{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T20:45:02Z","timestamp":1782333902085,"version":"3.54.5"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1006558","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,11,9]],"date-time":"2018-11-09T00:00:00Z","timestamp":1541721600000}}],"reference-count":89,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2018,10,30]],"date-time":"2018-10-30T00:00:00Z","timestamp":1540857600000},"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":["Award U01EB019416"],"award-info":[{"award-number":["Award U01EB019416"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["Award CBET 1511346"],"award-info":[{"award-number":["Award CBET 1511346"]}],"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.1006558","type":"journal-article","created":{"date-parts":[[2018,10,30]],"date-time":"2018-10-30T17:23:11Z","timestamp":1540920191000},"page":"e1006558","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":32,"title":["Suboptimal community growth mediated through metabolite crossfeeding promotes species diversity in the gut microbiota"],"prefix":"10.1371","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1969-4906","authenticated-orcid":true,"given":"Michael A.","family":"Henson","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Poonam","family":"Phalak","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2018,10,30]]},"reference":[{"issue":"4","key":"ref1","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1038\/nrmicro2974","article-title":"The gut microbiota\u2013masters of host development and physiology","volume":"11","author":"F Sommer","year":"2013","journal-title":"Nature Reviews Microbiology"},{"issue":"6","key":"ref2","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"},{"issue":"2","key":"ref3","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1080\/19490976.2016.1145374","article-title":"Chemical conversations in the gut microbiota","volume":"7","author":"JA Thompson","year":"2016","journal-title":"Gut microbes"},{"issue":"4","key":"ref4","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1016\/j.chom.2011.10.002","article-title":"Eating for two: how metabolism establishes interspecies interactions in the gut","volume":"10","author":"MA Fischbach","year":"2011","journal-title":"Cell host & microbe"},{"issue":"9","key":"ref5","doi-asserted-by":"crossref","first-page":"1331","DOI":"10.1038\/ijo.2015.84","article-title":"The role of short chain fatty acids in appetite regulation and energy homeostasis","volume":"39","author":"C Byrne","year":"2015","journal-title":"International journal of obesity"},{"issue":"3","key":"ref6","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1080\/19490976.2015.1134082","article-title":"Formation of short chain fatty acids by the gut microbiota and their impact on human metabolism","volume":"7","author":"DJ Morrison","year":"2016","journal-title":"Gut Microbes"},{"issue":"9","key":"ref7","doi-asserted-by":"crossref","first-page":"2325","DOI":"10.1194\/jlr.R036012","article-title":"The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism","volume":"54","author":"G den Besten","year":"2013","journal-title":"Journal of lipid research"},{"issue":"1","key":"ref8","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1097\/MOG.0000000000000139","article-title":"The gut microbiome in health and in disease","volume":"31","author":"AB Shreiner","year":"2015","journal-title":"Current opinion in gastroenterology"},{"issue":"2","key":"ref9","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1177\/0884533611436116","article-title":"Effects of gut microbes on nutrient absorption and energy regulation","volume":"27","author":"R Krajmalnik-Brown","year":"2012","journal-title":"Nutrition in Clinical Practice"},{"issue":"2","key":"ref10","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1159\/000186266","article-title":"Erythrocyte sedimentation rate and related factors in end-stage renal failure","volume":"57","author":"D Warner","year":"1991","journal-title":"Nephron"},{"issue":"4","key":"ref11","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1038\/nrmicro2540","article-title":"Unravelling the effects of the environment and host genotype on the gut microbiome","volume":"9","author":"A Spor","year":"2011","journal-title":"Nature Reviews Microbiology"},{"issue":"1","key":"ref12","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1038\/nrmicro3552","article-title":"Gut biogeography of the bacterial microbiota","volume":"14","author":"GP Donaldson","year":"2016","journal-title":"Nature Reviews Microbiology"},{"issue":"7430","key":"ref13","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1038\/nature11711","article-title":"Genomic variation landscape of the human gut microbiome","volume":"493","author":"S Schloissnig","year":"2013","journal-title":"Nature"},{"issue":"1","key":"ref14","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s13073-016-0307-y","article-title":"The healthy human microbiome","volume":"8","author":"J Lloyd-Price","year":"2016","journal-title":"Genome medicine"},{"issue":"7415","key":"ref15","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"},{"issue":"7","key":"ref16","doi-asserted-by":"crossref","first-page":"2103","DOI":"10.1111\/1462-2920.13318","article-title":"The human gut microbiome in health: establishment and resilience of microbiota over a lifetime","volume":"18","author":"K Greenhalgh","year":"2016","journal-title":"Environmental microbiology"},{"key":"ref17","article-title":"The gut microbiota and host health: a new clinical frontier","author":"JR Marchesi","year":"2015","journal-title":"Gut"},{"issue":"7402","key":"ref18","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","author":"C Huttenhower","year":"2012","journal-title":"Nature"},{"issue":"8","key":"ref19","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nbt.2942","article-title":"An integrated catalog of reference genes in the human gut microbiome","volume":"32","author":"J Li","year":"2014","journal-title":"Nature biotechnology"},{"issue":"1","key":"ref20","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s12865-016-0187-3","article-title":"Role of intestinal microbiota and metabolites on gut homeostasis and human diseases","volume":"18","author":"L Lin","year":"2017","journal-title":"BMC immunology"},{"issue":"11","key":"ref21","doi-asserted-by":"crossref","first-page":"1823","DOI":"10.1042\/BCJ20160510","article-title":"Introduction to the human gut microbiota","volume":"474","author":"E Thursby","year":"2017","journal-title":"Biochemical Journal"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1265","DOI":"10.3389\/fmicb.2017.01265","article-title":"Human gut microbiota: toward an ecology of disease","volume":"8","author":"S Selber-Hnatiw","year":"2017","journal-title":"Frontiers in microbiology"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.anaerobe.2016.05.006","article-title":"Structural and functional changes within the gut microbiota and susceptibility to Clostridium difficile infection","volume":"41","author":"CL Ross","year":"2016","journal-title":"Anaerobe"},{"issue":"2","key":"ref24","doi-asserted-by":"crossref","first-page":"20","DOI":"10.3390\/microorganisms4020020","article-title":"Microbiome, Metabolome and Inflammatory Bowel Disease","volume":"4","author":"I Ahmed","year":"2016","journal-title":"Microorganisms"},{"issue":"6","key":"ref25","first-page":"1219","article-title":"Recent advances in characterizing the gastrointestinal microbiome in Crohn\u2019s disease: a systematic review","volume":"21","author":"EK Wright","year":"2015","journal-title":"Inflammatory bowel diseases"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"563","DOI":"10.3389\/fmicb.2017.00563","article-title":"Gut microbiota modulation and its relationship with obesity using prebiotic fibers and probiotics: a review","volume":"8","author":"DK Dahiya","year":"2017","journal-title":"Frontiers in microbiology"},{"issue":"7","key":"ref27","doi-asserted-by":"crossref","first-page":"1183","DOI":"10.1161\/CIRCRESAHA.117.309715","article-title":"Gut microbiota in cardiovascular health and disease","volume":"120","author":"WW Tang","year":"2017","journal-title":"Circulation research"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"138","DOI":"10.3389\/fped.2017.00138","article-title":"The Microbiome and Blood Pressure: Can Microbes Regulate Our Blood Pressure?","volume":"5","author":"S Al Khodor","year":"2017","journal-title":"Frontiers in pediatrics"},{"key":"ref29","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":"3","key":"ref30","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1097\/PPO.0000000000000050","article-title":"Gut microbiome and colorectal adenomas","volume":"20","author":"S Dulal","year":"2014","journal-title":"Cancer journal (Sudbury, Mass)"},{"issue":"1","key":"ref31","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/s12866-017-0968-8","article-title":"The altered gut microbiota in adults with cystic fibrosis","volume":"17","author":"D Burke","year":"2017","journal-title":"BMC microbiology"},{"issue":"1","key":"ref32","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1097\/YCO.0000000000000117","article-title":"The gut microbiome and diet in psychiatry: focus on depression","volume":"28","author":"S Dash","year":"2015","journal-title":"Current opinion in psychiatry"},{"issue":"1","key":"ref33","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/msb4100131","article-title":"Metabolic modeling of a mutualistic microbial community","volume":"3","author":"S Stolyar","year":"2007","journal-title":"Molecular systems biology"},{"issue":"2","key":"ref34","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1080\/19490976.2015.1023494","article-title":"Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework","volume":"6","author":"A Heinken","year":"2015","journal-title":"Gut Microbes"},{"issue":"5","key":"ref35","doi-asserted-by":"crossref","first-page":"e64567","DOI":"10.1371\/journal.pone.0064567","article-title":"Community flux balance analysis for microbial consortia at balanced growth","volume":"8","author":"RA Khandelwal","year":"2013","journal-title":"PloS one"},{"issue":"2","key":"ref36","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/j.cmet.2015.07.001","article-title":"Quantifying diet-induced metabolic changes of the human gut microbiome","volume":"22","author":"S Shoaie","year":"2015","journal-title":"Cell metabolism"},{"issue":"2","key":"ref37","doi-asserted-by":"crossref","first-page":"e1002363","DOI":"10.1371\/journal.pcbi.1002363","article-title":"OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities","volume":"8","author":"AR Zomorrodi","year":"2012","journal-title":"PLoS computational biology"},{"issue":"5","key":"ref38","doi-asserted-by":"crossref","first-page":"e1005539","DOI":"10.1371\/journal.pcbi.1005539","article-title":"SteadyCom: Predicting microbial abundances while ensuring community stability","volume":"13","author":"SHJ Chan","year":"2017","journal-title":"PLoS computational biology"},{"issue":"6912","key":"ref39","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nature01149","article-title":"Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth","volume":"420","author":"RU Ibarra","year":"2002","journal-title":"Nature"},{"issue":"21","key":"ref40","doi-asserted-by":"crossref","first-page":"6400","DOI":"10.1128\/JB.185.21.6400-6408.2003","article-title":"Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model","volume":"185","author":"SS Fong","year":"2003","journal-title":"Journal of bacteriology"},{"issue":"124","key":"ref41","doi-asserted-by":"crossref","first-page":"20160627","DOI":"10.1098\/rsif.2016.0627","article-title":"Constraint-based stoichiometric modelling from single organisms to microbial communities","volume":"13","author":"W Gottstein","year":"2016","journal-title":"Journal of the Royal Society Interface"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"673","DOI":"10.3389\/fmicb.2016.00673","article-title":"Metabolic network modeling of microbial interactions in natural and engineered environmental systems","volume":"7","author":"O Perez-Garcia","year":"2016","journal-title":"Frontiers in microbiology"},{"issue":"5","key":"ref43","first-page":"317","article-title":"Metabolic network modeling of microbial communities","volume":"7","author":"MB Biggs","year":"2015","journal-title":"Wiley Interdisciplinary Reviews: Systems Biology and Medicine"},{"issue":"1","key":"ref44","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":"5","key":"ref45","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":"6","key":"ref46","doi-asserted-by":"crossref","first-page":"e32118","DOI":"10.1371\/journal.pone.0032118","article-title":"Analyses of the microbial diversity across the human microbiome","volume":"7","author":"K Li","year":"2012","journal-title":"PloS one"},{"issue":"6","key":"ref47","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1080\/19490976.2016.1241933","article-title":"Microbiome: Should we diversify from diversity?","volume":"7","author":"KVA Johnson","year":"2016","journal-title":"Gut microbes"},{"issue":"1","key":"ref48","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1111\/j.1574-6941.2003.tb01040.x","article-title":"Using ecological diversity measures with bacterial communities","volume":"43","author":"TC Hill","year":"2003","journal-title":"FEMS microbiology ecology"},{"issue":"1","key":"ref49","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1186\/1752-0509-6-127","article-title":"Comparative multi-goal tradeoffs in systems engineering of microbial metabolism","volume":"6","author":"D Byrne","year":"2012","journal-title":"BMC systems biology"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"14123","DOI":"10.1038\/ncomms14123","article-title":"Optimality and sub-optimality in a bacterial growth law","volume":"8","author":"BD Towbin","year":"2017","journal-title":"Nature communications"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"376","DOI":"10.3389\/fmicb.2017.00376","article-title":"Shaping the metabolism of intestinal Bacteroides population through diet to improve human health","volume":"8","author":"D Rios-Covian","year":"2017","journal-title":"Frontiers in microbiology"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"979","DOI":"10.3389\/fmicb.2016.00979","article-title":"Bifidobacteria and butyrate-producing colon bacteria: importance and strategies for their stimulation in the human gut","volume":"7","author":"A Rivi\u00e8re","year":"2016","journal-title":"Frontiers in microbiology"},{"issue":"2","key":"ref53","doi-asserted-by":"crossref","first-page":"e00889","DOI":"10.1128\/mBio.00889-14","article-title":"Revealing the bacterial butyrate synthesis pathways by analyzing (meta) genomic data","volume":"5","author":"M Vital","year":"2014","journal-title":"MBio"},{"issue":"6","key":"ref54","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1006\/anae.1997.0129","article-title":"Comparison of Batch Culture Growth and Fermentation of a PoultryVeillonellaIsolate and SelectedVeillonellaSpecies Grown in a Defined Medium","volume":"3","author":"J Durant","year":"1997","journal-title":"Anaerobe"},{"issue":"6252","key":"ref55","doi-asserted-by":"crossref","first-page":"1101","DOI":"10.1126\/science.aac4812","article-title":"Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples","volume":"349","author":"T Korem","year":"2015","journal-title":"Science"},{"key":"ref56","article-title":"Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates","author":"D Vandeputte","year":"2015","journal-title":"Gut"},{"issue":"3","key":"ref57","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1128\/JCM.02574-12","article-title":"Longitudinal analyses of gut mucosal microbiotas in ulcerative colitis in relation to patient age and disease severity and duration","volume":"51","author":"A Fite","year":"2013","journal-title":"Journal of clinical microbiology"},{"key":"ref58","article-title":"A microbial signature for Crohn\u2019s disease","author":"V Pascal","year":"2017","journal-title":"Gut"},{"issue":"1","key":"ref59","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/s13073-016-0331-y","article-title":"Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease","volume":"8","author":"KA Shaw","year":"2016","journal-title":"Genome medicine"},{"issue":"5","key":"ref60","doi-asserted-by":"crossref","first-page":"610","DOI":"10.1136\/gut.2006.111872","article-title":"The role of Escherichia coli in inflammatory bowel disease","volume":"56","author":"JM Rhodes","year":"2007","journal-title":"Gut"},{"issue":"10","key":"ref61","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":"3","key":"ref62","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.immuni.2011.03.008","article-title":"Experimental inflammatory bowel disease: insights into the host-microbiota dialog","volume":"34","author":"M Saleh","year":"2011","journal-title":"Immunity"},{"issue":"7","key":"ref63","doi-asserted-by":"crossref","first-page":"e41122","DOI":"10.1371\/journal.pone.0041122","article-title":"Multi-criteria optimization of regulation in metabolic networks","volume":"7","author":"C Higuera","year":"2012","journal-title":"PLoS one"},{"key":"ref64","first-page":"1217405","article-title":"Evolutionary trade-offs, Pareto optimality, and the geometry of phenotype space","author":"O Shoval","year":"2012","journal-title":"Science"},{"issue":"2","key":"ref65","doi-asserted-by":"crossref","first-page":"311","DOI":"10.3390\/metabo5020311","article-title":"Metabolism at evolutionary optimal States","volume":"5","author":"I Rabbers","year":"2015","journal-title":"Metabolites"},{"issue":"2","key":"ref66","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1038\/nrmicro821","article-title":"Bacterial biofilms: from the natural environment to infectious diseases","volume":"2","author":"L Hall-Stoodley","year":"2004","journal-title":"Nature reviews microbiology"},{"issue":"2","key":"ref67","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/s002480000057","article-title":"Spatial organization of microbial biofilm communities","volume":"40","author":"T Tolker-Nielsen","year":"2000","journal-title":"Microbial ecology"},{"issue":"10","key":"ref68","doi-asserted-by":"crossref","first-page":"913","DOI":"10.1002\/bies.201300073","article-title":"Intestinal colonization: how key microbial players become established in this dynamic process","volume":"35","author":"S El Aidy","year":"2013","journal-title":"Bioessays"},{"issue":"5","key":"ref69","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":"1","key":"ref70","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":"2017","journal-title":"Environmental microbiology"},{"issue":"3","key":"ref71","doi-asserted-by":"crossref","first-page":"e00209","DOI":"10.1128\/mSystems.00209-17","article-title":"From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota","volume":"3","author":"E Bauer","year":"2018","journal-title":"MSystems"},{"issue":"1","key":"ref72","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1186\/s40168-017-0299-x","article-title":"More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes","volume":"5","author":"KC van der Ark","year":"2017","journal-title":"Microbiome"},{"issue":"5","key":"ref73","doi-asserted-by":"crossref","first-page":"e1005544","DOI":"10.1371\/journal.pcbi.1005544","article-title":"BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities","volume":"13","author":"E Bauer","year":"2017","journal-title":"PLoS computational biology"},{"issue":"1","key":"ref74","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1186\/s12859-016-1230-3","article-title":"MMinte: an application for predicting metabolic interactions among the microbial species in a community","volume":"17","author":"H Mendes-Soares","year":"2016","journal-title":"BMC bioinformatics"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"2532","DOI":"10.1038\/srep02532","article-title":"Understanding the interactions between bacteria in the human gut through metabolic modeling","volume":"3","author":"S Shoaie","year":"2013","journal-title":"Scientific reports"},{"key":"ref76","first-page":"1","article-title":"Gut microbiota functions: metabolism of nutrients and other food components","author":"I Rowland","year":"2017","journal-title":"European journal of nutrition"},{"key":"ref77","first-page":"1","article-title":"Advances in Microbiology, Infectious Diseases and Public Health","author":"M Mikelsaar","year":"2016"},{"issue":"1","key":"ref78","doi-asserted-by":"crossref","first-page":"e0146162","DOI":"10.1371\/journal.pone.0146162","article-title":"Pglyrp-regulated gut microflora Prevotella falsenii, Parabacteroides distasonis and Bacteroides eggerthii enhance and Alistipes finegoldii attenuates colitis in mice","volume":"11","author":"R Dziarski","year":"2016","journal-title":"PloS one"},{"issue":"24","key":"ref79","doi-asserted-by":"crossref","first-page":"4137","DOI":"10.1042\/BCJ20160756","article-title":"Omics of bifidobacteria: research and insights into their health-promoting activities","volume":"474","author":"F Bottacini","year":"2017","journal-title":"Biochemical Journal"},{"issue":"6","key":"ref80","doi-asserted-by":"crossref","first-page":"3060","DOI":"10.1128\/AEM.71.6.3060-3067.2005","article-title":"Survival of probiotic lactobacilli in acidic environments is enhanced in the presence of metabolizable sugars","volume":"71","author":"B Corcoran","year":"2005","journal-title":"Applied and environmental microbiology"},{"issue":"4","key":"ref81","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1016\/j.chom.2016.09.001","article-title":"Stable engraftment of Bifidobacterium longum AH1206 in the human gut depends on individualized features of the resident microbiome","volume":"20","author":"MX Maldonado-G\u00f3mez","year":"2016","journal-title":"Cell host & microbe"},{"issue":"4","key":"ref82","doi-asserted-by":"crossref","first-page":"1366","DOI":"10.1111\/1462-2920.13659","article-title":"Microbial nutrient niches in the gut","volume":"19","author":"FC Pereira","year":"2017","journal-title":"Environmental microbiology"},{"issue":"2","key":"ref83","doi-asserted-by":"crossref","first-page":"e0171744","DOI":"10.1371\/journal.pone.0171744","article-title":"A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems","volume":"12","author":"M Budinich","year":"2017","journal-title":"PloS one"},{"issue":"1","key":"ref84","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1186\/s12918-017-0430-4","article-title":"Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism","volume":"11","author":"MJ Van Hoek","year":"2017","journal-title":"BMC systems biology"},{"issue":"1","key":"ref85","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1186\/1752-0509-5-167","article-title":"A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities","volume":"5","author":"E Tzamali","year":"2011","journal-title":"BMC systems biology"},{"key":"ref86","doi-asserted-by":"crossref","unstructured":"Requena T, Martinez-Cuesta MC, Pel\u00e1ez C. Diet and microbiota linked in health and disease. Food &amp; Function. 2018;.","DOI":"10.1039\/C7FO01820G"},{"issue":"2","key":"ref87","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1111\/apt.13248","article-title":"dietary fibre\u2013microbiota interactions","volume":"42","author":"HL Simpson","year":"2015","journal-title":"Alimentary pharmacology & therapeutics"},{"issue":"2","key":"ref88","doi-asserted-by":"crossref","first-page":"103","DOI":"10.3920\/BM2011.0003","article-title":"Intestinal health functions of colonic microbial metabolites: a review","volume":"2","author":"R Havenaar","year":"2011","journal-title":"Beneficial microbes"},{"issue":"12","key":"ref89","doi-asserted-by":"crossref","first-page":"1348","DOI":"10.3390\/nu9121348","article-title":"Short Chain Fatty Acids in the Colon and Peripheral Tissues: A Focus on Butyrate, Colon Cancer, Obesity and Insulin Resistance","volume":"9","author":"SM McNabney","year":"2017","journal-title":"Nutrients"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1006558","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2018,11,9]],"date-time":"2018-11-09T00:00:00Z","timestamp":1541721600000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006558","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,11]],"date-time":"2024-07-11T22:21:06Z","timestamp":1720736466000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1006558"}},"subtitle":[],"editor":[{"given":"Vassily","family":"Hatzimanikatis","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,10,30]]},"references-count":89,"journal-issue":{"issue":"10","published-online":{"date-parts":[[2018,10,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1006558","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pcbi.1006558","asserted-by":"object"}]},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,10,30]]}}}