{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T05:59:55Z","timestamp":1790315995993,"version":"4.1.0"},"reference-count":30,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T00:00:00Z","timestamp":1790294400000},"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. Antibiot."],"abstract":"<jats:p>\n                    Fecal microbiota transplantation (FMT) is an effective therapy for recurrent\n                    <jats:italic>Clostridioides difficile<\/jats:italic>\n                    infection (rCDI) and is increasingly explored for other dysbiosis-related disorders. However, its implementation as a regulated therapeutic strategy requires robust donor screening, biosafety frameworks, and standardized processing workflows. Here, we describe the establishment of the first fecal microbiota biobank in southern Brazil and evaluate the incorporation of metagenomic sequencing as a complementary layer of donor characterization and safety assessment. A structured donor selection pipeline based on international guidelines was implemented, integrating clinical screening, biochemical and serological testing, and microbiological analyses. Of 100 screened candidates, only four donors met all eligibility criteria and were included in the biobank, highlighting the stringency of the selection process. Shotgun metagenomic sequencing revealed a diverse resistome across all donors, including a shared core set of resistance genes alongside marked interindividual variability. Dominant resistance determinants included tetracycline-associated genes,\n                    <jats:italic>ermF<\/jats:italic>\n                    , CfxA-type \u03b2-lactamases, and aminoglycoside-modifying enzymes, which were associated with specific gut taxa. Genomic context analysis further identified four ARG-containing contigs with features compatible with potential mobility, although active horizontal gene transfer was beyond the scope of this study. Notably,\n                    <jats:italic>tet(Q)<\/jats:italic>\n                    and\n                    <jats:italic>ermF<\/jats:italic>\n                    were predominantly associated with\n                    <jats:italic>Bacteroides fragilis<\/jats:italic>\n                    , supporting its role as a reservoir of resistance determinants in the gut microbiota. These findings support the use of metagenomic profiling as a complementary approach to donor characterization and risk assessment rather than as a standalone criterion for donor exclusion. Overall, this study provides a framework for microbiota biobank implementation and highlights the potential of metagenomic analysis to complement conventional biosafety screening in FMT.\n                  <\/jats:p>","DOI":"10.3389\/frabi.2026.1905540","type":"journal-article","created":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T05:32:04Z","timestamp":1790314324000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Identification of antibiotic resistance genes in fecal microbiota selected donors during the establishment of a biobank in the south of Brazil"],"prefix":"10.3389","volume":"5","author":[{"given":"Lucas de Figueiredo","family":"Soveral","sequence":"first","affiliation":[{"name":"Laboratory of Immunoregulation, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"National Institute of Science and Technology for Mucosa and Skin","place":["Belo Horizonte, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liandra Raphaella de Lima","family":"Holanda","sequence":"additional","affiliation":[{"name":"Laboratory of Immunoregulation, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Izadora Borgmann Frizzo","family":"Assun\u00e7\u00e3o","sequence":"additional","affiliation":[{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Laboratory of Molecular Microbiology, Department of Clinical Analysis, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leticia Gon\u00e7alves","family":"Gomes","sequence":"additional","affiliation":[{"name":"Laboratory of Immunoregulation, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isabella Bittencourt","family":"de Souza","sequence":"additional","affiliation":[{"name":"Laboratory of Immunoregulation, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriella de Souza","family":"Rodrigues","sequence":"additional","affiliation":[{"name":"Laboratory of Immunoregulation, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"National Institute of Science and Technology for Mucosa and Skin","place":["Belo Horizonte, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patr\u00edcia Almeida","family":"Vanny","sequence":"additional","affiliation":[{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Clinical Specialties Unit, University Hospital Polydoro Ernani de S\u00e3o Thiago (HU-UFSC\/EBSERH), Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar","family":"Bruna-Romero","sequence":"additional","affiliation":[{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Laboratory of Applied Immunology, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jussara Kasuko","family":"Palmeiro","sequence":"additional","affiliation":[{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Laboratory of Molecular Microbiology, Department of Clinical Analysis, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mara Cristina","family":"Scheffer","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Biology, Microbiology and Serology, University Hospital Polydoro Ernani de S\u00e3o Thiago, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thais Cristine Marques","family":"Sincero","sequence":"additional","affiliation":[{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Laboratory of Molecular Microbiology, Department of Clinical Analysis, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos Rodrigo","family":"Z\u00e1rate-Blad\u00e9s","sequence":"additional","affiliation":[{"name":"Laboratory of Immunoregulation, Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"Center for Dysbiosis Control, Federal University of Santa Catarina","place":["Florian\u00f3polis, Brazil"]},{"name":"National Institute of Science and Technology for Mucosa and Skin","place":["Belo Horizonte, Brazil"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,25]]},"reference":[{"key":"B17","doi-asserted-by":"publisher","DOI":"10.3390\/jcm9061757","article-title":"Fecal microbiota transplantation: Screening and selection to choose the optimal donor","volume":"9","author":"Bibb\u00f2","year":"2020","journal-title":"J. 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Microbiol."},{"key":"B26","doi-asserted-by":"publisher","first-page":"2043","DOI":"10.1056\/NEJMoa1910437","article-title":"Drug-resistant E. coli bacteremia transmitted by fecal microbiota transplant","volume":"381","author":"DeFilipp","year":"2019","journal-title":"N. Engl. J. Med."},{"key":"B30","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1056\/nejmoa2106516","article-title":"SER-109, an oral microbiome therapy for recurrent Clostridioides difficile infection","volume":"386","author":"Feuerstadt","year":"2022","journal-title":"N. Engl. J. 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Hepatol."},{"key":"B12","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1111\/trf.15816","article-title":"How do I establish a stool bank for fecal microbiota transplantation within the blood\u2010 and tissue transplant service","volume":"60","author":"Kragsnaes","year":"2020","journal-title":"Transfusion"},{"key":"B16","doi-asserted-by":"publisher","first-page":"635","DOI":"10.1136\/gutjnl-2025-336532","article-title":"Towards optimising and standardising donor screening for faecal microbiota transplantion","volume":"75","author":"Liu","year":"2026","journal-title":"Gut"},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1556827","article-title":"Fecal microbiota transplantation: Application scenarios, efficacy prediction, and factors impacting donor-recipient interplay","volume":"16","author":"Liu","year":"2025","journal-title":"Front. Microbiol."},{"key":"B29","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1053\/j.gastro.2016.11.010","article-title":"Efficacy of sterile fecal filtrate transfer for treating patients with Clostridium difficile infection","volume":"152","author":"Ott","year":"2017","journal-title":"Gastroenterology"},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1016\/j.lfs.2022.120719","article-title":"Fecal microbiota transplantation for diseases: Therapeutic potential, methodology, risk management in clinical practice","volume":"304","author":"Qu","year":"2022","journal-title":"Life Sci."},{"key":"B2","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1111\/apt.14201","article-title":"Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection","volume":"46","author":"Quraishi","year":"2017","journal-title":"Aliment. Pharmacol. 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Gastroenterol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1590\/s0004-2803.202000000-79","article-title":"Structuring a fecal microbiota transplantation center in a university hospital in Brazil","volume":"57","author":"Terra","year":"2020","journal-title":"Arq Gastroenterol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"924","DOI":"10.1016\/j.cmi.2017.05.015","article-title":"How to: Establish and run a stool bank","volume":"23","author":"Terveer","year":"2017","journal-title":"Clin. Microbiol. Infect."},{"key":"B20","doi-asserted-by":"publisher","first-page":"1236","DOI":"10.1177\/2050640620957765","article-title":"Faecal microbiota transplantation for Clostridioides difficile infection: Four years\u2019 experience of the Netherlands Donor Feces Bank","volume":"8","author":"Terveer","year":"2020","journal-title":"United Eur. Gastroenterol. J."},{"key":"B1","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1056\/NEJMoa1205037","article-title":"Duodenal infusion of donor feces for recurrent Clostridium difficile","volume":"368","author":"van Nood","year":"2013","journal-title":"N. Engl. J. Med."},{"key":"B6","doi-asserted-by":"publisher","first-page":"2182","DOI":"10.1097\/MIB.0000000000000893","article-title":"Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn\u2019s disease","volume":"22","author":"Vaughn","year":"2016","journal-title":"Inflamm. Bowel Dis."},{"key":"B27","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abo2750","article-title":"Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement","volume":"15","author":"Woodworth","year":"2023","journal-title":"Sci. Transl. 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Commun."}],"container-title":["Frontiers in Antibiotics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/frabi.2026.1905540\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,25]],"date-time":"2026-09-25T05:32:05Z","timestamp":1790314325000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/frabi.2026.1905540\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,25]]},"references-count":30,"alternative-id":["10.3389\/frabi.2026.1905540"],"URL":"https:\/\/doi.org\/10.3389\/frabi.2026.1905540","relation":{},"ISSN":["2813-2467"],"issn-type":[{"value":"2813-2467","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,25]]},"article-number":"1905540"}}