{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,7]],"date-time":"2026-10-07T21:33:39Z","timestamp":1791408819293,"version":"4.3.3"},"reference-count":155,"publisher":"The Royal Society","issue":"8","license":[{"start":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:00:00Z","timestamp":1787097600000},"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":[[2026,8,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Inflammatory bowel diseases (IBDs) are a major public and veterinary health concern, but the causes are poorly understood. In this review, we discuss the potential of mycobacteria as causative factors for such diseases. We focus on similarities between the most common human IBD, Crohn's disease, and a common IBD in cattle, Johne's disease. Both are multifactorial diseases, leading to a chronic hyperinflammatory immune response of the intestines. However, the underlying genetic and environmental factors, such as variations in the intestinal microbiome, are still poorly understood. While Johne's disease has been shown to be caused by Mycobacterium avium subsp. paratuberculosis, the likeliness of mycobacteria as a causative factor of Crohn's disease is still heavily debated. In this review, we summarize the advances in research that could be used to further investigate the role of mycobacteria in intestinal diseases and to give better estimations about which mycobacterial species are most probably hazards for health. New advances in molecular, genetic and imaging methods give hope for better diagnostics, disease prevention, and development of new therapeutics. In addition, these techniques offer researchers a toolbox and general model systems for better understanding the mechanisms of intestinal diseases caused by mycobacteria and the role of the microbiome in the control of disease progression.<\/jats:p>","DOI":"10.1098\/rsob.250258","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:13:32Z","timestamp":1787098412000},"source":"Crossref","is-referenced-by-count":1,"title":["A modern toolbox to elucidate the role of the human microbiome in modulating mycobacterial gut infections"],"prefix":"10.1098","volume":"16","author":[{"given":"Chiara","family":"Foini","sequence":"first","affiliation":[{"name":"Department of Biology, Faculty of Science, Leiden University 1 , Leiden, The Netherlands"},{"name":"ISCB, Pasteur Institute 2 , Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ariane","family":"Briegel","sequence":"additional","affiliation":[{"name":"ISCB, Pasteur Institute 2 , Paris, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4128-9501","authenticated-orcid":false,"given":"Herman P.","family":"Spaink","sequence":"additional","affiliation":[{"name":"Department of Biology, Faculty of Science, Leiden University 1 , Leiden, The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"175","published-online":{"date-parts":[[2026,8,19]]},"reference":[{"key":"2026081820132607200_RSOB250258C1","doi-asserted-by":"crossref","first-page":"1367385","DOI":"10.3389\/fcimb.2024.1367385","article-title":"Development and application of one-step multiplex real-time PCR for detection of three main pathogens associated with bovine neonatal diarrhea","volume":"14","author":"Wang","year":"2024","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"2026081820132607200_RSOB250258C2","first-page":"619","article-title":"Prevalence of inflammatory bowel disease in pediatric and adult populations: recent estimates from large national databases in the United States, 2007-2016","volume":"26","author":"Ye","year":"2020","journal-title":"Inflamm. Bowel Dis."},{"key":"2026081820132607200_RSOB250258C3","doi-asserted-by":"crossref","first-page":"185","DOI":"10.2147\/DDDT.S11290","article-title":"Current and emerging drugs for the treatment of inflammatory bowel disease","volume":"5","author":"Triantafillidis","year":"2011","journal-title":"Drug Des. Devel. Ther."},{"key":"2026081820132607200_RSOB250258C4","doi-asserted-by":"crossref","first-page":"4089","DOI":"10.3390\/ijms24044089","article-title":"The gut\u2013organ-axis concept: advances the application of gut-on-chip technology","volume":"24","author":"Guo","year":"2023","journal-title":"Int. J. Mol. Sci."},{"key":"2026081820132607200_RSOB250258C5","first-page":"1","article-title":"Microbiota in health and diseases","volume":"7","author":"Hou","year":"2022","journal-title":"Signal Transduct. Target. Ther."},{"key":"2026081820132607200_RSOB250258C6","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":"2026081820132607200_RSOB250258C7","doi-asserted-by":"crossref","first-page":"578","DOI":"10.3390\/microorganisms10030578","article-title":"Gut microbiota dysbiosis: triggers, consequences, diagnostic and therapeutic options","volume":"10","author":"Hrncir","year":"2022","journal-title":"Microorganisms"},{"key":"2026081820132607200_RSOB250258C8","article-title":"Crohn's disease: complications of Crohn's disease","author":"NHS"},{"key":"2026081820132607200_RSOB250258C9","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.vetimm.2011.12.005","article-title":"Crohn's disease and Mycobacterium avium subsp. paratuberculosis: the need for a study is long overdue","volume":"145","author":"Davis","year":"2012","journal-title":"Vet. Immunol. Immunopathol."},{"key":"2026081820132607200_RSOB250258C10","doi-asserted-by":"crossref","first-page":"397","DOI":"10.1136\/flgastro-2020-101471","article-title":"Anti-Mycobacterium paratuberculosis (MAP) therapy for Crohn's disease: an overview and update","volume":"12","author":"Honap","year":"2020","journal-title":"Frontline Gastroenterol."},{"key":"2026081820132607200_RSOB250258C11","doi-asserted-by":"crossref","first-page":"2769","DOI":"10.1016\/S0140-6736(17)32448-0","article-title":"Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies","volume":"390","author":"Ng","year":"2017","journal-title":"Lancet"},{"key":"2026081820132607200_RSOB250258C12","doi-asserted-by":"crossref","first-page":"1810","DOI":"10.3748\/wjg.14.1810","article-title":"Colorectal cancer risk in Crohn's disease","volume":"14","author":"Freeman","year":"2008","journal-title":"World J. Gastroenterol."},{"key":"2026081820132607200_RSOB250258C13","doi-asserted-by":"crossref","first-page":"157","DOI":"10.5009\/gnl210118","article-title":"Long-term disease course of Crohn's disease: changes in disease location, phenotype, activities, and predictive factors","volume":"16","author":"Cho","year":"2021","journal-title":"Gut Liver"},{"key":"2026081820132607200_RSOB250258C14","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.1038\/ng.717","article-title":"Meta-analysis increases to 71 the tally of confirmed Crohn's disease susceptibility loci","volume":"42","author":"Franke","year":"2010","journal-title":"Nat. Genet."},{"key":"2026081820132607200_RSOB250258C15","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12916-023-02878-8","article-title":"Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study","volume":"21","author":"Xu","year":"2023","journal-title":"BMC Med."},{"key":"2026081820132607200_RSOB250258C16","doi-asserted-by":"crossref","first-page":"20","DOI":"10.1016\/j.disamonth.2017.07.001","article-title":"A comprehensive review and update on Crohn's disease","volume":"64","author":"Gajendran","year":"2018","journal-title":"Dis. Mon."},{"key":"2026081820132607200_RSOB250258C17","doi-asserted-by":"crossref","first-page":"3222","DOI":"10.3748\/wjg.v29.i21.3222","article-title":"Crohn's disease: why the ileum?","volume":"29","author":"Richard","year":"2023","journal-title":"World J. Gastroenterol."},{"key":"2026081820132607200_RSOB250258C18","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1038\/nm.2069","article-title":"NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation","volume":"16","author":"Cooney","year":"2010","journal-title":"Nat. Med."},{"key":"2026081820132607200_RSOB250258C19","doi-asserted-by":"crossref","first-page":"1590","DOI":"10.1016\/S0140-6736(12)60026-9","article-title":"Crohn's disease","volume":"380","author":"Baumgart","year":"2012","journal-title":"Lancet"},{"key":"2026081820132607200_RSOB250258C20","doi-asserted-by":"crossref","first-page":"1162473","DOI":"10.3389\/fimmu.2023.1162473","article-title":"Identifying immune cell infiltration and effective diagnostic biomarkers in Crohn's disease by bioinformatics analysis","volume":"14","author":"Huang","year":"2023","journal-title":"Front. Immunol."},{"key":"2026081820132607200_RSOB250258C21","doi-asserted-by":"crossref","first-page":"2195","DOI":"10.3748\/wjg.v22.i7.2195","article-title":"Role of regulatory T cell in the pathogenesis of inflammatory bowel disease","volume":"22","author":"Yamada","year":"2016","journal-title":"World J. Gastroenterol."},{"key":"2026081820132607200_RSOB250258C22","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":"2026081820132607200_RSOB250258C23","doi-asserted-by":"crossref","first-page":"536","DOI":"10.1002\/ibd.20335","article-title":"Changes in Crohn's disease phenotype over time in the Chinese population: validation of the Montreal classification system","volume":"14","author":"Chow","year":"2008","journal-title":"Inflamm. Bowel Dis."},{"key":"2026081820132607200_RSOB250258C24","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1016\/j.mayocp.2017.04.010","article-title":"Crohn disease: epidemiology, diagnosis, and management","volume":"92","author":"Feuerstein","year":"2017","journal-title":"Mayo Clin. Proc."},{"key":"2026081820132607200_RSOB250258C25","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1136\/gutjnl-2018-318081","article-title":"Assessment of Crohn's disease-associated small bowel strictures and fibrosis on cross-sectional imaging: a systematic review","volume":"68","author":"Bettenworth","year":"2019","journal-title":"Gut"},{"key":"2026081820132607200_RSOB250258C26","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1093\/ibd\/izad195","article-title":"Management of perianal fistulizing Crohn's disease","volume":"30","author":"Singh","year":"2024","journal-title":"Inflamm. Bowel Dis."},{"key":"2026081820132607200_RSOB250258C27","first-page":"438","article-title":"Ein eigenthuemlicher fall von tuberculose beim rind","volume-title":"Dtsch. Z. Tiermed. Pathol.","author":"Johne","year":"1895"},{"key":"2026081820132607200_RSOB250258C28","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/S0749-0720(15)30410-2","article-title":"Preclinical and clinical manifestations of paratuberculosis (including pathology)","volume":"12","author":"Whitlock","year":"1996","journal-title":"Vet. Clin. North Am. Food Anim. Pract."},{"key":"2026081820132607200_RSOB250258C29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s42523-021-00089-1","article-title":"MAP, Johne's disease and the microbiome; current knowledge and future considerations","volume":"3","author":"Matthews","year":"2021","journal-title":"Anim. Microbiome"},{"key":"2026081820132607200_RSOB250258C30","doi-asserted-by":"crossref","first-page":"3123","DOI":"10.3168\/jds.2020-19381","article-title":"Economic losses due to Johne's disease (paratuberculosis) in dairy cattle","volume":"104","author":"Rasmussen","year":"2021","journal-title":"J. Dairy Sci."},{"key":"2026081820132607200_RSOB250258C31","first-page":"243","article-title":"Farm factors associated with the presence of Mycobacterium paratuberculosis infection in dairy herds on the New York State Paratuberculosis Control Program","volume-title":"Prev. Vet. Med.","author":"Obasanjo","year":"1997"},{"key":"2026081820132607200_RSOB250258C32","first-page":"13","article-title":"Assessment of paratuberculosis international official reporting in Europe using the information supplied to the WOAH by the National Veterinary Services (NVS)","volume-title":"Veterinaria Italiana","author":"Fanelli","year":"2020"},{"key":"2026081820132607200_RSOB250258C33","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1093\/jb\/mvv121","article-title":"Intestinal M cells","volume":"159","author":"Ohno","year":"2015","journal-title":"J. Biochem."},{"key":"2026081820132607200_RSOB250258C34","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1177\/030098588802500205","article-title":"Role of M cells and macrophages in the entrance of Mycobacterium paratuberculosis into domes of ileal Peyer's patches in calves","volume":"25","author":"Momotani","year":"1988","journal-title":"Vet. Pathol."},{"key":"2026081820132607200_RSOB250258C35","doi-asserted-by":"crossref","first-page":"3570","DOI":"10.1128\/IAI.01411-09","article-title":"Peyer's patch-deficient mice demonstrate that Mycobacterium avium subsp. paratuberculosis translocates across the mucosal barrier via both M cells and enterocytes but has inefficient dissemination","volume":"78","author":"Bermudez","year":"2010","journal-title":"Infect. Immun."},{"key":"2026081820132607200_RSOB250258C36","doi-asserted-by":"crossref","first-page":"1370","DOI":"10.3390\/ani11051370","article-title":"Bovine intelectin 2 expression as a biomarker of paratuberculosis disease progression","volume":"11","author":"Blanco V\u00e1zquez","year":"2021","journal-title":"Animals"},{"key":"2026081820132607200_RSOB250258C37","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1016\/j.cvfa.2011.07.001","article-title":"Pathogenesis of paratuberculosis","volume":"27","author":"Sweeney","year":"2011","journal-title":"Vet. Clin. North Am. Food Anim. Pract."},{"key":"2026081820132607200_RSOB250258C38","doi-asserted-by":"crossref","first-page":"587","DOI":"10.3390\/ani13040587","article-title":"Evaluation of single nucleotide polymorphisms (SNPs) associated with genetic resistance to bovine paratuberculosis in Marchigiana beef cattle, an Italian native breed","volume":"13","author":"Mazzone","year":"2023","journal-title":"Animals"},{"key":"2026081820132607200_RSOB250258C39","doi-asserted-by":"crossref","first-page":"1118","DOI":"10.3390\/pathogens13121118","article-title":"The impact of Mycobacterium avium subsp. paratuberculosis on intestinal microbial community composition and diversity in small-tail han sheep","volume":"13","author":"Xue","year":"2024","journal-title":"Pathogens"},{"key":"2026081820132607200_RSOB250258C40","doi-asserted-by":"crossref","first-page":"24027","DOI":"10.1038\/s41598-024-74975-4","article-title":"Mycobacterium avium subspecies paratuberculosis (MAP) infection, and its impact on gut microbiome of individuals with multiple sclerosis","volume":"14","author":"Ashraf","year":"2024","journal-title":"Sci. Rep."},{"key":"2026081820132607200_RSOB250258C41","doi-asserted-by":"crossref","first-page":"103671","DOI":"10.1016\/j.msard.2022.103671","article-title":"Systematic review and meta-analysis of Mycobacterium avium subsp. paratuberculosis as environmental trigger of multiple sclerosis","volume":"59","author":"Ekundayo","year":"2022","journal-title":"Mult. Scler. Relat. Disord."},{"key":"2026081820132607200_RSOB250258C42","article-title":"The mucosal immune system","volume-title":"Immunobiology: the immune system in health and disease","author":"Janeway","year":"2001"},{"key":"2026081820132607200_RSOB250258C43","article-title":"Luminal nutrients and microbes in gut mucosal growth","volume-title":"Regulation of gastrointestinal mucosal growth","author":"Rao","year":"2010"},{"key":"2026081820132607200_RSOB250258C44","doi-asserted-by":"crossref","first-page":"886","DOI":"10.3390\/nu13030886","article-title":"The interplay between the gut microbiome and the immune system in the context of infectious diseases throughout life and the role of nutrition in optimizing treatment strategies","volume":"13","author":"Wiertsema","year":"2021","journal-title":"Nutrients"},{"key":"2026081820132607200_RSOB250258C45","article-title":"Johne's disease and Crohn's disease","volume-title":"Diagnosis and control of Johne's disease","author":"National Research Council (US) Committee on Diagnosis and Control of Johne's Disease","year":"2003"},{"key":"2026081820132607200_RSOB250258C46","doi-asserted-by":"crossref","first-page":"1323","DOI":"10.1001\/jama.1932.02740680019005","article-title":"Regional ileitis: a pathologic and clinical entity","volume":"99","author":"Crohn","year":"1932","journal-title":"J. Am. Med. Assoc."},{"key":"2026081820132607200_RSOB250258C47","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":"2026081820132607200_RSOB250258C48","doi-asserted-by":"crossref","first-page":"1239","DOI":"10.1111\/j.1939-1676.2012.01019.x","article-title":"Paratuberculosis (Johne's disease) in cattle and other susceptible species","volume":"26","author":"Sweeney","year":"2012","journal-title":"J. Vet. Intern. Med."},{"key":"2026081820132607200_RSOB250258C49","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1111\/j.1751-0813.2006.00001.x","article-title":"Losses of adult sheep due to ovine Johne's disease in 12 infected flocks over a 3-year period","volume":"84","author":"Bush","year":"2006","journal-title":"Aust. Vet. J."},{"key":"2026081820132607200_RSOB250258C50","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1016\/S0167-5877(99)00037-9","article-title":"Herd-level economic losses associated with Johne's disease on US dairy operations","volume":"40","author":"Ott","year":"1999","journal-title":"Prev. Vet. Med."},{"key":"2026081820132607200_RSOB250258C51","doi-asserted-by":"crossref","first-page":"7102","DOI":"10.1016\/j.vaccine.2007.07.054","article-title":"Comparative efficacy of an indigenous \u2018inactivated vaccine\u2019 using highly pathogenic field strain of Mycobacterium avium subspecies paratuberculosis \u2018Bison type\u2019 with a commercial vaccine for the control of Capri-paratuberculosis in India","volume":"25","author":"Singh","year":"2007","journal-title":"Vaccine"},{"key":"2026081820132607200_RSOB250258C52","doi-asserted-by":"crossref","first-page":"1086","DOI":"10.1177\/03009858211025790","article-title":"Apoptosis levels in bovine Johne's disease ileal lesions and association with bacterial numbers","volume":"58","author":"Lucena","year":"2021","journal-title":"Vet. Pathol."},{"key":"2026081820132607200_RSOB250258C53","doi-asserted-by":"crossref","first-page":"e065186","DOI":"10.1136\/bmjopen-2022-065186","article-title":"Global, regional and national burden of inflammatory bowel disease in 204 countries and territories from 1990 to 2019: a systematic analysis based on the Global Burden of Disease Study 2019","volume":"13","author":"Wang","year":"2023","journal-title":"BMJ Open"},{"key":"2026081820132607200_RSOB250258C54","doi-asserted-by":"crossref","first-page":"107430","DOI":"10.1016\/j.smallrumres.2025.107430","article-title":"Global prevalence of Mycobacterium avium subsp. paratuberculosis in sheep: systematic review and meta-analysis","volume":"243","author":"Magalh\u00e3es","year":"2025","journal-title":"Small Rumin. Res."},{"key":"2026081820132607200_RSOB250258C55","doi-asserted-by":"crossref","first-page":"544","DOI":"10.4161\/gmic.22156","article-title":"Role of commensal gut bacteria in inflammatory bowel diseases","volume":"3","author":"Loh","year":"2012","journal-title":"Gut Microbes"},{"key":"2026081820132607200_RSOB250258C56","author":"World Organization for Animal Health"},{"key":"2026081820132607200_RSOB250258C57","doi-asserted-by":"crossref","first-page":"1090","DOI":"10.1111\/j.1939-1676.2008.0147.x","article-title":"Detection of Mycobacterium avium subspecies paratuberculosis-specific DNA by PCR in intestinal biopsies of dogs","volume":"22","author":"Glanemann","year":"2008","journal-title":"J. Vet. Intern. Med."},{"key":"2026081820132607200_RSOB250258C58","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1007\/s10620-020-06653-0","article-title":"Putting Crohn's on the MAP: five common questions on the contribution of Mycobacterium avium subspecies paratuberculosis to the pathophysiology of Crohn's disease","volume":"66","author":"Agrawal","year":"2021","journal-title":"Dig. Dis. Sci."},{"key":"2026081820132607200_RSOB250258C59","doi-asserted-by":"crossref","first-page":"28","DOI":"10.21037\/tgh-23-16","article-title":"Mycobacterium avium subspecies paratuberculosis (MAP) and Crohn's disease: the debate continues","volume":"8","author":"Mintz","year":"2023","journal-title":"Transl. Gastroenterol. Hepatol."},{"key":"2026081820132607200_RSOB250258C60","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1757-4749-2-21","article-title":"Ulcerative colitis and Crohn's disease: is Mycobacterium avium subspecies paratuberculosis the common villain?","volume":"2","author":"Pierce","year":"2010","journal-title":"Gut Pathog."},{"key":"2026081820132607200_RSOB250258C61","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1007\/s00428-013-1474-5","article-title":"Lymphoid aggregates in Crohn's colitis and mucosal immunity","volume":"463","author":"Rubio","year":"2013","journal-title":"Virchows. Arch."},{"key":"2026081820132607200_RSOB250258C62","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1016\/S1473-3099(07)70211-6","article-title":"Mycobacterium avium subspecies paratuberculosis and Crohn's disease: a systematic review and meta-analysis","volume":"7","author":"Feller","year":"2007","journal-title":"Lancet Infect. Dis."},{"key":"2026081820132607200_RSOB250258C63","first-page":"e75663","article-title":"Endoscopic monitoring of treatment of indeterminate intestinal lesions in a prospective \u2018real-life\u2019 cohort in eastern India where tuberculosis remains endemic: distinguishing intestinal tuberculosis from Crohn's disease","volume":"16","author":"Deka","year":"2024","journal-title":"Cureus"},{"key":"2026081820132607200_RSOB250258C64","doi-asserted-by":"crossref","first-page":"2391","DOI":"10.2169\/internalmedicine.3093-23","article-title":"Significance of epidemiological background in preventing the misdiagnosis of intestinal tuberculosis as Crohn's disease","volume":"63","author":"Kaneko","year":"2024","journal-title":"Intern. Med."},{"key":"2026081820132607200_RSOB250258C65","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1186\/s13000-024-01566-2","article-title":"Is the identification of caseating granuloma in the intestine indicative of tuberculosis? A rare case of Crohn's disease","volume":"19","author":"Tao","year":"2024","journal-title":"Diagn. Pathol."},{"key":"2026081820132607200_RSOB250258C66","doi-asserted-by":"crossref","first-page":"1218","DOI":"10.1111\/apt.18522","article-title":"Crohn's disease with latent tuberculosis infection or intestinal tuberculosis: rapid discrimination by targeted next-generation sequencing","volume":"61","author":"Ye","year":"2025","journal-title":"Aliment. Pharmacol. Ther."},{"key":"2026081820132607200_RSOB250258C67","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s40588-020-00145-5","article-title":"Mycobacterium avium: an emerging pathogen for dog breeds with hereditary immunodeficiencies","volume":"7","author":"Ghielmetti","year":"2020","journal-title":"Curr. Clin. Microbiol. Rep."},{"key":"2026081820132607200_RSOB250258C68","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/1757-4749-1-15","article-title":"Mycobacterium avium subspecies paratuberculosis, Crohn's disease and the Doomsday scenario","volume":"1","author":"Hermon-Taylor","year":"2009","journal-title":"Gut Pathog."},{"key":"2026081820132607200_RSOB250258C69","article-title":"The possible involvement of Mycobacterium avium spp. paratuberculosis in the aetiology of Crohn's disease: a case control study in the Netherlands","author":"Herrewegh"},{"key":"2026081820132607200_RSOB250258C70","doi-asserted-by":"crossref","first-page":"141","DOI":"10.3109\/1040841X.2010.532480","article-title":"Current perspectives on Mycobacterium avium subsp. paratuberculosis, Johne's disease, and Crohn's disease: a review","volume":"37","author":"Over","year":"2011","journal-title":"Crit. Rev. Microbiol."},{"key":"2026081820132607200_RSOB250258C71","doi-asserted-by":"crossref","first-page":"2371","DOI":"10.3168\/jds.2009-2344","article-title":"Lack of association between the occurrence of Crohn's disease and occupational exposure to dairy and beef cattle herds infected with Mycobacterium avium subspecies paratuberculosis","volume":"93","author":"Qual","year":"2010","journal-title":"J. Dairy Sci."},{"key":"2026081820132607200_RSOB250258C72","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1155\/2010\/698362","article-title":"Mycobacterium avium\u00a0paratuberculosis and the etiology of Crohn's disease: a review of the controversy from the clinician's perspective","volume":"24","author":"Rosenfeld","year":"2010","journal-title":"Can. J. Gastroenterol."},{"key":"2026081820132607200_RSOB250258C73","doi-asserted-by":"crossref","first-page":"801892","DOI":"10.3389\/fmicb.2022.801892","article-title":"Bacterial species associated with human inflammatory bowel disease and their pathogenic mechanisms","volume":"13","author":"Zhang","year":"2022","journal-title":"Front. Microbiol."},{"key":"2026081820132607200_RSOB250258C74","doi-asserted-by":"crossref","first-page":"102267","DOI":"10.1016\/j.tube.2022.102267","article-title":"Nontuberculous mycobacteria in the environment","volume":"137","author":"Falkinham","year":"2022","journal-title":"Tuberculosis"},{"key":"2026081820132607200_RSOB250258C75","doi-asserted-by":"crossref","first-page":"2901","DOI":"10.3389\/fmicb.2018.02901","article-title":"Host variability in NTM disease: implications for research needs","volume":"9","author":"Swenson","year":"2018","journal-title":"Front. Microbiol."},{"key":"2026081820132607200_RSOB250258C76","doi-asserted-by":"crossref","first-page":"96","DOI":"10.3390\/biology10020096","article-title":"Drug resistance in nontuberculous mycobacteria: mechanisms and models","volume":"10","author":"Saxena","year":"2021","journal-title":"Biology"},{"key":"2026081820132607200_RSOB250258C77","doi-asserted-by":"crossref","first-page":"392","DOI":"10.1038\/s41579-020-0331-1","article-title":"Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus","volume":"18","author":"Johansen","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"2026081820132607200_RSOB250258C78","doi-asserted-by":"crossref","first-page":"e0007799","DOI":"10.1371\/journal.pntd.0007799","article-title":"Mycobacterium abscessus infection in the stomach of patients with various gastric symptoms","volume":"13","author":"Chouhan","year":"2019","journal-title":"PLoS Negl. Trop. Dis."},{"key":"2026081820132607200_RSOB250258C79","doi-asserted-by":"crossref","first-page":"7242","DOI":"10.1128\/IAI.69.12.7242-7249.2001","article-title":"Phenotypic and genomic analyses of the Mycobacterium avium complex reveal differences in gastrointestinal invasion and genomic composition","volume":"69","author":"McGarvey","year":"2001","journal-title":"Infect. Immun."},{"key":"2026081820132607200_RSOB250258C80","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1099\/mic.0.073379-0","article-title":"Long-term survival of tuberculosis complex mycobacteria in soil","volume":"160","author":"Ghodbane","year":"2014","journal-title":"Microbiology"},{"key":"2026081820132607200_RSOB250258C81","doi-asserted-by":"crossref","first-page":"1515","DOI":"10.1128\/IAI.69.3.1515-1520.2001","article-title":"Mycobacterium avium invades the intestinal mucosa primarily by interacting with enterocytes","volume":"69","author":"Sangari","year":"2001","journal-title":"Infect. Immun."},{"key":"2026081820132607200_RSOB250258C82","doi-asserted-by":"crossref","first-page":"e21","DOI":"10.1016\/S1473-3099(16)30139-6","article-title":"Zoonotic tuberculosis in human beings caused by Mycobacterium bovis: a call for action","volume":"17","author":"Olea-Popelka","year":"2017","journal-title":"Lancet Infect. Dis."},{"key":"2026081820132607200_RSOB250258C83","article-title":"Tuberculosis","author":"World Health Organization","year":"2026"},{"key":"2026081820132607200_RSOB250258C84","doi-asserted-by":"crossref","first-page":"1228","DOI":"10.3390\/pathogens11111228","article-title":"Mycobacterium tuberculosis transmission in high-incidence settings\u2014new paradigms and insights","volume":"11","author":"Coleman","year":"2022","journal-title":"Pathogens"},{"key":"2026081820132607200_RSOB250258C85","doi-asserted-by":"crossref","first-page":"20401","DOI":"10.1038\/s41598-024-70199-8","article-title":"Drug resistance and genomic variations among Mycobacterium tuberculosis isolates from the Nile Delta, Egypt","volume":"14","author":"Soliman","year":"2024","journal-title":"Sci. Rep."},{"key":"2026081820132607200_RSOB250258C86","article-title":"Leprosy","author":"World Health Organization","year":"2026"},{"key":"2026081820132607200_RSOB250258C87","doi-asserted-by":"crossref","first-page":"e0008276","DOI":"10.1371\/journal.pntd.0008276","article-title":"Reservoirs and transmission routes of leprosy; a systematic review","volume":"14","author":"Ploemacher","year":"2020","journal-title":"PLoS Negl. Trop. Dis."},{"key":"2026081820132607200_RSOB250258C88","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1080\/01652176.2018.1447171","article-title":"Mycobacterium marinum infection in fish and man: epidemiology, pathophysiology and management; a review","volume":"38","author":"Hashish","year":"2018","journal-title":"Vet. Q."},{"key":"2026081820132607200_RSOB250258C89","doi-asserted-by":"crossref","DOI":"10.1128\/microbiolspec.TNMI7-0038-2016","article-title":"Mycobacterium marinum","volume":"5","author":"Aubry","year":"2017","journal-title":"Microbiol. Spectr."},{"key":"2026081820132607200_RSOB250258C90","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1016\/B978-1-4377-0126-5.00024-0","article-title":"Nontuberculous mycobacterial skin infections","volume-title":"Netter's infectious disease","author":"Tulloch","year":"2012"},{"key":"2026081820132607200_RSOB250258C91","doi-asserted-by":"crossref","first-page":"159","DOI":"10.1016\/j.vetmic.2003.07.011","article-title":"Piscine mycobacteriosis: a literature review covering the agent and the disease it causes in fish and humans","volume":"99","author":"Decostere","year":"2004","journal-title":"Vet. Microbiol."},{"key":"2026081820132607200_RSOB250258C92","doi-asserted-by":"crossref","first-page":"12415","DOI":"10.1002\/jcp.28076","article-title":"Mycobacterium avium\u00a0paratuberculosis and Mycobacterium avium complex and related subspecies as causative agents of zoonotic and occupational diseases","volume":"234","author":"Eslami","year":"2019","journal-title":"J. Cell. Physiol."},{"key":"2026081820132607200_RSOB250258C93","first-page":"17","article-title":"Mycobacterium avium complex disease","author":"Hanna","year":"1995","journal-title":"BETA"},{"key":"2026081820132607200_RSOB250258C94","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.copbio.2019.03.010","article-title":"Nontuberculous mycobacteria in drinking water systems\u2014the challenges of characterization and risk mitigation","volume":"57","author":"Dowdell","year":"2019","journal-title":"Curr. Opin. Biotechnol."},{"key":"2026081820132607200_RSOB250258C95","doi-asserted-by":"crossref","first-page":"410362","DOI":"10.3389\/fmicb.2018.02029","article-title":"Global environmental nontuberculous mycobacteria and their contemporaneous man-made and natural niches","volume":"9","author":"Honda","year":"2018","journal-title":"Front. Microbiol."},{"key":"2026081820132607200_RSOB250258C96","doi-asserted-by":"crossref","first-page":"100374","DOI":"10.1016\/j.onehlt.2022.100374","article-title":"High rate of reinfection and possible transmission of Mycobacterium avium complex in northeast Thailand","volume":"14","author":"Boonjetsadaruhk","year":"2022","journal-title":"One Health"},{"key":"2026081820132607200_RSOB250258C97","doi-asserted-by":"crossref","first-page":"576","DOI":"10.3201\/eid2403.171554","article-title":"Global health estimate of invasive Mycobacterium chimaera infections associated with heater\u2013cooler devices in cardiac surgery","volume":"24","author":"Sommerstein","year":"2018","journal-title":"Emerg. Infect. Dis."},{"key":"2026081820132607200_RSOB250258C98","doi-asserted-by":"crossref","first-page":"204","DOI":"10.20506\/rst.20.1.1272","article-title":"Mycobacterium avium and Mycobacterium intracellulare infection in mammals","volume":"20","author":"Thorel","year":"2001","journal-title":"Rev. Sci. Tech."},{"key":"2026081820132607200_RSOB250258C99","doi-asserted-by":"crossref","first-page":"4407","DOI":"10.1128\/JCM.43.9.4407-4412.2005","article-title":"Clinical significance and epidemiologic analyses of Mycobacterium avium and Mycobacterium intracellulare among patients without AIDS","volume":"43","author":"Han","year":"2005","journal-title":"J. Clin. Microbiol."},{"key":"2026081820132607200_RSOB250258C100","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1128\/JCM.03399-13","article-title":"Subspecies identification and significance of 257 clinical strains of Mycobacterium avium","volume":"52","author":"Tran","year":"2014","journal-title":"J. Clin. Microbiol."},{"key":"2026081820132607200_RSOB250258C101","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/j.tube.2018.12.004","article-title":"Mycobacterium avium: an overview","volume":"114","author":"Busatto","year":"2019","journal-title":"Tuberculosis"},{"key":"2026081820132607200_RSOB250258C102","doi-asserted-by":"crossref","first-page":"e00402","DOI":"10.1128\/msystems.00402-19","article-title":"Global assessment of Mycobacterium avium subsp. hominissuis genetic requirement for growth and virulence","volume":"4","author":"Dragset","year":"2019","journal-title":"mSystems"},{"key":"2026081820132607200_RSOB250258C103","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1164\/rccm.201002-0310OC","article-title":"Nontuberculous mycobacterial lung disease prevalence at four integrated health care delivery systems","volume":"182","author":"Prevots","year":"2012","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"2026081820132607200_RSOB250258C104","first-page":"70","article-title":"Mycobacterium chelonae infection","volume":"8","author":"Akram","year":"2023","journal-title":"Infect. Dis. Newslett."},{"key":"2026081820132607200_RSOB250258C105","doi-asserted-by":"crossref","first-page":"1638","DOI":"10.3201\/2109.141634","article-title":"Mycobacterium abscessus complex infections in humans","volume":"21","author":"Lee","year":"2015","journal-title":"Emerg. Infect. Dis."},{"key":"2026081820132607200_RSOB250258C106","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1016\/j.ijregi.2022.02.004","article-title":"Non-tuberculous mycobacteria, not Mycobacterium bovis, are a significant cause of TB-like lesions observed in slaughtered cattle in Ghana","volume":"3","author":"Tingan","year":"2022","journal-title":"IJID Regions"},{"key":"2026081820132607200_RSOB250258C107","doi-asserted-by":"crossref","first-page":"550","DOI":"10.3201\/eid1703.101400","article-title":"Mycobacterium novocastrense-associated pulmonary and wound infections","volume":"17","author":"Shojaei","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"2026081820132607200_RSOB250258C108","doi-asserted-by":"crossref","first-page":"105297","DOI":"10.1016\/j.actatropica.2019.105297","article-title":"Identification and molecular characterization of mycobacteria isolated from animal sources in a developing country","volume":"204","author":"Dibaj","year":"2020","journal-title":"Acta Trop."},{"key":"2026081820132607200_RSOB250258C109","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1007\/s10393-022-01602-x","article-title":"Mycobacterium paratuberculosis zoonosis is a One Health emergency","volume":"19","author":"Dow","year":"2022","journal-title":"EcoHealth"},{"key":"2026081820132607200_RSOB250258C110","doi-asserted-by":"crossref","first-page":"3135","DOI":"10.1017\/S095026881500076X","article-title":"The zoonotic potential of Mycobacterium avium ssp. paratuberculosis: a systematic review and meta-analyses of the evidence","volume":"143","author":"Waddell","year":"2015","journal-title":"Epidemiol. Infect."},{"key":"2026081820132607200_RSOB250258C111","doi-asserted-by":"crossref","first-page":"549","DOI":"10.7861\/clinmed.2023-0493","article-title":"Crohn's disease: an update","volume":"23","author":"Cockburn","year":"2023","journal-title":"Clin. Med."},{"key":"2026081820132607200_RSOB250258C112","doi-asserted-by":"crossref","first-page":"e31892","DOI":"10.1097\/MD.0000000000031892","article-title":"An assessment of serum vitamin B12 and folate in patients with Crohn's disease","volume":"101","author":"Akbulut","year":"2022","journal-title":"Medicine"},{"key":"2026081820132607200_RSOB250258C113","doi-asserted-by":"crossref","first-page":"1384","DOI":"10.3390\/diagnostics14131384","article-title":"Diagnostic procedures for inflammatory bowel disease: laboratory, endoscopy, pathology, imaging, and beyond","volume":"14","author":"Hong","year":"2024","journal-title":"Diagnostics"},{"key":"2026081820132607200_RSOB250258C114","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1016\/S0378-1135(00)00316-3","article-title":"Parallel faecal and organ Mycobacterium avium subsp. paratuberculosis culture of different productivity types of cattle","volume":"77","author":"Pavlik","year":"2000","journal-title":"Vet. Microbiol."},{"key":"2026081820132607200_RSOB250258C115","first-page":"874","article-title":"Johne's disease in Canada: part I: clinical symptoms, pathophysiology, diagnosis, and prevalence in dairy herds","volume":"47","author":"Tiwari","year":"2006","journal-title":"Can. Vet. J."},{"key":"2026081820132607200_RSOB250258C116","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/j.rvsc.2015.07.017","article-title":"Interferon gamma response to Mycobacterium avium subsp. paratuberculosis specific lipopentapeptide antigen L5P in cattle","volume":"102","author":"Holbert","year":"2015","journal-title":"Res. Vet. Sci."},{"key":"2026081820132607200_RSOB250258C117","doi-asserted-by":"crossref","first-page":"158","DOI":"10.3390\/antibiotics13020158","article-title":"Mycobacterium avium ssp. paratuberculosis and Crohn's disease\u2014diagnostic microbiological investigations can inform new therapeutic approaches","volume":"13","author":"Aitken","year":"2024","journal-title":"Antibiotics"},{"key":"2026081820132607200_RSOB250258C118","doi-asserted-by":"crossref","first-page":"100244","DOI":"10.1016\/j.jctube.2021.100244","article-title":"Approach to the diagnosis and treatment of non-tuberculous mycobacterial disease","volume":"24","author":"Pennington","year":"2021","journal-title":"J. Clin. Tuberc. Other Mycobact. Dis."},{"key":"2026081820132607200_RSOB250258C119","doi-asserted-by":"crossref","first-page":"1349999","DOI":"10.3389\/fcimb.2024.1349999","article-title":"Droplet digital PCR as alternative to microbiological culture for Mycobacterium tuberculosis complex detection in bovine lymph node tissue samples","volume":"14","author":"S\u00e1nchez-Carvajal","year":"2024","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"2026081820132607200_RSOB250258C120","doi-asserted-by":"crossref","first-page":"103498","DOI":"10.1016\/j.autrev.2023.103498","article-title":"Global, regional, and national burden of inflammatory bowel disease and its associated anemia, 1990 to 2019 and predictions to 2050: an analysis of the global burden of disease study 2019","volume":"23","author":"Wang","year":"2024","journal-title":"Autoimmun. Rev."},{"key":"2026081820132607200_RSOB250258C121","doi-asserted-by":"crossref","first-page":"637841","DOI":"10.3389\/fvets.2021.637841","article-title":"Engineering synthetic lipopeptide antigen for specific detection of Mycobacterium avium subsp. paratuberculosis infection","volume":"8","author":"Bay","year":"2021","journal-title":"Front. Vet. Sci."},{"key":"2026081820132607200_RSOB250258C122","doi-asserted-by":"crossref","first-page":"704","DOI":"10.14202\/vetworld.2023.704-710","article-title":"Multiplex assay for the simultaneous detection of antibodies against small ruminant lentivirus, Mycobacterium avium subsp. paratuberculosis, and Brucella melitensis in goats","volume":"16","author":"N\u00e1jera-Rivera","year":"2023","journal-title":"Vet. World"},{"key":"2026081820132607200_RSOB250258C123","doi-asserted-by":"crossref","first-page":"62","DOI":"10.14745\/ccdr.v43i34a01","article-title":"Latent tuberculosis infection: an overview","volume":"43","author":"Kiazyk","year":"2017","journal-title":"Can. Commun. Dis. Rep."},{"key":"2026081820132607200_RSOB250258C124","doi-asserted-by":"crossref","first-page":"106807","DOI":"10.1016\/j.mimet.2023.106807","article-title":"A novel biphasic approach to reactivation of dormant Mycobacterium avium subspecies paratuberculosis","volume":"212","author":"Baradaran-Seyed","year":"2023","journal-title":"J. Microbiol. Methods"},{"key":"2026081820132607200_RSOB250258C125","doi-asserted-by":"crossref","first-page":"44765","DOI":"10.1038\/srep44765","article-title":"Inferring biomarkers for Mycobacterium avium subsp. paratuberculosis infection and disease progression in cattle using experimental data","volume":"7","author":"Magombedze","year":"2017","journal-title":"Sci. Rep."},{"key":"2026081820132607200_RSOB250258C126","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1016\/S0167-7012(00)00185-8","article-title":"Identification of cell wall deficient forms of M. avium subsp. paratuberculosis in paraffin embedded tissues from animals with Johne's disease by in situ hybridization","volume":"42","author":"Hulten","year":"2000","journal-title":"J. Microbiol. Methods"},{"key":"2026081820132607200_RSOB250258C127","doi-asserted-by":"crossref","first-page":"22593","DOI":"10.1038\/s41598-023-46062-7","article-title":"Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach","volume":"13","author":"Roume","year":"2023","journal-title":"Sci. Rep."},{"key":"2026081820132607200_RSOB250258C128","doi-asserted-by":"crossref","first-page":"493817","DOI":"10.3389\/fcimb.2020.00151","article-title":"Current sampling methods for gut microbiota: a call for more precise devices","volume":"10","author":"Tang","year":"2020","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"2026081820132607200_RSOB250258C129","doi-asserted-by":"crossref","first-page":"4042","DOI":"10.1038\/s41598-019-40182-9","article-title":"Effects of bowel preparation on the human gut microbiome and metabolome","volume":"9","author":"Nagata","year":"2019","journal-title":"Sci. Rep."},{"key":"2026081820132607200_RSOB250258C130","doi-asserted-by":"crossref","first-page":"101294","DOI":"10.1016\/j.mtbio.2024.101294","article-title":"Capsule robots for the monitoring, diagnosis, and treatment of intestinal diseases","volume":"29","author":"Wei","year":"2024","journal-title":"Mater. Today Bio"},{"key":"2026081820132607200_RSOB250258C131","doi-asserted-by":"crossref","first-page":"29490","DOI":"10.1038\/srep29490","article-title":"A crystal-clear zebrafish for in vivo imaging","volume":"6","author":"Antinucci","year":"2016","journal-title":"Sci. Rep."},{"key":"2026081820132607200_RSOB250258C132","doi-asserted-by":"crossref","first-page":"1862","DOI":"10.1038\/nprot.2008.186","article-title":"Methods for generating and colonizing gnotobiotic zebrafish","volume":"3","author":"Pham","year":"2008","journal-title":"Nat. Protoc."},{"key":"2026081820132607200_RSOB250258C133","doi-asserted-by":"crossref","first-page":"e13152","DOI":"10.1111\/cmi.13152","article-title":"The zebrafish as a model for gastrointestinal tract\u2013microbe interactions","volume":"22","author":"Flores","year":"2020","journal-title":"Cell. Microbiol."},{"key":"2026081820132607200_RSOB250258C134","doi-asserted-by":"crossref","first-page":"12008","DOI":"10.3390\/ijms252212008","article-title":"Zebrafish (Danio rerio) as a model system to investigate the role of the innate immune response in human infectious diseases","volume":"25","author":"Franza","year":"2024","journal-title":"Int. J. Mol. Sci."},{"key":"2026081820132607200_RSOB250258C135","doi-asserted-by":"crossref","first-page":"100042","DOI":"10.1016\/j.medmic.2021.100042","article-title":"Zebrafish model for human gut microbiome-related studies: advantages and limitations","volume":"8","author":"Lu","year":"2021","journal-title":"Med. Microecol."},{"key":"2026081820132607200_RSOB250258C136","doi-asserted-by":"crossref","first-page":"5359","DOI":"10.7150\/ijbs.124776","article-title":"The function of TLR2 and the microbiome in macrophage-dependent dissemination of nontuberculous mycobacterial gut infection","volume":"22","author":"Liu","year":"2026","journal-title":"Int. J. Biol. Sci."},{"key":"2026081820132607200_RSOB250258C137","doi-asserted-by":"crossref","first-page":"4633","DOI":"10.1038\/s41596-021-00589-z","article-title":"Intestinal organoid cocultures with microbes","volume":"16","author":"Puschhof","year":"2021","journal-title":"Nat. Protoc."},{"key":"2026081820132607200_RSOB250258C138","doi-asserted-by":"crossref","first-page":"2819154","DOI":"10.1155\/2018\/2819154","article-title":"Regulation of intestinal epithelial cells properties and functions by amino acids","volume":"2018","author":"Kong","year":"2018","journal-title":"Biomed Res. Int."},{"key":"2026081820132607200_RSOB250258C139","doi-asserted-by":"crossref","first-page":"C183","DOI":"10.1152\/ajpcell.1991.260.2.C183","article-title":"Functional biology of intestinal goblet cells","volume":"260","author":"Specian","year":"1991","journal-title":"Am. J. Physiol. Cell Physiol."},{"key":"2026081820132607200_RSOB250258C140","doi-asserted-by":"crossref","first-page":"e16427","DOI":"10.15252\/emmm.202216427","article-title":"Paneth cells as the cornerstones of intestinal and organismal health: a primer","volume":"15","author":"Wallaeys","year":"2023","journal-title":"EMBO Mol. Med."},{"key":"2026081820132607200_RSOB250258C141","doi-asserted-by":"crossref","first-page":"2702","DOI":"10.1016\/j.yexcr.2011.09.006","article-title":"Intestinal development and differentiation","volume":"317","author":"Noah","year":"2011","journal-title":"Exp. Cell Res."},{"key":"2026081820132607200_RSOB250258C142","doi-asserted-by":"crossref","first-page":"20170217","DOI":"10.1098\/rstb.2017.0217","article-title":"Intestinal organoids for modelling intestinal development and disease","volume":"373","author":"Fair","year":"2018","journal-title":"Phil. Trans. R. Soc. B"},{"key":"2026081820132607200_RSOB250258C143","doi-asserted-by":"crossref","first-page":"820","DOI":"10.3390\/cells13100820","article-title":"The imperative for innovative enteric nervous system\u2013intestinal organoid co-culture models: transforming GI disease modeling and treatment","volume":"13","author":"Llorente","year":"2024","journal-title":"Cells"},{"key":"2026081820132607200_RSOB250258C144","doi-asserted-by":"crossref","first-page":"e70531","DOI":"10.1002\/mco2.70531","article-title":"Immune and immune-integrated organoids as NextGeneration platforms for disease modeling","volume":"6","author":"Rashidan","year":"2025","journal-title":"MedComm"},{"key":"2026081820132607200_RSOB250258C145","doi-asserted-by":"crossref","first-page":"2630483","DOI":"10.1080\/19490976.2026.2630483","article-title":"Responses of intestinal organoids to infection by Mycobacterium avium resemble symptoms observed in Crohn's disease","volume":"18","author":"Hu","year":"2026","journal-title":"Gut Microbes"},{"key":"2026081820132607200_RSOB250258C146","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1111\/febs.12078","article-title":"Cryo-electron microscopy\u2014a primer for the non-microscopist","volume":"280","author":"Milne","year":"2013","journal-title":"FEBS J."},{"key":"2026081820132607200_RSOB250258C147","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1007\/s13199-022-00859-8","article-title":"Zooming in on host-symbiont interactions: advances in cryo-EM sample processing methods and future application to symbiotic tissues","volume":"87","author":"Gundlach","year":"2022","journal-title":"Symbiosis"},{"key":"2026081820132607200_RSOB250258C148","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1007\/978-1-0716-2639-9_13","article-title":"High-pressure freezing followed by freeze substitution: an optimal electron microscope technique to study Golgi apparatus organization and membrane trafficking","volume":"2557","author":"Liu","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"2026081820132607200_RSOB250258C149","doi-asserted-by":"crossref","first-page":"877","DOI":"10.1007\/s00418-008-0500-1","article-title":"Electron microscopy of high pressure frozen samples: bridging the gap between cellular ultrastructure and atomic resolution","volume":"130","author":"Studer","year":"2008","journal-title":"Histochem. Cell Biol."},{"key":"2026081820132607200_RSOB250258C150","doi-asserted-by":"crossref","first-page":"1684","DOI":"10.1038\/s41592-023-02113-5","article-title":"Serial lift-out: sampling the molecular anatomy of whole organisms","volume":"21","author":"Schi\u00f8tz","year":"2023","journal-title":"Nat. Methods"},{"key":"2026081820132607200_RSOB250258C151","doi-asserted-by":"crossref","first-page":"2591","DOI":"10.1038\/s41396-021-00952-8","article-title":"Microbial hitchhiking: how streptomyces spores are transported by motile soil bacteria","volume":"15","author":"Muok","year":"2021","journal-title":"ISME J."},{"key":"2026081820132607200_RSOB250258C152","doi-asserted-by":"crossref","first-page":"478","DOI":"10.4103\/ijmy.ijmy_190_23","article-title":"Identification of seven types of pili in Mycobacterium tuberculosis: using atomic force microscopy","volume":"12","author":"Farnia","year":"2023","journal-title":"Int. J. Mycobacteriol."},{"key":"2026081820132607200_RSOB250258C153","doi-asserted-by":"crossref","first-page":"247","DOI":"10.3390\/biology14030247","article-title":"Evolution of the PE_PGRS proteins of mycobacteria: are all equal or are some more equal than others?","volume":"14","author":"Chen","year":"2025","journal-title":"Biology"},{"key":"2026081820132607200_RSOB250258C154","doi-asserted-by":"crossref","first-page":"462","DOI":"10.1093\/ecco-jcc\/jjad178","article-title":"Matrix metalloproteinases in intestinal fibrosis","volume":"18","author":"Biel","year":"2023","journal-title":"J. Crohn's Colitis"},{"key":"2026081820132607200_RSOB250258C155","doi-asserted-by":"crossref","first-page":"2506","DOI":"10.3390\/ijms22052506","article-title":"Tight junctions as a key for pathogens invasion in intestinal epithelial cells","volume":"22","author":"Paradis","year":"2021","journal-title":"Int. J. Mol. Sci."}],"container-title":["Open Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/royalsocietypublishing.org\/rsob\/article-pdf\/doi\/10.1098\/rsob.250258\/6158932\/rsob.250258.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/royalsocietypublishing.org\/rsob\/article-pdf\/doi\/10.1098\/rsob.250258\/6158932\/rsob.250258.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T00:13:51Z","timestamp":1787098431000},"score":1,"resource":{"primary":{"URL":"https:\/\/royalsocietypublishing.org\/rsob\/article\/16\/8\/250258\/482826\/A-modern-toolbox-to-elucidate-the-role-of-the"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,19]]},"references-count":155,"journal-issue":{"issue":"8","published-print":{"date-parts":[[2026,8,19]]}},"URL":"https:\/\/doi.org\/10.1098\/rsob.250258","relation":{},"ISSN":["2046-2441"],"issn-type":[{"value":"2046-2441","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,19]]},"article-number":"250258"}}