{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T09:10:13Z","timestamp":1756804213422,"version":"3.44.0"},"reference-count":72,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T00:00:00Z","timestamp":1755475200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001411","name":"Indian Council of Medical Research (ICMR)-New Delhi","doi-asserted-by":"crossref","award":["5\/4\/8-1\/2019-NCD-II"],"award-info":[{"award-number":["5\/4\/8-1\/2019-NCD-II"]}],"id":[{"id":"10.13039\/501100001411","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Aims<\/jats:title>\n                  <jats:p>The study aims to assess the gut microbiota function and the status of bidirectional relationship of gut with other body organs in ulcerative colitis (UC).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods and Results<\/jats:title>\n                  <jats:p>The proteomic analysis of fecal samples revealed the presence of 2072 microbial proteins and 243 human proteins. Microbial proteins for pentose phosphate pathway (PPP) increased significantly in UC samples; whereas, decrease in proteins related to energy metabolism, transmembrane transporters and membrane proteins, and protein folding was noted. Interestingly, expression of proteins related to iron metabolism and oxidative stress indicates an oxidative gut environment that favors the growth of pathogenic microbes, enteric infections, and intestinal damage. Over-expression of host proteins such as neutrophil defensin 3, lactotransferrin, neutrophil elastase, azurocidin, protein S100-A8, protein S100-A9, and cathepsin G further indicate inflammation, and microbial infection in UC gut. The microbial (Omp)\u2013host (TLR4) protein interaction analysis by molecular docking suggests significant implications in immune modulation. Further, gas chromatography\u2013mass spectrometry investigation revealed altered concentration of microbial short chain fatty acids.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>The study revealed vital clues about the gut\u2013organ homeostasis in UC that contribute to the host physiology, disease pathogenesis and \u2018gut\u2013organ axis\u2019 fragmentation.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/jambio\/lxaf207","type":"journal-article","created":{"date-parts":[[2025,8,18]],"date-time":"2025-08-18T15:21:23Z","timestamp":1755530483000},"source":"Crossref","is-referenced-by-count":0,"title":["Gut\u2013organ axis is more fragmented in ulcerative colitis: a metaproteomics study"],"prefix":"10.1093","volume":"136","author":[{"given":"Asha","family":"Yadav","sequence":"first","affiliation":[{"name":"Maharshi Dayanand University Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, , Rohtak 124001 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pratik Balwant","family":"Shinde","sequence":"additional","affiliation":[{"name":"Maharshi Dayanand University Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, , Rohtak 124001 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Arush","family":"Behl","sequence":"additional","affiliation":[{"name":"Maharshi Dayanand University Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, , Rohtak 124001 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Deepti","family":"Singh","sequence":"additional","affiliation":[{"name":"Amity Institute of Microbial Technology, Amity University Rajasthan , Jaipur 303002 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Saurabh","family":"Kedia","sequence":"additional","affiliation":[{"name":"All India Institute of Medical Sciences New Delhi Department of Gastroenterology and Human Nutrition, , Ansari Nagar 110029 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1577-0118","authenticated-orcid":false,"given":"Vineet","family":"Ahuja","sequence":"additional","affiliation":[{"name":"All India Institute of Medical Sciences New Delhi Department of Gastroenterology and Human Nutrition, , Ansari Nagar 110029 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Krishna Kant","family":"Sharma","sequence":"additional","affiliation":[{"name":"Maharshi Dayanand University Laboratory of Enzymology and Gut Microbiology, Department of Microbiology, , Rohtak 124001 ,","place":["India"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,8,18]]},"reference":[{"key":"2025090204463087100_bib1","doi-asserted-by":"publisher","first-page":"636","DOI":"10.1111\/lam.13333","article-title":"Gut\u2013organ axis: a microbial outreach and networking","volume":"72","author":"Ahlawat","year":"2021","journal-title":"Lett Appl Microbiol"},{"key":"2025090204463087100_bib2","doi-asserted-by":"publisher","first-page":"254","DOI":"10.1080\/1040841X.2021.1876631","article-title":"Inflammatory bowel disease: tri-directional relationship between microbiota, immune system and intestinal epithelium","volume":"47","author":"Ahlawat","year":"2021","journal-title":"Crit Rev Microbiol"},{"key":"2025090204463087100_bib3","doi-asserted-by":"publisher","first-page":"e0240012","DOI":"10.1371\/journal.pone.0240012","article-title":"Proteins associated with neutrophil degranulation are upregulated in nasopharyngeal swabs from SARS-CoV-2 patients","volume":"15","author":"Akgun","year":"2020","journal-title":"PLoS One"},{"key":"2025090204463087100_bib4","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1111\/1462-2920.16238","article-title":"Metaproteomics to understand how microbiota function: the crystal ball predicts a promising future","volume":"25","author":"Armengaud","year":"2023","journal-title":"Environ Microbiol"},{"key":"2025090204463087100_bib5","doi-asserted-by":"publisher","first-page":"764","DOI":"10.1002\/hep.28356","article-title":"The severity of nonalcoholic fatty liver disease is associated with gut dysbiosis and shift in the metabolic function of the gut microbiota","volume":"63","author":"Boursier","year":"2016","journal-title":"Hepatology"},{"key":"2025090204463087100_bib6","doi-asserted-by":"publisher","first-page":"10062","DOI":"10.1038\/ncomms10062","article-title":"Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal","volume":"6","author":"Bui","year":"2015","journal-title":"Nat Commun"},{"key":"2025090204463087100_bib7","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4110\/in.2020.20.e15","article-title":"The role of butyrate in attenuating pathobiont-induced hyperinflammation","volume":"20","author":"Chen","year":"2020","journal-title":"Immune Netw"},{"key":"2025090204463087100_bib8","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1038\/s42003-019-0318-5","article-title":"Bridging human chaperonopathies and microbial chaperonins","volume":"2","author":"Conway\u00a0de\u00a0Macario","year":"2019","journal-title":"Commun Biol"},{"key":"2025090204463087100_bib9","doi-asserted-by":"publisher","first-page":"fnac072","DOI":"10.1093\/femsle\/fnac072","article-title":"Roles of intestinal Parabacteroides in human health and diseases","volume":"369","author":"Cui","year":"2022","journal-title":"FEMS Microbial Lett"},{"key":"2025090204463087100_bib10","doi-asserted-by":"publisher","first-page":"557","DOI":"10.1189\/jlb.1008647","article-title":"The endogenous Toll\u2013like receptor 4 agonist S100A8\/S100A9 (calprotectin) as innate amplifier of infection, autoimmunity, and cancer","volume":"86","author":"Ehrchen","year":"2009","journal-title":"J Leukoc Bio"},{"key":"2025090204463087100_bib11","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1016\/j.phrs.2019.01.019","article-title":"C\u00e2mara NO. The interplay among gut microbiota, hypertension and kidney diseases: the role of short-chain fatty acids","volume":"141","author":"Felizardo","year":"2019","journal-title":"Pharmacol Res"},{"key":"2025090204463087100_bib12","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1111\/j.1462-2920.2012.02845.x","article-title":"Microbiota from the distal guts of lean and obese adolescents exhibit partial functional redundancy besides clear differences in community structure","volume":"15","author":"Ferrer","year":"2013","journal-title":"Environ Microbiol"},{"key":"2025090204463087100_bib13","doi-asserted-by":"publisher","first-page":"3215","DOI":"10.1038\/s41467-023-39028-w","article-title":"Bacteriophage targeting microbiota alleviates non-alcoholic fatty liver disease induced by high alcohol-producing Klebsiella pneumonia","volume":"14","author":"Gan","year":"2023","journal-title":"Nat Commun"},{"key":"2025090204463087100_bib14","doi-asserted-by":"publisher","first-page":"322","DOI":"10.1016\/j.aninu.2024.05.001","article-title":"Double-side role of short chain fatty acids on host health via the gut\u2013organ axes","volume":"18","author":"Gao","year":"2024","journal-title":"Animal Nutrition"},{"key":"2025090204463087100_bib15","doi-asserted-by":"publisher","first-page":"1839","DOI":"10.1111\/febs.15511","article-title":"An alternative pentose phosphate pathway in human gut bacteria for the degradation of C5 sugars in dietary fibers","volume":"288","author":"Garschagen","year":"2021","journal-title":"FEBS J"},{"key":"2025090204463087100_bib16","doi-asserted-by":"publisher","first-page":"365","DOI":"10.3389\/fendo.2020.00365","article-title":"The role of the pentose phosphate pathway in diabetes and cancer","volume":"11","author":"Ge","year":"2020","journal-title":"Front Endocrinol"},{"key":"2025090204463087100_bib17","doi-asserted-by":"publisher","first-page":"416511","DOI":"10.1101\/416511","article-title":"Proteus: an R package for downstream analysis of MaxQuant output","author":"Gierlinski","year":"2018","journal-title":"Biorxiv"},{"key":"2025090204463087100_bib18","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1053\/j.gastro.2023.09.019","article-title":"Pathobionts in inflammatory bowel disease: origins, underlying mechanisms, and implications for clinical care","volume":"166","author":"Gilliland","year":"2023","journal-title":"Gastroenterology"},{"key":"2025090204463087100_bib19","doi-asserted-by":"publisher","first-page":"2714","DOI":"10.1002\/elps.1150181505","article-title":"SWISS-MODEL and the Swiss-Pdb Viewer: an environment for comparative protein modeling","volume":"18","author":"Guex","year":"1997","journal-title":"Electrophoresis"},{"key":"2025090204463087100_bib20","doi-asserted-by":"publisher","first-page":"563","DOI":"10.1016\/j.tim.2017.11.002","article-title":"Human gut microbiome: function matters","volume":"26","author":"Heintz-Buschart","year":"2018","journal-title":"Trends Microbiol"},{"key":"2025090204463087100_bib21","first-page":"92037","article-title":"AutoDock SF. and Vina with AutoDockTools: a Tutorial","volume":"10550","author":"Huey","year":"2012","journal-title":"Scripps Res Inst Mol Graph Lab"},{"key":"2025090204463087100_bib22","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1111\/apt.15314","article-title":"emerging role of the gut microbiome in the progression of nonalcoholic fatty liver disease and potential therapeutic implications","volume":"50","author":"Jayakumar","year":"2019","journal-title":"Aliment Pharmacol Ther"},{"key":"2025090204463087100_bib23","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1038\/s41467-017-00900-1","article-title":"The gut microbiome in atherosclerotic cardiovascular disease","volume":"8","author":"Jie","year":"2017","journal-title":"Nat Commun"},{"key":"2025090204463087100_bib24","doi-asserted-by":"publisher","first-page":"2499","DOI":"10.1007\/s00204-023-03562-9","article-title":"Reactive oxygen species, toxicity, oxidative stress, and antioxidants: chronic diseases and aging","volume":"97","author":"Jomova","year":"2023","journal-title":"Arch Toxicol"},{"key":"2025090204463087100_bib25","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1128\/IAI.00121-21","article-title":"Salmonella typhimurium adhesin OmpV activates host immunity to confer protection against systemic and gastrointestinal infection in mice","volume":"89","author":"Kaur","year":"2021","journal-title":"Infect Immun"},{"key":"2025090204463087100_bib26","doi-asserted-by":"publisher","first-page":"4768","DOI":"10.3390\/ijms23094768","article-title":"Role of the gut microbiota in the innate immune defense of the lungs and pathogenesis of the heterogeneous course of chronic obstructive pulmonary disease","volume":"23","author":"Kotlyarov","year":"2022","journal-title":"Int J Mol Sci"},{"key":"2025090204463087100_bib27","doi-asserted-by":"publisher","first-page":"904","DOI":"10.2174\/1389557517666170228115324","article-title":"Reactive oxygen and nitrogen species in carcinogenesis: implications of oxidative stress on the progression and development of several cancer types","volume":"17","author":"Kruk","year":"2017","journal-title":"MRMC"},{"key":"2025090204463087100_bib28","doi-asserted-by":"publisher","first-page":"6993","DOI":"10.1007\/s12010-024-04893-8","article-title":"Understanding the dynamics of human defensin antimicrobial peptides: pathogen resistance and commensal induction","volume":"196","author":"Kumaresan","year":"2024","journal-title":"Appl Biochem Biotechnol"},{"key":"2025090204463087100_bib29","doi-asserted-by":"publisher","first-page":"312","DOI":"10.3390\/pharmaceutics12050416","article-title":"Protein interactome of amyloid-\u03b2 as a therapeutic target","volume":"12","author":"Lazarev","year":"2023","journal-title":"Pharmaceutics"},{"key":"2025090204463087100_bib30","doi-asserted-by":"publisher","first-page":"1814107","DOI":"10.1080\/19490976.2020.1814107","article-title":"Young versus aged microbiota transplants to germ-free mice: increased short-chain fatty acids and improved cognitive performance","volume":"12","author":"Lee","year":"2020","journal-title":"Gut Microbes"},{"key":"2025090204463087100_bib31","doi-asserted-by":"publisher","first-page":"E240124226057","DOI":"10.2174\/0126662906273512231201050937","article-title":"Acetaldehyde and Butyrate: their Biological Effects on the Liver and the Gut Axis","volume":"03","author":"Liu","year":"2024","journal-title":"IJGHD"},{"key":"2025090204463087100_bib32","doi-asserted-by":"publisher","first-page":"304","DOI":"10.3390\/vaccines9030304","article-title":"Synthesis of Escherichia coli OmpA oral nanoparticles and evaluation of immune functions against the major etiologic agent of cow mastitis","volume":"9","author":"Liu","year":"2021","journal-title":"Vaccines"},{"key":"2025090204463087100_bib33","doi-asserted-by":"publisher","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":"2025090204463087100_bib34","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1038\/s41522-020-0123-4","article-title":"Metaproteomics characterizes human gut microbiome function in colorectal cancer","volume":"6","author":"Long","year":"2020","journal-title":"NPJ Biofilms Microbiomes"},{"key":"2025090204463087100_bib35","doi-asserted-by":"publisher","first-page":"e00678","DOI":"10.1002\/mbo3.678","article-title":"Altered gut microbiota and microbial biomarkers associated with chronic kidney disease","volume":"8","author":"Lun","year":"2019","journal-title":"MicrobiologyOpen"},{"key":"2025090204463087100_bib36","doi-asserted-by":"publisher","first-page":"599734","DOI":"10.3389\/fcimb.2021.599734","article-title":"Metagenome analysis of intestinal bacteria in healthy people, patients with inflammatory bowel disease and colorectal cancer","volume":"11","author":"Ma","year":"2021","journal-title":"Front Cell Infect Microbiol"},{"key":"2025090204463087100_bib37","doi-asserted-by":"publisher","first-page":"877533","DOI":"10.3389\/fimmu.2022.877533","article-title":"Distal consequences of mucosal infections in intestinal and lung inflammation","volume":"13","author":"Melo-Gonz\u00e1lez","year":"2022","journal-title":"Front Immunol"},{"key":"2025090204463087100_bib38","doi-asserted-by":"publisher","first-page":"1691","DOI":"10.3748\/wjg.v21.i6.1691","article-title":"Gut microbiota and liver diseases","volume":"21","author":"Minemura","year":"2015","journal-title":"WJG"},{"key":"2025090204463087100_bib39","doi-asserted-by":"publisher","first-page":"1262","DOI":"10.1126\/science.1223813","article-title":"Host\u2013gut microbiota metabolic interactions","volume":"336","author":"Nicholson","year":"2012","journal-title":"Science"},{"key":"2025090204463087100_bib40","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/j.cell.2019.02.022","article-title":"Pathogenic E. coli extracts nutrients from infected host cells utilizing injectisome components","volume":"177","author":"Pal","year":"2019","journal-title":"Cell"},{"key":"2025090204463087100_bib41","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1016\/j.biortech.2017.08.132","article-title":"Acetate-assisted increase of butyrate production by Eubacterium limosum KIST612 during carbon monoxide fermentation","volume":"245","author":"Park","year":"2017","journal-title":"Bioresour Technol"},{"key":"2025090204463087100_bib42","doi-asserted-by":"publisher","first-page":"734","DOI":"10.1007\/s10517-017-3700-7","article-title":"Analysis of gut microbiota in patients with Parkinson's disease","volume":"162","author":"Petrov","year":"2017","journal-title":"Bull Exp Biol Med"},{"key":"2025090204463087100_bib43","doi-asserted-by":"publisher","first-page":"2131","DOI":"10.1093\/ecco-jcc\/jjab102","article-title":"Inflammatory bowel disease-associated colorectal cancer: translational risks from mechanisms to medicines","volume":"15","author":"Porter","year":"2021","journal-title":"J Crohns Colitis"},{"key":"2025090204463087100_bib44","doi-asserted-by":"publisher","first-page":"2259033","DOI":"10.1080\/19490976.2023.2259033","article-title":"Human gut microbiome and metabolite dynamics under simulated microgravity","volume":"15","author":"Ramos-Nascimento","year":"2023","journal-title":"Gut Microbes"},{"key":"2025090204463087100_bib45","doi-asserted-by":"publisher","first-page":"65","DOI":"10.3390\/ijms22010065","article-title":"Butyrate and propionate restore the cytokine and house dust mite compromised barrier function of human bronchial airway epithelial cells","volume":"22","author":"Richards","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2025090204463087100_bib46","doi-asserted-by":"publisher","first-page":"1993","DOI":"10.3390\/nu12071993","article-title":"Iron supplementation influence on the gut microbiota and probiotic intake effect in iron deficiency\u2014a literature-based review","volume":"12","author":"Rusu","year":"2020","journal-title":"Nutrients"},{"key":"2025090204463087100_bib47","doi-asserted-by":"publisher","first-page":"350","DOI":"10.1002\/mds.26069","article-title":"Gut microbiota are related to Parkinson's disease and clinical phenotype","volume":"30","author":"Scheperjans","year":"2015","journal-title":"Mov Disord"},{"key":"2025090204463087100_bib48","doi-asserted-by":"publisher","first-page":"lxad016","DOI":"10.1093\/jambio\/lxad016","article-title":"Functional analysis of metalloenzymes from human gut microbiota and their role in ulcerative colitis","volume":"134","author":"Shinde","year":"2023","journal-title":"J Appl Microbiol"},{"key":"2025090204463087100_bib49","doi-asserted-by":"publisher","first-page":"4154","DOI":"10.2174\/1381612824666181001153605","article-title":"Protective mechanisms of butyrate on inflammatory bowel disease","volume":"24","author":"Silva","year":"2018","journal-title":"CPD"},{"key":"2025090204463087100_bib50","doi-asserted-by":"publisher","first-page":"137643","DOI":"10.1016\/j.ijbiomac.2024.137643","article-title":"Refolding dynamics and immunoinformatic insights into Vibrio cholerae OmpA, OmpK, and OmpV for vaccine applications","volume":"283","author":"Singh","year":"2024","journal-title":"Int J Biol Macromol"},{"key":"2025090204463087100_bib51","doi-asserted-by":"publisher","first-page":"4112","DOI":"10.1111\/jam.15504","article-title":"Balancing reactive oxygen species generation by rebooting gut microbiota","volume":"132","author":"Singh","year":"2022","journal-title":"J Appl Microbiol"},{"key":"2025090204463087100_bib52","doi-asserted-by":"publisher","first-page":"3350","DOI":"10.1111\/febs.15327","article-title":"Glycolysis\u2013a key player in the inflammatory response","volume":"287","author":"Soto-Heredero","year":"2020","journal-title":"FEBS J"},{"key":"2025090204463087100_bib53","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/j.mib.2014.11.002","article-title":"Neutrophil serine proteases in antibacterial defense","volume":"23","author":"Stapels","year":"2015","journal-title":"Curr Opin Microbiol"},{"key":"2025090204463087100_bib54","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1136\/jim-2020-001715","article-title":"Quantitative increase in short-chain fatty acids, especially butyrate protects kidney from ischemia\/reperfusion injury","volume":"70","author":"Sun","year":"2022","journal-title":"J Investig Med"},{"key":"2025090204463087100_bib55","doi-asserted-by":"publisher","first-page":"D607","DOI":"10.1093\/nar\/gky1131","article-title":"STRING v11: protein\u2013protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets","volume":"47","author":"Szklarczyk","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2025090204463087100_bib56","doi-asserted-by":"publisher","first-page":"54","DOI":"10.3892\/mmr.2019.9848","article-title":"Metaproteomic portrait of the healthy human gut microbiota","volume":"10","author":"Tanca","year":"2024","journal-title":"Mol Med Report"},{"key":"2025090204463087100_bib57","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1038\/s41598-017-01033-7","article-title":"Direct recognition of LPS drive TLR4 expressing CD8+ T cell activation in patients with rheumatoid arthritis","volume":"7","author":"Tripathy","year":"2017","journal-title":"Sci Rep"},{"key":"2025090204463087100_bib58","doi-asserted-by":"publisher","first-page":"2301","DOI":"10.1038\/nprot.2016.136","article-title":"The MaxQuant computational platform for mass spectrometry-based shotgun proteomics","volume":"11","author":"Tyanova","year":"2016","journal-title":"Nat Protoc"},{"key":"2025090204463087100_bib59","doi-asserted-by":"crossref","first-page":"13537","DOI":"10.1038\/s41598-017-13601-y","article-title":"Gut microbiome alterations in Alzheimer's disease","volume":"7","author":"Vogt","year":"2017","journal-title":"Sci Rep"},{"key":"2025090204463087100_bib60","doi-asserted-by":"publisher","first-page":"2814","DOI":"10.21037\/jgo-21-624","article-title":"Correlation of ulcerative colitis and colorectal cancer: a systematic review and meta-analysis","volume":"12","author":"Wang","year":"2021","journal-title":"J Gastrointest Oncol"},{"key":"2025090204463087100_bib61","doi-asserted-by":"crossref","first-page":"5.6.1","DOI":"10.1002\/cpbi.3","article-title":"Comparative protein structure modeling using MOD ELLER","volume":"54","author":"Webb","year":"2016","journal-title":"Curr Protoc Bioinformatics"},{"key":"2025090204463087100_bib62","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12876-016-0534-0","article-title":"Cirrhosis related functionality characteristic of the fecal microbiota as revealed by a metaproteomic approach","volume":"16","author":"Wei","year":"2016","journal-title":"BMC Gastroenterol"},{"key":"2025090204463087100_bib63","doi-asserted-by":"publisher","first-page":"W407","DOI":"10.1093\/nar\/gkm290","article-title":"ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins","volume":"35","author":"Wiederstein","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2025090204463087100_bib64","doi-asserted-by":"publisher","first-page":"2333","DOI":"10.3390\/nu5072333","article-title":"Intestinal iron homeostasis and colon tumorigenesis","volume":"5","author":"Xue","year":"2013","journal-title":"Nutrients"},{"key":"2025090204463087100_bib65","doi-asserted-by":"publisher","first-page":"lxad280","DOI":"10.1093\/jambio\/lxad280","article-title":"Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study","volume":"134","author":"Yadav","year":"2023","journal-title":"J Appl Microbiol"},{"key":"2025090204463087100_bib66","doi-asserted-by":"publisher","first-page":"107289","DOI":"10.1016\/j.ijantimicag.2024.107289","article-title":"Gut colonization with antibiotic-resistant Escherichia coli pathobionts leads to disease severity in ulcerative colitis","volume":"64","author":"Yadav","year":"2024","journal-title":"Int J Antimicrob Agents"},{"key":"2025090204463087100_bib67","doi-asserted-by":"publisher","first-page":"573475","DOI":"10.3389\/fphar.2020.573475","article-title":"Propionic acid targets the TLR4\/NF-\u03ba B signaling pathway and inhibits LPS-induced intestinal barrier dysfunction: in vitro and in vivo studies","volume":"11","author":"Yang","year":"2020","journal-title":"Front Pharmacol"},{"key":"2025090204463087100_bib68","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1053\/j.sempedsurg.2017.10.003","article-title":"Clinical presentation of Crohn\u2019s, ulcerative colitis, and indeterminate colitis: symptoms, extraintestinal manifestations, and disease phenotypes","volume":"26","author":"Yangyang","year":"2017","journal-title":"Semin Pediatr Surg"},{"key":"2025090204463087100_bib69","doi-asserted-by":"publisher","first-page":"1242","DOI":"10.3748\/wjg.v26.i12.1242","article-title":"Roles of G protein-coupled receptors in inflammatory bowel disease","volume":"26","author":"Zeng","year":"2020","journal-title":"WJG"},{"key":"2025090204463087100_bib70","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1016\/j.talanta.2018.12.049","article-title":"A sensitive GC\/MS detection method for analyzing microbial metabolites short chain fatty acids in fecal and serum samples","volume":"196","author":"Zhang","year":"2019","journal-title":"Talanta"},{"key":"2025090204463087100_bib71","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-016-0176-z","article-title":"MetaPro-IQ: a universal metaproteomic approach to studying human and mouse gut microbiota","volume":"4","author":"Zhang","year":"2016","journal-title":"Microbiome"},{"key":"2025090204463087100_bib72","doi-asserted-by":"publisher","first-page":"389","DOI":"10.1016\/j.aninu.2020.09.002","article-title":"Interplay between gut microbiota and antimicrobial peptides","volume":"6","author":"Zong","year":"2020","journal-title":"Animal Nutrition"}],"container-title":["Journal of Applied Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jambio\/advance-article-pdf\/doi\/10.1093\/jambio\/lxaf207\/64078685\/lxaf207.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jambio\/article-pdf\/136\/9\/lxaf207\/64078685\/lxaf207.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jambio\/article-pdf\/136\/9\/lxaf207\/64078685\/lxaf207.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,2]],"date-time":"2025-09-02T08:46:37Z","timestamp":1756802797000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jambio\/article\/doi\/10.1093\/jambio\/lxaf207\/8237445"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,18]]},"references-count":72,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2025,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/jambio\/lxaf207","relation":{},"ISSN":["1365-2672"],"issn-type":[{"type":"electronic","value":"1365-2672"}],"subject":[],"published-other":{"date-parts":[[2025,9]]},"published":{"date-parts":[[2025,8,18]]},"article-number":"lxaf207"}}