{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:21:03Z","timestamp":1787008863563,"version":"build-2736575974"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2017,6,26]],"date-time":"2017-06-26T00:00:00Z","timestamp":1498435200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The inflammatory intestinal disorder Crohn's disease (CD) has become a health challenge worldwide. The gut microbiota closely interacts with the host immune system, but its functional impact in CD is unclear. Except for studies on a small number of CD patients, analyses of the gut microbiota in CD have used 16S rDNA amplicon sequencing. Here we employed metagenomic shotgun sequencing to provide a detailed characterization of the compositional and functional features of the CD microbiota, comprising also unannotated bacteria, and investigated its modulation by exclusive enteral nutrition. Based on signature taxa, CD microbiotas clustered into 2 distinct metacommunities, indicating individual variability in CD microbiome structure. Metacommunity-specific functional shifts in CD showed enrichment in producers of the pro-inflammatory hexa-acylated lipopolysaccharide variant and a reduction in the potential to synthesize short-chain fatty acids. Disruption of ecological networks was evident in CD, coupled with reduction in growth rates of many bacterial species. Short-term exclusive enteral nutrition elicited limited impact on the overall composition of the CD microbiota, although functional changes occurred following treatment. The microbiotas in CD patients can be stratified into 2 distinct metacommunities, with the most severely perturbed metacommunity exhibiting functional potentials that deviate markedly from that of the healthy individuals, with possible implication in relation to CD pathogenesis.<\/jats:p>","DOI":"10.1093\/gigascience\/gix050","type":"journal-article","created":{"date-parts":[[2017,6,26]],"date-time":"2017-06-26T00:17:05Z","timestamp":1498436225000},"source":"Crossref","is-referenced-by-count":94,"title":["Two distinct metacommunities characterize the gut microbiota in Crohn's disease patients"],"prefix":"10.1093","volume":"6","author":[{"given":"Qing","family":"He","sequence":"first","affiliation":[{"name":"1Department of Gastroenterology, The Sixth Affiliated Hospital of The Sun Yat-sen University, Guangzhou 510610, China"},{"name":"2Department of Nutrition, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510610, China"},{"name":"3Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510610, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Gao","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuye","family":"Jie","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinlei","family":"Yu","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Janne Marie","family":"Laursen","sequence":"additional","affiliation":[{"name":"6Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Xiao","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Li","sequence":"additional","affiliation":[{"name":"1Department of Gastroenterology, The Sixth Affiliated Hospital of The Sun Yat-sen University, Guangzhou 510610, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingling","family":"Li","sequence":"additional","affiliation":[{"name":"2Department of Nutrition, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510610, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faming","family":"Zhang","sequence":"additional","affiliation":[{"name":"7Digestive Endoscopy and Medical Center for Digestive Diseases, the Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu Province, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiang","family":"Feng","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"8Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaoping","family":"Li","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinghong","family":"Yu","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chuan","family":"Liu","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Lan","sequence":"additional","affiliation":[{"name":"1Department of Gastroenterology, The Sixth Affiliated Hospital of The Sun Yat-sen University, Guangzhou 510610, China"},{"name":"3Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510610, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ting","family":"Yan","sequence":"additional","affiliation":[{"name":"2Department of Nutrition, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou 510610, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Liu","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xun","family":"Xu","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huanming","family":"Yang","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"9James D. Watson Institute of Genome Sciences, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jian","family":"Wang","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"9James D. Watson Institute of Genome Sciences, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lise","family":"Madsen","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"10Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark"},{"name":"11National Institute of Nutrition and Seafood Research, Bergen, Norway"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Susanne","family":"Brix","sequence":"additional","affiliation":[{"name":"6Department of Biotechnology and Biomedicine, Technical University of Denmark (DTU), Kongens Lyngby, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianping","family":"Wang","sequence":"additional","affiliation":[{"name":"1Department of Gastroenterology, The Sixth Affiliated Hospital of The Sun Yat-sen University, Guangzhou 510610, China"},{"name":"3Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, the Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510610, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karsten","family":"Kristiansen","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"10Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Universitetsparken 13, 2100 Copenhagen, Denmark"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huijue","family":"Jia","sequence":"additional","affiliation":[{"name":"4BGI-Shenzhen, Shenzhen 518083, China"},{"name":"5China National Genebank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China"},{"name":"12Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen 518083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,6,26]]},"reference":[{"key":"2024111706562753900_bib1","article-title":"Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease","author":"Imhann","year":"2016","journal-title":"Gut"},{"key":"2024111706562753900_bib2","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1097\/MOG.0b013e3280105a38","article-title":"Adherent-invasive Escherichia coli and Crohn's disease","volume":"23","author":"Barnich","year":"2007","journal-title":"Curr Opin Gastroenterol"},{"key":"2024111706562753900_bib3","doi-asserted-by":"crossref","first-page":"521","DOI":"10.1155\/2000\/798305","article-title":"Causation of Crohn's disease by Mycobacterium avium subspecies paratuberculosis","volume":"14","author":"Hermon-Taylor","year":"2000","journal-title":"Can J Gastroenterol"},{"key":"2024111706562753900_bib4","doi-asserted-by":"crossref","first-page":"173","DOI":"10.2147\/CEG.S33858","article-title":"Gut bacterial profile in patients newly diagnosed with treatment-naive Crohn's disease","volume":"5","author":"Ricanek","year":"2012","journal-title":"Clin Exp Gastroenterol"},{"key":"2024111706562753900_bib5","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's disease","volume":"15","author":"Gevers","year":"2014","journal-title":"Cell Host Microbe"},{"key":"2024111706562753900_bib6","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":"Morgan","year":"2012","journal-title":"Genome Biol"},{"key":"2024111706562753900_bib7","doi-asserted-by":"crossref","first-page":"636785","DOI":"10.1155\/2013\/636785","article-title":"Dominant fecal microbiota in newly diagnosed untreated inflammatory bowel disease patients","volume":"2013","author":"Thorkildsen","year":"2013","journal-title":"Gastroenterol Res Pract"},{"key":"2024111706562753900_bib8","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":"Li","year":"2014","journal-title":"Nat Biotechnol"},{"key":"2024111706562753900_bib9","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.1038\/ajg.2015.357","article-title":"Extensive modulation of the fecal metagenome in children with Crohn's disease during exclusive enteral nutrition","volume":"110","author":"Quince","year":"2015","journal-title":"Am J Gastroenterol"},{"issue":"10080","key":"2024111706562753900_bib10","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.1016\/S0140-6736(16)31711-1","article-title":"Crohn's disease","volume":"389","author":"Torres","year":"2017","journal-title":"Lancet"},{"key":"2024111706562753900_bib11","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1097\/00004836-200110000-00006","article-title":"Side effects of corticosteroid therapy","volume":"33","author":"Buchman","year":"2001","journal-title":"J Clin Gastroenterol"},{"key":"2024111706562753900_bib12","doi-asserted-by":"crossref","first-page":"7652","DOI":"10.3748\/wjg.v19.i43.7652","article-title":"Use of exclusive enteral nutrition in adults with Crohn's disease: a review","volume":"19","author":"Wall","year":"2013","journal-title":"World J Gastroenterol"},{"key":"2024111706562753900_bib13","doi-asserted-by":"crossref","first-page":"6809","DOI":"10.3748\/wjg.v21.i22.6809","article-title":"Exclusive enteral nutrition in children with Crohn's disease","volume":"21","author":"Day","year":"2015","journal-title":"World J Gastroenterol"},{"key":"2024111706562753900_bib14","doi-asserted-by":"crossref","first-page":"e71","DOI":"10.1038\/ctg.2014.21","article-title":"Effect of exclusive enteral nutrition on the microbiota of children with newly diagnosed Crohn's disease","volume":"6","author":"Kaakoush","year":"2015","journal-title":"Clin Translat Gastroenterol"},{"key":"2024111706562753900_bib15","article-title":"The gut microbiome in Crohn's disease and modulation by exclusive enteral nutrition","author":"He Q","year":"2016","journal-title":"In. EMBL-EBI"},{"key":"2024111706562753900_bib16","doi-asserted-by":"crossref","first-page":"822","DOI":"10.1038\/nbt.2939","article-title":"Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes","volume":"32","author":"Nielsen","year":"2014","journal-title":"Nat Biotechnol"},{"key":"2024111706562753900_bib17","doi-asserted-by":"crossref","first-page":"e30126","DOI":"10.1371\/journal.pone.0030126","article-title":"Dirichlet multinomial mixtures: generative models for microbial metagenomics","volume":"7","author":"Holmes","year":"2012","journal-title":"PLoS One"},{"key":"2024111706562753900_bib18","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":"Segata","year":"2011","journal-title":"Genome Biol"},{"key":"2024111706562753900_bib19","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1126\/science.1198469","article-title":"Induction of colonic regulatory T cells by indigenous Clostridium species","volume":"331","author":"Atarashi","year":"2011","journal-title":"Science"},{"key":"2024111706562753900_bib20","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1146\/annurev.biochem.71.110601.135414","article-title":"Lipopolysaccharide endotoxins","volume":"71","author":"Raetz","year":"2002","journal-title":"Annu Rev Biochem"},{"key":"2024111706562753900_bib21","doi-asserted-by":"crossref","first-page":"1191","DOI":"10.1038\/nature07830","article-title":"The structural basis of lipopolysaccharide recognition by the TLR4\u2013MD-2 complex","volume":"458","author":"Park","year":"2009","journal-title":"Nature"},{"key":"2024111706562753900_bib22","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.jaci.2014.09.036","article-title":"Metagenomic heterogeneity explains dual immune effects of endotoxins","volume":"135","author":"Brix","year":"2015","journal-title":"J Allergy Clin Immunol"},{"key":"2024111706562753900_bib23","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1097\/MCO.0000000000000025","article-title":"Biological significance of short-chain fatty acid metabolism by the intestinal microbiome","volume":"17","author":"Puertollano","year":"2014","journal-title":"Curr Opin Clin Nutr Metab Care"},{"key":"2024111706562753900_bib24","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":"Korem","year":"2015","journal-title":"Science"},{"key":"2024111706562753900_bib25","doi-asserted-by":"crossref","first-page":"446","DOI":"10.1038\/nature12721","article-title":"Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells","volume":"504","author":"Furusawa","year":"2013","journal-title":"Nature"},{"key":"2024111706562753900_bib26","doi-asserted-by":"crossref","first-page":"128","DOI":"10.1016\/j.immuni.2013.12.007","article-title":"Activation of Gpr109a, receptor for niacin and the commensal metabolite butyrate, suppresses colonic inflammation and carcinogenesis","volume":"40","author":"Singh","year":"2014","journal-title":"Immunity"},{"key":"2024111706562753900_bib27","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1016\/j.ijmm.2015.10.002","article-title":"Distinct inflammatory and cytopathic characteristics of Escherichia coli isolates from inflammatory bowel disease patients","volume":"305","author":"Jensen","year":"2015","journal-title":"Int J Med Microbiol"},{"key":"2024111706562753900_bib28","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nri2515","article-title":"The gut microbiota shapes intestinal immune responses during health and disease","volume":"9","author":"Round","year":"2009","journal-title":"Nat Rev Immunol"},{"key":"2024111706562753900_bib29","first-page":"5A","article-title":"Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: Report of a Working Party of the 2005 Montreal World Congress of Gastroenterology","volume":"19","author":"Silverberg","year":"2005","journal-title":"Can J Gastroenterol Hepatol"},{"key":"2024111706562753900_bib30","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":"Qin","year":"2012","journal-title":"Nature"},{"key":"2024111706562753900_bib31","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/2047-217X-1-18","article-title":"SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler","volume":"1","author":"Luo","year":"2012","journal-title":"Gigascience"},{"key":"2024111706562753900_bib32","doi-asserted-by":"crossref","first-page":"2685","DOI":"10.1073\/pnas.0406811102","article-title":"Uncovering transcriptional regulation of metabolism by using metabolic network topology","volume":"102","author":"Patil","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024111706562753900_bib33","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1038\/nature11319","article-title":"Gut microbiota composition correlates with diet and health in the elderly","volume":"488","author":"Claesson","year":"2012","journal-title":"Nature"},{"key":"2024111706562753900_bib34","doi-asserted-by":"crossref","first-page":"541","DOI":"10.1038\/nature12506","article-title":"Richness of human gut microbiome correlates with metabolic markers","volume":"500","author":"Le Chatelier","year":"2013","journal-title":"Nature"},{"key":"2024111706562753900_bib35","doi-asserted-by":"crossref","first-page":"19430","DOI":"10.1073\/pnas.0609333103","article-title":"Multivariate regression analysis of distance matrices for testing associations between gene expression patterns and related variables","volume":"103","author":"Zapala","year":"2006","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2024111706562753900_bib36"},{"key":"2024111706562753900_bib37","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":"Friedman","year":"2012","journal-title":"PLoS Comput Biol"},{"key":"2024111706562753900_bib38","doi-asserted-by":"crossref","unstructured":"He Q GY, Jie Z, Yu X, Supporting data for \u201cTwo distinct metacommunities characterize the gut microbiota in Crohn's disease patients.\u201d \u00a0Gigascience Database \u00a02017. 10.5524\/100317.","DOI":"10.1093\/gigascience\/gix050"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/6\/7\/gix050\/60712113\/gigascience_6_7_gix050.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/6\/7\/gix050\/60712113\/gigascience_6_7_gix050.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,17]],"date-time":"2024-11-17T01:57:26Z","timestamp":1731808646000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/gix050\/3888814"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,6,26]]},"references-count":38,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2017,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gigascience\/gix050","relation":{},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,7]]},"published":{"date-parts":[[2017,6,26]]},"article-number":"gix050"}}