{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T23:39:37Z","timestamp":1792366777194,"version":"4.4.0"},"reference-count":48,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T00:00:00Z","timestamp":1783900800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"},{"start":{"date-parts":[[2026,10,19]],"date-time":"2026-10-19T00:00:00Z","timestamp":1792368000000},"content-version":"vor","delay-in-days":98,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0"}],"funder":[{"name":"Israeli Science Foundation","award":["grant 1571\/17 and 3165\/20"],"award-info":[{"award-number":["grant 1571\/17 and 3165\/20"]}]},{"name":"Israel Cancer Research Fund Research Career Development Award"},{"DOI":"10.13039\/100015545","name":"Seerave Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100015545","id-type":"DOI","asserted-by":"publisher"}]},{"name":"CIFAR Azrieli Global Scholars","award":["grant FL-000969\/FL-001245\/FL-001381"],"award-info":[{"award-number":["grant FL-000969\/FL-001245\/FL-001381"]}]},{"name":"Human Frontier Science Program Career Development Award","award":["grant CDA00025\/2019-C"],"award-info":[{"award-number":["grant CDA00025\/2019-C"]}]},{"name":"Gutwirth Foundation award"},{"name":"the European Union","award":["ERC, ExtractABact, 101078712"],"award-info":[{"award-number":["ERC, ExtractABact, 101078712"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Microbiol"],"DOI":"10.1186\/s12866-026-05354-4","type":"journal-article","created":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T08:05:19Z","timestamp":1783929919000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Microbiome changes associated with FMT-mediated clearance of antibiotic-resistant Klebsiella pneumoniae in a murine carriage model"],"prefix":"10.1186","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5770-9801","authenticated-orcid":false,"given":"Shaqed","family":"Carasso","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5968-0547","authenticated-orcid":false,"given":"Tal","family":"Gefen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rozan","family":"Bakria","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haggai","family":"Bar-Yoseph","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7303-854X","authenticated-orcid":false,"given":"Naama","family":"Geva-Zatorsky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,7,13]]},"reference":[{"key":"5354_CR1","unstructured":"O\u2019Neill J. (2016). Tackling Drug-resistant Infections Globally: Final Report and Recommendations. The Review on Antimicrobial Resistance. London: HM Government and the Wellcome Trust. 2016."},{"key":"5354_CR2","doi-asserted-by":"publisher","unstructured":"Davies J. (1996). Origins and evolution of antibiotic resistance. Preprint at American Society for Microbiology (ASM). https:\/\/doi.org\/10.1128\/mmbr.00016-10","DOI":"10.1128\/mmbr.00016-10"},{"key":"5354_CR3","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1016\/j.jhin.2016.05.018","volume":"94","author":"Y Dickstein","year":"2016","unstructured":"Dickstein Y, Edelman R, Dror T, Hussein K, Bar-Lavie Y, Paul M. Carbapenem-resistant Enterobacteriaceae colonization and infection in critically ill patients: a retrospective matched cohort comparison with non-carriers. J Hosp Infect. 2016;94:54\u20139. https:\/\/doi.org\/10.1016\/j.jhin.2016.05.018.","journal-title":"J Hosp Infect"},{"key":"5354_CR4","doi-asserted-by":"publisher","unstructured":"Rock C, Donnenberg MS. (2014). Human Pathogenic Enterobacteriaceae. In Reference Module in Biomedical Sciences (Elsevier). https:\/\/doi.org\/10.1016\/b978-0-12-801238-3.00136-7","DOI":"10.1016\/b978-0-12-801238-3.00136-7"},{"key":"5354_CR5","doi-asserted-by":"publisher","first-page":"122","DOI":"10.3390\/antibiotics8030122","volume":"8","author":"B Suay-Garc\u00eda","year":"2019","unstructured":"Suay-Garc\u00eda B, P\u00e9rez-Gracia MT. Present and Future of Carbapenem-resistant Enterobacteriaceae (CRE) Infections. Antibiotics. 2019;8:122. https:\/\/doi.org\/10.3390\/antibiotics8030122.","journal-title":"Antibiotics"},{"key":"5354_CR6","doi-asserted-by":"publisher","first-page":"2133","DOI":"10.1093\/jac\/dkv086","volume":"70","author":"M Tumbarello","year":"2015","unstructured":"Tumbarello M, Trecarichi EM, De Rosa FG, Giannella M, Giacobbe DR, Bassetti M, Losito AR, Bartoletti M, Del Bono V, Corcione S, et al. Infections caused by KPC-producing Klebsiella pneumoniae: differences in therapy and mortality in a multicentre study. J Antimicrob Chemother. 2015;70:2133\u201343. https:\/\/doi.org\/10.1093\/jac\/dkv086.","journal-title":"J Antimicrob Chemother"},{"key":"5354_CR7","doi-asserted-by":"publisher","first-page":"1099","DOI":"10.1086\/592412","volume":"29","author":"G Patel","year":"2008","unstructured":"Patel G, Huprikar S, Factor SH, Jenkins SG, Calfee DP. Outcomes of Carbapenem-Resistant Klebsiella pneumoniae Infection and the Impact of Antimicrobial and Adjunctive Therapies. Infect Control Hosp Epidemiol. 2008;29:1099\u2013106. https:\/\/doi.org\/10.1086\/592412.","journal-title":"Infect Control Hosp Epidemiol"},{"key":"5354_CR8","doi-asserted-by":"publisher","DOI":"10.1186\/cc13949","author":"M Yamamoto","year":"2014","unstructured":"Yamamoto M, Pop-Vicas AE. Treatment for infections with carbapenem-resistant Enterobacteriaceae: What options do we still have? Preprint BioMed Cent Ltd. 2014. https:\/\/doi.org\/10.1186\/cc13949. https:\/\/doi.org\/10.1186\/cc13949.","journal-title":"Preprint BioMed Cent Ltd"},{"key":"5354_CR9","doi-asserted-by":"publisher","first-page":"1357","DOI":"10.1111\/1469-0691.12747","volume":"20","author":"M Giannella","year":"2014","unstructured":"Giannella M, Trecarichi EM, De Rosa FG, Del Bono V, Bassetti M, Lewis RE, Losito AR, Corcione S, Saffioti C, Bartoletti M, et al. Risk factors for carbapenem-resistant Klebsiella pneumoniae bloodstream infection among rectal carriers: A prospective observational multicentre study. Clin Microbiol Infect. 2014;20:1357\u201362. https:\/\/doi.org\/10.1111\/1469-0691.12747.","journal-title":"Clin Microbiol Infect"},{"key":"5354_CR10","doi-asserted-by":"publisher","unstructured":"Bar-Yoseph H, Hussein K, Braun E, Paul M. Natural history and decolonization strategies for ESBL\/carbapenem-resistant Enterobacteriaceae carriage: Systematic review and meta-analysis. Preprint at Oxford University; 2016. https:\/\/doi.org\/10.1093\/jac\/dkw221.","DOI":"10.1093\/jac\/dkw221"},{"key":"5354_CR11","doi-asserted-by":"publisher","unstructured":"Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: A major worldwide source and shuttle for antibiotic resistance. Preprint at Oxford University; 2017. https:\/\/doi.org\/10.1093\/femsre\/fux013.","DOI":"10.1093\/femsre\/fux013"},{"key":"5354_CR12","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1016\/J.JIPH.2023.01.009","volume":"16","author":"A Mascolo","year":"2023","unstructured":"Mascolo A, Carannante N, Mauro G, di, Sarno M, Costanzo M, Licciardi F, Bernardo M, Capoluongo N, Perrella A, Capuano A. Decolonization of drug-resistant Enterobacteriaceae carriers: A scoping review of the literature. J Infect Public Health. 2023;16:376\u201383. https:\/\/doi.org\/10.1016\/J.JIPH.2023.01.009.","journal-title":"J Infect Public Health"},{"key":"5354_CR13","doi-asserted-by":"publisher","first-page":"e3000465","DOI":"10.1371\/journal.pbio.3000465","volume":"18","author":"M Baumgartner","year":"2020","unstructured":"Baumgartner M, Bayer F, Pfrunder-Cardozo KR, Buckling A, Hall AR. Resident microbial communities inhibit growth and antibiotic-resistance evolution of Escherichia coli in human gut microbiome samples. PLoS Biol. 2020;18:e3000465. https:\/\/doi.org\/10.1371\/journal.pbio.3000465.","journal-title":"PLoS Biol"},{"key":"5354_CR14","doi-asserted-by":"publisher","unstructured":"Korach-Rechtman H, Hreish M, Fried C, Gerassy-Vainberg S, Azzam ZS, Kashi Y, Berger G. (2020). Intestinal Dysbiosis in Carriers of Carbapenem-Resistant Enterobacteriaceae. mSphere 5. https:\/\/doi.org\/10.1128\/msphere.00173-20","DOI":"10.1128\/msphere.00173-20"},{"key":"5354_CR15","doi-asserted-by":"publisher","unstructured":"Yadegar A, Bar-Yoseph H, Monaghan TM, Pakpour S, Severino A, Kuijper EJ, Smits WK, Terveer EM, Neupane S, Nabavi-Rad A, et al. Fecal microbiota transplantation: current challenges and future landscapes. Clin Microbiol Rev. 2024;37. https:\/\/doi.org\/10.1128\/cmr.00060-22.","DOI":"10.1128\/cmr.00060-22"},{"key":"5354_CR16","doi-asserted-by":"publisher","unstructured":"Merrick B, Prossomariti D, Allen E, Bisnauthsing K, Kertanegara M, Sergaki C, Le Guennec AD, Delord M, Bell JT, Conte MR, et al. Faecal microbiota transplant to ERadicate gastrointestinal carriage of Antibiotic-Resistant Organisms (FERARO): A feasibility randomised controlled trial. J Infect. 2025;91. https:\/\/doi.org\/10.1016\/j.jinf.2025.106504.","DOI":"10.1016\/j.jinf.2025.106504"},{"key":"5354_CR17","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1556\/1886.2019.00002","volume":"9","author":"K Mrazek","year":"2019","unstructured":"Mrazek K, Bereswill S, Heimesaat MM. Fecal microbiota transplantation decreases intestinal loads of multi-drug resistant Pseudomonas aeruginosa in murine carriers. Eur J Microbiol Immunol (Bp). 2019;9:14\u201322. https:\/\/doi.org\/10.1556\/1886.2019.00002.","journal-title":"Eur J Microbiol Immunol (Bp)"},{"key":"5354_CR18","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1016\/j.cmi.2018.12.009","volume":"25","author":"BD Huttner","year":"2019","unstructured":"Huttner BD, de Lastours V, Wassenberg M, Maharshak N, Mauris A, Galperine T, Zanichelli V, Kapel N, Bellanger A, Olearo F, et al. A 5-day course of oral antibiotics followed by faecal transplantation to eradicate carriage of multidrug-resistant Enterobacteriaceae: a randomized clinical trial. Clin Microbiol Infect. 2019;25:830\u20138. https:\/\/doi.org\/10.1016\/j.cmi.2018.12.009.","journal-title":"Clin Microbiol Infect"},{"key":"5354_CR19","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1038\/S41522-025-00791-X","volume":"11","author":"J Yang","year":"2025","unstructured":"Yang J, Zhou Y, Du A, Zhang Z, Wang B, Tian Y, Liu H, Cai L, Pang F, Li Y, et al. Microbiome-mediated colonization resistance to carbapenem-resistant Klebsiella pneumoniae in ICU patients. NPJ Biofilms Microbiomes. 2025;11:157. https:\/\/doi.org\/10.1038\/S41522-025-00791-X.","journal-title":"NPJ Biofilms Microbiomes"},{"key":"5354_CR20","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1084\/JEM.20181639","volume":"216","author":"MT Sorbara","year":"2019","unstructured":"Sorbara MT, Dubin K, Littmann ER, Moody TU, Fontana E, Seok R, Leiner IM, Taur Y, Peled JU, Van Den Brink MRM, et al. Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification. J Exp Med. 2019;216:84. https:\/\/doi.org\/10.1084\/JEM.20181639.","journal-title":"J Exp Med"},{"key":"5354_CR21","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1126\/science.aan3706","volume":"359","author":"B Routy","year":"2018","unstructured":"Routy B, Le Chatelier E, Derosa L, Duong CPM, Alou MT, Daill\u00e8re R, Fluckiger A, Messaoudene M, Rauber C, Roberti MP, et al. Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors. Sci (1979). 2018;359:91\u20137. https:\/\/doi.org\/10.1126\/science.aan3706.","journal-title":"Sci (1979)"},{"issue":"1 12","key":"5354_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41467-021-24448-3","volume":"12","author":"MMC Lam","year":"2021","unstructured":"Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL, Holt KE. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nat Commun 2021. 2021;12(1 12):1\u201316. https:\/\/doi.org\/10.1038\/s41467-021-24448-3.","journal-title":"Nat Commun 2021"},{"key":"5354_CR23","doi-asserted-by":"publisher","unstructured":"Liu Q, Zuo T, Lu W, Yeoh YK, Su Q, Xu Z, Tang W, Yang K, Zhang F, Lau LHS, et al. Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae. mSystems. 2022;7. https:\/\/doi.org\/10.1128\/MSYSTEMS.01510-21.","DOI":"10.1128\/MSYSTEMS.01510-21"},{"key":"5354_CR24","doi-asserted-by":"publisher","unstructured":"Tang HJ, Chen CC, Lu YC, Huang HL, Chen HJ, Chuang YC, Lai CC, Chao CM. The effect of Lactobacillus with prebiotics on KPC-2-producing Klebsiella pneumoniae. Front Microbiol. 2022;13. https:\/\/doi.org\/10.3389\/FMICB.2022.1050247.","DOI":"10.3389\/FMICB.2022.1050247"},{"key":"5354_CR25","doi-asserted-by":"publisher","unstructured":"Chen CC, Lai CC, Huang HL, Huang WY, Toh HS, Weng TC, Chuang YC, Lu YC, Tang HJ. Antimicrobial Activity of Lactobacillus Species Against Carbapenem-Resistant Enterobacteriaceae. Front Microbiol. 2019;10. https:\/\/doi.org\/10.3389\/FMICB.2019.00789.","DOI":"10.3389\/FMICB.2019.00789"},{"key":"5354_CR26","doi-asserted-by":"publisher","first-page":"2133","DOI":"10.1080\/14786419.2014.989844","volume":"29","author":"CP De Oliveira","year":"2015","unstructured":"De Oliveira CP, Da Silva JA, De Siqueira JP. Nature of the antimicrobial activity of Lactobacillus casei Bifidobacterium bifidum and Bifidobacterium animalis against foodborne pathogenic and spoilage microorganisms. Nat Prod Res. 2015;29:2133\u20136. https:\/\/doi.org\/10.1080\/14786419.2014.989844.","journal-title":"Nat Prod Res"},{"key":"5354_CR27","doi-asserted-by":"publisher","unstructured":"Bondue P, Cr\u00e8vecoeur S, Brose F, Daube G, Seghaye MC, Griffiths MW, LaPointe G, Delcenserie V. Cell-free spent media obtained from Bifidobacterium bifidum and Bifidobacterium crudilactis grown in media supplemented with 3\u2019-sialyllactose modulate virulence gene expression in Escherichia coli O157: H7 and Salmonella Typhimurium. Front Microbiol. 2016;7. https:\/\/doi.org\/10.3389\/fmicb.2016.01460.","DOI":"10.3389\/fmicb.2016.01460"},{"key":"5354_CR28","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1111\/j.1574-6941.2011.01279.x","volume":"80","author":"AR Smith","year":"2012","unstructured":"Smith AR, Macfarlane GT, Reynolds N, O\u2019May GA, Bahrami B, Macfarlane S. Effect of a synbiotic on microbial community structure in a continuous culture model of the gastric microbiota in enteral nutrition patients. FEMS Microbiol Ecol. 2012;80:135\u201345. https:\/\/doi.org\/10.1111\/j.1574-6941.2011.01279.x.","journal-title":"FEMS Microbiol Ecol"},{"key":"5354_CR29","doi-asserted-by":"publisher","first-page":"878","DOI":"10.1038\/S41586-024-07960-6","volume":"633","author":"M Furuichi","year":"2024","unstructured":"Furuichi M, Kawaguchi T, Pust M-M, Yasuma-Mitobe K, Plichta DR, Hasegawa N, Ohya T, Bhattarai SK, Sasajima S, Aoto Y, et al. Commensal consortia decolonize Enterobacteriaceae via ecological control. Nature. 2024;633:878. https:\/\/doi.org\/10.1038\/S41586-024-07960-6.","journal-title":"Nature"},{"key":"5354_CR30","doi-asserted-by":"publisher","first-page":"e00781","DOI":"10.1128\/MSPHERE.00781-23","volume":"9","author":"KC Chang","year":"2024","unstructured":"Chang KC, Nagarajan N, Gan Y-H. Short-chain fatty acids of various lengths differentially inhibit Klebsiella pneumoniae and Enterobacteriaceae species. mSphere. 2024;9:e00781\u201323. https:\/\/doi.org\/10.1128\/MSPHERE.00781-23.","journal-title":"mSphere"},{"key":"5354_CR31","doi-asserted-by":"publisher","unstructured":"Fang Q, Feng Y, McNally A, Zong Z. Characterization of phage resistance and phages capable of intestinal decolonization of carbapenem-resistant Klebsiella pneumoniae in mice. Commun Biol. 2022;5. https:\/\/doi.org\/10.1038\/S42003-022-03001-Y.","DOI":"10.1038\/S42003-022-03001-Y"},{"key":"5354_CR32","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1053\/j.gastro.2016.11.010","volume":"152","author":"SJ Ott","year":"2017","unstructured":"Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, Cassidy L, Tholey A, Fickenscher H, Seegert D, et al. Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. Gastroenterology. 2017;152:799\u2013e8117. https:\/\/doi.org\/10.1053\/j.gastro.2016.11.010.","journal-title":"Gastroenterology"},{"key":"5354_CR33","doi-asserted-by":"publisher","first-page":"986","DOI":"10.1016\/S2468-1253(25)00190-6","volume":"10","author":"D Kao","year":"2025","unstructured":"Kao D, Wong K, Lee C, Steiner T, Franz R, McDougall C, Silva M, Schmidt TSB, Walter J, Loebenberg R, et al. Effects of lyophilised faecal filtrate compared with lyophilised donor stool on Clostridioides difficile recurrence: a multicentre, randomised, double-blinded, non-inferiority trial. Lancet Gastroenterol Hepatol. 2025;10:986\u201397. https:\/\/doi.org\/10.1016\/S2468-1253(25)00190-6.","journal-title":"Lancet Gastroenterol Hepatol"},{"key":"5354_CR34","doi-asserted-by":"publisher","unstructured":"Michaud E, Waeckel L, Gayet R, Goguyer-Deschaumes R, Chanut B, Jospin F, Bathany K, Monnoye M, Genet C, Prier A, et al. Alteration of microbiota antibody-mediated immune selection contributes to dysbiosis in inflammatory bowel diseases. EMBO Mol Med. 2022;14. https:\/\/doi.org\/10.15252\/EMMM.202115386.","DOI":"10.15252\/EMMM.202115386"},{"key":"5354_CR35","doi-asserted-by":"publisher","unstructured":"DuPont HL, Jiang ZD, Alexander AS, DuPont AW, Brown EL. (2022). Intestinal IgA-Coated Bacteria in Healthy- and Altered-Microbiomes (Dysbiosis) and Predictive Value in Successful Fecal Microbiota Transplantation. Microorganisms 11, 93. https:\/\/doi.org\/10.3390\/MICROORGANISMS11010093","DOI":"10.3390\/MICROORGANISMS11010093"},{"key":"5354_CR36","doi-asserted-by":"publisher","first-page":"1862027","DOI":"10.1080\/19490976.2020.1862027","volume":"13","author":"KE Huus","year":"2020","unstructured":"Huus KE, Frankowski M, Pu\u010di\u0107-Bakovi\u0107 M, Vu\u010dkovi\u0107 F, Lauc G, Mullish BH, Marchesi JR, Monaghan TM, Kao D, Finlay BB. Changes in IgA-targeted microbiota following fecal transplantation for recurrent Clostridioides difficile infection. Gut Microbes. 2020;13:1862027. https:\/\/doi.org\/10.1080\/19490976.2020.1862027.","journal-title":"Gut Microbes"},{"key":"5354_CR37","doi-asserted-by":"publisher","unstructured":"Ramos-Ramos JC, L\u00e1zaro-Perona F, Arribas JR, Garc\u00eda-Rodr\u00edguez J, Mingorance J, Ruiz-Carrascoso G, Borobia AM, Pa\u00f1o-Pardo JR, Herruzo R, Arnalich F. Proof-of-concept trial of the combination of lactitol with Bifidobacterium bifidum and Lactobacillus acidophilus for the eradication of intestinal OXA-48-producing Enterobacteriaceae. Gut Pathog. 2020;12. https:\/\/doi.org\/10.1186\/s13099-020-00354-9.","DOI":"10.1186\/s13099-020-00354-9"},{"key":"5354_CR38","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa737","author":"H Bar-Yoseph","year":"2020","unstructured":"Bar-Yoseph H, Carasso S, Shklar S, Korytny A, Even Dar R, Daoud H, Nassar R, Maharshak N, Hussein K, Geffen Y, et al. Oral Capsulized Fecal Microbiota Transplantation for Eradication of Carbapenemase-producing Enterobacteriaceae Colonization With a Metagenomic Perspective. Clin Infect Dis. 2020. https:\/\/doi.org\/10.1093\/cid\/ciaa737.","journal-title":"Clin Infect Dis"},{"key":"5354_CR39","doi-asserted-by":"publisher","first-page":"1721","DOI":"10.1101\/gr.210641.116","volume":"26","author":"D Kim","year":"2016","unstructured":"Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: Rapid and sensitive classification of metagenomic sequences. Genome Res. 2016;26:1721\u20139. https:\/\/doi.org\/10.1101\/gr.210641.116.","journal-title":"Genome Res"},{"key":"5354_CR40","doi-asserted-by":"publisher","first-page":"1674","DOI":"10.1093\/BIOINFORMATICS\/BTV033","volume":"31","author":"D Li","year":"2015","unstructured":"Li D, Liu CM, Luo R, Sadakane K, Lam TW. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674\u20136. https:\/\/doi.org\/10.1093\/BIOINFORMATICS\/BTV033.","journal-title":"Bioinformatics"},{"key":"5354_CR41","doi-asserted-by":"publisher","unstructured":"Kang DD, Froula J, Egan R, Wang Z. (2015). MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 2015, e1165. https:\/\/doi.org\/10.7717\/PEERJ.1165\/SUPP-2","DOI":"10.7717\/PEERJ.1165\/SUPP-2"},{"key":"5354_CR42","doi-asserted-by":"publisher","unstructured":"Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE. Identification of Klebsiella capsule synthesis loci from whole genome data. Microb Genom. 2016;2(e000102). https:\/\/doi.org\/10.1099\/MGEN.0.000102\/CITE\/REFWORKS.","DOI":"10.1099\/MGEN.0.000102\/CITE\/REFWORKS"},{"key":"5354_CR43","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":"5354_CR44","doi-asserted-by":"publisher","first-page":"W180","DOI":"10.1093\/nar\/gkx295","volume":"45","author":"A Dhariwal","year":"2017","unstructured":"Dhariwal A, Chong J, Habib S, King IL, Agellon LB, Xia J. MicrobiomeAnalyst: A web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data. Nucleic Acids Res. 2017;45:W180\u20138. https:\/\/doi.org\/10.1093\/nar\/gkx295.","journal-title":"Nucleic Acids Res"},{"key":"5354_CR45","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/JOURNAL.PONE.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie PJ, Holmes S. phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data. PLoS ONE. 2013;8:e61217. https:\/\/doi.org\/10.1371\/JOURNAL.PONE.0061217.","journal-title":"PLoS ONE"},{"key":"5354_CR46","unstructured":"Oksanen J, Blanchet FG, Friendly M, Kindt R, Legendre P, Mcglinn D, Minchin PR, O\u2019hara RB, Simpson GL, Solymos P et al. (2020). vegan: Community Ecology Package, vegan: Community Ecology Package. R package version 2.5-6. https:\/\/CRAN.R-project.org\/package=vegan"},{"key":"5354_CR47","doi-asserted-by":"publisher","first-page":"R60","DOI":"10.1186\/GB-2011-12-6-R60","volume":"12","author":"N Segata","year":"2011","unstructured":"Segata N, Izard J, Waldron L, Gevers D, Miropolsky L, Garrett WS, Huttenhower C. Metagenomic biomarker discovery and explanation. Genome Biol. 2011;12:R60. https:\/\/doi.org\/10.1186\/GB-2011-12-6-R60.","journal-title":"Genome Biol"},{"key":"5354_CR48","doi-asserted-by":"publisher","first-page":"4027","DOI":"10.1093\/BIOINFORMATICS\/BTAC438","volume":"38","author":"Y Cao","year":"2022","unstructured":"Cao Y, Dong Q, Wang D, Zhang P, Liu Y, Niu C. microbiomeMarker: an R\/Bioconductor package for microbiome marker identification and visualization. Bioinformatics. 2022;38:4027\u20139. https:\/\/doi.org\/10.1093\/BIOINFORMATICS\/BTAC438.","journal-title":"Bioinformatics"}],"container-title":["BMC Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-026-05354-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-05354-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12866-026-05354-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,18]],"date-time":"2026-10-18T22:56:00Z","timestamp":1792364160000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12866-026-05354-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,13]]},"references-count":48,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2026,12]]}},"alternative-id":["5354"],"URL":"https:\/\/doi.org\/10.1186\/s12866-026-05354-4","relation":{},"ISSN":["1471-2180"],"issn-type":[{"value":"1471-2180","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,13]]},"assertion":[{"value":"24 March 2026","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 June 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"13 July 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The use of animals and experimental protocols were approved by the Technion's Institutional Animal Care and Use Committee, (approval number. IL1100817).","order":1,"name":"Ethics","label":"Ethics approval and consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Consent to publication","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":3,"name":"Ethics","label":"Competing interests","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"898"}}