{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T14:11:31Z","timestamp":1793283091157,"version":"4.5.0"},"reference-count":74,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2020,7,7]],"date-time":"2020-07-07T00:00:00Z","timestamp":1594080000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007658","name":"Crohn's and Colitis Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100007658","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","cmghjournal.org","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cellular and Molecular Gastroenterology and Hepatology"],"published-print":{"date-parts":[[2021]]},"DOI":"10.1016\/j.jcmgh.2020.07.003","type":"journal-article","created":{"date-parts":[[2020,7,10]],"date-time":"2020-07-10T11:51:54Z","timestamp":1594381914000},"page":"77-98","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":63,"title":["Muc2 Mucin and Nonmucin Microbiota Confer Distinct Innate Host Defense in Disease Susceptibility and Colonic Injury"],"prefix":"10.1016","volume":"11","author":[{"given":"Aralia","family":"Leon-Coria","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Manish","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6415-2797","authenticated-orcid":false,"given":"Matthew","family":"Workentine","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"France","family":"Moreau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Surette","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kris","family":"Chadee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jcmgh.2020.07.003_bib1","doi-asserted-by":"crossref","first-page":"688","DOI":"10.1038\/sj.embor.7400731","article-title":"The gut flora as a forgotten organ","volume":"7","author":"O\u2019Hara","year":"2006","journal-title":"EMBO Rep"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib2","doi-asserted-by":"crossref","first-page":"8787","DOI":"10.3748\/wjg.v21.i29.8787","article-title":"Role of the normal gut microbiota","volume":"21","author":"Jandhyala","year":"2015","journal-title":"World J Gastroenterol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib3","doi-asserted-by":"crossref","first-page":"122","DOI":"10.1016\/j.clim.2015.05.014","article-title":"Immune\u2013microbiota interactions in health and disease","volume":"159","author":"Palm","year":"2015","journal-title":"Clin Immunol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib4","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1038\/nrgastro.2014.156","article-title":"Decade in review\u2014gut microbiota: The gut microbiota era marches on","volume":"11","author":"Guarner","year":"2014","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib5","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1111\/cei.12474","article-title":"Immune homeostasis, dysbiosis and therapeutic modulation of the gut microbiota","volume":"179","author":"Peterson","year":"2015","journal-title":"Clin Exp Immunol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib6","doi-asserted-by":"crossref","first-page":"E2930","DOI":"10.1073\/pnas.1423854112","article-title":"Identifying personal microbiomes using metagenomic codes","volume":"112","author":"Franzosa","year":"2015","journal-title":"Proc Natl Acad Sci"},{"issue":"7402","key":"10.1016\/j.jcmgh.2020.07.003_bib7","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1038\/nature11234","article-title":"Structure, function and diversity of the healthy human microbiome","volume":"486","year":"2012","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib8","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1136\/gutjnl-2015-309990","article-title":"The gut microbiota and host health: a new clinical frontier","volume":"65","author":"Marchesi","year":"2016","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib9","first-page":"26191","article-title":"Dysbiosis of the gut microbiota in disease","volume":"26","author":"Carding","year":"2015","journal-title":"Microb Ecol Health Dis"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib10","first-page":"1","article-title":"The central role of the gut microbiota in chronic inflammatory diseases","volume":"1","author":"Ferreira","year":"2014","journal-title":"J\u00a0Immunol Res"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib11","doi-asserted-by":"crossref","first-page":"13780","DOI":"10.1073\/pnas.0706625104","article-title":"Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases","volume":"104","author":"Frank","year":"2007","journal-title":"Proc Natl Acad Sci"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib12","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1136\/gut.2003.025403","article-title":"Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease","volume":"53","author":"Ott","year":"2004","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib13","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1038\/nrgastro.2013.35","article-title":"The gastrointestinal mucus system in health and disease","volume":"10","author":"Johansson","year":"2013","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib14","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1136\/gutjnl-2012-303207","article-title":"Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis","volume":"63","author":"Johansson","year":"2014","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib15","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1136\/gutjnl-2017-314903","article-title":"Adherent-invasive Escherichia coli in inflammatory bowel disease","volume":"67","author":"Palmela","year":"2018","journal-title":"Gut"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib16","doi-asserted-by":"crossref","first-page":"2124","DOI":"10.1097\/MIB.0000000000000117","article-title":"Mucus layers in inflammatory bowel disease","volume":"20","author":"Johansson","year":"2014","journal-title":"Inflamm Bowel Dis"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib17","doi-asserted-by":"crossref","first-page":"G34","DOI":"10.1152\/ajpgi.00298.2016","article-title":"The probiotic mixture VSL#3 reduces colonic inflammation and improves intestinal barrier function in Muc2 mucin deficient mice","volume":"312","author":"Kumar","year":"2017","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib18","doi-asserted-by":"crossref","first-page":"8543","DOI":"10.1074\/jbc.M117.789305","article-title":"Intestinal mucin activates human dendritic cells and IL-8 production in a glycan-specific manner","volume":"293","author":"Melo-Gonzalez","year":"2018","journal-title":"J\u00a0Bio Chem"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib19","doi-asserted-by":"crossref","first-page":"928","DOI":"10.1016\/j.cell.2017.01.022","article-title":"Mining the human gut microbiota for immunomodulatory organisms","volume":"168","author":"Geva-Zatorsky","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib20","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1016\/j.ajpath.2012.11.035","article-title":"Entamoeba histolytica exacerbates epithelial tight junction permeability and proinflammatory responses in Muc2\u2212\/\u2212 mice","volume":"182","author":"Kissoon-Singh","year":"2013","journal-title":"Am J Pathol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib21","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1000902","article-title":"Muc2 Protects against lethal infectious colitis by disassociating pathogenic and commensal bacteria from the colonic mucosa","volume":"6","author":"Bergstrom","year":"2010","journal-title":"PLoS Pathog"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib22","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1053\/j.gastro.2006.04.020","article-title":"Muc2-deficient mice spontaneously develop colitis, indicating that MUC2 is critical for colonic protection","volume":"131","author":"Van der Sluis","year":"2006","journal-title":"Gastroenterology"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib23","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0017996","article-title":"Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression","volume":"6","author":"Reikvam","year":"2011","journal-title":"PLoS One"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib24","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1016\/S0002-9440(10)62264-X","article-title":"Interferon-gamma and tumor necrosis factor-alpha synergize to induce intestinal epithelial barrier dysfunction by up-regulating myosin light chain kinase expression","volume":"166","author":"Wang","year":"2005","journal-title":"Am J Pathol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib25","doi-asserted-by":"crossref","first-page":"684","DOI":"10.1038\/embor.2012.96","article-title":"Innate immune signalling at the intestinal epithelium in homeostasis and disease","volume":"13","author":"Pott","year":"2012","journal-title":"EMBO Rep"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib26","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1126\/science.1223813","article-title":"Host-gut microbiota metabolic interactions","volume":"336","author":"Nicholson","year":"2012","journal-title":"Science"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib27","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1038\/nature18848","article-title":"The microbiota in adaptive immune homeostasis and disease","volume":"535","author":"Honda","year":"2016","journal-title":"Nature"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib28","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1097\/MIB.0000000000000319","article-title":"IL-22-STAT3 pathway plays a key role in the maintenance of ileal homeostasis in mice lacking secreted mucus barrier","volume":"21","author":"Sovran","year":"2015","journal-title":"Inflamm Bowel Dis"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib29","doi-asserted-by":"crossref","first-page":"1883","DOI":"10.1097\/MIB.0000000000000422","article-title":"Ecobiotherapy rich in firmicutes decreases susceptibility to colitis in a humanized gnotobiotic mouse model","volume":"21","author":"Natividad","year":"2015","journal-title":"Inflamm Bowel Dis"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib30","doi-asserted-by":"crossref","first-page":"19967","DOI":"10.1073\/pnas.1014669107","article-title":"MyD88 signaling in nonhematopoietic cells protects mice against induced colitis by regulating specific EGF receptor ligands","volume":"107","author":"Brandl","year":"2010","journal-title":"Proc Natl Acad Sci"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib31","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0130750","article-title":"CD103+CD11b+ dendritic cells induce Th17 T Cells in Muc2-deficient mice with extensively spread colitis","volume":"10","author":"Wenzel","year":"2015","journal-title":"PLoS One"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib32","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib33","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1111\/j.1365-2982.2012.01921.x","article-title":"Intestinal barrier function in health and gastrointestinal disease","volume":"24","author":"Camilleri","year":"2012","journal-title":"Neurogastroenterol Motil"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib34","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/nrgastro.2014.201","article-title":"IBD pathogenesis in 2014: Molecular pathways controlling barrier function in IBD","volume":"12","author":"Atreya","year":"2014","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib35","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.chom.2015.04.008","article-title":"An integrative view of microbiome-host interactions in inflammatory bowel diseases","volume":"17","author":"Wlodarska","year":"2015","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib36","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1007\/s00281-014-0454-4","article-title":"The gut microbiota and inflammatory bowel disease","volume":"37","author":"Matsuoka","year":"2015","journal-title":"Semin Immunopathol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib37","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/ni.3332","article-title":"Complementarity and redundancy of IL-22-producing innate lymphoid cells","volume":"17","author":"Rankin","year":"2016","journal-title":"Nat Immunol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib38","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1016\/j.cell.2015.08.061","article-title":"An IL-23R\/IL-22 circuit regulates epithelial serum amyloid A to promote local effector Th17 responses","volume":"163","author":"Sano","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib39","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.3389\/fimmu.2017.01296","article-title":"Innate lymphoid cells in intestinal inflammation","volume":"8","author":"Geremia","year":"2017","journal-title":"Front Immunol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib40","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.ppat.1003698","article-title":"IL-22 mediates goblet cell hyperplasia and worm expulsion in intestinal helminth infection","volume":"9","author":"Turner","year":"2013","journal-title":"PLoS Pathog"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib41","doi-asserted-by":"crossref","first-page":"411","DOI":"10.4161\/gmic.29330","article-title":"The interplay between the gut microbiota and the immune system","volume":"5","author":"Geuking","year":"2014","journal-title":"Gut Microbes"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib42","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/j.anaerobe.2013.03.011","article-title":"Diet, the human gut microbiota, and IBD","volume":"24","author":"Wu","year":"2013","journal-title":"Anaerobe"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib43","doi-asserted-by":"crossref","first-page":"3098","DOI":"10.1002\/eji.201343740","article-title":"Dendritic cell subsets in the intestinal lamina propria: ontogeny and function","volume":"43","author":"Persson","year":"2013","journal-title":"Eur J Immunol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib44","doi-asserted-by":"crossref","first-page":"412","DOI":"10.1016\/j.it.2011.06.003","article-title":"Intestinal CD103+ dendritic cells: master regulators of tolerance?","volume":"32","author":"Scott","year":"2011","journal-title":"Trends Immunol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib45","first-page":"h6420","article-title":"Antibiotic resistance in Enterobacteriaceae: mechanisms and clinical implications","volume":"351","author":"Iredell","year":"2015","journal-title":"BMJ"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib46","first-page":"1","volume":"4","year":"2015","journal-title":"Investigation of Enterobacteriaceae"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib47","doi-asserted-by":"crossref","first-page":"826","DOI":"10.1097\/MIB.0000000000000688","article-title":"Identification of commensal species positively correlated with early stress responses to a compromised mucus barrier","volume":"22","author":"Sovran","year":"2016","journal-title":"Inflamm Bowel Dis"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib48","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3390\/microorganisms6030075","article-title":"Akkermansia muciniphila in the human gastrointestinal tract\u202f: when, where, and how?","volume":"6","author":"Geerlings","year":"2018","journal-title":"Microorganisms"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib49","doi-asserted-by":"crossref","first-page":"S21","DOI":"10.1017\/S0007114512005235","article-title":"Linking the gut microbiota to human health","volume":"109","author":"Robles Alonso","year":"2013","journal-title":"Br J Nutr"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib50","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1203\/PDR.0b013e3181827c0f","article-title":"The probiotic Lactobacillus GG may augment intestinal host defense by regulating apoptosis and promoting cytoprotective responses in the developing murine gut","volume":"64","author":"Lin","year":"2008","journal-title":"Pediatr Res"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib51","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1016\/j.chom.2015.10.007","article-title":"Normalization of host intestinal mucus layers requires long-term microbial colonization","volume":"18","author":"Johansson","year":"2015","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib52","doi-asserted-by":"crossref","first-page":"1503","DOI":"10.1016\/j.chembiol.2012.10.022","article-title":"Molecular basis of in-vivo biofilm formation by bacterial pathogens","volume":"19","author":"Joo","year":"2013","journal-title":"Chem Biol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib53","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib54","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE\u202f: highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat Methods"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib55","doi-asserted-by":"crossref","first-page":"3476","DOI":"10.1093\/bioinformatics\/btv401","article-title":"Error filtering , pair assembly and error correction for next-generation sequencing reads","volume":"31","author":"Edgar","year":"2015","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib56","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Na\u0131ve bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl Environ Microbiol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib57","doi-asserted-by":"crossref","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","article-title":"Snakemake \u2014 a scalable bioinformatics workflow engine","volume":"28","author":"K\u00f6ster","year":"2012","journal-title":"Bioinformatics"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib58","series-title":"R\u202f: a language and environment for statistical computing","year":"2011"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib59","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0061217","article-title":"Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib60","author":"Oksanen","year":"2015","journal-title":"Package \u2018vegan\u2019"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib61","first-page":"379","volume":"27","author":"Shannon","year":"1948","journal-title":"A\u00a0mathematical theory of communication"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib62","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate\u202f: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J\u00a0R Stat Soc Ser B"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib63","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib64","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1003531","article-title":"Waste not, want not: why rarefying microbiome data is inadmissible","volume":"10","author":"McMurdie","year":"2014","journal-title":"PLOS Comput Biol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib65","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat Methhods"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib66","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis\u202f: A knowledge-based approach for interpreting genome-wide","volume":"102","author":"Subramanian","year":"2005","journal-title":"Pro Nat Aca Sci"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib67","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler\u202f: an R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"Omi A J Integr Biol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib68","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1513\/AnnalsATS.201310-351OC","article-title":"The loss of topography in the microbial communities of the upper respiratory tract in the elderly","volume":"11","author":"Whelan","year":"2014","journal-title":"Ann Am Thorac Soc"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib69","doi-asserted-by":"crossref","first-page":"3846","DOI":"10.1128\/AEM.02772-10","article-title":"Generation of multimillion-sequence 16S rRNA gene libraries from complex microbial communities by assembling paired-end Illumina reads","volume":"77","author":"Bartram","year":"2011","journal-title":"Appl Environ Microbiol"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib70","first-page":"229","article-title":"Preservation of mucus in histological sections, immunostaining of mucins in fixed tissue, and localization of bacteria with FISH","volume":"842","author":"Johansson","year":"2012"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib71","doi-asserted-by":"crossref","first-page":"360","DOI":"10.1186\/1756-0500-6-360","article-title":"Dextran sodium sulfate inhibits the activities of both polymerase and reverse transcriptase: Lithium chloride purification, a rapid and efficient technique to purify RNA","volume":"6","author":"Viennois","year":"2013","journal-title":"BMC Res Notes"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib72","doi-asserted-by":"crossref","first-page":"2307","DOI":"10.1038\/nprot.2007.315","article-title":"Isolation and subsequent analysis of murine lamina propria mononuclear cells from colonic tissue","volume":"2","author":"Weigmann","year":"2007","journal-title":"Nat Protoc"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib73","doi-asserted-by":"crossref","first-page":"386","DOI":"10.1006\/meth.2001.1261","article-title":"An overview of real-time quantitative PCR: applications to quantify cytokine gene expression","volume":"25","author":"Giulietti","year":"2001","journal-title":"Methods"},{"key":"10.1016\/j.jcmgh.2020.07.003_bib74","doi-asserted-by":"crossref","first-page":"1152","DOI":"10.1038\/labinvest.2010.91","article-title":"Enterohemorrhagic E.\u00a0coli alters murine intestinal epithelial tight junction protein expression and barrier function in Shiga toxin independent manner","volume":"90","author":"Roxas","year":"2010","journal-title":"Lab Invest"}],"container-title":["Cellular and Molecular Gastroenterology and Hepatology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352345X20301090?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2352345X20301090?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T18:27:28Z","timestamp":1762453648000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2352345X20301090"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021]]},"references-count":74,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021]]}},"alternative-id":["S2352345X20301090"],"URL":"https:\/\/doi.org\/10.1016\/j.jcmgh.2020.07.003","relation":{},"ISSN":["2352-345X"],"issn-type":[{"value":"2352-345X","type":"print"}],"subject":[],"published":{"date-parts":[[2021]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Muc2 Mucin and Nonmucin Microbiota Confer Distinct Innate Host Defense in Disease Susceptibility and Colonic Injury","name":"articletitle","label":"Article Title"},{"value":"Cellular and Molecular Gastroenterology and Hepatology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jcmgh.2020.07.003","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Authors. Published by Elsevier Inc. on behalf of the AGA Institute.","name":"copyright","label":"Copyright"}]}}