{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T16:24:38Z","timestamp":1791390278419,"version":"4.3.3"},"update-to":[{"DOI":"10.1371\/journal.ppat.1009537","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,5,12]],"date-time":"2021-05-12T00:00:00Z","timestamp":1620777600000}}],"reference-count":132,"publisher":"Public Library of Science (PLoS)","issue":"4","license":[{"start":{"date-parts":[[2021,4,30]],"date-time":"2021-04-30T00:00:00Z","timestamp":1619740800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI125307"],"award-info":[{"award-number":["AI125307"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI130608"],"award-info":[{"award-number":["AI130608"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI007528"],"award-info":[{"award-number":["AI007528"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006108","name":"National Center for Advancing Translational Sciences","doi-asserted-by":"publisher","award":["UL1TR002240"],"award-info":[{"award-number":["UL1TR002240"]}],"id":[{"id":"10.13039\/100006108","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>\n                    <jats:italic>Klebsiella pneumoniae<\/jats:italic>\n                    (Kp) is an important cause of healthcare-associated infections, which increases patient morbidity, mortality, and hospitalization costs. Gut colonization by Kp is consistently associated with subsequent Kp disease, and patients are predominantly infected with their colonizing strain. Our previous comparative genomics study, between disease-causing and asymptomatically colonizing Kp isolates, identified a plasmid-encoded tellurite (TeO\n                    <jats:sub>3<\/jats:sub>\n                    <jats:sup>-2<\/jats:sup>\n                    )-resistance (\n                    <jats:italic>ter<\/jats:italic>\n                    ) operon as strongly associated with infection. However, TeO\n                    <jats:sub>3<\/jats:sub>\n                    <jats:sup>-2<\/jats:sup>\n                    is extremely rare and toxic to humans. Thus, we used a multidisciplinary approach to determine the biological link between\n                    <jats:italic>ter<\/jats:italic>\n                    and Kp infection. First, we used a genomic and bioinformatic approach to extensively characterize Kp plasmids encoding the\n                    <jats:italic>ter<\/jats:italic>\n                    locus. These plasmids displayed substantial variation in plasmid incompatibility type and gene content. Moreover, the\n                    <jats:italic>ter<\/jats:italic>\n                    operon was genetically independent of other plasmid-encoded virulence and antibiotic resistance loci, both in our original patient cohort and in a large set (n = 88) of publicly available\n                    <jats:italic>ter<\/jats:italic>\n                    operon-encoding Kp plasmids, indicating that the\n                    <jats:italic>ter<\/jats:italic>\n                    operon is likely playing a direct, but yet undescribed role in Kp disease. Next, we employed multiple mouse models of infection and colonization to show that 1) the\n                    <jats:italic>ter<\/jats:italic>\n                    operon is dispensable during bacteremia, 2) the\n                    <jats:italic>ter<\/jats:italic>\n                    operon enhances fitness in the gut, 3) this phenotype is dependent on the colony of origin of mice, and 4) antibiotic disruption of the gut microbiota eliminates the requirement for\n                    <jats:italic>ter<\/jats:italic>\n                    . Furthermore, using 16S rRNA gene sequencing, we show that the\n                    <jats:italic>ter<\/jats:italic>\n                    operon enhances Kp fitness in the gut in the presence of specific indigenous microbiota, including those predicted to produce short chain fatty acids. Finally, administration of exogenous short-chain fatty acids in our mouse model of colonization was sufficient to reduce fitness of a\n                    <jats:italic>ter<\/jats:italic>\n                    mutant. These findings indicate that the\n                    <jats:italic>ter<\/jats:italic>\n                    operon, strongly associated with human infection, encodes factors that resist stress induced by the indigenous gut microbiota during colonization. This work represents a substantial advancement in our molecular understanding of Kp pathogenesis and gut colonization, directly relevant to Kp disease in healthcare settings.\n                  <\/jats:p>","DOI":"10.1371\/journal.ppat.1009537","type":"journal-article","created":{"date-parts":[[2021,4,30]],"date-time":"2021-04-30T13:47:32Z","timestamp":1619790452000},"page":"e1009537","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":39,"title":["A plasmid locus associated with Klebsiella clinical infections encodes a microbiome-dependent gut fitness factor"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1685-302X","authenticated-orcid":true,"given":"Jay","family":"Vornhagen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6047-0678","authenticated-orcid":true,"given":"Christine M.","family":"Bassis","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Srividya","family":"Ramakrishnan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8670-0160","authenticated-orcid":true,"given":"Robert","family":"Hein","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4030-508X","authenticated-orcid":true,"given":"Sophia","family":"Mason","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4262-7173","authenticated-orcid":true,"given":"Yehudit","family":"Bergman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4197-7913","authenticated-orcid":true,"given":"Nicole","family":"Sunshine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3765-5313","authenticated-orcid":true,"given":"Yunfan","family":"Fan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5818-148X","authenticated-orcid":true,"given":"Caitlyn L.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2083-6027","authenticated-orcid":true,"given":"Winston","family":"Timp","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4118-4446","authenticated-orcid":true,"given":"Michael C.","family":"Schatz","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3687-2364","authenticated-orcid":true,"given":"Vincent B.","family":"Young","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6134-151X","authenticated-orcid":true,"given":"Patricia J.","family":"Simner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael A.","family":"Bachman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,4,30]]},"reference":[{"issue":"13","key":"ppat.1009537.ref001","doi-asserted-by":"crossref","first-page":"1198","DOI":"10.1056\/NEJMoa1306801","article-title":"Multistate Point-Prevalence Survey of Health Care\u2013Associated Infections.","volume":"370","author":"SS Magill","year":"2014","journal-title":"New England Journal of Medicine"},{"issue":"4","key":"ppat.1009537.ref002","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1128\/CMR.11.4.589","article-title":"Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors","volume":"11","author":"R Podschun","year":"1998","journal-title":"Clinical microbiology reviews"},{"key":"ppat.1009537.ref003","author":"CDC","year":"2009","journal-title":"The Direct Medical Costs of Healthcare-Associated Infections in U.S. Hospitals and the Benefits of Prevention"},{"key":"ppat.1009537.ref004","author":"O\u2019Neill","year":"2016","journal-title":"Tackling Drug-Resistant Infections Globally: final report and recommendations"},{"issue":"2","key":"ppat.1009537.ref005","doi-asserted-by":"crossref","first-page":"160","DOI":"10.3201\/eid0802.010025","article-title":"Community-acquired Klebsiella pneumoniae bacteremia: global differences in clinical patterns","volume":"8","author":"WC Ko","year":"2002","journal-title":"Emerging infectious diseases"},{"issue":"4","key":"ppat.1009537.ref006","doi-asserted-by":"crossref","first-page":"e1008114","DOI":"10.1371\/journal.pgen.1008114","article-title":"Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae","volume":"15","author":"KL Wyres","year":"2019","journal-title":"PLoS genetics"},{"key":"ppat.1009537.ref007","article-title":"Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15","author":"MMC Lam","year":"2019","journal-title":"J Antimicrob Chemother"},{"issue":"7","key":"ppat.1009537.ref008","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00517-19","article-title":"Two Hypervirulent Klebsiella pneumoniae Isolates Producing a bla KPC-2 Carbapenemase from a Canadian Patient","volume":"63","author":"LF Mataseje","year":"2019","journal-title":"Antimicrobial agents and chemotherapy"},{"issue":"7","key":"ppat.1009537.ref009","doi-asserted-by":"crossref","DOI":"10.1128\/AAC.00519-19","article-title":"Identification of a Carbapenemase-Producing Hypervirulent Klebsiella pneumoniae Isolate in the United States","volume":"63","author":"M Karlsson","year":"2019","journal-title":"Antimicrobial agents and chemotherapy"},{"issue":"3","key":"ppat.1009537.ref010","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00015-18","article-title":"Identification of Pathogenicity-Associated Loci in Klebsiella pneumoniae from Hospitalized Patients","volume":"3","author":"RM Martin","year":"2018","journal-title":"mSystems"},{"issue":"5","key":"ppat.1009537.ref011","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00261-16","article-title":"Molecular Epidemiology of Colonizing and Infecting Isolates of Klebsiella pneumoniae","volume":"1","author":"RM Martin","year":"2016","journal-title":"mSphere"},{"issue":"2","key":"ppat.1009537.ref012","doi-asserted-by":"crossref","first-page":"208","DOI":"10.1093\/cid\/cix270","article-title":"Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients.","volume":"65","author":"CL Gorrie","year":"2017","journal-title":"Clinical infectious diseases: an official publication of the Infectious Diseases Society of America"},{"issue":"7","key":"ppat.1009537.ref013","doi-asserted-by":"crossref","first-page":"384","DOI":"10.1038\/nrmicro.2017.64","article-title":"Genome watch: Klebsiella pneumoniae: when a colonizer turns bad.","volume":"15","author":"MJ Dorman","year":"2017","journal-title":"Nature reviews Microbiology"},{"key":"ppat.1009537.ref014","doi-asserted-by":"crossref","first-page":"230","DOI":"10.3389\/fmicb.2019.00230","article-title":"Dynamic Colonization of Klebsiella pneumoniae Isolates in Gastrointestinal Tract of Intensive Care Patients","volume":"10","author":"QL Sun","year":"2019","journal-title":"Front Microbiol."},{"issue":"11","key":"ppat.1009537.ref015","doi-asserted-by":"crossref","DOI":"10.1128\/IAI.00071-20","article-title":"Animal Model To Study Klebsiella pneumoniae Gastrointestinal Colonization and Host-to-Host Transmission","volume":"88","author":"TM Young","year":"2020","journal-title":"Infection and immunity"},{"issue":"2","key":"ppat.1009537.ref016","doi-asserted-by":"crossref","first-page":"304","DOI":"10.1038\/s41564-019-0640-1","article-title":"Commensal Bacteroidetes protect against Klebsiella pneumoniae colonization and transmission through IL-36 signalling","volume":"5","author":"RP Sequeira","year":"2020","journal-title":"Nat Microbiol."},{"issue":"2","key":"ppat.1009537.ref017","doi-asserted-by":"crossref","first-page":"e0116704","DOI":"10.1371\/journal.pone.0116704","article-title":"Effects of vendor and genetic background on the composition of the fecal microbiota of inbred mice","volume":"10","author":"AC Ericsson","year":"2015","journal-title":"PloS one"},{"issue":"7610","key":"ppat.1009537.ref018","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nature18849","article-title":"Interactions between the microbiota and pathogenic bacteria in the gut","volume":"535","author":"AJ Baumler","year":"2016","journal-title":"Nature"},{"issue":"6","key":"ppat.1009537.ref019","doi-asserted-by":"crossref","first-page":"1057","DOI":"10.1038\/s41564-019-0407-8","article-title":"Endogenous Enterobacteriaceae underlie variation in susceptibility to Salmonella infection","volume":"4","author":"EM Velazquez","year":"2019","journal-title":"Nat Microbiol"},{"issue":"6","key":"ppat.1009537.ref020","doi-asserted-by":"crossref","first-page":"682","DOI":"10.1016\/j.chom.2017.05.005","article-title":"Enhancement of IFNgamma Production by Distinct Commensals Ameliorates Salmonella-Induced Disease","volume":"21","author":"S Thiemann","year":"2017","journal-title":"Cell host & microbe"},{"issue":"12","key":"ppat.1009537.ref021","doi-asserted-by":"crossref","first-page":"3142","DOI":"10.1039\/c2mb25239b","article-title":"Ter-dependent stress response systems: novel pathways related to metal sensing, production of a nucleoside-like metabolite, and DNA-processing","volume":"8","author":"V Anantharaman","year":"2012","journal-title":"Molecular bioSystems"},{"issue":"6","key":"ppat.1009537.ref022","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1002\/path.1700350603","article-title":"On the specific antibacterial properties of penicillin and potassium tellurite. Incorporating a method of demonstrating some bacterial antagonisms","volume":"35","author":"A Fleming","year":"1932","journal-title":"The Journal of Pathology and Bacteriology"},{"issue":"10","key":"ppat.1009537.ref023","doi-asserted-by":"crossref","first-page":"917","DOI":"10.2105\/AJPH.4.10.917","article-title":"POTASSIUM TELLURITE AS AN INDICATOR OF MICROBIAL LIFE.","volume":"4","author":"WE King","year":"1914","journal-title":"Am J Public Health (N Y)."},{"issue":"7","key":"ppat.1009537.ref024","doi-asserted-by":"crossref","first-page":"739","DOI":"10.2105\/AJPH.36.7.739","article-title":"Use of a Potassium Tellurite Medium in the Detection of Corynebacterium diphtheriae.","volume":"36","author":"DK Kellogg","year":"1946","journal-title":"American journal of public health and the nation\u2019s health"},{"issue":"2","key":"ppat.1009537.ref025","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1099\/00222615-39-2-155","article-title":"Use of tellurite for the selection of verocytotoxigenic Escherichia coli O157","volume":"39","author":"PM Zadik","year":"1993","journal-title":"J Med Microbiol"},{"issue":"3","key":"ppat.1009537.ref026","doi-asserted-by":"crossref","first-page":"894","DOI":"10.1128\/JCM.03121-12","article-title":"Evaluation of CHROMagar STEC and STEC O104 chromogenic agar media for detection of Shiga Toxin-producing Escherichia coli in stool specimens","volume":"51","author":"M Gouali","year":"2013","journal-title":"Journal of clinical microbiology"},{"issue":"3","key":"ppat.1009537.ref027","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1016\/S0966-842X(99)01454-7","article-title":"Bacterial tellurite resistance","volume":"7","author":"DE Taylor","year":"1999","journal-title":"Trends in microbiology"},{"issue":"17","key":"ppat.1009537.ref028","doi-asserted-by":"crossref","first-page":"5016","DOI":"10.1128\/JB.177.17.5016-5027.1995","article-title":"Phage inhibition, colicin resistance, and tellurite resistance are encoded by a single cluster of genes on the IncHI2 plasmid R478","volume":"177","author":"KF Whelan","year":"1995","journal-title":"Journal of bacteriology"},{"issue":"Pt 5","key":"ppat.1009537.ref029","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1099\/mic.0.25981-0","article-title":"An inducible tellurite-resistance operon in Proteus mirabilis","volume":"149","author":"A Toptchieva","year":"2003","journal-title":"Microbiology (Reading, England)."},{"issue":"1\u20132","key":"ppat.1009537.ref030","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1016\/j.vetmic.2010.12.025","article-title":"Intracellular Yersinia pestis expresses general stress response and tellurite resistance proteins in mouse macrophages","volume":"150","author":"D Ponnusamy","year":"2011","journal-title":"Vet Microbiol"},{"issue":"11","key":"ppat.1009537.ref031","doi-asserted-by":"crossref","first-page":"e0141984","DOI":"10.1371\/journal.pone.0141984","article-title":"Role of Tellurite Resistance Operon in Filamentous Growth of Yersinia pestis in Macrophages","volume":"10","author":"D Ponnusamy","year":"2015","journal-title":"PloS one."},{"issue":"1","key":"ppat.1009537.ref032","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1007\/s00284-014-0550-7","article-title":"Transcriptional regulation mechanism of ter operon by OxyR in Yersinia pestis","volume":"69","author":"B Ni","year":"2014","journal-title":"Current microbiology"},{"key":"ppat.1009537.ref033","doi-asserted-by":"crossref","first-page":"e4402","DOI":"10.7717\/peerj.4402","article-title":"Comparative genomic analysis of a new tellurite-resistant Psychrobacter strain isolated from the Antarctic Peninsula","volume":"6","author":"CM Munoz-Villagran","year":"2018","journal-title":"PeerJ"},{"issue":"17","key":"ppat.1009537.ref034","doi-asserted-by":"crossref","first-page":"4690","DOI":"10.1128\/JB.184.17.4690-4698.2002","article-title":"Genomic Variability of O Islands Encoding Tellurite Resistance in Enterohemorrhagic Escherichia coli O157:H7 Isolates","volume":"184","author":"DE Taylor","year":"2002","journal-title":"Journal of bacteriology"},{"issue":"4","key":"ppat.1009537.ref035","doi-asserted-by":"crossref","first-page":"1380","DOI":"10.1128\/JCM.03053-14","article-title":"Association of tellurite resistance with hypervirulent clonal groups of Klebsiella pneumoniae","volume":"53","author":"V Passet","year":"2015","journal-title":"Journal of clinical microbiology"},{"key":"ppat.1009537.ref036","first-page":"32","article-title":"Hypervirulent Klebsiella pneumoniae.","author":"TA Russo","year":"2019","journal-title":"Clinical microbiology reviews"},{"key":"ppat.1009537.ref037","article-title":"A conjugative plasmid that augments virulence in Klebsiella pneumoniae","author":"X Yang","year":"2019","journal-title":"Nat Microbiol"},{"issue":"4","key":"ppat.1009537.ref038","doi-asserted-by":"crossref","first-page":"725","DOI":"10.1038\/nprot.2010.5","article-title":"I-TASSER: a unified platform for automated protein structure and function prediction","volume":"5","author":"A Roy","year":"2010","journal-title":"Nature protocols"},{"issue":"1","key":"ppat.1009537.ref039","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1038\/nmeth.3213","article-title":"The I-TASSER Suite: protein structure and function prediction","volume":"12","author":"J Yang","year":"2015","journal-title":"Nature methods"},{"key":"ppat.1009537.ref040","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1186\/1471-2105-9-40","article-title":"I-TASSER server for protein 3D structure prediction","volume":"9","author":"Y Zhang","year":"2008","journal-title":"BMC bioinformatics"},{"issue":"D1","key":"ppat.1009537.ref041","first-page":"D606","article-title":"The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities","volume":"48","author":"JJ Davis","year":"2020","journal-title":"Nucleic acids research"},{"issue":"1","key":"ppat.1009537.ref042","doi-asserted-by":"crossref","DOI":"10.1093\/ofid\/ofaa012","article-title":"Epidemiological and Microbiome Associations Between Klebsiella pneumoniae and Vancomycin-Resistant Enterococcus Colonization in Intensive Care Unit Patients","volume":"7","author":"A Collingwood","year":"2020","journal-title":"Open forum infectious diseases"},{"issue":"4","key":"ppat.1009537.ref043","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1093\/infdis\/jiy534","article-title":"Klebsiella pneumoniae Type VI Secretion System Contributes to Bacterial Competition, Cell Invasion, Type-1 Fimbriae Expression, and In Vivo Colonization","volume":"219","author":"PF Hsieh","year":"2019","journal-title":"The Journal of infectious diseases"},{"key":"ppat.1009537.ref044","doi-asserted-by":"crossref","first-page":"442","DOI":"10.3389\/fcimb.2017.00442","article-title":"Identification and Characterization of an Antibacterial Type VI Secretion System in the Carbapenem-Resistant Strain Klebsiella pneumoniae HS11286","volume":"7","author":"L Liu","year":"2017","journal-title":"Frontiers in cellular and infection microbiology"},{"issue":"8","key":"ppat.1009537.ref045","doi-asserted-by":"crossref","first-page":"e23500","DOI":"10.1371\/journal.pone.0023500","article-title":"Isolation of genes involved in biofilm formation of a Klebsiella pneumoniae strain causing pyogenic liver abscess","volume":"6","author":"MC Wu","year":"2011","journal-title":"PloS one"},{"issue":"7","key":"ppat.1009537.ref046","doi-asserted-by":"crossref","first-page":"2464","DOI":"10.1128\/IAI.06247-11","article-title":"Cellobiose-specific phosphotransferase system of Klebsiella pneumoniae and its importance in biofilm formation and virulence","volume":"80","author":"MC Wu","year":"2012","journal-title":"Infection and immunity"},{"issue":"11","key":"ppat.1009537.ref047","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1080\/STA-200066418","article-title":"A Similarity Measure Based on Species Proportions","volume":"34","author":"JC Yue","year":"2005","journal-title":"Communications in Statistics\u2014Theory and Methods"},{"issue":"3","key":"ppat.1009537.ref048","doi-asserted-by":"crossref","first-page":"173","DOI":"10.15430\/JCP.2019.24.3.173","article-title":"Sex-related Alterations of Gut Microbiota in the C57BL\/6 Mouse Model of Inflammatory Bowel Disease.","volume":"24","author":"HJ Son","year":"2019","journal-title":"J Cancer Prev"},{"issue":"4","key":"ppat.1009537.ref049","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1080\/19490976.2016.1203502","article-title":"Sex differences and hormonal effects on gut microbiota composition in mice","volume":"7","author":"E Org","year":"2016","journal-title":"Gut Microbes"},{"issue":"2","key":"ppat.1009537.ref050","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1016\/j.cmet.2018.09.023","article-title":"The Mouse Microbiome Is Required for Sex-Specific Diurnal Rhythms of Gene Expression and Metabolism.","volume":"29","author":"BD Weger","year":"2019","journal-title":"Cell Metab"},{"issue":"6","key":"ppat.1009537.ref051","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"N Segata","year":"2011","journal-title":"Genome Biol"},{"issue":"10","key":"ppat.1009537.ref052","doi-asserted-by":"crossref","first-page":"16131","DOI":"10.1038\/nmicrobiol.2016.131","article-title":"The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota","volume":"1","author":"I Lagkouvardos","year":"2016","journal-title":"Nature Microbiology"},{"issue":"42","key":"ppat.1009537.ref053","doi-asserted-by":"crossref","DOI":"10.1128\/genomeA.00758-17","article-title":"High-Quality Whole-Genome Sequences of the Oligo-Mouse-Microbiota Bacterial Community","volume":"5","author":"D Garzetti","year":"2017","journal-title":"Genome announcements"},{"issue":"1","key":"ppat.1009537.ref054","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1186\/s40168-019-0637-2","article-title":"Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family","volume":"7","author":"I Lagkouvardos","year":"2019","journal-title":"Microbiome"},{"issue":"1","key":"ppat.1009537.ref055","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1186\/s40168-016-0181-2","article-title":"Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals","volume":"4","author":"KL Ormerod","year":"2016","journal-title":"Microbiome"},{"issue":"3","key":"ppat.1009537.ref056","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00470-17","article-title":"Gut Microbiota Mediates the Protective Effects of Dietary Capsaicin against Chronic Low-Grade Inflammation and Associated Obesity Induced by High-Fat Diet.","volume":"8","author":"C Kang","year":"2017","journal-title":"mBio"},{"issue":"40","key":"ppat.1009537.ref057","doi-asserted-by":"crossref","first-page":"E5934","DOI":"10.1073\/pnas.1612559113","article-title":"High-fat diet modifies the PPAR-gamma pathway leading to disruption of microbial and physiological ecosystem in murine small intestine","volume":"113","author":"J Tomas","year":"2016","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7533","key":"ppat.1009537.ref058","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/nature13828","article-title":"Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile","volume":"517","author":"CG Buffie","year":"2015","journal-title":"Nature"},{"key":"ppat.1009537.ref059","first-page":"672295","article-title":"PICRUSt2: An improved and customizable approach for metagenome inference","volume":"2020","author":"GM Douglas","journal-title":"bioRxiv"},{"issue":"D1","key":"ppat.1009537.ref060","doi-asserted-by":"crossref","first-page":"D633","DOI":"10.1093\/nar\/gkx935","article-title":"The MetaCyc database of metabolic pathways and enzymes","volume":"46","author":"R Caspi","year":"2018","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"ppat.1009537.ref061","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1038\/mi.2017.118","article-title":"GPR43 mediates microbiota metabolite SCFA regulation of antimicrobial peptide expression in intestinal epithelial cells via activation of mTOR and STAT3","volume":"11","author":"Y Zhao","year":"2018","journal-title":"Mucosal Immunol"},{"issue":"5","key":"ppat.1009537.ref062","doi-asserted-by":"crossref","first-page":"662","DOI":"10.1016\/j.chom.2015.03.005","article-title":"Crosstalk between Microbiota-Derived Short-Chain Fatty Acids and Intestinal Epithelial HIF Augments Tissue Barrier Function","volume":"17","author":"CJ Kelly","year":"2015","journal-title":"Cell Host Microbe"},{"issue":"2","key":"ppat.1009537.ref063","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1053\/j.gastro.2013.04.056","article-title":"Short-chain fatty acids activate GPR41 and GPR43 on intestinal epithelial cells to promote inflammatory responses in mice","volume":"145","author":"MH Kim","year":"2013","journal-title":"Gastroenterology"},{"key":"ppat.1009537.ref064","doi-asserted-by":"crossref","first-page":"142","DOI":"10.3389\/fimmu.2018.00142","article-title":"The Metabolic Sensor GPR43 Receptor Plays a Role in the Control of Klebsiella pneumoniae Infection in the Lung","volume":"9","author":"I Galvao","year":"2018","journal-title":"Front Immunol"},{"issue":"1","key":"ppat.1009537.ref065","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1084\/jem.20181639","article-title":"Inhibiting antibiotic-resistant Enterobacteriaceae by microbiota-mediated intracellular acidification","volume":"216","author":"MT Sorbara","year":"2019","journal-title":"J Exp Med"},{"issue":"5","key":"ppat.1009537.ref066","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1179\/1973947814Y.0000000199","article-title":"Risk factors for tracheobronchial acquisition of resistant Gram-negative bacterial pathogens in mechanically ventilated ICU patients","volume":"27","author":"I Papakonstantinou","year":"2015","journal-title":"J Chemother"},{"issue":"3","key":"ppat.1009537.ref067","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1128\/AM.30.3.381-395.1975","article-title":"Distribution and persistence of Staphylococcus and Micrococcus species and other aerobic bacteria on human skin","volume":"30","author":"WE Kloos","year":"1975","journal-title":"Appl Microbiol"},{"issue":"1","key":"ppat.1009537.ref068","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1086\/653079","article-title":"CadC regulates cad and tdc operons in response to gastrointestinal stresses and enhances intestinal colonization of Klebsiella pneumoniae","volume":"202","author":"PF Hsieh","year":"2010","journal-title":"The Journal of infectious diseases"},{"issue":"Pt 1","key":"ppat.1009537.ref069","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1099\/mic.0.25833-0","article-title":"Application of a novel multi-screening signature-tagged mutagenesis assay for identification of Klebsiella pneumoniae genes essential in colonization and infection","volume":"149","author":"C Struve","year":"2003","journal-title":"Microbiology (Reading, England)."},{"issue":"8","key":"ppat.1009537.ref070","doi-asserted-by":"crossref","first-page":"4729","DOI":"10.1128\/IAI.70.8.4729-4734.2002","article-title":"Identification of Klebsiella pneumoniae genes involved in intestinal colonization and adhesion using signature-tagged mutagenesis","volume":"70","author":"N Maroncle","year":"2002","journal-title":"Infection and immunity"},{"issue":"2","key":"ppat.1009537.ref071","article-title":"Genome-Wide Screening for Enteric Colonization Factors in Carbapenem-Resistant ST258 Klebsiella pneumoniae","volume":"10","author":"HJ Jung","year":"2019","journal-title":"mBio"},{"issue":"1","key":"ppat.1009537.ref072","doi-asserted-by":"crossref","first-page":"132","DOI":"10.3181\/00379727-86-21030","article-title":"Effect of streptomycin on susceptibility of intestinal tract to experimental Salmonella infection","volume":"86","author":"M Bohnhoff","year":"1954","journal-title":"Proc Soc Exp Biol Med"},{"issue":"3","key":"ppat.1009537.ref073","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1128\/IAI.02768-14","article-title":"Dynamics and establishment of Clostridium difficile infection in the murine gastrointestinal tract","volume":"83","author":"MJ Koenigsknecht","year":"2015","journal-title":"Infection and immunity"},{"issue":"1","key":"ppat.1009537.ref074","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1111\/imr.12563","article-title":"The intestinal microbiota: Antibiotics, colonization resistance, and enteric pathogens","volume":"279","author":"S Kim","year":"2017","journal-title":"Immunol Rev"},{"issue":"7609","key":"ppat.1009537.ref075","doi-asserted-by":"crossref","first-page":"697","DOI":"10.1038\/nature18597","article-title":"Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion","volume":"534","author":"F Faber","year":"2016","journal-title":"Nature"},{"issue":"5","key":"ppat.1009537.ref076","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1179\/2047773214Y.0000000148","article-title":"Prevalence of antibiotic resistant bacteria in healthy adults, foods, food animals, and the environment in selected areas in Thailand.","volume":"108","author":"A Boonyasiri","year":"2014","journal-title":"Pathog Glob Health"},{"key":"ppat.1009537.ref077","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.jgar.2017.02.014","article-title":"Extended-spectrum beta-lactamase-producing Escherichia coli isolated from healthy humans in Mexico, including subclone ST131-B2-O25:H4-H30-Rx","volume":"9","author":"G Cortes-Cortes","year":"2017","journal-title":"J Glob Antimicrob Resist"},{"issue":"3","key":"ppat.1009537.ref078","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1292\/jvms.16-0639","article-title":"Antimicrobial resistance profiles and molecular characterization of Escherichia coli strains isolated from healthy adults in Ho Chi Minh City, Vietnam","volume":"79","author":"PH Hoang","year":"2017","journal-title":"J Vet Med Sci"},{"issue":"12","key":"ppat.1009537.ref079","doi-asserted-by":"crossref","first-page":"3416","DOI":"10.1093\/jac\/dkw328","article-title":"Detection of the plasmid-mediated colistin-resistance gene mcr-1 in faecal metagenomes of Dutch travellers","volume":"71","author":"CJ von Wintersdorff","year":"2016","journal-title":"J Antimicrob Chemother"},{"issue":"4","key":"ppat.1009537.ref080","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1016\/S1473-3099(16)30527-8","article-title":"Prevalence, risk factors, outcomes, and molecular epidemiology of mcr-1-positive Enterobacteriaceae in patients and healthy adults from China: an epidemiological and clinical study","volume":"17","author":"Y Wang","year":"2017","journal-title":"The Lancet Infectious diseases"},{"issue":"1","key":"ppat.1009537.ref081","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41385-018-0053-0","article-title":"Interbacterial mechanisms of colonization resistance and the strategies pathogens use to overcome them","volume":"12","author":"MT Sorbara","year":"2019","journal-title":"Mucosal immunology"},{"issue":"1","key":"ppat.1009537.ref082","first-page":"204","article-title":"Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces","volume":"6","author":"NK Singh","year":"2018","journal-title":"MicrobiomePubMed Central PMCID"},{"issue":"17","key":"ppat.1009537.ref083","doi-asserted-by":"crossref","first-page":"8499","DOI":"10.1073\/pnas.1820594116","article-title":"Klebsiella and Providencia emerge as lone survivors following long-term starvation of oral microbiota","volume":"116","author":"JL Baker","year":"2019","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"3","key":"ppat.1009537.ref084","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1080\/08927014.2018.1434876","article-title":"Role of nutrient limitation in the competition between uropathogenic strains of Klebsiella pneumoniae and Escherichia coli in mixed biofilms","volume":"34","author":"GE Juarez","year":"2018","journal-title":"Biofouling"},{"issue":"8","key":"ppat.1009537.ref085","doi-asserted-by":"crossref","first-page":"1294","DOI":"10.1093\/infdis\/jiy615","article-title":"A Novel Role for the Klebsiella pneumoniae Sap (Sensitivity to Antimicrobial Peptides) Transporter in Intestinal Cell Interactions, Innate Immune Responses, Liver Abscess, and Virulence","volume":"219","author":"CR Hsu","year":"2019","journal-title":"The Journal of infectious diseases"},{"issue":"1","key":"ppat.1009537.ref086","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/s12866-019-1494-7","article-title":"Changes in the gut microbiome and fermentation products concurrent with enhanced longevity in acarbose-treated mice","volume":"19","author":"BJ Smith","year":"2019","journal-title":"BMC Microbiol"},{"issue":"1","key":"ppat.1009537.ref087","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1128\/JB.129.1.276-281.1977","article-title":"Plasmid-determined resistance to tellurium compounds","volume":"129","author":"AO Summers","year":"1977","journal-title":"Journal of bacteriology"},{"issue":"3","key":"ppat.1009537.ref088","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1128\/AEM.01771-08","article-title":"Metabolomic investigation of the bacterial response to a metal challenge","volume":"75","author":"V Tremaroli","year":"2009","journal-title":"Appl Environ Microbiol"},{"issue":"1","key":"ppat.1009537.ref089","doi-asserted-by":"crossref","first-page":"40","DOI":"10.1016\/j.polar.2014.01.001","article-title":"Isolation, identification and characterization of highly tellurite-resistant, tellurite-reducing bacteria from Antarctica","volume":"8","year":"2014","journal-title":"Polar Science"},{"issue":"2","key":"ppat.1009537.ref090","doi-asserted-by":"crossref","first-page":"e211","DOI":"10.1371\/journal.pone.0000211","article-title":"Bacterial toxicity of potassium tellurite: unveiling an ancient enigma","volume":"2","author":"JM Perez","year":"2007","journal-title":"PloS one."},{"issue":"Pt 12","key":"ppat.1009537.ref091","doi-asserted-by":"crossref","first-page":"3133","DOI":"10.1099\/13500872-141-12-3133","article-title":"The tellurite-resistance determinants tehAtehB and klaAklaBtelB have different biochemical requirements","volume":"141","author":"RJ Turner","year":"1995","journal-title":"Microbiology (Reading)."},{"key":"ppat.1009537.ref092","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1016\/j.micres.2015.05.002","article-title":"Escherichia coli 6-phosphogluconate dehydrogenase aids in tellurite resistance by reducing the toxicant in a NADPH-dependent manner","volume":"177","author":"JM Sandoval","year":"2015","journal-title":"Microbiol Res"},{"key":"ppat.1009537.ref093","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.jprot.2016.01.003","article-title":"Proteomic analysis of the TerC interactome: Novel links to tellurite resistance and pathogenicity","volume":"136","author":"L Turkovicova","year":"2016","journal-title":"J Proteomics"},{"issue":"12","key":"ppat.1009537.ref094","doi-asserted-by":"crossref","first-page":"843","DOI":"10.1038\/nrmicro2454","article-title":"Swimming against the tide: progress and challenges in our understanding of colicin translocation.","volume":"8","author":"C Kleanthous","year":"2010","journal-title":"Nature reviews Microbiology"},{"issue":"2","key":"ppat.1009537.ref095","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1016\/j.chom.2018.07.002","article-title":"A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection.","volume":"24","author":"A Jacobson","year":"2018","journal-title":"Cell host & microbe"},{"issue":"6","key":"ppat.1009537.ref096","doi-asserted-by":"crossref","first-page":"1332","DOI":"10.1016\/j.cell.2016.05.041","article-title":"From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites","volume":"165","author":"A Koh","year":"2016","journal-title":"Cell"},{"issue":"4","key":"ppat.1009537.ref097","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/j.chom.2016.03.004","article-title":"Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella.","volume":"19","author":"F Rivera-Chavez","year":"2016","journal-title":"Cell host & microbe"},{"issue":"6351","key":"ppat.1009537.ref098","doi-asserted-by":"crossref","first-page":"570","DOI":"10.1126\/science.aam9949","article-title":"Microbiota-activated PPAR-gamma signaling inhibits dysbiotic Enterobacteriaceae expansion","volume":"357","author":"MX Byndloss","year":"2017","journal-title":"Science"},{"issue":"9","key":"ppat.1009537.ref099","doi-asserted-by":"crossref","first-page":"819","DOI":"10.1136\/gut.19.9.819","article-title":"Short chain fatty acid absorption by the human large intestine","volume":"19","author":"NI McNeil","year":"1978","journal-title":"Gut"},{"issue":"10","key":"ppat.1009537.ref100","doi-asserted-by":"crossref","first-page":"3145","DOI":"10.1093\/jn\/133.10.3145","article-title":"Fecal acetate is inversely related to acetate absorption from the human rectum and distal colon","volume":"133","author":"JA Vogt","year":"2003","journal-title":"The Journal of nutrition"},{"issue":"27","key":"ppat.1009537.ref101","doi-asserted-by":"crossref","first-page":"E3574","DOI":"10.1073\/pnas.1501049112","article-title":"Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health","volume":"112","author":"KE Holt","year":"2015","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ppat.1009537.ref102","volume-title":"Guide for the Care and Use of Laboratory Animals","author":"NR Council","year":"2011","edition":"8"},{"issue":"7","key":"ppat.1009537.ref103","doi-asserted-by":"crossref","first-page":"3783","DOI":"10.1128\/IAI.72.7.3783-3792.2004","article-title":"Isolation of a chromosomal region of Klebsiella pneumoniae associated with allantoin metabolism and liver infection","volume":"72","author":"HC Chou","year":"2004","journal-title":"Infection and immunity"},{"issue":"12","key":"ppat.1009537.ref104","doi-asserted-by":"crossref","first-page":"6640","DOI":"10.1073\/pnas.120163297","article-title":"One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products","volume":"97","author":"KA Datsenko","year":"2000","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"3","key":"ppat.1009537.ref105","doi-asserted-by":"crossref","first-page":"e00775","DOI":"10.1128\/mBio.00775-15","article-title":"Genome-Wide Identification of Klebsiella pneumoniae Fitness Genes during Lung Infection","volume":"6","author":"MA Bachman","year":"2015","journal-title":"mBio"},{"issue":"3","key":"ppat.1009537.ref106","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"SF Altschul","year":"1990","journal-title":"Journal of molecular biology"},{"issue":"1","key":"ppat.1009537.ref107","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: Scalable analysis of bacterial genome variation at the population level.","volume":"11","author":"KA Jolley","year":"2010","journal-title":"BMC bioinformatics"},{"issue":"12","key":"ppat.1009537.ref108","doi-asserted-by":"crossref","first-page":"4073","DOI":"10.1128\/JCM.01924-13","article-title":"wzi Gene sequencing, a rapid method for determination of capsular type for Klebsiella strains","volume":"51","author":"S Brisse","year":"2013","journal-title":"Journal of clinical microbiology"},{"issue":"5","key":"ppat.1009537.ref109","doi-asserted-by":"crossref","first-page":"722","DOI":"10.1101\/gr.215087.116","article-title":"Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation","volume":"27","author":"S Koren","year":"2017","journal-title":"Genome research"},{"issue":"11","key":"ppat.1009537.ref110","doi-asserted-by":"crossref","first-page":"e112963","DOI":"10.1371\/journal.pone.0112963","article-title":"Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement","volume":"9","author":"BJ Walker","year":"2014","journal-title":"PloS one"},{"issue":"4","key":"ppat.1009537.ref111","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nature methods"},{"issue":"6","key":"ppat.1009537.ref112","doi-asserted-by":"crossref","first-page":"1037","DOI":"10.1093\/bioinformatics\/btx713","article-title":"DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication","volume":"34","author":"Y Tanizawa","year":"2018","journal-title":"Bioinformatics"},{"issue":"13","key":"ppat.1009537.ref113","doi-asserted-by":"crossref","first-page":"1658","DOI":"10.1093\/bioinformatics\/btl158","article-title":"Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences","volume":"22","author":"W Li","year":"2006","journal-title":"Bioinformatics"},{"issue":"14","key":"ppat.1009537.ref114","doi-asserted-by":"crossref","first-page":"3059","DOI":"10.1093\/nar\/gkf436","article-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform","volume":"30","author":"K Katoh","year":"2002","journal-title":"Nucleic acids research"},{"issue":"22","key":"ppat.1009537.ref115","doi-asserted-by":"crossref","first-page":"3501","DOI":"10.1093\/bioinformatics\/btw474","article-title":"MSAViewer: interactive JavaScript visualization of multiple sequence alignments","volume":"32","author":"G Yachdav","year":"2016","journal-title":"Bioinformatics"},{"issue":"1","key":"ppat.1009537.ref116","doi-asserted-by":"crossref","first-page":"8365","DOI":"10.1038\/srep08365","article-title":"RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes","volume":"5","author":"T Brettin","year":"2015","journal-title":"Scientific Reports"},{"issue":"D1","key":"ppat.1009537.ref117","doi-asserted-by":"crossref","first-page":"D535","DOI":"10.1093\/nar\/gkw1017","article-title":"Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center","volume":"45","author":"AR Wattam","year":"2017","journal-title":"Nucleic acids research"},{"issue":"6145","key":"ppat.1009537.ref118","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1126\/science.1241165","article-title":"The microbial metabolites, short-chain fatty acids, regulate colonic Treg cell homeostasis","volume":"341","author":"PM Smith","year":"2013","journal-title":"Science"},{"issue":"10","key":"ppat.1009537.ref119","doi-asserted-by":"crossref","first-page":"3838","DOI":"10.1128\/IAI.00459-15","article-title":"Fecal Microbiota Transplantation Eliminates Clostridium difficile in a Murine Model of Relapsing Disease","volume":"83","author":"AM Seekatz","year":"2015","journal-title":"Infection and immunity"},{"issue":"17","key":"ppat.1009537.ref120","doi-asserted-by":"crossref","first-page":"5112","DOI":"10.1128\/AEM.01043-13","article-title":"Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform","volume":"79","author":"JJ Kozich","year":"2013","journal-title":"Appl Environ Microbiol"},{"issue":"23","key":"ppat.1009537.ref121","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"PD Schloss","year":"2009","journal-title":"Appl Environ Microbiol"},{"issue":"2","key":"ppat.1009537.ref122","doi-asserted-by":"crossref","DOI":"10.1128\/mSphereDirect.00073-17","article-title":"OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units","volume":"2","author":"SL Westcott","year":"2017","journal-title":"mSphere"},{"issue":"12","key":"ppat.1009537.ref123","doi-asserted-by":"crossref","first-page":"e8230","DOI":"10.1371\/journal.pone.0008230","article-title":"A high-throughput DNA sequence aligner for microbial ecology studies","volume":"4","author":"PD Schloss","year":"2009","journal-title":"PloS one"},{"issue":"1","key":"ppat.1009537.ref124","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","author":"MJ Anderson","year":"2001","journal-title":"Austral Ecology"},{"key":"ppat.1009537.ref125","doi-asserted-by":"crossref","first-page":"D633","DOI":"10.1093\/nar\/gkt1244","article-title":"Ribosomal Database Project: data and tools for high throughput rRNA analysis","volume":"42","author":"JR Cole","year":"2014","journal-title":"Nucleic acids research"},{"issue":"16","key":"ppat.1009537.ref126","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Q Wang","year":"2007","journal-title":"Appl Environ Microbiol"},{"issue":"D1","key":"ppat.1009537.ref127","doi-asserted-by":"crossref","first-page":"D666","DOI":"10.1093\/nar\/gky901","article-title":"IMG\/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes","volume":"47","author":"IA Chen","year":"2019","journal-title":"Nucleic Acids Res"},{"issue":"2","key":"ppat.1009537.ref128","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1093\/sysbio\/syy054","article-title":"EPA-ng: Massively Parallel Evolutionary Placement of Genetic Sequences","volume":"68","author":"P Barbera","year":"2019","journal-title":"Syst Biol"},{"issue":"5","key":"ppat.1009537.ref129","doi-asserted-by":"crossref","first-page":"e0217050","DOI":"10.1371\/journal.pone.0217050","article-title":"Scalable methods for analyzing and visualizing phylogenetic placement of metagenomic samples","volume":"14","author":"L Czech","year":"2019","journal-title":"PLoS One"},{"issue":"6","key":"ppat.1009537.ref130","doi-asserted-by":"crossref","first-page":"1053","DOI":"10.1093\/bioinformatics\/btx701","article-title":"Efficient comparative phylogenetics on large trees","volume":"34","author":"S Louca","year":"2018","journal-title":"Bioinformatics"},{"issue":"8","key":"ppat.1009537.ref131","doi-asserted-by":"crossref","first-page":"e1000465","DOI":"10.1371\/journal.pcbi.1000465","article-title":"A parsimony approach to biological pathway reconstruction\/inference for genomes and metagenomes","volume":"5","author":"Y Ye","year":"2009","journal-title":"PLoS Comput Biol."},{"issue":"9","key":"ppat.1009537.ref132","doi-asserted-by":"crossref","first-page":"5953","DOI":"10.1128\/IAI.69.9.5953-5957.2001","article-title":"Development of a competitive index assay to evaluate the virulence of Listeria monocytogenes actA mutants during primary and secondary infection of mice","volume":"69","author":"V Auerbuch","year":"2001","journal-title":"Infection and immunity"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1009537","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,5,12]],"date-time":"2021-05-12T00:00:00Z","timestamp":1620777600000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1009537","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,11,2]],"date-time":"2023-11-02T23:44:59Z","timestamp":1698968699000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1009537"}},"subtitle":[],"editor":[{"given":"Joan","family":"Mecsas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2021,4,30]]},"references-count":132,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2021,4,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1009537","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2020.02.26.963322","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,4,30]]}}}