{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,4]],"date-time":"2026-11-04T21:52:38Z","timestamp":1793829158559,"version":"4.6.1"},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"8","license":[{"start":{"date-parts":[[2021,7,5]],"date-time":"2021-07-05T00:00:00Z","timestamp":1625443200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,7,5]],"date-time":"2021-07-05T00:00:00Z","timestamp":1625443200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Microbiol"],"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Antimicrobial resistance poses a substantial threat to human health. The gut microbiome is considered a reservoir for potential spread of resistance genes from commensals to pathogens, termed the gut resistome. The impact of probiotics, commonly consumed by many in health or in conjunction with the administration of antibiotics, on the gut resistome is elusive. Reanalysis of gut metagenomes from healthy antibiotics-na\u00efve humans supplemented with an 11-probiotic-strain preparation, allowing direct assessment of the gut resistome in situ along the gastrointestinal (GI) tract, demonstrated that probiotics reduce the number of antibiotic resistance genes exclusively in the gut of colonization-permissive individuals. In mice and in a separate cohort of humans, a course of antibiotics resulted in expansion of the lower GI tract resistome, which was mitigated by autologous faecal microbiome transplantation or during spontaneous recovery. In contrast, probiotics further exacerbated resistome expansion in the GI mucosa by supporting the bloom of strains carrying vancomycin resistance genes but not resistance genes encoded by the probiotic strains. Importantly, the aforementioned effects were not reflected in stool samples, highlighting the importance of direct sampling to analyse the effect of probiotics and antibiotics on the gut resistome. Analysing antibiotic resistance gene content in additional published clinical trials with probiotics further highlighted the importance of person-specific metagenomics-based profiling of the gut resistome using direct sampling. Collectively, these findings suggest opposing person-specific and antibiotic-dependent effects of probiotics on the resistome, whose contribution to the spread of antimicrobial resistance genes along the human GI tract merit further studies.<\/jats:p>","DOI":"10.1038\/s41564-021-00920-0","type":"journal-article","created":{"date-parts":[[2021,7,5]],"date-time":"2021-07-05T16:03:03Z","timestamp":1625500983000},"page":"1043-1054","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":243,"title":["Probiotics impact the antibiotic resistance gene reservoir along the human GI tract in a person-specific and antibiotic-dependent manner"],"prefix":"10.1038","volume":"6","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2313-1172","authenticated-orcid":false,"given":"Emmanuel","family":"Montassier","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0737-5425","authenticated-orcid":false,"given":"Rafael","family":"Vald\u00e9s-Mas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eric","family":"Batard","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niv","family":"Zmora","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mally","family":"Dori-Bachash","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3836-972X","authenticated-orcid":false,"given":"Jotham","family":"Suez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5775-2110","authenticated-orcid":false,"given":"Eran","family":"Elinav","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,7,5]]},"reference":[{"key":"920_CR1","unstructured":"No Time to Wait: Securing the Future from Drug-Resistant Infections. Report to the Secretary-General of the United Nations (Interagency Coordination Group on Antimicrobial Resistance, 2019)."},{"key":"920_CR2","doi-asserted-by":"publisher","first-page":"1128","DOI":"10.1126\/science.1176950","volume":"325","author":"MOA Sommer","year":"2009","unstructured":"Sommer, M. O. A., Dantas, G. & Church, G. M. Functional characterization of the antibiotic resistance reservoir in the human microflora. Science 325, 1128\u20131131 (2009).","journal-title":"Science"},{"key":"920_CR3","doi-asserted-by":"publisher","first-page":"2285","DOI":"10.1038\/s41564-019-0550-2","volume":"4","author":"AJ Gasparrini","year":"2019","unstructured":"Gasparrini, A. J. et al. Persistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome. Nat. Microbiol. 4, 2285\u20132297 (2019).","journal-title":"Nat. Microbiol."},{"key":"920_CR4","doi-asserted-by":"publisher","first-page":"1584","DOI":"10.1038\/s41396-020-0634-2","volume":"14","author":"TP Campbell","year":"2020","unstructured":"Campbell, T. P. et al. The microbiome and resistome of chimpanzees, gorillas, and humans across host lifestyle and geography. ISME J. 14, 1584\u20131599 (2020).","journal-title":"ISME J."},{"key":"920_CR5","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1128\/AAC.50.3.1054-1062.2006","volume":"50","author":"A Launay","year":"2006","unstructured":"Launay, A., Ballard, S. A., Johnson, P. D. R., Grayson, M. L. & Lambert, T. Transfer of vancomycin resistance transposon Tn1549 from Clostridium symbiosum to Enterococcus spp. in the gut of gnotobiotic mice. Antimicrob. Agents Chemother. 50, 1054\u20131062 (2006).","journal-title":"Antimicrob. Agents Chemother."},{"key":"920_CR6","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1002\/bies.201300143","volume":"36","author":"K Forslund","year":"2014","unstructured":"Forslund, K., Sunagawa, S., Coelho, L. P. & Bork, P. Metagenomic insights into the human gut resistome and the forces that shape it. Bioessays 36, 316\u2013329 (2014).","journal-title":"Bioessays"},{"key":"920_CR7","doi-asserted-by":"publisher","first-page":"16024","DOI":"10.1038\/nmicrobiol.2016.24","volume":"1","author":"MK Gibson","year":"2016","unstructured":"Gibson, M. K. et al. Developmental dynamics of the preterm infant gut microbiota and antibiotic resistome. Nat. Microbiol. 1, 16024 (2016).","journal-title":"Nat. Microbiol."},{"key":"920_CR8","doi-asserted-by":"publisher","first-page":"1269","DOI":"10.1073\/pnas.1113246109","volume":"109","author":"B Stecher","year":"2012","unstructured":"Stecher, B. et al. Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae. Proc. Natl Acad. Sci. USA 109, 1269\u20131274 (2012).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"920_CR9","doi-asserted-by":"publisher","first-page":"1086","DOI":"10.1093\/jac\/dkn323","volume":"62","author":"S Schj\u00f8rring","year":"2008","unstructured":"Schj\u00f8rring, S., Struve, C. & Krogfelt, K. A. Transfer of antimicrobial resistance plasmids from Klebsiella pneumoniae to Escherichia coli in the mouse intestine. J. Antimicrob. Chemother. 62, 1086\u20131093 (2008).","journal-title":"J. Antimicrob. Chemother."},{"key":"920_CR10","doi-asserted-by":"publisher","first-page":"981","DOI":"10.1128\/iai.28.3.981-990.1980","volume":"28","author":"Y Duval-Iflah","year":"1980","unstructured":"Duval-Iflah, Y., Raibaud, P., Tancrede, C. & Rousseau, M. R-plasmic transfer from Serratia liquefaciens to Escherichia coli in vitro and in vivo in the digestive tract of gnotobiotic mice associated with human fecal flora. Infect. Immun. 28, 981\u2013990 (1980).","journal-title":"Infect. Immun."},{"key":"920_CR11","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1111\/j.1472-765X.2011.03182.x","volume":"54","author":"M Sparo","year":"2012","unstructured":"Sparo, M. et al. High-level resistance to gentamicin: genetic transfer between Enterococcus faecalis isolated from food of animal origin and human microbiota. Lett. Appl. Microbiol. 54, 119\u2013125 (2012).","journal-title":"Lett. Appl. Microbiol."},{"key":"920_CR12","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1111\/j.1574-6968.2004.tb09614.x","volume":"235","author":"CH Lester","year":"2004","unstructured":"Lester, C. H., Frimodt-Moller, N. & Hammerum, A. M. Conjugal transfer of aminoglycoside and macrolide resistance between Enterococcus faecium isolates in the intestine of streptomycin-treated mice. FEMS Microbiol. Lett. 235, 385\u2013391 (2004).","journal-title":"FEMS Microbiol. Lett."},{"key":"920_CR13","doi-asserted-by":"publisher","first-page":"1808","DOI":"10.1093\/cid\/civ191","volume":"60","author":"S G\u00f6ttig","year":"2015","unstructured":"G\u00f6ttig, S., Gruber, T. M., Stecher, B., Wichelhaus, T. A. & Kempf, V. A. J. In vivo horizontal gene transfer of the carbapenemase OXA-48 during a nosocomial outbreak. Clin. Infect. Dis. 60, 1808\u20131815 (2015).","journal-title":"Clin. Infect. Dis."},{"key":"920_CR14","doi-asserted-by":"publisher","first-page":"1014","DOI":"10.3201\/eid1606.091671","volume":"16","author":"MG Goren","year":"2010","unstructured":"Goren, M. G. et al. Transfer of carbapenem-resistant plasmid from Klebsiella pneumoniae ST258 to Escherichia coli in patient. Emerg. Infect. Dis. 16, 1014\u20131017 (2010).","journal-title":"Emerg. Infect. Dis."},{"key":"920_CR15","doi-asserted-by":"publisher","first-page":"1142","DOI":"10.1093\/jac\/dkm327","volume":"60","author":"N Karami","year":"2007","unstructured":"Karami, N. et al. Transfer of an ampicillin resistance gene between two Escherichia coli strains in the bowel microbiota of an infant treated with antibiotics. J. Antimicrob. Chemother. 60, 1142\u20131145 (2007).","journal-title":"J. Antimicrob. Chemother."},{"key":"920_CR16","doi-asserted-by":"publisher","first-page":"1041","DOI":"10.1093\/jac\/dkr547","volume":"67","author":"L Cr\u00e9met","year":"2012","unstructured":"Cr\u00e9met, L. et al. Nosocomial outbreak of carbapenem-resistant Enterobacter cloacae highlighting the interspecies transferability of the blaOXA-48 gene in the gut flora. J. Antimicrob. Chemother. 67, 1041\u20131043 (2012).","journal-title":"J. Antimicrob. Chemother."},{"key":"920_CR17","doi-asserted-by":"publisher","first-page":"50","DOI":"10.3389\/fmicb.2020.00050","volume":"11","author":"C Tsigalou","year":"2020","unstructured":"Tsigalou, C., Konstantinidis, T., Stavropoulou, E., Bezirtzoglou, E. E. & Tsakris, A. Potential elimination of human gut resistome by exploiting the benefits of functional foods. Front. Microbiol. 11, 50 (2020).","journal-title":"Front. Microbiol."},{"key":"920_CR18","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1016\/j.jgar.2020.02.007","volume":"22","author":"J Selvin","year":"2020","unstructured":"Selvin, J., Maity, D., Sajayan, A. & Kiran, G. S. Revealing antibiotic resistance in therapeutic and dietary probiotic supplements. J. Glob. Antimicrob. Resist. 22, 202\u2013205 (2020).","journal-title":"J. Glob. Antimicrob. Resist."},{"key":"920_CR19","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1016\/j.foodres.2014.01.025","volume":"57","author":"P Sharma","year":"2014","unstructured":"Sharma, P., Tomar, S. K., Goswami, P., Sangwan, V. & Singh, R. Antibiotic resistance among commercially available probiotics. Food Res. Int. 57, 176\u2013195 (2014).","journal-title":"Food Res. Int."},{"key":"920_CR20","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1111\/j.1574-6941.2006.00212.x","volume":"59","author":"L Jacobsen","year":"2007","unstructured":"Jacobsen, L. et al. Horizontal transfer of tet(M) and erm(B) resistance plasmids from food strains of Lactobacillus plantarum to Enterococcus faecalis JH2-2 in the gastrointestinal tract of gnotobiotic rats. FEMS Microbiol. Ecol. 59, 158\u2013166 (2007).","journal-title":"FEMS Microbiol. Ecol."},{"key":"920_CR21","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1038\/s41591-019-0439-x","volume":"25","author":"J Suez","year":"2019","unstructured":"Suez, J., Zmora, N., Segal, E. & Elinav, E. The pros, cons, and many unknowns of probiotics. Nat. Med. 25, 716\u2013729 (2019).","journal-title":"Nat. Med."},{"key":"920_CR22","doi-asserted-by":"publisher","first-page":"e00231-15","DOI":"10.1128\/mBio.00231-15","volume":"6","author":"EA Eloe-Fadrosh","year":"2015","unstructured":"Eloe-Fadrosh, E. A. Functional dynamics of the gut microbiome in elderly people during probiotic consumption. mBio 6, e00231-15 (2015).","journal-title":"mBio"},{"key":"920_CR23","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-29229-5","volume":"8","author":"CW MacPherson","year":"2018","unstructured":"MacPherson, C. W. et al. Gut bacterial microbiota and its resistome rapidly recover to basal state levels after short-term amoxicillin-clavulanic acid treatment in healthy adults. Sci. Rep. 8, 11192 (2018).","journal-title":"Sci. Rep."},{"key":"920_CR24","doi-asserted-by":"publisher","first-page":"347","DOI":"10.3389\/fped.2018.00347","volume":"6","author":"E Esaiassen","year":"2018","unstructured":"Esaiassen, E. et al. Effects of probiotic supplementation on the gut microbiota and antibiotic resistome development in preterm infants. Front. Pediatr. 6, 347 (2018).","journal-title":"Front. Pediatr."},{"key":"920_CR25","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/nrmicro3552","volume":"14","author":"GP Donaldson","year":"2016","unstructured":"Donaldson, G. P., Lee, S. M. & Mazmanian, S. K. Gut biogeography of the bacterial microbiota. Nat. Rev. Microbiol. 14, 20\u201332 (2016).","journal-title":"Nat. Rev. Microbiol."},{"key":"920_CR26","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1016\/j.cell.2018.08.041","volume":"174","author":"N Zmora","year":"2018","unstructured":"Zmora, N. et al. Personalized gut mucosal colonization resistance to empiric probiotics is associated with unique host and microbiome features. Cell 174, 1388\u20131405 (2018).","journal-title":"Cell"},{"key":"920_CR27","doi-asserted-by":"publisher","first-page":"1406","DOI":"10.1016\/j.cell.2018.08.047","volume":"174","author":"J Suez","year":"2018","unstructured":"Suez, J. et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell 174, 1406\u20131423 (2018).","journal-title":"Cell"},{"key":"920_CR28","doi-asserted-by":"publisher","first-page":"2263","DOI":"10.1093\/bioinformatics\/bty053","volume":"34","author":"X Yin","year":"2018","unstructured":"Yin, X. et al. ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes. Bioinformatics 34, 2263\u20132270 (2018).","journal-title":"Bioinformatics"},{"key":"920_CR29","doi-asserted-by":"publisher","first-page":"D517","DOI":"10.1093\/nar\/gkz1136","volume":"48","author":"BP Alcock","year":"2020","unstructured":"Alcock, B. P. et al. CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res. 48, D517\u2013D525 (2020).","journal-title":"Nucleic Acids Res."},{"key":"920_CR30","doi-asserted-by":"publisher","first-page":"e1004557","DOI":"10.1371\/journal.pcbi.1004557","volume":"11","author":"J Kaminski","year":"2015","unstructured":"Kaminski, J. et al. High-specificity targeted functional profiling in microbial communities with ShortBRED. PLoS Comput. Biol. 11, e1004557 (2015).","journal-title":"PLoS Comput. Biol."},{"key":"920_CR31","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1080\/19490976.2019.1586039","volume":"11","author":"J Suez","year":"2020","unstructured":"Suez, J., Zmora, N. & Elinav, E. Probiotics in the next-generation sequencing era. Gut Microbes 11, 77\u201393 (2020).","journal-title":"Gut Microbes"},{"key":"920_CR32","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/s40168-018-0401-z","volume":"6","author":"G Arango-Argoty","year":"2018","unstructured":"Arango-Argoty, G. et al. DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome 6, 23 (2018).","journal-title":"Microbiome"},{"key":"920_CR33","doi-asserted-by":"publisher","first-page":"3601","DOI":"10.1093\/bioinformatics\/bty387","volume":"34","author":"WPM Rowe","year":"2018","unstructured":"Rowe, W. P. M. & Winn, M. D. Indexed variation graphs for efficient and accurate resistome profiling. Bioinformatics 34, 3601\u20133608 (2018).","journal-title":"Bioinformatics"},{"key":"920_CR34","doi-asserted-by":"publisher","DOI":"10.1186\/s40168-019-0703-9","volume":"7","author":"GA Arango-Argoty","year":"2019","unstructured":"Arango-Argoty, G. A. et al. NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes. Microbiome 7, 88 (2019).","journal-title":"Microbiome"},{"key":"920_CR35","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1080\/19490976.2020.1722054","volume":"11","author":"J Zhang","year":"2020","unstructured":"Zhang, J. et al. Probiotics maintain the intestinal microbiome homeostasis of the sailors during a long sea voyage. Gut Microbes 11, 930\u2013943 (2020).","journal-title":"Gut Microbes"},{"key":"920_CR36","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1016\/j.chom.2016.09.001","volume":"20","author":"MX Maldonado-G\u00f3mez","year":"2016","unstructured":"Maldonado-G\u00f3mez, M. X. et al. Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome. Cell Host Microbe 20, 515\u2013526 (2016).","journal-title":"Cell Host Microbe"},{"key":"920_CR37","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-18414-8","volume":"11","author":"Y Zhang","year":"2020","unstructured":"Zhang, Y. et al. Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study). Nat. Commun. 11, 5015 (2020).","journal-title":"Nat. Commun."},{"key":"920_CR38","doi-asserted-by":"publisher","first-page":"2235","DOI":"10.1038\/ismej.2016.13","volume":"10","author":"C Zhang","year":"2016","unstructured":"Zhang, C. et al. Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes. ISME J. 10, 2235\u20132245 (2016).","journal-title":"ISME J."},{"key":"920_CR39","doi-asserted-by":"publisher","first-page":"596","DOI":"10.1128\/AAC.50.2.596-599.2006","volume":"50","author":"CH Lester","year":"2006","unstructured":"Lester, C. H., Frimodt-M\u00f8ller, N., S\u00f8rensen, T. L., Monnet, D. L. & Hammerum, A. M. In vivo transfer of the vanA resistance gene from an Enterococcus faecium isolate of animal origin to an E. faecium isolate of human origin in the intestines of human volunteers. Antimicrob. Agents Chemother. 50, 596\u2013599 (2006).","journal-title":"Antimicrob. Agents Chemother."},{"key":"920_CR40","doi-asserted-by":"publisher","first-page":"26S","DOI":"10.1016\/S0002-9343(98)00354-4","volume":"106","author":"TM Perl","year":"1999","unstructured":"Perl, T. M. The threat of vancomycin resistance. Am. J. Med. 106, 26S\u201337S (1999).","journal-title":"Am. J. Med."},{"key":"920_CR41","unstructured":"Antibiotic Resistance Threats in the United States, 2013 (CDC & U. S. Department of Health and Human Services, 2013)."},{"key":"920_CR42","doi-asserted-by":"publisher","first-page":"1268","DOI":"10.1038\/s41559-020-1235-1","volume":"4","author":"L Le\u00f3nidas Cardoso","year":"2020","unstructured":"Le\u00f3nidas Cardoso, L., Dur\u00e3o, P., Amicone, M. & Gordo, I. Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut. Nat. Ecol. Evol. 4, 1268\u20131278 (2020).","journal-title":"Nat. Ecol. Evol."},{"key":"920_CR43","doi-asserted-by":"publisher","first-page":"2002","DOI":"10.1056\/NEJMoa1802598","volume":"379","author":"D Schnadower","year":"2018","unstructured":"Schnadower, D. et al. Lactobacillus rhamnosus GG versus placebo for acute gastroenteritis in children. N. Engl. J. Med. 379, 2002\u20132014 (2018).","journal-title":"N. Engl. J. Med."},{"key":"920_CR44","doi-asserted-by":"publisher","first-page":"2015","DOI":"10.1056\/NEJMoa1802597","volume":"379","author":"SB Freedman","year":"2018","unstructured":"Freedman, S. B. et al. Multicenter trial of a combination probiotic for children with gastroenteritis. N. Engl. J. Med. 379, 2015\u20132026 (2018).","journal-title":"N. Engl. J. Med."},{"key":"920_CR45","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1016\/S0140-6736(13)61218-0","volume":"382","author":"SJ Allen","year":"2013","unstructured":"Allen, S. J. et al. Lactobacilli and bifidobacteria in the prevention of antibiotic-associated diarrhoea and Clostridium difficile diarrhoea in older inpatients (PLACIDE): a randomised, double-blind, placebo-controlled, multicentre trial. Lancet 382, 1249\u20131257 (2013).","journal-title":"Lancet"},{"key":"920_CR46","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1038\/nature23480","volume":"548","author":"P Panigrahi","year":"2017","unstructured":"Panigrahi, P. et al. A randomized synbiotic trial to prevent sepsis among infants in rural India. Nature 548, 407\u2013412 (2017).","journal-title":"Nature"},{"key":"920_CR47","doi-asserted-by":"publisher","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","volume":"34","author":"S Chen","year":"2018","unstructured":"Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884\u2013i890 (2018).","journal-title":"Bioinformatics"},{"key":"920_CR48","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357\u2013359 (2012).","journal-title":"Nat. Methods"},{"key":"920_CR49","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019).","journal-title":"Genome Biol."},{"key":"920_CR50","doi-asserted-by":"publisher","first-page":"e104","DOI":"10.7717\/peerj-cs.104","volume":"3","author":"J Lu","year":"2017","unstructured":"Lu, J., Breitwieser, F. P., Thielen, P. & Salzberg, S. L. Bracken: estimating species abundance in metagenomics data. PeerJ Comput. Sci. 3, e104 (2017).","journal-title":"PeerJ Comput. Sci."},{"key":"920_CR51","doi-asserted-by":"publisher","first-page":"e102","DOI":"10.1002\/cpbi.102","volume":"70","author":"A Prjibelski","year":"2020","unstructured":"Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A. & Korobeynikov, A. Using SPAdes de novo assembler. Curr. Protoc. Bioinformatics 70, e102 (2020).","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"920_CR52","doi-asserted-by":"publisher","first-page":"52","DOI":"10.3389\/fmicb.2020.00052","volume":"11","author":"LG Panunzi","year":"2020","unstructured":"Panunzi, L. G. SraX: a novel comprehensive resistome analysis tool. Front. Microbiol. 11, 52 (2020).","journal-title":"Front. Microbiol."},{"key":"920_CR53","doi-asserted-by":"publisher","first-page":"2966","DOI":"10.1093\/bioinformatics\/btaa095","volume":"36","author":"GA Arango-Argoty","year":"2020","unstructured":"Arango-Argoty, G. A. et al. ARGminer: a web platform for the crowdsourcing-based curation of antibiotic resistance genes. Bioinformatics 36, 2966\u20132973 (2020).","journal-title":"Bioinformatics"},{"key":"920_CR54","doi-asserted-by":"publisher","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","volume":"8","author":"PJ McMurdie","year":"2013","unstructured":"McMurdie, P. J. & Holmes, S. phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PLoS ONE 8, e61217 (2013).","journal-title":"PLoS ONE"},{"key":"920_CR55","unstructured":"J. Oksanen et al. vegan: Community ecology package. R package version 2.5-6 https:\/\/CRAN.R-project.org\/package=vegan (2019)."}],"container-title":["Nature Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00920-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00920-0","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00920-0.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,3]],"date-time":"2022-12-03T00:46:45Z","timestamp":1670028405000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41564-021-00920-0"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,7,5]]},"references-count":55,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,8]]}},"alternative-id":["920"],"URL":"https:\/\/doi.org\/10.1038\/s41564-021-00920-0","relation":{},"ISSN":["2058-5276"],"issn-type":[{"value":"2058-5276","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,7,5]]},"assertion":[{"value":"9 July 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 May 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 July 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 October 2021","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Update","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"In the version of this article initially published online, the following metadata was omitted and has now been included: Open access funding provided by Deutsches Krebsforschungszentrum (DKFZ)","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"E.E. is a consultant to DayTwo and BiomX. None of the topics related to this work involve these or other commercial entities. The remaining authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}