{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T02:32:26Z","timestamp":1786933946332,"version":"build-2736575974"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,7,29]],"date-time":"2024-07-29T00:00:00Z","timestamp":1722211200000},"content-version":"vor","delay-in-days":210,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Inflammatory bowel disease (IBD), including Crohn\u2019s disease (CD) and ulcerative colitis (UC), is associated with a loss or an imbalance of host\u2013microorganism interactions. However, such interactions at protein levels remain largely unknown. Here, we applied a depletion-assisted metaproteomics approach to obtain in-depth host\u2013microbiome association networks of IBD, where the core host proteins shifted from those maintaining mucosal homeostasis in controls to those involved in inflammation, proteolysis, and intestinal barrier in IBD. Microbial nodes such as short-chain fatty-acid producer-related host\u2013microbial crosstalk were lost or suppressed by inflammatory proteins in IBD. Guided by protein\u2013protein association networks, we employed proteomics and lipidomics to investigate the effects of UC-related core proteins S100A8, S100A9, and cytokines (IL-1\u03b2, IL-6, and TNF-\u03b1) on gut bacteria. These proteins suppressed purine nucleotide biosynthesis in stool-derived in vitro communities, which was also reduced in IBD stool samples. Single species study revealed that S100A8, S100A9, and cytokines can synergistically or antagonistically alter gut bacteria intracellular and secreted proteome, with combined S100A8 and S100A9 potently inhibiting beneficial Bifidobacterium adolescentis. Furthermore, these inflammatory proteins only altered the extracellular but not intracellular proteins of Ruminococcus gnavus. Generally, S100A8 induced more significant bacterial proteome changes than S100A9, IL-1\u03b2, IL-6, and TNF-\u03b1 but gut bacteria degrade significantly more S100A8 than S100A9 in the presence of both proteins. Among the investigated species, distinct lipid alterations were only observed in Bacteroides vulgatus treated with combined S100A8, S100A9, and cytokines. These results provided a valuable resource of inflammatory protein-centric host\u2013microbial molecular interactions.<\/jats:p>","DOI":"10.1093\/ismejo\/wrae146","type":"journal-article","created":{"date-parts":[[2024,7,30]],"date-time":"2024-07-30T00:09:10Z","timestamp":1722298150000},"source":"Crossref","is-referenced-by-count":14,"title":["Core microbiome-associated proteins associated with ulcerative colitis interact with cytokines for synergistic or antagonistic effects on gut bacteria"],"prefix":"10.1093","volume":"18","author":[{"given":"Ting","family":"Zhang","sequence":"first","affiliation":[{"name":"Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Meihua East Road, Zhuhai, Guangdong 519000 , China"},{"name":"Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hang","family":"Zhong","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Meihua East Road, Zhuhai, Guangdong 519000 , China"},{"name":"Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lu","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyan","family":"Zhang","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Meihua East Road, Zhuhai, Guangdong 519000 , China"},{"name":"Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kewen","family":"Xue","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Meihua East Road, Zhuhai, Guangdong 519000 , China"},{"name":"Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feixiang","family":"He","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Meihua East Road, Zhuhai, Guangdong 519000 , China"},{"name":"Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingshu","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Panpan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhi","family":"Zhao","sequence":"additional","affiliation":[{"name":"Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Cong","sequence":"additional","affiliation":[{"name":"Department of Endocrinology and Metabolism, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Pang","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Meihua East Road, Zhuhai, Guangdong 519000 , China"},{"name":"Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaofeng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hong","family":"Shan","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Meihua East Road, Zhuhai, Guangdong 519000 , China"},{"name":"Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhixiang","family":"Yan","sequence":"additional","affiliation":[{"name":"Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) , Meihua East Road, Zhuhai, Guangdong 519000 , China"},{"name":"Guangdong-Hong Kong-Macao University Joint Laboratory of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University , Meihua East Road, Zhuhai, Guangdong 519000 , China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2024,7,29]]},"reference":[{"key":"2024082915092139600_ref1","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/s41579-019-0213-6","article-title":"Microbial genes and pathways in inflammatory bowel disease","volume":"17","author":"Schirmer","year":"2019","journal-title":"Nat Rev Microbiol"},{"key":"2024082915092139600_ref2","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1038\/nrgastro.2015.34","article-title":"Epidemiology and risk factors for IBD","volume":"12","author":"Ananthakrishnan","year":"2015","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"2024082915092139600_ref3","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1016\/j.jaci.2019.11.003","article-title":"The microbiome and inflammatory bowel disease","volume":"145","author":"Glassner","year":"2020","journal-title":"J Allergy Clin Immunol"},{"key":"2024082915092139600_ref4","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","article-title":"Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases","volume":"569","author":"Lloyd-Price","year":"2019","journal-title":"Nature"},{"key":"2024082915092139600_ref5","doi-asserted-by":"crossref","first-page":"17004","DOI":"10.1038\/nmicrobiol.2017.4","article-title":"Dynamics of the human gut microbiome in inflammatory bowel disease","volume":"2","author":"Halfvarson","year":"2017","journal-title":"Nat Microbiol"},{"key":"2024082915092139600_ref6","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/s41564-017-0089-z","article-title":"Dynamics of metatranscription in the inflammatory bowel disease gut microbiome","volume":"3","author":"Schirmer","year":"2018","journal-title":"Nat Microbiol"},{"key":"2024082915092139600_ref7","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1186\/s40168-020-00967-x","article-title":"A semi-tryptic peptide centric metaproteomic mining approach and its potential utility in capturing signatures of gut microbial proteolysis","volume":"9","author":"Yan","year":"2021","journal-title":"Microbiome."},{"key":"2024082915092139600_ref8","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1038\/ismej.2008.108","article-title":"Shotgun metaproteomics of the human distal gut microbiota","volume":"3","author":"Verberkmoes","year":"2009","journal-title":"ISME J"},{"key":"2024082915092139600_ref9","doi-asserted-by":"crossref","first-page":"4203","DOI":"10.1021\/ac303053e","article-title":"Metaproteomics: harnessing the power of high performance mass spectrometry to identify the suite of proteins that control metabolic activities in microbial communities","volume":"85","author":"Hettich","year":"2013","journal-title":"Anal Chem"},{"key":"2024082915092139600_ref10","doi-asserted-by":"crossref","first-page":"9407","DOI":"10.1021\/acs.analchem.7b02224","article-title":"Deep metaproteomics approach for the study of human microbiomes","volume":"89","author":"Zhang","year":"2017","journal-title":"Anal Chem"},{"key":"2024082915092139600_ref11","doi-asserted-by":"crossref","first-page":"72","DOI":"10.1186\/s40168-017-0290-6","article-title":"Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life","volume":"5","author":"Xiong","year":"2017","journal-title":"Microbiome"},{"key":"2024082915092139600_ref12","doi-asserted-by":"crossref","first-page":"4982","DOI":"10.1021\/pr100646w","article-title":"Depletion of abundant plasma proteins and limitations of plasma proteomics","volume":"9","author":"Tu","year":"2010","journal-title":"J Proteome Res"},{"key":"2024082915092139600_ref13","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1038\/85686","article-title":"Large-scale analysis of the yeast proteome by multidimensional protein identification technology","volume":"19","author":"Washburn","year":"2001","journal-title":"Nat Biotechnol"},{"key":"2024082915092139600_ref14","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1002\/elps.200800639","article-title":"Liquid-phase-based separation systems for depletion, prefractionation and enrichment of proteins in biological fluids for in-depth proteomics analysis","volume":"30","author":"Jmeian","year":"2009","journal-title":"Electrophoresis"},{"key":"2024082915092139600_ref15","doi-asserted-by":"crossref","first-page":"1573","DOI":"10.1074\/mcp.M113.035170","article-title":"Confetti: a multiprotease map of the HeLa proteome for comprehensive proteomics","volume":"13","author":"Guo","year":"2014","journal-title":"Mol Cell Proteomics"},{"key":"2024082915092139600_ref16","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1038\/nmeth.2250","article-title":"Digestion and depletion of abundant proteins improves proteomic coverage","volume":"10","author":"Fonslow","year":"2013","journal-title":"Nat Methods"},{"key":"2024082915092139600_ref17","doi-asserted-by":"crossref","first-page":"4383","DOI":"10.1021\/acs.analchem.0c03931","article-title":"Simple and sensitive method for deep profiling of host cell proteins in therapeutic antibodies by combining ultra-low trypsin concentration digestion, long chromatographic gradients, and BoxCar mass spectrometry acquisition","volume":"93","author":"Nie","year":"2021","journal-title":"Anal Chem"},{"key":"2024082915092139600_ref18","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1093\/ecco-jcc\/jjw168","article-title":"3rd European evidence-based consensus on the diagnosis and management of Crohn's disease 2016: part 1: diagnosis and medical management","volume":"11","author":"Gomollon","year":"2017","journal-title":"J Crohns Colitis"},{"key":"2024082915092139600_ref19","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1002\/ibd.21048","article-title":"World gastroenterology organization practice guidelines for the diagnosis and management of IBD in 2010","volume":"16","author":"Bernstein","year":"2010","journal-title":"Inflamm Bowel Dis"},{"key":"2024082915092139600_ref20","first-page":"439","article-title":"Development of a Crohn's disease activity index","volume":"70","author":"Best","year":"1976","journal-title":"National Cooperative Crohn's Disease Study Gastroenterology"},{"key":"2024082915092139600_ref21","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1177\/147323000503300111","article-title":"Ulcerative colitis activity index: a useful prognostic factor for predicting ulcerative colitis outcome","volume":"33","author":"Gurel","year":"2005","journal-title":"J Int Med Res"},{"key":"2024082915092139600_ref22","doi-asserted-by":"crossref","first-page":"749","DOI":"10.1136\/gut.2005.082909","article-title":"The Montreal classification of inflammatory bowel disease: controversies, consensus, and implications","volume":"55","author":"Satsangi","year":"2006","journal-title":"Gut"},{"key":"2024082915092139600_ref23","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/s43705-023-00245-5","article-title":"Optimizing ex vivo culture conditions to study human gut microbiome","volume":"3","author":"Tao","year":"2023","journal-title":"ISME Commun"},{"key":"2024082915092139600_ref24","doi-asserted-by":"crossref","first-page":"4146","DOI":"10.1038\/s41467-019-12087-8","article-title":"An in vitro model maintaining taxon-specific functional activities of the gut microbiome","volume":"10","author":"Li","year":"2019","journal-title":"Nat Commun"},{"key":"2024082915092139600_ref25","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1021\/acs.jproteome.8b00716","article-title":"Unipept 4.0: functional analysis of metaproteome data","volume":"18","author":"Gurdeep Singh","year":"2019","journal-title":"J Proteome Res"},{"key":"2024082915092139600_ref26","doi-asserted-by":"crossref","first-page":"e25","DOI":"10.1002\/imt2.25","article-title":"iMetaLab suite: a one-stop toolset for metaproteomics","volume":"1","author":"Li","year":"2022","journal-title":"iMeta"},{"key":"2024082915092139600_ref27","doi-asserted-by":"crossref","DOI":"10.1002\/cpbi.86","article-title":"Using MetaboAnalyst 4.0 for comprehensive and integrative metabolomics data analysis","volume":"68","author":"Chong","year":"2019","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024082915092139600_ref28","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009442","article-title":"Multivariable association discovery in population-scale meta-omics studies","volume":"17","author":"Mallick","year":"2021","journal-title":"PLoS Comput Biol"},{"key":"2024082915092139600_ref29","doi-asserted-by":"crossref","first-page":"e5","DOI":"10.1002\/imt2.5","article-title":"ImageGP: an easy-to-use data visualization web server for scientific researchers","volume":"1","author":"Chen","year":"2022","journal-title":"iMeta"},{"key":"2024082915092139600_ref30","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1111\/jgh.12164","article-title":"Incidence and clinical characteristics of inflammatory bowel disease in a developed region of Guangdong Province, China: a prospective population-based study","volume":"28","author":"Zeng","year":"2013","journal-title":"J Gastroenterol Hepatol"},{"key":"2024082915092139600_ref31","article-title":"The incidence of inflammatory bowel disease in northern China: a prospective population-based study","volume":"9","author":"Yang","year":"2014","journal-title":"PLoS One"},{"key":"2024082915092139600_ref32","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1016\/j.vetmic.2012.08.019","article-title":"The OmpA family of proteins: roles in bacterial pathogenesis and immunity","volume":"163","author":"Confer","year":"2013","journal-title":"Vet Microbiol"},{"key":"2024082915092139600_ref33","doi-asserted-by":"crossref","first-page":"277","DOI":"10.3389\/fimmu.2019.00277","article-title":"Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases","volume":"10","author":"Parada Venegas","year":"2019","journal-title":"Front Immunol"},{"key":"2024082915092139600_ref34","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1038\/s41591-018-0308-z","article-title":"Microbial network disturbances in relapsing refractory Crohn's disease","volume":"25","author":"Yilmaz","year":"2019","journal-title":"Nat Med"},{"key":"2024082915092139600_ref35","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1186\/s40168-018-0603-4","article-title":"A comparative study of the gut microbiota in immune-mediated inflammatory diseases-does a common dysbiosis exist?","volume":"6","author":"Forbes","year":"2018","journal-title":"Microbiome"},{"key":"2024082915092139600_ref36","doi-asserted-by":"crossref","first-page":"631","DOI":"10.1136\/gut.2010.223263","article-title":"Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives","volume":"60","author":"Joossens","year":"2011","journal-title":"Gut"},{"key":"2024082915092139600_ref37","doi-asserted-by":"crossref","DOI":"10.1093\/femsre\/fuad039","article-title":"Faecalibacterium: a bacterial genus with promising human health applications","volume":"47","author":"Martin","year":"2023","journal-title":"FEMS Microbiol Rev"},{"key":"2024082915092139600_ref38","doi-asserted-by":"crossref","first-page":"720","DOI":"10.3945\/jn.108.101675","article-title":"Intestinal inflammation increases gastrointestinal threonine uptake and mucin synthesis in enterally fed minipigs","volume":"139","author":"Remond","year":"2009","journal-title":"J Nutr"},{"key":"2024082915092139600_ref39","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1097\/01.MIB.0000442681.85545.31","article-title":"Clinical utility of fecal biomarkers for the diagnosis and management of inflammatory bowel disease","volume":"20","author":"Kopylov","year":"2014","journal-title":"Inflamm Bowel Dis"},{"key":"2024082915092139600_ref40","doi-asserted-by":"crossref","first-page":"13566","DOI":"10.3748\/wjg.v21.i48.13566","article-title":"Fecal calprotectin correlated with endoscopic remission for Asian inflammatory bowel disease patients","volume":"21","author":"Lin","year":"2015","journal-title":"World J Gastroenterol"},{"key":"2024082915092139600_ref41","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/s41579-018-0036-x","article-title":"Interactions of commensal and pathogenic microorganisms with the intestinal mucosal barrier","volume":"16","author":"Martens","year":"2018","journal-title":"Nat Rev Microbiol"},{"key":"2024082915092139600_ref42","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1038\/mi.2016.75","article-title":"Mechanisms of inflammation-driven bacterial dysbiosis in the gut","volume":"10","author":"Zeng","year":"2017","journal-title":"Mucosal Immunol"},{"key":"2024082915092139600_ref43","doi-asserted-by":"crossref","first-page":"2923","DOI":"10.1111\/j.1572-0241.1999.01439.x","article-title":"Rectal dialysate and fecal concentrations of neutrophil gelatinase-associated lipocalin, interleukin-8, and tumor necrosis factor-alpha in ulcerative colitis","volume":"94","author":"Nielsen","year":"1999","journal-title":"Am J Gastroenterol"},{"key":"2024082915092139600_ref44","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1136\/jcp.46.8.757","article-title":"Cytokines in stools of children with inflammatory bowel disease or infective diarrhoea","volume":"46","author":"Nicholls","year":"1993","journal-title":"J Clin Pathol"},{"key":"2024082915092139600_ref45","first-page":"107","article-title":"Detection of calprotectin in inflammatory bowel disease: Fecal and serum levels and immunohistochemical localization","volume":"41","author":"Fukunaga","year":"2018","journal-title":"Int J Mol Med"},{"key":"2024082915092139600_ref46","doi-asserted-by":"crossref","first-page":"262","DOI":"10.1038\/s41564-021-01050-3","article-title":"Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity","volume":"7","author":"Mills","year":"2022","journal-title":"Nat Microbiol"},{"key":"2024082915092139600_ref47","doi-asserted-by":"crossref","first-page":"12672","DOI":"10.1073\/pnas.1904099116","article-title":"Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide","volume":"116","author":"Henke","year":"2019","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024082915092139600_ref48","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature09922","article-title":"Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease","volume":"472","author":"Wang","year":"2011","journal-title":"Nature"},{"key":"2024082915092139600_ref49","doi-asserted-by":"crossref","first-page":"11246","DOI":"10.3748\/wjg.v21.i40.11246","article-title":"Disease monitoring in inflammatory bowel disease","volume":"21","author":"Chang","year":"2015","journal-title":"World J Gastroenterol"},{"key":"2024082915092139600_ref50","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2020.595877","article-title":"Gene networks underlying the resistance of bifidobacterium longum to inflammatory factors","volume":"11","author":"Veselovsky","year":"2020","journal-title":"Front Immunol"},{"key":"2024082915092139600_ref51","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1164\/ajrccm.160.3.9807080","article-title":"Cytokines IL-1beta, IL-6, and TNF-alpha enhance in vitro growth of bacteria","volume":"160","author":"Meduri","year":"1999","journal-title":"Am J Respir Crit Care Med"},{"key":"2024082915092139600_ref52","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1128\/iai.61.3.830-835.1993","article-title":"Tumor necrosis factor alpha binding to bacteria: evidence for a high-affinity receptor and alteration of bacterial virulence properties","volume":"61","author":"Luo","year":"1993","journal-title":"Infect Immun"},{"key":"2024082915092139600_ref53","doi-asserted-by":"crossref","first-page":"3841","DOI":"10.1073\/pnas.1220341110","article-title":"Molecular basis for manganese sequestration by calprotectin and roles in the innate immune response to invading bacterial pathogens","volume":"110","author":"Damo","year":"2013","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024082915092139600_ref54","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2221121120","article-title":"Engineered calprotectin-sensing probiotics for IBD surveillance in humans","volume":"120","author":"Xia","year":"2023","journal-title":"Proc Natl Acad Sci USA"},{"key":"2024082915092139600_ref55","doi-asserted-by":"crossref","first-page":"158","DOI":"10.1016\/j.chom.2011.07.004","article-title":"Nutrient metal sequestration by calprotectin inhibits bacterial superoxide defense, enhancing neutrophil killing of Staphylococcus aureus","volume":"10","author":"Kehl-Fie","year":"2011","journal-title":"Cell Host Microbe"},{"key":"2024082915092139600_ref56","doi-asserted-by":"crossref","first-page":"13694","DOI":"10.1038\/srep13694","article-title":"Myeloid-related protein 8 induces self-tolerance and cross-tolerance to bacterial infection via TLR4- and TLR2-mediated signal pathways","volume":"5","author":"Coveney","year":"2015","journal-title":"Sci Rep"},{"key":"2024082915092139600_ref57","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1016\/j.reth.2022.06.010","article-title":"S100A8 accelerates wound healing by promoting adipose stem cell proliferation and suppressing inflammation","volume":"21","author":"Su","year":"2022","journal-title":"Regen Ther"}],"container-title":["The ISME Journal"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ismej\/advance-article-pdf\/doi\/10.1093\/ismejo\/wrae146\/58679564\/wrae146.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismej\/advance-article-pdf\/doi\/10.1093\/ismejo\/wrae146\/58859207\/wrae146.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismej\/advance-article-pdf\/doi\/10.1093\/ismejo\/wrae146\/58859207\/wrae146.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,29]],"date-time":"2024-08-29T21:02:27Z","timestamp":1724965347000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismej\/article\/doi\/10.1093\/ismejo\/wrae146\/7723479"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1]]},"references-count":57,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1,8]]}},"URL":"https:\/\/doi.org\/10.1093\/ismejo\/wrae146","relation":{},"ISSN":["1751-7362","1751-7370"],"issn-type":[{"value":"1751-7362","type":"print"},{"value":"1751-7370","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,1]]},"published":{"date-parts":[[2024,1]]},"article-number":"wrae146"}}