]],"date-time":"2026-11-01T07:07:52Z","timestamp":1793516872591,"version":"4.5.0"},"reference-count":56,"publisher":"MDPI AG","issue":"5","license":[{"start":{"date-parts":[[2026,5,17]],"date-time":"2026-05-17T00:00:00Z","timestamp":1778976000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Russian state-funded project for ICBFM SB RAS","award":["125012300671-8"],"award-info":[{"award-number":["125012300671-8"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background\/Objectives: Soil microbiomes in agroecosystems are natural reservoirs of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), creating conditions for horizontal gene transfer (HGT) to clinically relevant bacteria. Southern West Siberia\u2014a globally significant grain-producing region\u2014lacks metagenomic characterization of its soil resistome. This study aimed to establish the first baseline profile of resistome and mobilome composition for West Siberian agricultural soils. Methods: Twelve composite soil samples were collected from agroecosystems under seven crop types across diverse soil types in southern West Siberia (September 2022). Shotgun metagenomics was performed on an Illumina NovaSeq 6000 platform. Taxonomic profiling used Kraken2\/Bracken; ARG annotation used Prokka\/DeepARG (identity \u2265 70%, probability score \u2265 0.8); while MGE characterization used Platon, HMMER v3.3.2, and Prokka-based integrase annotation. Resistome load was normalized to the single-copy housekeeping gene rpoB; ARG\u2013MGE associations were defined as co-localization within 10 kb on the same contig. Results: Microbial communities were dominated by Pseudomonadota and Bacillota, with a stable core of Streptomycetaceae, Nitrobacteraceae, and Sphingomonadaceae. Normalized resistome load (N\/rpoB 2.30\u20135.37) indicated moderate anthropogenic pressure. Dominant ARGs included efflux pumps (emrA, drrA, tetA, bcr, fsr), target modification (lnrL), and lipid A modification (arnA) genes. Class 1 integron integrase (intI1\/rpoB 0.64\u20131.59) was detected in all 12 samples, exceeding unity in 9 of 12. ARG\u2013MGE co-localizations were found in 11 of 12 samples. In sample Mg_155, genes emrA\u2013emrB and bcr (NODE_16) and arnA and lnrL (NODE_6) were each independently associated with distinct prophage IntA integrase copies within Pseudomonas contigs, documenting multiple parallel horizontal transfer events encompassing resistance to five antibiotic classes. Conclusions: This work establishes the first metagenomic baseline of resistome and mobilome for West Siberian agroecosystems. The obtained data indicate moderate anthropogenic pressure on soil microbiomes, consistent with temperate agricultural systems with limited organic fertilizer input. The detected ARG\u2013MGE co-localizations and evidence of prophage-mediated transfer of resistance determinants beyond their natural hosts suggest that mobilization potential in the region warrants consideration in future AMR monitoring programs.<\/jats:p>","DOI":"10.3390\/antibiotics15050502","type":"journal-article","created":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T08:55:28Z","timestamp":1779180928000},"page":"502","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["West Siberian Soil Resistome: Mobile Antibiotic Resistance in Agricultural Microbiomes"],"prefix":"10.3390","volume":"15","author":[{"given":"Anna Evgenevna","family":"Skotareva","sequence":"first","affiliation":[{"name":"Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia"},{"name":"Department of Molecular Biology and Biotechnology, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4852-5661","authenticated-orcid":false,"given":"Ekaterina Alexeevna","family":"Sokolova","sequence":"additional","affiliation":[{"name":"Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia"},{"name":"Department of Molecular Biology and Biotechnology, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3405-6980","authenticated-orcid":false,"given":"Elena Nikolaevna","family":"Voronina","sequence":"additional","affiliation":[{"name":"Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia"},{"name":"Department of Molecular Biology and Biotechnology, Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,17]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Von Wintersdorff, C.J.H., Penders, J., van Niekerk, J.M., Mills, N.D., Majumder, S., van Alphen, L.B., Savelkoul, P.H.M., and Wolffs, P.F.G. 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