{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T08:13:11Z","timestamp":1774685591002,"version":"3.50.1"},"reference-count":68,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2013,12,12]],"date-time":"2013-12-12T00:00:00Z","timestamp":1386806400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1003388","type":"journal-article","created":{"date-parts":[[2013,12,12]],"date-time":"2013-12-12T21:28:40Z","timestamp":1386883720000},"page":"e1003388","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":580,"title":["Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota"],"prefix":"10.1371","volume":"9","author":[{"given":"Richard R.","family":"Stein","sequence":"first","affiliation":[]},{"given":"Vanni","family":"Bucci","sequence":"additional","affiliation":[]},{"given":"Nora C.","family":"Toussaint","sequence":"additional","affiliation":[]},{"given":"Charlie G.","family":"Buffie","sequence":"additional","affiliation":[]},{"given":"Gunnar","family":"R\u00e4tsch","sequence":"additional","affiliation":[]},{"given":"Eric G.","family":"Pamer","sequence":"additional","affiliation":[]},{"given":"Chris","family":"Sander","sequence":"additional","affiliation":[]},{"given":"Jo\u00e3o B.","family":"Xavier","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2013,12,12]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/nature09944","article-title":"Enterotypes of the human gut microbiome","volume":"473","author":"M Arumugam","year":"2011","journal-title":"Nature"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.trsl.2012.05.003","article-title":"The human gut microbiome: current knowledge, challenges, and future directions","volume":"160","author":"M Dave","year":"2012","journal-title":"Transl Res"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1038\/nrmicro2973","article-title":"The microbiome explored: recent insights and future challenges","volume":"11","author":"M Blaser","year":"2013","journal-title":"Nature Rev Microbiol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"S128","DOI":"10.1097\/MCG.0b013e31821f44c4","article-title":"Obesity and the gut microbiota","volume":"45","author":"H Flint","year":"2011","journal-title":"J Clin Gastroenterol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"R79","DOI":"10.1186\/gb-2012-13-9-r79","article-title":"Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment","volume":"13","author":"XC Morgan","year":"2012","journal-title":"Genome Biol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"e9085","DOI":"10.1371\/journal.pone.0009085","article-title":"Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults","volume":"5","author":"N Larsen","year":"2010","journal-title":"PLoS One"},{"key":"ref7","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"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"5354","DOI":"10.1073\/pnas.1019378108","article-title":"Microbiota regulates immune defense against respiratory tract inuenza a virus infection","volume":"108","author":"T Ichinohe","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1093\/infdis\/110.1.38","article-title":"In vivo and in vitro antagonism of intestinal bacteria against shigella exneri: II. the inhibitory mechanism","volume":"110","author":"R Freter","year":"1962","journal-title":"J Infect Dis"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"805","DOI":"10.1084\/jem.120.5.805","article-title":"Resistance of the mouse's intestinal tract to experimental salmonella infection I. factors which interfere with the initiation of infection by oral inoculation","volume":"120","author":"M Bohnhoff","year":"1964","journal-title":"J Exp Med"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1038\/nrg3182","article-title":"The human microbiome: at the interface of health and disease","volume":"13","author":"I Cho","year":"2012","journal-title":"Nature Rev Genet"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1016\/j.cell.2012.01.035","article-title":"The impact of the gut microbiota on human health: an integrative view","volume":"148","author":"JC Clemente","year":"2012","journal-title":"Cell"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1635","DOI":"10.1126\/science.1110591","article-title":"Diversity of the human intestinal microbial ora","volume":"308","author":"PB Eckburg","year":"2005","journal-title":"Science"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/nature11550","article-title":"Diversity, stability and resilience of the human gut microbiota","volume":"489","author":"CA Lozupone","year":"2012","journal-title":"Nature"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"R50","DOI":"10.1186\/gb-2011-12-5-r50","article-title":"Moving pictures of the human microbiome","volume":"12","author":"JG Caporaso","year":"2011","journal-title":"Genome Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1111\/j.1753-4887.2012.00489.x","article-title":"The human microbiome: ecosystem resilience and health","volume":"70","author":"DA Relman","year":"2012","journal-title":"Nutr Rev"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1038\/ismej.2010.118","article-title":"Dominant and dietresponsive groups of bacteria within the human colonic microbiota","volume":"5","author":"AW Walker","year":"2010","journal-title":"ISME J"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"4554","DOI":"10.1073\/pnas.1000087107","article-title":"Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation","volume":"108","author":"L Dethlefsen","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1128\/IAI.05496-11","article-title":"Profound alterations of intestinal microbiota following a single dose of clindamycin results in sustained susceptibility to clostridium difficile-induced colitis","volume":"80","author":"CG Buffie","year":"2012","journal-title":"Infect Immun"},{"key":"ref20","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","volume":"55","author":"Y Taur","year":"2012","journal-title":"Clin Infect Dis"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/ismej.2007.3","article-title":"Long-term ecological impacts of antibiotic administration on the human intestinal microbiota","volume":"1","author":"C Jernberg","year":"2007","journal-title":"ISME J"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"11512","DOI":"10.1073\/pnas.0801925105","article-title":"Resistance, resilience, and redundancy in microbial communities","volume":"105","author":"SD Allison","year":"2008","journal-title":"Proc Natl Acad Sci"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1044","DOI":"10.1016\/j.cgh.2011.08.014","article-title":"Treating clostridium difficile infection with fecal microbiota transplantation","volume":"9","author":"JS Bakken","year":"2011","journal-title":"Clin Gastroenterol Hepatol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1056\/NEJMoa1205037","article-title":"Duodenal infusion of donor feces for recurrent clostridium difficile","volume":"368","author":"E van Nood","year":"2013","journal-title":"New Engl J Med"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"965","DOI":"10.1128\/IAI.01197-12","article-title":"Intestinal microbiota containing barnesiella cures vancomycin-resistant enterococcus faecium colonization","volume":"81","author":"C Ubeda","year":"2013","journal-title":"Infect Immun"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e1002606","DOI":"10.1371\/journal.pcbi.1002606","article-title":"Microbial co-occurrence relationships in the human microbiome","volume":"8","author":"K Faust","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"E162","DOI":"10.1086\/662668","article-title":"The evolution of bacteriocin production in bacterial biofilms","volume":"178","author":"V Bucci","year":"2011","journal-title":"Amer Nat"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"e1002497","DOI":"10.1371\/journal.pcbi.1002497","article-title":"Social interaction, noise and antibiotic-mediated switches in the intestinal microbiota","volume":"8","author":"V Bucci","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1016\/j.mib.2013.03.009","article-title":"Disruption of the gut microbiome as a risk factor for microbial infections","volume":"16","author":"A Khosravi","year":"2013","journal-title":"Curr Opin Microbiol"},{"key":"ref30","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"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"1518","DOI":"10.1126\/science.1205438","article-title":"Detecting novel associations in large data sets","volume":"334","author":"DN Reshef","year":"2011","journal-title":"Science"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"e1002687","DOI":"10.1371\/journal.pcbi.1002687","article-title":"Inferring correlation networks from genomic survey data","volume":"8","author":"J Friedman","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"666","DOI":"10.1038\/msb.2013.22","article-title":"Computational metaomics for microbial community studies","volume":"9","author":"N Segata","year":"2013","journal-title":"Mol Sys Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"2532","DOI":"10.1093\/bioinformatics\/btl417","article-title":"Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors","volume":"22","author":"Q Ruan","year":"2006","journal-title":"Bioinformatics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"S15","DOI":"10.1186\/1752-0509-5-S2-S15","article-title":"Extended local similarity analysis (elsa) of microbial community and other time series data with replicates","volume":"5","author":"L Xia","year":"2011","journal-title":"BMC Syst Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1093\/bioinformatics\/bts668","article-title":"Efficient statistical significance approximation for local similarity analysis of high-throughput time series data","volume":"29","author":"LC Xia","year":"2013","journal-title":"Bioinformatics"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e1002624","DOI":"10.1371\/journal.pcbi.1002624","article-title":"Inferring dynamic signatures of microbes in complex host ecosystems","volume":"8","author":"GK Gerber","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1128\/AEM.01338-07","article-title":"Microbial interactions within a cheese microbial community","volume":"74","author":"J Mounier","year":"2008","journal-title":"Appl Environ Microbiol"},{"key":"ref39","doi-asserted-by":"crossref","unstructured":"Hofbauer J, Sigmund K (1998) Evolutionary games and population dynamics. Cambridge University Press.","DOI":"10.1017\/CBO9781139173179"},{"key":"ref40","doi-asserted-by":"crossref","unstructured":"May RM (2001) Stability and complexity in model ecosystems, volume 6. Princeton University Press.","DOI":"10.1515\/9780691206912"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"6163","DOI":"10.1073\/pnas.092576199","article-title":"Reverse engineering gene networks using singular value decomposition and robust regression","volume":"99","author":"MKS Yeung","year":"2002","journal-title":"Proc Natl Acad Sci"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1126\/science.1081900","article-title":"Inferring genetic networks and identifying compound mode of action via expression profiling","volume":"301","author":"TS Gardner","year":"2003","journal-title":"Science"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"R36","DOI":"10.1186\/gb-2006-7-5-r36","article-title":"The inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo","volume":"7","author":"R Bonneau","year":"2006","journal-title":"Genome Biol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1093\/bioinformatics\/btl003","article-title":"Inference of gene regulatory networks and compound mode of action from time course gene expression profiles","volume":"22","author":"M Bansal","year":"2006","journal-title":"Bioinformatics"},{"key":"ref45","unstructured":"White JR (2010) Novel Methods for Metagenomic Analysis. Ph.D. thesis, University of Maryland."},{"key":"ref46","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1038\/nrmicro2832","article-title":"Microbial interactions: from networks to models","volume":"10","author":"K Faust","year":"2012","journal-title":"Nature Rev Microbiol"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"4680","DOI":"10.1073\/pnas.1002611107","article-title":"Vaginal microbiome of reproductive-age women","volume":"108","author":"J Ravel","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"ref48","unstructured":"Tikhonov A, Arsenin VY (1977) Solution of Ill-posed Problems. VH Winston & Sons."},{"key":"ref49","doi-asserted-by":"crossref","unstructured":"Aster RC, Borchers B, Thurber CH (2012) Parameter estimation and inverse problems. Academic Press.","DOI":"10.1016\/B978-0-12-385048-5.00010-0"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1090\/S0002-9939-1995-1264833-2","article-title":"Extinction in competitive Lotka\u2013Volterra systems","volume":"123","author":"ML Zeeman","year":"1995","journal-title":"Proc Amer Math Soc"},{"key":"ref51","first-page":"147","article-title":"Coexistence in competitive Lotka\u2013Volterra systems","volume":"11","author":"JG Kim","year":"1996","journal-title":"Comm Kor Math Soc"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1093\/jn\/116.1.164","article-title":"Using density rather than mass to express the concentration of gastrointestinal tract constituents","volume":"116","author":"JR Lupton","year":"1986","journal-title":"J Nutr"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1007\/s12223-012-0138-1","article-title":"The antimicrobial action of chitosan, low molar mass chitosan, and chitooligosaccharides on human colonic bacteria","volume":"57","author":"J \u0160im\u016dnek","year":"2012","journal-title":"Folia Microbiol"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"802","DOI":"10.3201\/eid0808.010418","article-title":"Antecedent treatment with different antibiotic agents as a risk factor for vancomycin-resistant enterococcus","volume":"8","author":"MH Samore","year":"2002","journal-title":"Emerg Infect Dis"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1086\/502207","article-title":"Colonization and infection with multiple nosocomial pathogens among patients colonized with vancomycin-resistant enterococcus","volume":"24","author":"CJ Donskey","year":"2003","journal-title":"Infect Control Hosp Epidemiol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"2391","DOI":"10.1088\/0951-7715\/19\/10\/006","article-title":"Chaos in low-dimensional Lotka\u2013Volterra models of competition","volume":"19","author":"J Vano","year":"2006","journal-title":"Nonlinearity"},{"key":"ref57","doi-asserted-by":"crossref","unstructured":"Amann H (1990) Ordinary differential equations: an introduction to nonlinear analysis, volume 13. de Gruyter.","DOI":"10.1515\/9783110853698"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1016\/S0169-5347(02)02495-3","article-title":"Community ecology theory as a framework for biological invasions","volume":"17","author":"K Shea","year":"2002","journal-title":"Trends Ecol Evol"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"417","DOI":"10.3389\/fmicb.2012.00417","article-title":"Fundamentals of microbial community resistance and resilience","volume":"3","author":"A Shade","year":"2012","journal-title":"FMICB"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"1175","DOI":"10.1126\/science.1219805","article-title":"Generic indicators for loss of resilience before a tipping point leading to population collapse","volume":"336","author":"L Dai","year":"2012","journal-title":"Science"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"789","DOI":"10.1086\/284105","article-title":"On the evidence needed to judge ecological stability or persistence","volume":"121","author":"JH Connell","year":"1983","journal-title":"Amer Nat"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"4158","DOI":"10.1073\/pnas.1015676108","article-title":"Bacterial community structures are unique and resilient in full-scale bioenergy systems","volume":"108","author":"JJ Werner","year":"2011","journal-title":"Proc Natl Acad Sci"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1038\/ismej.2011.162","article-title":"The western english channel contains a persistent microbial seed bank","volume":"6","author":"JG Caporaso","year":"2011","journal-title":"ISME J"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"6158","DOI":"10.1128\/AEM.00764-11","article-title":"Soil microbial community successional patterns during forest ecosystem restoration","volume":"77","author":"NC Banning","year":"2011","journal-title":"Appl Environ Microbiol"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The human microbiome project","volume":"449","author":"PJ Turnbaugh","year":"2007","journal-title":"Nature"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"e1000711","DOI":"10.1371\/journal.ppat.1000711","article-title":"Like will to like: abundances of closely related species can predict susceptibility to intestinal colonization by pathogenic and commensal bacteria","volume":"6","author":"B Stecher","year":"2010","journal-title":"PLoS Pathog"},{"key":"ref67","doi-asserted-by":"crossref","unstructured":"Barenblatt GI (1996) Scaling, self-similarity, and intermediate asymptotics: dimensional analysis and intermediate asymptotics, volume 14. Cambridge University Press.","DOI":"10.1017\/CBO9781107050242"},{"key":"ref68","unstructured":"Bishop CM (2006) Pattern recognition and machine learning. Springer New York."}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003388","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,8,12]],"date-time":"2020-08-12T01:15:15Z","timestamp":1597194915000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1003388"}},"subtitle":[],"editor":[{"given":"Christian","family":"von Mering","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2013,12,12]]},"references-count":68,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2013,12,12]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1003388","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,12,12]]}}}