{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T07:04:19Z","timestamp":1789974259568,"version":"4.0.1"},"reference-count":76,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100014825","name":"Biotechnology Industry Research Assistance Council","doi-asserted-by":"publisher","award":["INSACOG"],"award-info":[{"award-number":["INSACOG"]}],"id":[{"id":"10.13039\/501100014825","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001407","name":"Department of Biotechnology, Ministry of Science and Technology, India","doi-asserted-by":"publisher","award":["BT\/PR50613\/MED\/32\/981\/2023"],"award-info":[{"award-number":["BT\/PR50613\/MED\/32\/981\/2023"]}],"id":[{"id":"10.13039\/501100001407","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Gut Pathog"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    The human microbiome serves as a reservoir of antibiotic resistance genes (ARGs), collectively known as the resistome, which has crucial implications for human health. However, the distribution of ARGs across diverse bacterial taxa and their variation across populations, disease states, and body sites remain less well understood. Here, we comprehensively profiled the human resistome using genomic and metagenomic data. Our analysis included 4,744 species-representative gut bacterial genomes and 452 oral bacterial genomes, along with gut metagenomic data from 10,230 individuals across 58 studies encompassing 5,388 healthy and 4,842 disease-associated samples, including underexplored non-Western cohorts. Our analysis revealed variation in the gut resistome across population groups and countries. The oral microbiome exhibited a distinct resistome profile with lower ARG prevalence compared to the gut. Across multiple datasets, ARG abundance was generally higher in inflammatory bowel disease samples compared to healthy samples. Pathogenic taxa such as\n                    <jats:italic>Enterobacter<\/jats:italic>\n                    ,\n                    <jats:italic>Citrobacter<\/jats:italic>\n                    ,\n                    <jats:italic>Escherichia<\/jats:italic>\n                    , and\n                    <jats:italic>Klebsiella<\/jats:italic>\n                    carried the highest number of ARGs, including clinically relevant ARGs, whereas abundant commensals like\n                    <jats:italic>Bacteroides<\/jats:italic>\n                    and\n                    <jats:italic>Prevotella<\/jats:italic>\n                    contributed to the baseline resistome. Notably, population-level differences in ARG composition appeared to be linked to microbial community structure. Shared ARGs between commensal and pathogenic bacteria provided clues to horizontal gene transfer. These findings provide crucial insights into the ecological and population-level factors shaping the gut resistome, highlighting the roles of both pathogens and commensals in the maintenance and dissemination of antimicrobial resistance.\n                  <\/jats:p>","DOI":"10.1186\/s13099-026-00860-2","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T10:04:42Z","timestamp":1789466682000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Insights into the dynamics of antibiotic resistance genes in the human gut microbiome across populations"],"prefix":"10.1186","volume":"18","author":[{"given":"Deepika","family":"Pateriya","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anjli","family":"Tanwar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2958-6215","authenticated-orcid":false,"given":"Vineet K.","family":"Sharma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,15]]},"reference":[{"key":"860_CR1","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1016\/S0140-6736(24)01867-1","volume":"404","author":"M Naghavi","year":"2024","unstructured":"Naghavi M, Vollset SE, Ikuta KS, Swetschinski LR, Gray AP, Wool EE, Aguilar GR, Mestrovic T, Smith G, Han C, et al. Global Burden of Bacterial Antimicrobial Resistance 1990\u20132021: A Systematic Analysis with Forecasts to 2050. Lancet. 2024;404:1199\u2013226. https:\/\/doi.org\/10.1016\/S0140-6736(24)01867-1.","journal-title":"Lancet"},{"key":"860_CR2","doi-asserted-by":"publisher","first-page":"102150","DOI":"10.1016\/J.MIB.2022.102150","volume":"68","author":"LE Lamberte","year":"2022","unstructured":"Lamberte LE, van Schaik W. Antibiotic Resistance in the Commensal Human Gut Microbiota. Curr Opin Microbiol. 2022;68:102150. https:\/\/doi.org\/10.1016\/J.MIB.2022.102150.","journal-title":"Curr Opin Microbiol"},{"key":"860_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-022-29096-9","volume":"2022 131","author":"SC Forster","year":"2022","unstructured":"Forster SC, Liu J, Kumar N, Gulliver EL, Gould JA, Escobar-Zepeda A, Mkandawire T, Pike LJ, Shao Y, Stares MD, et al. Strain-Level Characterization of Broad Host Range Mobile Genetic Elements Transferring Antibiotic Resistance from the Human Microbiome. Nat Commun. 2022;2022 131:1\u20139. https:\/\/doi.org\/10.1038\/s41467-022-29096-9.","journal-title":"Nat Commun"},{"key":"860_CR4","doi-asserted-by":"publisher","first-page":"100409","DOI":"10.1016\/J.ENVADV.2023.100409","volume":"13","author":"S Bobate","year":"2023","unstructured":"Bobate S, Mahalle S, Dafale NA, Bajaj A. Emergence of Environmental Antibiotic Resistance: Mechanism, Monitoring and Management. Environ Adv. 2023;13:100409. https:\/\/doi.org\/10.1016\/J.ENVADV.2023.100409.","journal-title":"Environ Adv"},{"key":"860_CR5","doi-asserted-by":"publisher","first-page":"1445155","DOI":"10.3389\/FMICB.2024.1445155","volume":"15","author":"R Agudo","year":"2024","unstructured":"Agudo R, Reche MP. Revealing Antibiotic Resistance\u2019s Ancient Roots: Insights from Pristine Ecosystems. Front Microbiol. 2024;15:1445155. https:\/\/doi.org\/10.3389\/FMICB.2024.1445155","journal-title":"Front Microbiol"},{"key":"860_CR6","doi-asserted-by":"publisher","first-page":"114734","DOI":"10.1016\/J.ECOENV.2023.114734","volume":"254","author":"D Ding","year":"2023","unstructured":"Ding D, Wang B, Zhang X, Zhang J, Zhang H, Liu X, Gao Z, Yu Z. The Spread of Antibiotic Resistance to Humans and Potential Protection Strategies. Ecotoxicol Environ Saf. 2023;254:114734. https:\/\/doi.org\/10.1016\/J.ECOENV.2023.114734.","journal-title":"Ecotoxicol Environ Saf"},{"key":"860_CR7","doi-asserted-by":"publisher","unstructured":"Tao S, Chen H, Li N, Wang T, Liang W. The Spread of Antibiotic Resistance Genes In Vivo Model. Can J Infect Dis Med Microbiol. 2022;2022(3348695). https:\/\/doi.org\/10.1155\/2022\/3348695.","DOI":"10.1155\/2022\/3348695"},{"key":"860_CR8","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1038\/S41467-020-14422-W","volume":"11","author":"VR Carr","year":"2020","unstructured":"Carr VR, Witherden EA, Lee S, Shoaie S, Mullany P, Proctor GB, Gomez-Cabrero D, Moyes DL. Abundance and Diversity of Resistomes Differ between Healthy Human Oral Cavities and Gut. Nat Commun. 2020;11:693. https:\/\/doi.org\/10.1038\/S41467-020-14422-W.","journal-title":"Nat Commun"},{"key":"860_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S41467-023-36633-7","volume":"14","author":"K Lee","year":"2023","unstructured":"Lee K, Raguideau S, Sir\u00e9n K, Asnicar F, Cumbo F, Hildebrand F, Segata N, Cha CJ, Quince C. Population-Level Impacts of Antibiotic Usage on the Human Gut Microbiome. Nat Commun. 2023;14:1\u201319. https:\/\/doi.org\/10.1038\/S41467-023-36633-7","journal-title":"Nat Commun"},{"key":"860_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s42003-022-04187-x","volume":"5","author":"Q Lin","year":"2022","unstructured":"Lin Q, Xavier BB, Alako BTF, Mitchell AL, Rajakani SG, Glupczynski Y, Finn RD, Cochrane G, Malhotra-Kumar S. Screening of Global Microbiomes Implies Ecological Boundaries Impacting the Distribution and Dissemination of Clinically Relevant Antimicrobial Resistance Genes. Commun Biol. 2022;5:1\u20139. https:\/\/doi.org\/10.1038\/s42003-022-04187-x","journal-title":"Commun Biol"},{"key":"860_CR11","doi-asserted-by":"publisher","unstructured":"Patangia DV, Grimaud G, Wang S, Ross RP, Stanton C. Influence of Age, Socioeconomic Status, and Location on the Infant Gut Resistome across Populations. Gut Microbes. 2024;16. https:\/\/doi.org\/10.1080\/19490976.2023.2297837.","DOI":"10.1080\/19490976.2023.2297837"},{"key":"860_CR12","doi-asserted-by":"publisher","first-page":"1163","DOI":"10.1101\/GR.155465.113","volume":"23","author":"K Forslund","year":"2013","unstructured":"Forslund K, Sunagawa S, Kultima JR, Mende DR, Arumugam M, Typas A, Bork P. Country-Specific Antibiotic Use Practices Impact the Human Gut Resistome. Genome Res. 2013;23:1163\u20139. https:\/\/doi.org\/10.1101\/GR.155465.113.","journal-title":"Genome Res"},{"key":"860_CR13","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1038\/s41587-020-0603-3","volume":"39","author":"A Almeida","year":"2021","unstructured":"Almeida A, Nayfach S, Boland M, Strozzi F, Beracochea M, Shi ZJ, Pollard KS, Sakharova E, Parks DH, Hugenholtz P, et al. A Unified Catalog of 204,938 Reference Genomes from the Human Gut Microbiome. Nat Biotechnol. 2021;39:105\u201314. https:\/\/doi.org\/10.1038\/s41587-020-0603-3.","journal-title":"Nat Biotechnol"},{"key":"860_CR14","doi-asserted-by":"publisher","first-page":"D777","DOI":"10.1093\/NAR\/GKAB1019","volume":"50","author":"D Dai","year":"2022","unstructured":"Dai D, Zhu J, Sun C, Li M, Liu J, Wu S, Ning K, He LJ, Zhao XM, Chen WH. GMrepo v2: A Curated Human Gut Microbiome Database with Special Focus on Disease Markers and Cross-Dataset Comparison. Nucleic Acids Res. 2022;50:D777\u201384. https:\/\/doi.org\/10.1093\/NAR\/GKAB1019.","journal-title":"Nucleic Acids Res"},{"key":"860_CR15","doi-asserted-by":"publisher","first-page":"1023","DOI":"10.1038\/nmeth.4468","volume":"2017 1411","author":"E Pasolli","year":"2017","unstructured":"Pasolli E, Schiffer L, Manghi P, Renson A, Obenchain V, Truong DT, Beghini F, Malik F, Ramos M, Dowd JB, et al. Accessible, Curated Metagenomic Data through ExperimentHub. Nat Methods. 2017;2017 1411:1023\u20134. https:\/\/doi.org\/10.1038\/nmeth.4468.","journal-title":"Nat Methods"},{"key":"860_CR16","doi-asserted-by":"publisher","first-page":"D19","DOI":"10.1093\/NAR\/GKQ1019","volume":"39","author":"R Leinonen","year":"2011","unstructured":"Leinonen R, Sugawara H, Shumway M. Collaboration, on behalf of the I.N.S.D. The Sequence Read Archive. Nucleic Acids Res. 2011;39:D19\u201321. https:\/\/doi.org\/10.1093\/NAR\/GKQ1019.","journal-title":"Nucleic Acids Res"},{"key":"860_CR17","doi-asserted-by":"publisher","first-page":"D28","DOI":"10.1093\/NAR\/GKQ967","volume":"39","author":"R Leinonen","year":"2010","unstructured":"Leinonen R, Akhtar R, Birney E, Bower L, Cerdeno-T\u00e1rraga A, Cheng Y, Cleland I, Faruque N, Goodgame N, Gibson R, et al. The European Nucleotide Archive. Nucleic Acids Res. 2010;39:D28. https:\/\/doi.org\/10.1093\/NAR\/GKQ967.","journal-title":"Nucleic Acids Res"},{"key":"860_CR18","doi-asserted-by":"publisher","first-page":"3137","DOI":"10.1093\/BIOINFORMATICS\/BTX373","volume":"33","author":"J Brown","year":"2017","unstructured":"Brown J, Pirrung M, Mccue LAFQC, Dashboard. Integrates FastQC Results into a Web-Based, Interactive, and Extensible FASTQ Quality Control Tool. Bioinformatics. 2017;33:3137\u20139. https:\/\/doi.org\/10.1093\/BIOINFORMATICS\/BTX373.","journal-title":"Bioinformatics"},{"key":"860_CR19","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/BIOINFORMATICS\/BTU170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger AM, Lohse M, Usadel B, Trimmomatic. A Flexible Trimmer for Illumina Sequence Data. Bioinformatics. 2014;30:2114\u201320. https:\/\/doi.org\/10.1093\/BIOINFORMATICS\/BTU170.","journal-title":"Bioinformatics"},{"key":"860_CR20","unstructured":"Rotmistrovsky K and Agarwala R. 2011. BMTagger: Best Match Tagger for removing human reads from metagenomics datasets. https:\/\/ftp.ncbi.nlm.nih.gov\/pub\/agarwala\/bmtagger"},{"key":"860_CR21","doi-asserted-by":"publisher","unstructured":"Pateriya D, K. VPP, Scaria J, Sharma VK. Landscape of Flavonoid Metabolism in Human Gut Microbiome and Its Association with Health and Disease. Gut Microbes Rep. 2025;2. https:\/\/doi.org\/10.1080\/29933935.2025.2520788.","DOI":"10.1080\/29933935.2025.2520788"},{"key":"860_CR22","doi-asserted-by":"publisher","first-page":"e0163962","DOI":"10.1371\/JOURNAL.PONE.0163962","volume":"11","author":"W Shen","year":"2016","unstructured":"Shen W, Le S, Li Y, Hu F, SeqKit:. A Cross-Platform and Ultrafast Toolkit for FASTA\/Q File Manipulation. PLoS ONE. 2016;11:e0163962. https:\/\/doi.org\/10.1371\/JOURNAL.PONE.0163962.","journal-title":"PLoS ONE"},{"key":"860_CR23","doi-asserted-by":"publisher","first-page":"110592","DOI":"10.1016\/J.COMPBIOMED.2025.110592","volume":"195","author":"D Pateriya","year":"2025","unstructured":"Pateriya D, Malwe AS, Sharma VK, CRCpred. An AI-ML Tool for Colorectal Cancer Prediction Using Gut Microbiome. Comput Biol Med. 2025;195:110592. https:\/\/doi.org\/10.1016\/J.COMPBIOMED.2025.110592.","journal-title":"Comput Biol Med"},{"key":"860_CR24","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood DE, Lu J, Langmead B. Improved Metagenomic Analysis with Kraken 2. Genome Biol. 2019;20:1\u201313. https:\/\/doi.org\/10.1186\/S13059-019-1891-0","journal-title":"Genome Biol"},{"key":"860_CR25","doi-asserted-by":"publisher","first-page":"e104","DOI":"10.7717\/PEERJ-CS.104","volume":"2017","author":"J Lu","year":"2017","unstructured":"Lu J, Breitwieser FP, Thielen P, Salzberg SL, Bracken. Estimating Species Abundance in Metagenomics Data. PeerJ Comput Sci. 2017;2017:e104. https:\/\/doi.org\/10.7717\/PEERJ-CS.104","journal-title":"PeerJ Comput Sci"},{"key":"860_CR26","doi-asserted-by":"publisher","first-page":"D690","DOI":"10.1093\/NAR\/GKAC920","volume":"51","author":"BP Alcock","year":"2023","unstructured":"Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR, Wlodarski MA, Edalatmand A, Petkau A, Syed SA, Tsang KK, et al. CARD 2023: Expanded Curation, Support for Machine Learning, and Resistome Prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res. 2023;51:D690\u20139. https:\/\/doi.org\/10.1093\/NAR\/GKAC920.","journal-title":"Nucleic Acids Res"},{"key":"860_CR27","doi-asserted-by":"publisher","unstructured":"Hyatt D, Chen GL, LoCascio PF, Land ML, Larimer FW, Hauser LJ, Prodigal. Prokaryotic Gene Recognition and Translation Initiation Site Identification. BMC Bioinformatics. 2010;11:1\u201311. https:\/\/doi.org\/10.1186\/1471-2105-11-119","DOI":"10.1186\/1471-2105-11-119"},{"key":"860_CR28","doi-asserted-by":"publisher","unstructured":"Buchfink B, Xie C, Huson DH. Fast and Sensitive Protein Alignment Using Diamond. 2015, 12, https:\/\/doi.org\/10.1038\/nmeth.3176","DOI":"10.1038\/nmeth.3176"},{"key":"860_CR29","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/ismej.2014.106","volume":"9","author":"MK Gibson","year":"2014","unstructured":"Gibson MK, Forsberg KJ, Dantas G. Improved Annotation of Antibiotic Resistance Determinants Reveals Microbial Resistomes Cluster by Ecology. ISME J. 2014;9:207\u201316. https:\/\/doi.org\/10.1038\/ismej.2014.106.","journal-title":"ISME J"},{"key":"860_CR30","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12859-018-2336-6","volume":"19","author":"PTLC Clausen","year":"2018","unstructured":"Clausen PTLC, Aarestrup FM, Lund O. Rapid and Precise Alignment of Raw Reads against Redundant Databases with KMA. BMC Bioinformatics. 2018;19:1\u20138. https:\/\/doi.org\/10.1186\/S12859-018-2336-6","journal-title":"BMC Bioinformatics"},{"key":"860_CR31","doi-asserted-by":"publisher","unstructured":"Barbosa da Costa N, H\u00e9bert M-P, Fug\u00e8re V, Terrat Y, Fussmann GF, Gonzalez A, Shapiro BJ. A Glyphosate-Based Herbicide Cross-Selects for Antibiotic Resistance Genes in Bacterioplankton Communities. mSystems. 2022;7. https:\/\/doi.org\/10.1128\/MSYSTEMS.01482-21.","DOI":"10.1128\/MSYSTEMS.01482-21"},{"key":"860_CR32","doi-asserted-by":"publisher","unstructured":"Guitor AK, Raphenya AR, Klunk J, Kuch M, Alcock B, Surette MG, McArthur AG, Poinar HN, Wright GD. Capturing the Resistome: A Targeted Capture Method to Reveal Antibiotic Resistance Determinants in Metagenomes. Antimicrob Agents Chemother. 2020;64. https:\/\/doi.org\/10.1128\/AAC.01324-19.","DOI":"10.1128\/AAC.01324-19"},{"key":"860_CR33","doi-asserted-by":"publisher","unstructured":"Brown CL, Mullet J, Hindi F, Stoll JE, Gupta S, Choi M, Keenum I, Vikesland P, Pruden A, Zhang L. MobileOG-Db: A Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements. Appl Environ Microbiol. 2022;88. https:\/\/doi.org\/10.1128\/AEM.00991-22\/.","DOI":"10.1128\/AEM.00991-22\/"},{"key":"860_CR34","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-024-45638-9","volume":"2024 151","author":"R Maddamsetti","year":"2024","unstructured":"Maddamsetti R, Yao Y, Wang T, Gao J, Huang VT, Hamrick GS, Son HI, You L. Duplicated Antibiotic Resistance Genes Reveal Ongoing Selection and Horizontal Gene Transfer in Bacteria. Nat Commun. 2024;2024 151:1\u201315. https:\/\/doi.org\/10.1038\/s41467-024-45638-9.","journal-title":"Nat Commun"},{"key":"860_CR35","doi-asserted-by":"publisher","first-page":"2099","DOI":"10.1038\/S41396-022-01258-Z","volume":"16","author":"X Yi","year":"2022","unstructured":"Yi X, Liang JL, Su JQ, Jia P, li Lu J, Zheng J, Wang Z, wei Feng S, hao Luo Z, xia Ai H, et al. Globally Distributed Mining-Impacted Environments Are Underexplored Hotspots of Multidrug Resistance Genes. ISME J. 2022;16:2099\u2013113. https:\/\/doi.org\/10.1038\/S41396-022-01258-Z.","journal-title":"ISME J"},{"key":"860_CR36","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1016\/J.CSBJ.2023.11.047","volume":"23","author":"Y Sheng","year":"2024","unstructured":"Sheng Y, Wang J, Gao Y, Peng Y, Li X, Huang W, Zhou H, Liu R, Zhang W. Combined Analysis of Cross-Population Healthy Adult Human Microbiome Reveals Consistent Differences in Gut Microbial Characteristics between Western and Non-Western Countries. Comput Struct Biotechnol J. 2024;23:87\u201395. https:\/\/doi.org\/10.1016\/J.CSBJ.2023.11.047.","journal-title":"Comput Struct Biotechnol J"},{"key":"860_CR37","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41522-021-00248-x","volume":"2021 71","author":"P Prasoodanan","year":"2021","unstructured":"Prasoodanan P, K V, Sharma AK, Mahajan S, Dhakan DB, Maji A, Scaria J, Sharma VK. Western and Non-Western Gut Microbiomes Reveal New Roles of Prevotella in Carbohydrate Metabolism and Mouth\u2013Gut Axis. npj Biofilms Microbiomes. 2021;2021 71:1\u201317. https:\/\/doi.org\/10.1038\/s41522-021-00248-x.","journal-title":"npj Biofilms Microbiomes"},{"key":"860_CR38","doi-asserted-by":"publisher","first-page":"e100","DOI":"10.1002\/CPBI.100","volume":"70","author":"M Estaki","year":"2020","unstructured":"Estaki M, Jiang L, Bokulich NA, McDonald D, Gonz\u00e1lez A, Kosciolek T, Martino C, Zhu Q, Birmingham A, V\u00e1zquez-Baeza Y, et al. QIIME 2 Enables Comprehensive End-to-End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data. Curr Protoc Bioinforma. 2020;70:e100. https:\/\/doi.org\/10.1002\/CPBI.100.","journal-title":"Curr Protoc Bioinforma"},{"key":"860_CR39","doi-asserted-by":"publisher","unstructured":"Khleborodova A, Gamboa-Tuz SD, Ramos M, Segata N, Waldron L, Oh S. Lefser: Implementation of Metagenomic Biomarker Discovery Tool, LEfSe, in R. Bioinformatics. 2024;40. https:\/\/doi.org\/10.1093\/BIOINFORMATICS\/BTAE707.","DOI":"10.1093\/BIOINFORMATICS\/BTAE707"},{"key":"860_CR40","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1016\/J.MIB.2020.02.002","volume":"53","author":"RS McInnes","year":"2020","unstructured":"McInnes RS, McCallum GE, Lamberte LE, van Schaik W. Horizontal Transfer of Antibiotic Resistance Genes in the Human Gut Microbiome. Curr Opin Microbiol. 2020;53:35\u201343. https:\/\/doi.org\/10.1016\/J.MIB.2020.02.002.","journal-title":"Curr Opin Microbiol"},{"key":"860_CR41","doi-asserted-by":"publisher","unstructured":"Crits-Christoph A, Hallowell HA, Koutouvalis K, Suez JG, Microbes. Bad Genes? The Dissemination of Antimicrobial Resistance in the Human Microbiome. Gut Microbes. 2022;14\u2063\u2063\u2063 . https:\/\/doi.org\/10.1080\/19490976.2022.2055944","DOI":"10.1080\/19490976.2022.2055944"},{"key":"860_CR42","doi-asserted-by":"publisher","first-page":"627","DOI":"10.3390\/ANTIBIOTICS13070627","volume":"13","author":"AT Aboushady","year":"2024","unstructured":"Aboushady AT, Manigart O, Sow A, Fuller W, Ouedraogo AS, Ebruke C, Babin FX, Gahimbare L, Sombi\u00e9 I, Stelling J. Surveillance of Antimicrobial Resistance in the ECOWAS Region: Setting the Scene for Critical Interventions Needed. Antibiotics. 2024;13:627. https:\/\/doi.org\/10.3390\/ANTIBIOTICS13070627","journal-title":"Antibiotics"},{"key":"860_CR43","doi-asserted-by":"publisher","first-page":"943","DOI":"10.3390\/ANTIBIOTICS13100943","volume":"13","author":"AA Yahaya","year":"2024","unstructured":"Yahaya AA, Fuller W, Kithinji D, Mazengiya YD, Gahimbare L, Bishikwabo-Nsarhaza K. Perspectives on the Regional Strategy for Implementation of National Action Plans on Antimicrobial Resistance in the WHO African Region. Antibiotics. 2024;13:943. https:\/\/doi.org\/10.3390\/ANTIBIOTICS13100943.","journal-title":"Antibiotics"},{"key":"860_CR44","doi-asserted-by":"publisher","first-page":"188","DOI":"10.1016\/J.ECOENV.2014.04.037","volume":"106","author":"A Machado","year":"2014","unstructured":"Machado A, Bordalo AA. Prevalence of Antibiotic Resistance in Bacteria Isolated from Drinking Well Water Available in Guinea-Bissau (West Africa). Ecotoxicol Environ Saf. 2014;106:188\u201394. https:\/\/doi.org\/10.1016\/J.ECOENV.2014.04.037.","journal-title":"Ecotoxicol Environ Saf"},{"key":"860_CR45","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1111\/J.1469-0691.2010.03182.X","volume":"16","author":"J Li\u00f1ares","year":"2010","unstructured":"Li\u00f1ares J, Ardanuy C, Pallares R, Fenoll A. Changes in Antimicrobial Resistance, Serotypes and Genotypes in Streptococcus Pneumoniae over a 30-Year Period. Clin Microbiol Infect. 2010;16:402\u201310. https:\/\/doi.org\/10.1111\/J.1469-0691.2010.03182.X.","journal-title":"Clin Microbiol Infect"},{"key":"860_CR46","doi-asserted-by":"crossref","unstructured":"Song, J.H.; Chang, H.H.; Suh, J.Y.; of \u2026 K.S.K.-J.; undefined 2004 Macrolide Resistance and Genotypic Characterization of Streptococcus Pneumoniae in Asian Countries: A Study of the Asian Network for Surveillance of Resistant. Acad. Song, HH Chang. JY Suh, KS Ko, SI Jung, WS Oh, KR Peck, NY Lee, Y YangJournal Antimicrob. Chemother. 2004\u2022academic.oup.com 2004, doi:10.1093\/jac\/dkh118.","DOI":"10.1093\/jac\/dkh118"},{"key":"860_CR47","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12879-020-05000-Y","volume":"20","author":"EXL Loo","year":"2020","unstructured":"Loo EXL, Zain A, Yap GC, Purbojati RW, Drautz-Moses DI, Koh YQ, Chong YS, Tan KH, Gluckman PD, Yap F, et al. Longitudinal Assessment of Antibiotic Resistance Gene Profiles in Gut Microbiomes of Infants at Risk of Eczema. BMC Infect Dis. 2020;20:1\u201312. https:\/\/doi.org\/10.1186\/S12879-020-05000-Y","journal-title":"BMC Infect Dis"},{"key":"860_CR48","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1007\/S10096-016-2842-2","volume":"36","author":"S Zangenah","year":"2017","unstructured":"Zangenah S, Andersson AF, \u00d6zenci V, Bergman P. Genomic Analysis Reveals the Presence of a Class D Beta-Lactamase with Broad Substrate Specificity in Animal Bite Associated Capnocytophaga Species. Eur J Clin Microbiol Infect Dis. 2017;36:657\u201362. https:\/\/doi.org\/10.1007\/S10096-016-2842-2","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"860_CR49","doi-asserted-by":"publisher","unstructured":"Zhang X, Zhou Q, Tang M, Pu J, Zhang J, Lu J, Zhang Y, Gao Y. Aminoglycoside Resistance and Possible Mechanisms in Campylobacter Spp. Isolated From Chicken and Swine in Jiangsu, China. Front Microbiol. 2021;12. https:\/\/doi.org\/10.3389\/FMICB.2021.716185.","DOI":"10.3389\/FMICB.2021.716185"},{"key":"860_CR50","doi-asserted-by":"publisher","unstructured":"Dhakan DB, Maji A, Sharma AK, Saxena R, Pulikkan J, Grace T, Gomez A, Scaria J, Amato KR, Sharma VK. The Unique Composition of Indian Gut Microbiome, Gene Catalogue, and Associated Fecal Metabolome Deciphered Using Multi-Omics Approaches. Gigascience. 2019;8. https:\/\/doi.org\/10.1093\/GIGASCIENCE\/GIZ004.","DOI":"10.1093\/GIGASCIENCE\/GIZ004"},{"key":"860_CR51","doi-asserted-by":"publisher","unstructured":"Tett A, Huang KD, Asnicar F, Fehlner-Peach H, Pasolli E, Karcher N, Armanini F, Manghi P, Bonham K, Zolfo M, et al. The Prevotella Copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations. Cell Host Microbe. 2019;26:666\u2013e6797. https:\/\/doi.org\/10.1016\/j.chom.2019.08.018.","DOI":"10.1016\/j.chom.2019.08.018"},{"key":"860_CR52","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1038\/nature17672","volume":"533","author":"EC Pehrsson","year":"2016","unstructured":"Pehrsson EC, Tsukayama P, Patel S, Mej\u00eda-Bautista M, Sosa-Soto G, Navarrete KM, Calderon M, Cabrera L, Hoyos-Arango W, Bertoli MT, et al. Interconnected Microbiomes and Resistomes in Low-Income Human Habitats. Nature. 2016;533:212\u20136. https:\/\/doi.org\/10.1038\/nature17672.","journal-title":"Nature"},{"key":"860_CR53","doi-asserted-by":"publisher","first-page":"1246","DOI":"10.1080\/19490976.2020.1747329","volume":"11","author":"Z Dan","year":"2020","unstructured":"Dan Z, Mao X, Liu Q, Guo M, Zhuang Y, Liu Z, Chen K, Chen J, Xu R, Tang J, et al. Altered Gut Microbial Profile Is Associated with Abnormal Metabolism Activity of Autism Spectrum Disorder. Gut Microbes. 2020;11:1246\u201367. https:\/\/doi.org\/10.1080\/19490976.2020.1747329.","journal-title":"Gut Microbes"},{"key":"860_CR54","doi-asserted-by":"publisher","first-page":"910","DOI":"10.1136\/GUTJNL-2020-324015","volume":"71","author":"Y Wan","year":"2022","unstructured":"Wan Y, Zuo T, Xu Z, Zhang F, Zhan H, Chan D, Leung TF, Yeoh YK, Chan FKL, Chan R, et al. Underdevelopment of the Gut Microbiota and Bacteria Species as Non-Invasive Markers of Prediction in Children with Autism Spectrum Disorder. Gut. 2022;71:910\u20138. https:\/\/doi.org\/10.1136\/GUTJNL-2020-324015.","journal-title":"Gut"},{"key":"860_CR55","doi-asserted-by":"publisher","first-page":"10291","DOI":"10.1038\/S41467-024-54797-8","volume":"15","author":"S Akiyama","year":"2024","unstructured":"Akiyama S, Nishijima S, Kojima Y, Kimura M, Ohsugi M, Ueki K, Mizokami M, Hattori M, Tsuchiya K, Uemura N, et al. Multi-Biome Analysis Identifies Distinct Gut Microbial Signatures and Their Crosstalk in Ulcerative Colitis and Crohn\u2019s Disease. Nat Commun. 2024;15:10291. https:\/\/doi.org\/10.1038\/S41467-024-54797-8.","journal-title":"Nat Commun"},{"key":"860_CR56","doi-asserted-by":"publisher","unstructured":"Li T, Yin Y. Critical Assessment of Pan-Genomic Analysis of Metagenome-Assembled Genomes. Brief Bioinform. 2022;23. https:\/\/doi.org\/10.1093\/BIB\/BBAC413.","DOI":"10.1093\/BIB\/BBAC413"},{"key":"860_CR57","doi-asserted-by":"publisher","first-page":"106815","DOI":"10.1016\/J.MIMET.2023.106815","volume":"213","author":"C Lee","year":"2023","unstructured":"Lee C, Polo RO, Zaheer R, Van Domselaar G, Zovoilis A, McAllister TA. Evaluation of Metagenomic Assembly Methods for the Detection and Characterization of Antimicrobial Resistance Determinants and Associated Mobilizable Elements. J Microbiol Methods. 2023;213:106815. https:\/\/doi.org\/10.1016\/J.MIMET.2023.106815.","journal-title":"J Microbiol Methods"},{"key":"860_CR58","doi-asserted-by":"publisher","unstructured":"Ducarmon QR, Zwittink RD, Hornung BVH, van Schaik W, Young VB, Kuijper EJ. Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection. Microbiol Mol Biol Rev. 2019;83. https:\/\/doi.org\/10.1128\/MMBR.00007-19.","DOI":"10.1128\/MMBR.00007-19"},{"key":"860_CR59","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/NRMICRO2312","volume":"8","author":"HK Allen","year":"2010","unstructured":"Allen HK, Donato J, Wang HH, Cloud-Hansen KA, Davies J, Handelsman J. Call of the Wild: Antibiotic Resistance Genes in Natural Environments. Nat Rev Microbiol. 2010;8:251\u20139. https:\/\/doi.org\/10.1038\/NRMICRO2312","journal-title":"Nat Rev Microbiol"},{"key":"860_CR60","doi-asserted-by":"publisher","first-page":"135882","DOI":"10.1016\/J.SCITOTENV.2019.135882","volume":"705","author":"BAT Nguyen","year":"2020","unstructured":"Nguyen BAT, Chen QL, He JZ, Hu HW. Microbial Regulation of Natural Antibiotic Resistance: Understanding the Protist-Bacteria Interactions for Evolution of Soil Resistome. Sci Total Environ. 2020;705:135882. https:\/\/doi.org\/10.1016\/J.SCITOTENV.2019.135882.","journal-title":"Sci Total Environ"},{"key":"860_CR61","doi-asserted-by":"publisher","first-page":"940","DOI":"10.1016\/j.tim.2022.04.004","volume":"30","author":"M Derrien","year":"2022","unstructured":"Derrien M, Turroni F, Ventura M, van Sinderen D. Insights into Endogenous Bifidobacterium Species in the Human Gut Microbiota during Adulthood. Trends Microbiol. 2022;30:940\u20137. https:\/\/doi.org\/10.1016\/j.tim.2022.04.004.","journal-title":"Trends Microbiol"},{"key":"860_CR62","doi-asserted-by":"publisher","unstructured":"Aog\u00e1in MM, Lau KJX, Cai Z, Narayana JK, Purbojati RW, Drautz-Moses DI, Gaultier NE, Jaggi TK, Tiew PY, Ong TH, et al. Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease. Am J Respir Crit Care Med. 2020;202:433\u201347. https:\/\/doi.org\/10.1164\/RCCM.201911-2202OC","DOI":"10.1164\/RCCM.201911-2202OC"},{"key":"860_CR63","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1128\/AAC.00672-10","volume":"55","author":"MI Garvey","year":"2011","unstructured":"Garvey MI, Baylay AJ, Wong RL, Piddock LJ. V Overexpression of PatA and PatB, Which Encode ABC Transporters, Is Associated with Fluoroquinolone Resistance in Clinical Isolates of Streptococcus Pneumoniae. Antimicrob Agents Chemother. 2011;55:190\u20136. https:\/\/doi.org\/10.1128\/AAC.00672-10","journal-title":"Antimicrob Agents Chemother"},{"key":"860_CR64","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S41522-024-00507-7","volume":"10","author":"NK Brar","year":"2024","unstructured":"Brar NK, Dhariwal A, \u00c5mdal HA, Junges R, Salvadori G, Baker JL, Edlund A, Petersen FC. Exploring Ex Vivo Biofilm Dynamics: Consequences of Low Ampicillin Concentrations on the Human Oral Microbiome. npj Biofilms Microbiomes. 2024;10:1\u201310. https:\/\/doi.org\/10.1038\/S41522-024-00507-7","journal-title":"npj Biofilms Microbiomes"},{"key":"860_CR65","doi-asserted-by":"publisher","first-page":"47","DOI":"10.1164\/rccm.202306-1059OC","volume":"210","author":"MM Aog\u00e1in","year":"2024","unstructured":"Aog\u00e1in MM, Ivan FX, Jaggi TK, Richardson H, Shoemark A, Narayana JK, Dicker AJ, Koh MS, Lee KCH, How OT, et al. Airway Resistotypes and Clinical Outcomes in Bronchiectasis. Am J Respir Crit Care Med. 2024;210:47\u201362. https:\/\/doi.org\/10.1164\/RCCM.202306-1059OC","journal-title":"Am J Respir Crit Care Med"},{"key":"860_CR66","doi-asserted-by":"publisher","first-page":"102688","DOI":"10.1016\/J.ANAEROBE.2022.102688","volume":"79","author":"S Yokoyama","year":"2023","unstructured":"Yokoyama S, Hayashi M, Goto T, Muto Y, Tanaka K. Identification of CfxA Gene Variants and Susceptibility Patterns in $\u03b2$-Lactamase-Producing Prevotella Strains. Anaerobe. 2023;79:102688. https:\/\/doi.org\/10.1016\/J.ANAEROBE.2022.102688.","journal-title":"Anaerobe"},{"key":"860_CR67","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S12941-023-00585-Z","volume":"22","author":"AC Anderson","year":"2023","unstructured":"Anderson AC, von Ohle C, Frese C, Boutin S, Bridson C, Schoilew K, Peikert SA, Hellwig E, Pelz K, Wittmer A, et al. The Oral Microbiota Is a Reservoir for Antimicrobial Resistance: Resistome and Phenotypic Resistance Characteristics of Oral Biofilm in Health, Caries, and Periodontitis. Ann Clin Microbiol Antimicrob. 2023;22:1\u201319. https:\/\/doi.org\/10.1186\/S12941-023-00585-Z","journal-title":"Ann Clin Microbiol Antimicrob"},{"key":"860_CR68","doi-asserted-by":"publisher","first-page":"355","DOI":"10.1111\/1462-2920.14009","volume":"20","author":"J Feng","year":"2018","unstructured":"Feng J, Li B, Jiang X, Yang Y, Wells GF, Zhang T, Li X. Antibiotic Resistome in a Large-Scale Healthy Human Gut Microbiota Deciphered by Metagenomic and Network Analyses. Environ Microbiol. 2018;20:355\u201368. https:\/\/doi.org\/10.1111\/1462-2920.14009","journal-title":"Environ Microbiol"},{"key":"860_CR69","doi-asserted-by":"publisher","first-page":"590018","DOI":"10.3389\/FMOLB.2020.590018","volume":"7","author":"Q Qiu","year":"2020","unstructured":"Qiu Q, Wang J, Yan Y, Roy B, Chen Y, Shang X, Dou T, Han L. Metagenomic Analysis Reveals the Distribution of Antibiotic Resistance Genes in a Large-Scale Population of Healthy Individuals and Patients With Varied Diseases. Front Mol Biosci. 2020;7:590018. https:\/\/doi.org\/10.3389\/FMOLB.2020.590018","journal-title":"Front Mol Biosci"},{"key":"860_CR70","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/S41467-023-44289-6","volume":"14","author":"X Li","year":"2023","unstructured":"Li X, Brejnrod A, Thorsen J, Zachariasen T, Trivedi U, Russel J, Vestergaard GA, Stokholm J, Rasmussen MA, S\u00f8rensen SJ. Differential Responses of the Gut Microbiome and Resistome to Antibiotic Exposures in Infants and Adults. Nat Commun. 2023;14:1\u201316. https:\/\/doi.org\/10.1038\/S41467-023-44289-6","journal-title":"Nat Commun"},{"key":"860_CR71","doi-asserted-by":"publisher","unstructured":"Bavumiragira JP, Eheneden I, Yin H, Mumbi AW, Gerald; Quoie DS, Uyisaba P, Wang R, Zhao J. Insight on Prioritization of Antibiotics in China, Their Occurrence, and Removal by Different Wastewater Treatment Technologies. Discov. Environ. 2024 21 2024, 2, 1\u201334. https:\/\/doi.org\/10.1007\/S44274-024-00047-Z","DOI":"10.1007\/S44274-024-00047-Z"},{"key":"860_CR72","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/S40168-017-0338-7","volume":"5","author":"K Winglee","year":"2017","unstructured":"Winglee K, Howard AG, Sha W, Gharaibeh RZ, Liu J, Jin D, Fodor AA, Gordon-Larsen P. Recent Urbanization in China Is Correlated with a Westernized Microbiome Encoding Increased Virulence and Antibiotic Resistance Genes. Microbiome. 2017;5:1\u201313. https:\/\/doi.org\/10.1186\/S40168-017-0338-7","journal-title":"Microbiome"},{"key":"860_CR73","doi-asserted-by":"publisher","unstructured":"Li J, Liu L, Zhang H, Guo J, Wei X, Xue M, Ma X. Severe Problem of Macrolides Resistance to Common Pathogens in China. Front Cell Infect Microbiol. 2023;13. https:\/\/doi.org\/10.3389\/FCIMB.2023.1181633\/FULL.","DOI":"10.3389\/FCIMB.2023.1181633\/FULL"},{"key":"860_CR74","doi-asserted-by":"publisher","first-page":"e00031723","DOI":"10.1590\/0102-311XES031723","volume":"40","author":"EST Villalobos","year":"2024","unstructured":"Villalobos EST, Ossa JAMD, MezaY.P.Gulloso, A.C.R. Nine-Year Trend in Escherichia Coli Resistance to Ciprofloxacin: Cross-Sectional Study in a Hospital in Colombia. Cad Saude Publica. 2024;40:e00031723. https:\/\/doi.org\/10.1590\/0102-311XES031723","journal-title":"Cad Saude Publica"},{"key":"860_CR75","doi-asserted-by":"publisher","first-page":"686472","DOI":"10.3389\/FCIMB.2021.686472","volume":"11","author":"EA Rodr\u00edguez","year":"2021","unstructured":"Rodr\u00edguez EA, Pino NJ, Jim\u00e9nez JN. Climatological and Epidemiological Conditions Are Important Factors Related to the Abundance of Bla KPC and Other Antibiotic Resistance Genes (ARGs) in Wastewater Treatment Plants and Their Effluents, in an Endemic Country. Front Cell Infect Microbiol. 2021;11:686472. https:\/\/doi.org\/10.3389\/FCIMB.2021.686472","journal-title":"Front Cell Infect Microbiol"},{"key":"860_CR76","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1128\/MMBR.00016-10","volume":"74","author":"J Davies","year":"2010","unstructured":"Davies J, Davies D. Origins and Evolution of Antibiotic Resistance. Microbiol Mol Biol Rev. 2010;74:417. https:\/\/doi.org\/10.1128\/MMBR.00016-10.","journal-title":"Microbiol Mol Biol Rev"}],"container-title":["Gut Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13099-026-00860-2","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13099-026-00860-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13099-026-00860-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T06:43:49Z","timestamp":1789973029000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1186\/s13099-026-00860-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,15]]},"references-count":76,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["860"],"URL":"https:\/\/doi.org\/10.1186\/s13099-026-00860-2","relation":{},"ISSN":["1757-4749"],"issn-type":[{"value":"1757-4749","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,15]]},"assertion":[{"value":"1 January 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"3 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 September 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"76"}}