{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T13:18:44Z","timestamp":1790687924261,"version":"4.1.0"},"reference-count":58,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2018,8,1]],"date-time":"2018-08-01T00:00:00Z","timestamp":1533081600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["DK111847"],"award-info":[{"award-number":["DK111847"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009560","name":"American Gastroenterological Association","doi-asserted-by":"publisher","award":["Research Scholar Award"],"award-info":[{"award-number":["Research Scholar Award"]}],"id":[{"id":"10.13039\/100009560","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0200322","type":"journal-article","created":{"date-parts":[[2018,8,1]],"date-time":"2018-08-01T13:30:50Z","timestamp":1533130250000},"page":"e0200322","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":61,"title":["Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens"],"prefix":"10.1371","volume":"13","author":[{"given":"Alexandra E.","family":"Livanos","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erik J.","family":"Snider","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susan","family":"Whittier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David H.","family":"Chong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy C.","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julian A.","family":"Abrams","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2023-2899","authenticated-orcid":true,"given":"Daniel E.","family":"Freedberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,8,1]]},"reference":[{"issue":"11","key":"ref1","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/nri3535","article-title":"Microbiota-mediated colonization resistance against intestinal pathogens","volume":"13","author":"CG Buffie","year":"2013","journal-title":"Nat Rev Immunol"},{"issue":"1","key":"ref2","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/S2213-2600(15)00427-0","article-title":"The microbiome and critical illness","volume":"4","author":"RP Dickson","year":"2016","journal-title":"Lancet Respir Med"},{"issue":"2","key":"ref3","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.ccc.2015.11.004","article-title":"The Gut as the Motor of Multiple Organ Dysfunction in Critical Illness","volume":"32","author":"NJ Klingensmith","year":"2016","journal-title":"Crit Care Clin"},{"issue":"5","key":"ref4","doi-asserted-by":"crossref","first-page":"475","DOI":"10.1097\/SHK.0000000000000534","article-title":"The Shift of an Intestinal &quot;Microbiome&quot; to a &quot;Pathobiome&quot; Governs the Course and Outcome of Sepsis Following Surgical Injury","volume":"45","author":"MA Krezalek","year":"2016","journal-title":"Shock"},{"issue":"21","key":"ref5","doi-asserted-by":"crossref","first-page":"1137","DOI":"10.1056\/NEJM196911202812101","article-title":"Changing pharyngeal bacterial flora of hospitalized patients. Emergence of gram-negative bacilli","volume":"281","author":"WG Johanson","year":"1969","journal-title":"N Engl J Med"},{"issue":"6","key":"ref6","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1097\/SHK.0000000000000691","article-title":"Dysbiosis Across Multiple Body Sites in Critically Ill Adult Surgical Patients","volume":"46","author":"A Yeh","year":"2016","journal-title":"Shock"},{"issue":"5","key":"ref7","doi-asserted-by":"crossref","first-page":"e01361","DOI":"10.1128\/mBio.01361-14","article-title":"Membership and behavior of ultra-low-diversity pathogen communities present in the gut of humans during prolonged critical illness","volume":"5","author":"A Zaborin","year":"2014","journal-title":"MBio"},{"issue":"7","key":"ref8","doi-asserted-by":"crossref","first-page":"905","DOI":"10.1093\/cid\/cis580","article-title":"Intestinal domination and the risk of bacteremia in patients undergoing allogeneic hematopoietic stem cell transplantation. Clinical infectious diseases: an official publication of the","volume":"55","author":"Y Taur","year":"2012","journal-title":"Infectious Diseases Society of America"},{"issue":"12","key":"ref9","doi-asserted-by":"crossref","first-page":"4332","DOI":"10.1172\/JCI43918","article-title":"Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans","volume":"120","author":"C Ubeda","year":"2010","journal-title":"J Clin Invest"},{"issue":"1","key":"ref10","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"},{"key":"ref11","first-page":"156","article-title":"The effect of antibiotic therapy on susceptibility to an experimental enteric infection","volume":"67","author":"CP Miller","year":"1954","journal-title":"Trans Assoc Am Physicians"},{"issue":"5","key":"ref12","doi-asserted-by":"crossref","first-page":"2839","DOI":"10.1128\/IAI.71.5.2839-2858.2003","article-title":"Pretreatment of mice with streptomycin provides a Salmonella enterica serovar Typhimurium colitis model that allows analysis of both pathogen and host","volume":"71","author":"M Barthel","year":"2003","journal-title":"Infect Immun"},{"issue":"1","key":"ref13","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1757-4749-5-23","article-title":"Commensal Clostridia: leading players in the maintenance of gut homeostasis","volume":"5","author":"LR Lopetuso","year":"2013","journal-title":"Gut Pathog"},{"issue":"4","key":"ref14","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1007\/s10620-010-1418-8","article-title":"Altered gut flora are associated with septic complications and death in critically ill patients with systemic inflammatory response syndrome","volume":"56","author":"K Shimizu","year":"2011","journal-title":"Dig Dis Sci"},{"issue":"4","key":"ref15","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00199-16","article-title":"Extreme Dysbiosis of the Microbiome in Critical Illness","volume":"1","author":"D McDonald","year":"2016","journal-title":"mSphere"},{"issue":"8","key":"ref16","doi-asserted-by":"crossref","first-page":"2361","DOI":"10.1007\/s10620-011-1649-3","article-title":"Dramatic changes of the gut flora immediately after severe and sudden insults","volume":"56","author":"M Hayakawa","year":"2011","journal-title":"Dig Dis Sci"},{"issue":"7","key":"ref17","doi-asserted-by":"crossref","first-page":"e101344","DOI":"10.1371\/journal.pone.0101344","article-title":"Rectal swabs for analysis of the intestinal microbiota","volume":"9","author":"AE Budding","year":"2014","journal-title":"PLoS One"},{"issue":"7872","key":"ref18","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/S0140-6736(74)91639-0","article-title":"Assessment of coma and impaired consciousness. A practical scale","volume":"2","author":"G Teasdale","year":"1974","journal-title":"Lancet"},{"issue":"5","key":"ref19","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1097\/01.CCM.0000215112.84523.F0","article-title":"Acute Physiology and Chronic Health Evaluation (APACHE) IV: hospital mortality assessment for today&apos;s critically ill patients","volume":"34","author":"JE Zimmerman","year":"2006","journal-title":"Crit Care Med"},{"issue":"1","key":"ref20","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1038\/nrg3129","article-title":"Experimental and analytical tools for studying the human microbiome","volume":"13","author":"J Kuczynski","year":"2011","journal-title":"Nat Rev Genet"},{"issue":"Suppl 1","key":"ref21","doi-asserted-by":"crossref","first-page":"4516","DOI":"10.1073\/pnas.1000080107","article-title":"Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample","volume":"108","author":"JG Caporaso","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7402","key":"ref22","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"issue":"23","key":"ref23","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":"3","key":"ref24","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1038\/ismej.2011.139","article-title":"An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea","volume":"6","author":"D McDonald","year":"2012","journal-title":"ISME J"},{"issue":"19","key":"ref25","doi-asserted-by":"crossref","first-page":"2460","DOI":"10.1093\/bioinformatics\/btq461","article-title":"Search and clustering orders of magnitude faster than BLAST","volume":"26","author":"RC Edgar","year":"2010","journal-title":"Bioinformatics"},{"issue":"3","key":"ref26","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2014approximately maximum-likelihood trees for large alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PLoS One"},{"issue":"5","key":"ref27","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"JG Caporaso","year":"2010","journal-title":"Nat Methods"},{"issue":"12","key":"ref28","doi-asserted-by":"crossref","first-page":"8228","DOI":"10.1128\/AEM.71.12.8228-8235.2005","article-title":"UniFrac: a new phylogenetic method for comparing microbial communities","volume":"71","author":"C Lozupone","year":"2005","journal-title":"Appl Environ Microbiol"},{"issue":"6","key":"ref29","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":"4","key":"ref30","doi-asserted-by":"crossref","first-page":"812","DOI":"10.1099\/00207713-44-4-812","article-title":"The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations","volume":"44","author":"MD Collins","year":"1994","journal-title":"Int J Syst Bacteriol"},{"issue":"1","key":"ref31","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s40168-017-0309-z","article-title":"Comparative gut microbiota and resistome profiling of intensive care patients receiving selective digestive tract decontamination and healthy subjects","volume":"5","author":"E Buelow","year":"2017","journal-title":"Microbiome"},{"issue":"1","key":"ref32","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/s00134-016-4613-z","article-title":"Critically ill patients demonstrate large interpersonal variation in intestinal microbiota dysregulation: a pilot study","volume":"43","author":"JM Lankelma","year":"2017","journal-title":"Intensive Care Med"},{"issue":"6351","key":"ref33","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":"5","key":"ref34","doi-asserted-by":"crossref","first-page":"592","DOI":"10.1016\/j.chom.2017.04.002","article-title":"Cooperating Commensals Restore Colonization Resistance to Vancomycin-Resistant Enterococcus faecium","volume":"21","author":"S Caballero","year":"2017","journal-title":"Cell Host Microbe"},{"issue":"7","key":"ref35","doi-asserted-by":"crossref","first-page":"1174","DOI":"10.1182\/blood-2014-02-554725","article-title":"The effects of intestinal tract bacterial diversity on mortality following allogeneic hematopoietic stem cell transplantation","volume":"124","author":"Y Taur","year":"2014","journal-title":"Blood"},{"issue":"5","key":"ref36","doi-asserted-by":"crossref","first-page":"569","DOI":"10.1177\/0148607114529596","article-title":"Rapid and Sustained Long-Term Decrease of Fecal Short-Chain Fatty Acids in Critically Ill Patients With Systemic Inflammatory Response Syndrome","volume":"39","author":"T Yamada","year":"2015","journal-title":"JPEN J Parenter Enteral Nutr"},{"issue":"5","key":"ref37","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1016\/j.cmet.2014.07.003","article-title":"Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates","volume":"20","author":"ED Sonnenburg","year":"2014","journal-title":"Cell Metab"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"6342","DOI":"10.1038\/ncomms7342","article-title":"Fat, fibre and cancer risk in African Americans and rural Africans","volume":"6","author":"SJ O'Keefe","year":"2015","journal-title":"Nat Commun"},{"issue":"7461","key":"ref39","doi-asserted-by":"crossref","first-page":"232","DOI":"10.1038\/nature12331","article-title":"Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota","volume":"500","author":"K Atarashi","year":"2013","journal-title":"Nature"},{"issue":"1\u20132","key":"ref40","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1016\/j.cell.2013.12.016","article-title":"Microbiota-generated metabolites promote metabolic benefits via gut-brain neural circuits","volume":"156","author":"F De Vadder","year":"2014","journal-title":"Cell"},{"issue":"5","key":"ref41","doi-asserted-by":"crossref","first-page":"1339","DOI":"10.1016\/j.cell.2016.10.043","article-title":"A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility","volume":"167","author":"MS Desai","year":"2016","journal-title":"Cell"},{"issue":"7","key":"ref42","doi-asserted-by":"crossref","first-page":"1117","DOI":"10.1093\/infdis\/jix011","article-title":"Protective Factors in the Intestinal Microbiome Against Clostridium difficile Infection in Recipients of Allogeneic Hematopoietic Stem Cell Transplantation","volume":"215","author":"YJ Lee","year":"2017","journal-title":"J Infect Dis"},{"issue":"4","key":"ref43","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1097\/MCC.0000000000000321","article-title":"Role of the microbiome, probiotics, and &apos;dysbiosis therapy&apos; in critical illness","volume":"22","author":"PE Wischmeyer","year":"2016","journal-title":"Curr Opin Crit Care"},{"issue":"6285","key":"ref44","doi-asserted-by":"crossref","first-page":"560","DOI":"10.1126\/science.aad3503","article-title":"Population-level analysis of gut microbiome variation","volume":"352","author":"G Falony","year":"2016","journal-title":"Science"},{"issue":"6285","key":"ref45","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1126\/science.aad3369","article-title":"Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity","volume":"352","author":"A Zhernakova","year":"2016","journal-title":"Science"},{"issue":"6","key":"ref46","doi-asserted-by":"crossref","first-page":"138","DOI":"10.4291\/wjgp.v2.i6.138","article-title":"Effect of fiber supplementation on the microbiota in critically ill patients","volume":"2","author":"SJ O'Keefe","year":"2011","journal-title":"World J Gastrointest Pathophysiol"},{"issue":"21","key":"ref47","doi-asserted-by":"crossref","first-page":"2323","DOI":"10.1001\/jama.2009.1754","article-title":"International study of the prevalence and outcomes of infection in intensive care units","volume":"302","author":"JL Vincent","year":"2009","journal-title":"JAMA"},{"issue":"7","key":"ref48","doi-asserted-by":"crossref","first-page":"1303","DOI":"10.1097\/00003246-200107000-00002","article-title":"Epidemiology of severe sepsis in the United States: analysis of incidence, outcome, and associated costs of care","volume":"29","author":"DC Angus","year":"2001","journal-title":"Crit Care Med"},{"issue":"7","key":"ref49","doi-asserted-by":"crossref","first-page":"2879","DOI":"10.1128\/AAC.49.7.2879-2886.2005","article-title":"Colonization and resistance dynamics of gram-negative bacteria in patients during and after hospitalization","volume":"49","author":"PM Filius","year":"2005","journal-title":"Antimicrobial agents and chemotherapy"},{"issue":"3","key":"ref50","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1128\/IAI.01197-12","article-title":"Intestinal microbiota containing Barnesiella species cures vancomycin-resistant Enterococcus faecium colonization","volume":"81","author":"C Ubeda","year":"2013","journal-title":"Infect Immun"},{"issue":"6335","key":"ref51","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1126\/science.aag2029","article-title":"Neonatal acquisition of Clostridia species protects against colonization by bacterial pathogens","volume":"356","author":"YG Kim","year":"2017","journal-title":"Science"},{"issue":"5","key":"ref52","doi-asserted-by":"crossref","first-page":"e516","DOI":"10.1097\/CCM.0000000000002291","article-title":"Dietary Supplementation With Nonfermentable Fiber Alters the Gut Microbiota and Confers Protection in Murine Models of Sepsis","volume":"45","author":"MJ Morowitz","year":"2017","journal-title":"Crit Care Med"},{"issue":"9613","key":"ref53","doi-asserted-by":"crossref","first-page":"651","DOI":"10.1016\/S0140-6736(08)60207-X","article-title":"Probiotic prophylaxis in predicted severe acute pancreatitis: a randomised, double-blind, placebo-controlled trial","volume":"371","author":"MG Besselink","year":"2008","journal-title":"Lancet"},{"issue":"5","key":"ref54","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1007\/s00134-008-1368-1","article-title":"Effect of synbiotic therapy on the incidence of ventilator associated pneumonia in critically ill patients: a randomised, double-blind, placebo-controlled trial","volume":"35","author":"DJ Knight","year":"2009","journal-title":"Intensive Care Med"},{"issue":"12","key":"ref55","doi-asserted-by":"crossref","first-page":"3290","DOI":"10.1097\/CCM.0b013e318260cc33","article-title":"Probiotics in the critically ill: a systematic review of the randomized trial evidence","volume":"40","author":"EO Petrof","year":"2012","journal-title":"Crit Care Med"},{"key":"ref56","article-title":"Gastrointestinal carriage is a major reservoir of K. pneumoniae infection in intensive care patients","author":"CL Gorrie","year":"2017","journal-title":"Clin Infect Dis"},{"issue":"10","key":"ref57","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1097\/01.CCM.0000182798.39709.84","article-title":"Early changes in organ function predict eventual survival in severe sepsis","volume":"33","author":"MM Levy","year":"2005","journal-title":"Crit Care Med"},{"issue":"7602","key":"ref58","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1038\/nature17626","article-title":"The evolution of cooperation within the gut microbiota","volume":"533","author":"S Rakoff-Nahoum","year":"2016","journal-title":"Nature"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0200322","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T09:46:54Z","timestamp":1540201614000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0200322"}},"subtitle":[],"editor":[{"given":"Brenda A.","family":"Wilson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,1]]},"references-count":58,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2018,8,1]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0200322","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,8,1]]}}}