{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T20:29:44Z","timestamp":1775593784089,"version":"3.50.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1005939","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,1,26]],"date-time":"2018-01-26T00:00:00Z","timestamp":1516924800000}}],"reference-count":114,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2018,1,16]],"date-time":"2018-01-16T00:00:00Z","timestamp":1516060800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Simons Foundation (US)","award":["409704"],"award-info":[{"award-number":["409704"]}]},{"DOI":"10.13039\/100007161","name":"Boston University","doi-asserted-by":"publisher","award":["Startup fund"],"award-info":[{"award-number":["Startup fund"]}],"id":[{"id":"10.13039\/100007161","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Rafik B. Hariri Institute","award":["Graduate fellowship"],"award-info":[{"award-number":["Graduate fellowship"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DBI-1559829"],"award-info":[{"award-number":["DBI-1559829"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1005939","type":"journal-article","created":{"date-parts":[[2018,1,16]],"date-time":"2018-01-16T13:25:29Z","timestamp":1516109129000},"page":"e1005939","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["Interactions between species introduce spurious associations in microbiome studies"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4767-0971","authenticated-orcid":true,"given":"Rajita","family":"Menon","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vivek","family":"Ramanan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1988-0645","authenticated-orcid":true,"given":"Kirill S.","family":"Korolev","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2018,1,16]]},"reference":[{"issue":"7164","key":"ref1","doi-asserted-by":"crossref","first-page":"804","DOI":"10.1038\/nature06244","article-title":"The human microbiome project: exploring the microbial part of ourselves in a changing world","volume":"449","author":"PJ Turnbaugh","year":"2007","journal-title":"Nature"},{"issue":"7402","key":"ref2","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1038\/nature11053","article-title":"Human gut microbiome viewed across age and geography","volume":"486","author":"T Yatsunenko","year":"2012","journal-title":"Nature"},{"issue":"4","key":"ref3","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 Reviews Genetics"},{"issue":"7500","key":"ref4","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nature13178","article-title":"Dynamics and associations of microbial community types across the human body","volume":"509","author":"T Ding","year":"2014","journal-title":"Nature"},{"issue":"1","key":"ref5","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1186\/s12915-014-0069-1","article-title":"The Earth Microbiome project: successes and aspirations","volume":"12","author":"JA Gilbert","year":"2014","journal-title":"BMC biology"},{"issue":"12","key":"ref6","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":"Clinical Gastroenterology and Hepatology"},{"issue":"7521","key":"ref7","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1038\/nature13793","article-title":"Artificial sweeteners induce glucose intolerance by altering the gut microbiota","volume":"514","author":"J Suez","year":"2014","journal-title":"Nature"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"58","DOI":"10.3945\/ajcn.110.010132","article-title":"Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans","volume":"94","author":"R Jumpertz","year":"2011","journal-title":"The American journal of clinical nutrition"},{"issue":"7122","key":"ref9","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1038\/nature05414","article-title":"An obesity-associated gut microbiome with increased capacity for energy harvest","volume":"444","author":"PJ Turnbaugh","year":"2006","journal-title":"nature"},{"issue":"05","key":"ref10","doi-asserted-by":"crossref","first-page":"755","DOI":"10.1017\/S0007114510004319","article-title":"Assessment of psychotropic-like properties of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects","volume":"105","author":"M Messaoudi","year":"2011","journal-title":"British Journal of Nutrition"},{"issue":"3","key":"ref11","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1111\/j.1365-2982.2010.01664.x","article-title":"The microbiome-gut-brain axis: from bowel to behavior","volume":"23","author":"JF Cryan","year":"2011","journal-title":"Neurogastroenterology & Motility"},{"issue":"5","key":"ref12","doi-asserted-by":"crossref","first-page":"1000","DOI":"10.1016\/j.cell.2014.08.006","article-title":"Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease","volume":"158","author":"NW Palm","year":"2014","journal-title":"Cell"},{"issue":"6","key":"ref13","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1016\/j.cell.2016.11.018","article-title":"Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson\u2019s Disease","volume":"167","author":"TR Sampson","year":"2016","journal-title":"Cell"},{"issue":"7418","key":"ref14","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nature11450","article-title":"A metagenome-wide association study of gut microbiota in type 2 diabetes","volume":"490","author":"J Qin","year":"2012","journal-title":"Nature"},{"issue":"2","key":"ref15","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.chom.2015.01.001","article-title":"The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes","volume":"17","author":"AD Kostic","year":"2015","journal-title":"Cell host & microbe"},{"issue":"1","key":"ref16","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1038\/ismej.2010.92","article-title":"Toward defining the autoimmune microbiome for type 1 diabetes","volume":"5","author":"A Giongo","year":"2011","journal-title":"The ISME journal"},{"issue":"1","key":"ref17","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1097\/BOR.0000000000000008","article-title":"Microbiome and mucosal inflammation as extra-articular triggers for rheumatoid arthritis and autoimmunity","volume":"26","author":"SB Brusca","year":"2014","journal-title":"Current opinion in rheumatology"},{"issue":"22","key":"ref18","doi-asserted-by":"crossref","first-page":"4244","DOI":"10.1016\/j.febslet.2014.05.034","article-title":"Arthritis susceptibility and the gut microbiome","volume":"588","author":"V Taneja","year":"2014","journal-title":"FEBS letters"},{"issue":"1","key":"ref19","doi-asserted-by":"crossref","first-page":"e00261","DOI":"10.1128\/mBio.00261-11","article-title":"Application of novel PCR-based methods for detection, quantitation, and phylogenetic characterization of Sutterella species in intestinal biopsy samples from children with autism and gastrointestinal disturbances","volume":"3","author":"BL Williams","year":"2012","journal-title":"MBio"},{"issue":"1","key":"ref20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2040-2392-4-42","article-title":"Ruminococcus torques in feces of children with autism spectrum disorder","volume":"4","author":"L Wang","year":"2013","journal-title":"Molecular autism"},{"issue":"3","key":"ref21","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1016\/j.chom.2014.02.005","article-title":"The treatment-naive microbiome in new-onset Crohn\u2019s disease","volume":"15","author":"D Gevers","year":"2014","journal-title":"Cell Host \u2018I&\u2019 Microbe"},{"key":"ref22","first-page":"1","article-title":"Fungal Microbiota Profile in Newly Diagnosed Treatment-na\u00efve Children with Crohn\u2019s disease","author":"M El Mouzan","year":"2017","journal-title":"Journal of Crohn\u2019s and Colitis"},{"issue":"7610","key":"ref23","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/nature18850","article-title":"Microbiome-wide association studies link dynamic microbial consortia to disease","volume":"535","author":"JA Gilbert","year":"2016","journal-title":"Nature"},{"issue":"10","key":"ref24","doi-asserted-by":"crossref","first-page":"e0137725","DOI":"10.1371\/journal.pone.0137725","article-title":"Comparison of fecal microbiota in children with autism spectrum disorders and neurotypical siblings in the Simons Simplex Collection","volume":"10","author":"JS Son","year":"2015","journal-title":"PloS ONE"},{"issue":"4","key":"ref25","doi-asserted-by":"crossref","first-page":"945","DOI":"10.1016\/j.celrep.2015.12.088","article-title":"Detecting Microbial Dysbiosis Associated with Pediatric Crohn Disease Despite the High Variability of the Gut Microbiota","volume":"14","author":"F Wang","year":"2016","journal-title":"Cell Reports"},{"issue":"2","key":"ref26","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1002\/ibd.21751","article-title":"Characterization of the gastrointestinal microbiota in health and inflammatory bowel disease","volume":"18","author":"P De Cruz","year":"2012","journal-title":"Inflammatory bowel diseases"},{"issue":"6261","key":"ref27","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1126\/science.aad2602","article-title":"The ecology of the microbiome: networks, competition, and stability","volume":"350","author":"KZ Coyte","year":"2015","journal-title":"Science"},{"issue":"7602","key":"ref28","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"},{"issue":"5","key":"ref29","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1111\/j.1462-2920.2007.01281.x","article-title":"Interactions and competition within the microbial community of the human colon: links between diet and health","volume":"9","author":"HJ Flint","year":"2007","journal-title":"Environmental microbiology"},{"issue":"7606","key":"ref30","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/nature18301","article-title":"Universality of human microbial dynamics","volume":"534","author":"A Bashan","year":"2016","journal-title":"Nature"},{"issue":"7","key":"ref31","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":"ref32","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1038\/nbt.3703","article-title":"Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota","volume":"35","author":"S Magn\u00fasd\u00f3ttir","year":"2017","journal-title":"Nature Biotechnology"},{"issue":"12","key":"ref33","doi-asserted-by":"crossref","first-page":"1004","DOI":"10.1038\/nchembio.2207","article-title":"Discovery of MRSA active antibiotics using primary sequence from the human microbiome","volume":"12","author":"J Chu","year":"2016","journal-title":"Nature Chemical Biology"},{"issue":"4","key":"ref34","doi-asserted-by":"crossref","first-page":"690","DOI":"10.1046\/j.1420-9101.2003.00575.x","article-title":"A phylogenetic approach to assessing the targets of microbial warfare","volume":"16","author":"MA Riley","year":"2003","journal-title":"Journal of evolutionary biology"},{"issue":"2","key":"ref35","doi-asserted-by":"crossref","first-page":"786","DOI":"10.1073\/pnas.012399899","article-title":"Chemical warfare between microbes promotes biodiversity","volume":"99","author":"TL Cz\u00e1r\u00e1n","year":"2002","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"9","key":"ref36","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1016\/j.tree.2006.06.013","article-title":"Assembly of the human intestinal microbiota","volume":"21","author":"L Dethlefsen","year":"2006","journal-title":"Trends in ecology & evolution"},{"key":"ref37","first-page":"13","article-title":"Gastrointestinal microbiology","author":"RI Mackie","year":"1997"},{"issue":"7","key":"ref38","doi-asserted-by":"crossref","first-page":"e1004182","DOI":"10.1371\/journal.pcbi.1004182","article-title":"Inferring pairwise interactions from biological data using maximum-entropy probability models","volume":"11","author":"RR Stein","year":"2015","journal-title":"PLoS Comput Biol"},{"key":"ref39","article-title":"Biophysics: searching for principles","author":"W Bialek","year":"2012"},{"issue":"9","key":"ref40","doi-asserted-by":"crossref","first-page":"1","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 biology"},{"key":"ref41","article-title":"A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis","author":"K Machiels","year":"2013","journal-title":"Gut"},{"issue":"9","key":"ref42","doi-asserted-by":"crossref","first-page":"1","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 biology"},{"issue":"6","key":"ref43","doi-asserted-by":"crossref","first-page":"e01286","DOI":"10.1128\/genomeA.01286-15","article-title":"Complete genome sequence of the human gut symbiont Roseburia hominis","volume":"3","author":"AJ Travis","year":"2015","journal-title":"Genome announcements"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1081","DOI":"10.3389\/fmicb.2016.01081","article-title":"The gut microbiota in immune-mediated inflammatory diseases","volume":"7","author":"JD Forbes","year":"2016","journal-title":"Frontiers in Microbiology"},{"issue":"5","key":"ref45","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1136\/gut.2010.223263","article-title":"Dysbiosis of the faecal microbiota in patients with Crohn\u2019s disease and their unaffected relatives","volume":"60","author":"M Joossens","year":"2011","journal-title":"Gut"},{"issue":"8","key":"ref46","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1002\/ibd.20903","article-title":"Low counts of Faecalibacterium prausnitzii in colitis microbiota","volume":"15","author":"H Sokol","year":"2009","journal-title":"Inflammatory bowel diseases"},{"issue":"1","key":"ref47","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1159\/000441768","article-title":"Reduced abundance of butyrate-producing bacteria species in the fecal microbial community in Crohn\u2019s disease","volume":"93","author":"K Takahashi","year":"2016","journal-title":"Digestion"},{"key":"ref48","article-title":"Equilibrium statistical physics","author":"M Plischke","year":"1994"},{"key":"ref49","doi-asserted-by":"crossref","DOI":"10.1093\/acprof:oso\/9780199593415.001.0001","article-title":"Maximum entropy and ecology: a theory of abundance, distribution, and energetics","author":"J Harte","year":"2011"},{"issue":"7087","key":"ref50","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1038\/nature04701","article-title":"Weak pairwise correlations imply strongly correlated network states in a neural population","volume":"440","author":"E Schneidman","year":"2006","journal-title":"Nature"},{"issue":"33","key":"ref51","doi-asserted-by":"crossref","first-page":"13854","DOI":"10.1073\/pnas.0903244106","article-title":"Inferring species interactions in tropical forests","volume":"106","author":"I Volkov","year":"2009","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"12","key":"ref52","doi-asserted-by":"crossref","first-page":"1153","DOI":"10.1038\/nphys3846","article-title":"Local equilibrium in bird flocks","volume":"12","author":"T Mora","year":"2016","journal-title":"Nature Physics"},{"issue":"49","key":"ref53","doi-asserted-by":"crossref","first-page":"E1293","DOI":"10.1073\/pnas.1111471108","article-title":"Direct-coupling analysis of residue coevolution captures native contacts across many protein families","volume":"108","author":"F Morcos","year":"2011","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"28","key":"ref54","doi-asserted-by":"crossref","first-page":"11530","DOI":"10.1073\/pnas.1105315108","article-title":"Coordinate linkage of HIV evolution reveals regions of immunological vulnerability","volume":"108","author":"V Dahirel","year":"2011","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"4","key":"ref55","doi-asserted-by":"crossref","first-page":"e1005435","DOI":"10.1371\/journal.pcbi.1005435","article-title":"Variable habitat conditions drive species covariation in the human microbiota","volume":"13","author":"CK Fisher","year":"2017","journal-title":"PLOS Computational Biology"},{"issue":"9","key":"ref56","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 computational biology"},{"key":"ref57","doi-asserted-by":"crossref","DOI":"10.1007\/978-94-009-4109-0","article-title":"The statistical analysis of compositional data","author":"J Aitchison","year":"1986"},{"key":"ref58","doi-asserted-by":"crossref","DOI":"10.1002\/9781119976462","article-title":"Compositional data analysis: Theory and applications","author":"V Pawlowsky-Glahn","year":"2011"},{"issue":"3","key":"ref59","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1023\/A:1023818214614","article-title":"Isometric logratio transformations for compositional data analysis","volume":"35","author":"JJ Egozcue","year":"2003","journal-title":"Mathematical Geology"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","author":"Y Benjamini","year":"1995","journal-title":"Journal of the royal statistical society Series B (Methodological)"},{"issue":"16","key":"ref61","doi-asserted-by":"crossref","first-page":"9440","DOI":"10.1073\/pnas.1530509100","article-title":"Statistical significance for genomewide studies","volume":"100","author":"JD Storey","year":"2003","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"ref62","article-title":"Microbial genome-wide association studies: lessons from human GWAS","author":"RA Power","year":"2016","journal-title":"Nature Reviews Genetics"},{"issue":"5","key":"ref63","doi-asserted-by":"crossref","first-page":"e19416","DOI":"10.1371\/journal.pone.0019416","article-title":"Behavior of QQ-plots and genomic control in studies of gene-environment interaction","volume":"6","author":"A Voorman","year":"2011","journal-title":"PloS one"},{"key":"ref64","doi-asserted-by":"crossref","unstructured":"Ho TK. Random decision forests. In: Document Analysis and Recognition, 1995., Proceedings of the Third International Conference on. vol. 1. IEEE; 1995. p. 278\u2013282.","DOI":"10.1109\/ICDAR.1995.598994"},{"issue":"1","key":"ref65","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1023\/A:1010933404324","article-title":"Random forests","volume":"45","author":"L Breiman","year":"2001","journal-title":"Machine learning"},{"issue":"3","key":"ref66","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1007\/BF00994018","article-title":"Support-vector networks","volume":"20","author":"C Cortes","year":"1995","journal-title":"Machine learning"},{"issue":"7422","key":"ref67","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1038\/nature11582","article-title":"Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease","volume":"491","author":"L Jostins","year":"2012","journal-title":"Nature"},{"issue":"7152","key":"ref68","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1038\/nature06005","article-title":"Unravelling the pathogenesis of inflammatory bowel disease","volume":"448","author":"R Xavier","year":"2007","journal-title":"Nature"},{"issue":"43","key":"ref69","doi-asserted-by":"crossref","first-page":"16731","DOI":"10.1073\/pnas.0804812105","article-title":"Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients","volume":"105","author":"H Sokol","year":"2008","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"10","key":"ref70","doi-asserted-by":"crossref","first-page":"e109146","DOI":"10.1371\/journal.pone.0109146","article-title":"Faecalibacterium prausnitzii inhibits interleukin-17 to ameliorate colorectal colitis in rats","volume":"9","author":"M Zhang","year":"2014","journal-title":"PloS one"},{"issue":"11","key":"ref71","doi-asserted-by":"crossref","first-page":"e558","DOI":"10.1016\/j.crohns.2013.04.002","article-title":"Faecalibacterium prausnitzii upregulates regulatory T cells and anti-inflammatory cytokines in treating TNBS-induced colitis","volume":"7","author":"X Qiu","year":"2013","journal-title":"Journal of Crohn\u2019s and Colitis"},{"key":"ref72","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2016.01081","article-title":"The gut microbiota in immune-mediated inflammatory diseases","volume":"7","author":"JD Forbes","year":"2016","journal-title":"Frontiers in Microbiology"},{"issue":"5","key":"ref73","doi-asserted-by":"crossref","first-page":"429","DOI":"10.1016\/S0171-2985(00)80102-3","article-title":"Bifidobacterium adolescentis modulates the specific immune response to another human gut bacterium, Bacteroides thetaiotaomicron, in gnotobiotic rats","volume":"202","author":"L Scharek","year":"2000","journal-title":"Immunobiology"},{"issue":"2","key":"ref74","first-page":"123","article-title":"Review-Potential of probiotics as biotherapeutic agents targeting the innate immune system","volume":"4","author":"VO Oyetayo","year":"2005","journal-title":"African Journal of Biotechnology"},{"key":"ref75","doi-asserted-by":"crossref","DOI":"10.1038\/srep23971","article-title":"Evaluation of genetic diversity among strains of the human gut commensal Bifidobacterium adolescentis","volume":"6","author":"S Duranti","year":"2016","journal-title":"Scientific reports"},{"key":"ref76","article-title":"Lactic acid bacteria and bifidobacteria: current progress in advanced research","author":"K Sonomoto","year":"2011"},{"key":"ref77","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1111\/1462-2920.13589","article-title":"Formation of propionate and butyrate by the human colonic microbiota","volume":"19","author":"P Louis","year":"2016","journal-title":"Environmental Microbiology"},{"key":"ref78","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2016.00783","article-title":"Capturing One of the Human Gut Microbiome\u2019s Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data","volume":"7","author":"P Jeraldo","year":"2016","journal-title":"Frontiers in Microbiology"},{"issue":"9","key":"ref79","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1038\/nrgastro.2012.85","article-title":"Contributions of the microbial hydrogen economy to colonic homeostasis","volume":"9","author":"F Carbonero","year":"2012","journal-title":"Nature Reviews Gastroenterology and Hepatology"},{"issue":"10","key":"ref80","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1038\/nrmicro3344","article-title":"The gut microbiota, bacterial metabolites and colorectal cancer","volume":"12","author":"P Louis","year":"2014","journal-title":"Nature reviews Microbiology"},{"issue":"5","key":"ref81","doi-asserted-by":"crossref","first-page":"1615","DOI":"10.1111\/1462-2920.12599","article-title":"Modelling the emergent dynamics and major metabolites of the human colonic microbiota","volume":"17","author":"H Kettle","year":"2015","journal-title":"Environmental microbiology"},{"issue":"4","key":"ref82","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1111\/j.1751-7915.2010.00244.x","article-title":"Butyrate production in phylogenetically diverse Firmicutes isolated from the chicken caecum","volume":"4","author":"V Eeckhaut","year":"2011","journal-title":"Microbial biotechnology"},{"issue":"1","key":"ref83","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6968.2009.01514.x","article-title":"Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine","volume":"294","author":"P Louis","year":"2009","journal-title":"FEMS microbiology letters"},{"issue":"3","key":"ref84","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1111\/1462-2920.13658","article-title":"Oscillospira and related bacteria\u2014From metagenomic species to metabolic features","volume":"19","author":"U Gophna","year":"2017","journal-title":"Environmental microbiology"},{"issue":"8","key":"ref85","doi-asserted-by":"crossref","first-page":"3617","DOI":"10.1172\/JCI75436","article-title":"Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature","volume":"124","author":"Y Haberman","year":"2014","journal-title":"The Journal of clinical investigation"},{"issue":"10","key":"ref86","doi-asserted-by":"crossref","first-page":"3258","DOI":"10.1128\/JCM.01396-12","article-title":"Microbial dysbiosis in pediatric patients with Crohn\u2019s disease","volume":"50","author":"NO Kaakoush","year":"2012","journal-title":"Journal of clinical microbiology"},{"issue":"22","key":"ref87","doi-asserted-by":"crossref","first-page":"4223","DOI":"10.1016\/j.febslet.2014.09.039","article-title":"Meta-analyses of human gut microbes associated with obesity and IBD","volume":"588","author":"WA Walters","year":"2014","journal-title":"FEBS letters"},{"issue":"12","key":"ref88","doi-asserted-by":"crossref","DOI":"10.1002\/oby.20466","article-title":"Human intestinal microbiota composition is associated with local and systemic inflammation in obesity","volume":"21","author":"FJ Verdam","year":"2013","journal-title":"Obesity"},{"issue":"4","key":"ref89","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1038\/ismej.2012.146","article-title":"Microbiota conservation and BMI signatures in adult monozygotic twins","volume":"7","author":"S Tims","year":"2013","journal-title":"The ISME journal"},{"issue":"2","key":"ref90","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1002\/hep.26093","article-title":"Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH","volume":"57","author":"L Zhu","year":"2013","journal-title":"Hepatology"},{"issue":"6","key":"ref91","doi-asserted-by":"crossref","first-page":"874","DOI":"10.1111\/1758-2229.12319","article-title":"Interactions between the intestinal microbiota and bile acids in gallstones patients","volume":"7","author":"N Keren","year":"2015","journal-title":"Environmental microbiology reports"},{"key":"ref92","doi-asserted-by":"crossref","DOI":"10.1038\/srep25945","article-title":"Gut microbiota composition and Clostridium difficile infection in hospitalized elderly individuals: a metagenomic study","volume":"6","author":"C Milani","year":"2016","journal-title":"Scientific reports"},{"issue":"1","key":"ref93","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1016\/j.micinf.2015.09.008","article-title":"Identification of key taxa that favor intestinal colonization of Clostridium difficile in an adult Chinese population","volume":"18","author":"S Gu","year":"2016","journal-title":"Microbes and infection"},{"issue":"1","key":"ref94","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1080\/19490976.2014.997612","article-title":"Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease","volume":"6","author":"Y Minamoto","year":"2015","journal-title":"Gut microbes"},{"key":"ref95","article-title":"Depletion of luminal iron alters the gut microbiota and prevents Crohn\u2019s disease-like ileitis","author":"T Werner","year":"2010","journal-title":"Gut"},{"issue":"3","key":"ref96","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1128\/AEM.01561-09","article-title":"Bacteria associated with immunoregulatory cells in mice","volume":"76","author":"LL Presley","year":"2010","journal-title":"Applied and environmental microbiology"},{"issue":"33","key":"ref97","doi-asserted-by":"crossref","first-page":"9345","DOI":"10.1073\/pnas.1606631113","article-title":"Early gut colonizers shape parasite susceptibility and microbiota composition in honey bee workers","volume":"113","author":"RS Schwarz","year":"2016","journal-title":"Proceedings of the National Academy of Sciences"},{"issue":"8","key":"ref98","first-page":"ZE13","article-title":"Aggregatibacter actinomycetemcomitans\u2014A tooth killer?","volume":"8","author":"M Raja","year":"2014","journal-title":"Journal of clinical and diagnostic research: JCDR"},{"issue":"1","key":"ref99","doi-asserted-by":"crossref","first-page":"66","DOI":"10.1111\/j.1600-0765.1995.tb01254.x","article-title":"Predominant microflora of severe, moderate and minimal periodontal lesions in young adults with rapidly progressive periodontitis","volume":"30","author":"J Kamma","year":"1995","journal-title":"Journal of periodontal research"},{"issue":"4","key":"ref100","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1177\/039463201302600411","article-title":"Periodontal bacteria in the genital tract: are they related to adverse pregnancy outcome?","volume":"26","author":"M Cassini","year":"2013","journal-title":"International journal of immunopathology and pharmacology"},{"key":"ref101","article-title":"Fungal microbiota dysbiosis in IBD","author":"H Sokol","year":"2016","journal-title":"Gut"},{"key":"ref102","article-title":"Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers","author":"A Lavelle","year":"2015","journal-title":"Gut"},{"issue":"1","key":"ref103","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.femsec.2004.05.005","article-title":"Molecular inventory of faecal microflora in patients with Crohn\u2019s disease","volume":"50","author":"I Mangin","year":"2004","journal-title":"FEMS microbiology ecology"},{"issue":"11","key":"ref104","doi-asserted-by":"crossref","first-page":"4136","DOI":"10.1128\/JCM.01004-06","article-title":"Differences between tissue-associated intestinal microfloras of patients with Crohn\u2019s disease and ulcerative colitis","volume":"44","author":"U Gophna","year":"2006","journal-title":"Journal of clinical microbiology"},{"issue":"9","key":"ref105","doi-asserted-by":"crossref","first-page":"e66934","DOI":"10.1371\/journal.pone.0066934","article-title":"Characterization of the gut-associated microbiome in inflammatory pouch complications following ileal pouch-anal anastomosis","volume":"8","author":"AD Tyler","year":"2013","journal-title":"PloS one"},{"issue":"3","key":"ref106","doi-asserted-by":"crossref","first-page":"e58825","DOI":"10.1371\/journal.pone.0058825","article-title":"The microaerophilic microbiota of de-novo paediatric inflammatory bowel disease: the BISCUIT study","volume":"8","author":"R Hansen","year":"2013","journal-title":"PLoS One"},{"key":"ref107","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2016.01706","article-title":"Mucosal prevalence and interactions with the epithelium indicate commensalism of Sutterella spp","volume":"7","author":"K Hiippala","year":"2016","journal-title":"Frontiers in microbiology"},{"issue":"10","key":"ref108","doi-asserted-by":"crossref","first-page":"e27076","DOI":"10.1371\/journal.pone.0027076","article-title":"A comprehensive evaluation of colonic mucosal isolates of Sutterella wadsworthensis from inflammatory bowel disease","volume":"6","author":"I Mukhopadhya","year":"2011","journal-title":"PLoS One"},{"issue":"11","key":"ref109","doi-asserted-by":"crossref","first-page":"e112023","DOI":"10.1371\/journal.pone.0112023","article-title":"Gut microbiome in Down syndrome","volume":"9","author":"E Biagi","year":"2014","journal-title":"PLoS one"},{"issue":"4","key":"ref110","doi-asserted-by":"crossref","first-page":"551","DOI":"10.1137\/1035134","article-title":"On the early history of the singular value decomposition","volume":"35","author":"GW Stewart","year":"1993","journal-title":"SIAM review"},{"issue":"Oct","key":"ref111","first-page":"2825","article-title":"Scikit-learn: Machine learning in Python","volume":"12","author":"F Pedregosa","year":"2011","journal-title":"Journal of Machine Learning Research"},{"issue":"7","key":"ref112","doi-asserted-by":"crossref","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"TZ DeSantis","year":"2006","journal-title":"Applied and environmental microbiology"},{"issue":"May","key":"ref113","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":"1","author":"JG Caporaso","year":"2010","journal-title":"Nature methods"},{"issue":"12","key":"ref114","doi-asserted-by":"crossref","first-page":"1200","DOI":"10.1038\/nmeth.2658","article-title":"Differential abundance analysis for microbial marker-gene surveys","volume":"10","author":"JN Paulson","year":"2013","journal-title":"Nature methods"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1005939","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,1,26]],"date-time":"2018-01-26T00:00:00Z","timestamp":1516924800000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005939","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,29]],"date-time":"2025-06-29T17:51:10Z","timestamp":1751219470000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005939"}},"subtitle":[],"editor":[{"given":"Stefano","family":"Allesina","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,1,16]]},"references-count":114,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2018,1,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005939","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/176677","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,1,16]]}}}