{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T09:55:21Z","timestamp":1790848521432,"version":"4.1.0"},"reference-count":40,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["enviromicro-journals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Environ Microbiol Rep"],"published-print":{"date-parts":[[2026,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>\n                    Antimicrobial resistance (AMR) in environmental systems represents an emerging One Health challenge, with anaerobic digesters potentially serving as reservoirs of resistance\u2010associated genetic features. This study analysed four publicly available anaerobic digester shotgun metagenomic datasets (M2, M3, M12 and M17) retrieved from the NCBI Sequence Read Archive to characterise microbial functions, resistance\u2010associated annotations and antibiotic target loci. The datasets were generated using Illumina HiSeq 2000 sequencing and analysed through quality assessment, assembly, functional annotation and resistome profiling. A total of 1082 resistance\u2010associated annotations were identified, with the highest abundance detected in M2 (348), followed by M12 (276), M17 (259) and M3 (205). Detected annotations were associated with diverse antimicrobial categories, including aminoglycosides, quinolones, beta\u2010lactams, tetracyclines, glycopeptides, macrolides and sulfonamides. Several frequently detected loci, including\n                    <jats:italic>rpoB<\/jats:italic>\n                    ,\n                    <jats:italic>rpoC<\/jats:italic>\n                    ,\n                    <jats:italic>gyrA<\/jats:italic>\n                    ,\n                    <jats:italic>gyrB<\/jats:italic>\n                    , EF\u2010Tu, EF\u2010G, Ddl and KasA, were interpreted as antibiotic target or housekeeping loci rather than confirmed acquired resistance genes. Exploratory co\u2010abundance analysis identified strong associations among functionally linked loci, including\n                    <jats:italic>rpoB\u2010rpoC<\/jats:italic>\n                    and\n                    <jats:italic>gyrA\u2010gyrB<\/jats:italic>\n                    , likely reflecting shared genomic occurrence or functional relationships. These findings highlight the resistome potential of anaerobic digesters while emphasising the need for host\u2010resolved metagenomics, mobile genetic element analysis and mutation\u2010level characterisation to clarify environmental AMR risks.\n                  <\/jats:p>","DOI":"10.1111\/1758-2229.70400","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T09:09:28Z","timestamp":1790845768000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Metagenomic Characterisation of Antibiotic Resistance in Anaerobic Digesters and Their Implications for Environmental Health"],"prefix":"10.1111","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-9323-1790","authenticated-orcid":false,"given":"Olasunbo Aina","family":"Olasupo","sequence":"first","affiliation":[{"name":"Department of Microbiology Osun State University  Osogbo Nigeria"},{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-4857-2142","authenticated-orcid":false,"given":"Oluwaseyi Paul","family":"Olaniyan","sequence":"additional","affiliation":[{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"},{"name":"Multidisciplinary Research Laboratory Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2212-1930","authenticated-orcid":false,"given":"Sunday Babatunde","family":"Akinde","sequence":"additional","affiliation":[{"name":"Department of Microbiology Osun State University  Osogbo Nigeria"},{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ademola Ayodele","family":"Adesoye","sequence":"additional","affiliation":[{"name":"Department of Microbiology Osun State University  Osogbo Nigeria"},{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatimah Adenike","family":"Ajadi","sequence":"additional","affiliation":[{"name":"Department of Microbiology Federal University of Health Sciences  Ila\u2010Orangun Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0702-3243","authenticated-orcid":false,"given":"Omokaro","family":"Obire","sequence":"additional","affiliation":[{"name":"Department of Microbiology Rivers State University  Port Harcourt Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9646-5122","authenticated-orcid":false,"given":"Elijah Kolawole","family":"Oladipo","sequence":"additional","affiliation":[{"name":"Molecular Biology, Immunology and Bioinformatics Laboratory, Department of Microbiology Adeleke University  Ede Nigeria"},{"name":"Genomics Unit Helix Biogen Institute  Ogbomoso Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3921-6832","authenticated-orcid":false,"given":"Waidi Folorunso","family":"Sule","sequence":"additional","affiliation":[{"name":"Department of Microbiology Osun State University  Osogbo Nigeria"},{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2434-2089","authenticated-orcid":false,"given":"Olamilekan Emmanuel","family":"Oyinloye","sequence":"additional","affiliation":[{"name":"Department of Microbiology Osun State University  Osogbo Nigeria"},{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-3391-5193","authenticated-orcid":false,"given":"Adedolapo Aishat","family":"Salami","sequence":"additional","affiliation":[{"name":"Department of Microbiology Osun State University  Osogbo Nigeria"},{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emmanuel Sunday","family":"Fajoyegbe","sequence":"additional","affiliation":[{"name":"Department of Microbiology Osun State University  Osogbo Nigeria"},{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-8121-1113","authenticated-orcid":false,"given":"Adejoke Janet","family":"Ajani","sequence":"additional","affiliation":[{"name":"Department of Microbiology Osun State University  Osogbo Nigeria"},{"name":"Microbial Biotechnology and One Health Research Laboratory, Osun State University  Osogbo Nigeria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6632-2155","authenticated-orcid":false,"given":"Olabisi","family":"Ojo","sequence":"additional","affiliation":[{"name":"Department of Natural Sciences Albany State University  Albany Georgia USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,10,1]]},"reference":[{"issue":"1","key":"e_1_2_12_2_1","doi-asserted-by":"crossref","first-page":"959","DOI":"10.1186\/s12864-024-10876-0","article-title":"Metagenomic Assemblies Tend to Break Around Antibiotic Resistance Genes","volume":"25","author":"Abramova A.","year":"2024","journal-title":"BMC 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Colombia: The Role of gyrA Mutations in Fluoroquinolone Resistance","volume":"15","author":"\u00c1lvarez\u2010Aldana A.","year":"2026","journal-title":"Antibiotics"},{"issue":"4","key":"e_1_2_12_6_1","doi-asserted-by":"crossref","first-page":"374","DOI":"10.3390\/antibiotics10040374","article-title":"Potential Environmental and Human Health Risks Caused by Antibiotic\u2010Resistant Bacteria (ARB), Antibiotic Resistance Genes (ARGs) and Emerging Contaminants (ECs) From Municipal Solid Waste (MSW) Landfill","volume":"10","author":"Anand U.","year":"2021","journal-title":"Antibiotics"},{"issue":"14","key":"e_1_2_12_7_1","doi-asserted-by":"crossref","first-page":"4126","DOI":"10.1093\/bioinformatics\/btaa490","article-title":"Metaviral SPAdes: Assembly of Viruses From Metagenomic Data","volume":"36","author":"Antipov 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Close Genetic Relatedness, and Favorable Living Conditions Benefit Species Co\u2010Occurrence of Gut Microbiota in Brandt's Vole","volume":"15","author":"Cheng C.","year":"2024","journal-title":"Frontiers in Microbiology"},{"issue":"1","key":"e_1_2_12_13_1","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1038\/s41579-021-00602-y","article-title":"Interactions Between Bacterial and Phage Communities in Natural Environments","volume":"20","author":"Chevallereau A.","year":"2022","journal-title":"Nature Reviews Microbiology"},{"issue":"6","key":"e_1_2_12_14_1","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1111\/1755-0998.13079","article-title":"Incorporating Phylogenetic Metrics Into Microbial Co\u2010Occurrence Networks Based on Amplicon Sequences to Discern Community Assembly Processes","volume":"19","author":"Goberna M.","year":"2019","journal-title":"Molecular Ecology 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P.","year":"2025","journal-title":"Discover Chemistry"},{"key":"e_1_2_12_28_1","doi-asserted-by":"publisher","DOI":"10.1186\/s40816\u2010021\u201000311\u20102"},{"issue":"3","key":"e_1_2_12_29_1","doi-asserted-by":"crossref","DOI":"10.3390\/antibiotics14030296","article-title":"Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements With a Focus on the Complex Role of Phages","volume":"14","author":"Olsen N. 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