{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T13:05:05Z","timestamp":1789477505384,"version":"build-2803163510"},"reference-count":73,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T00:00:00Z","timestamp":1789430400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"INNODOCTO 2024","award":["INNTA3\/2024\/13"],"award-info":[{"award-number":["INNTA3\/2024\/13"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>As a central regulator of nutrient absorption, immune homeostasis and overall health, the gastrointestinal tract has become a major focus of biomedical research. However, developing in vitro models that accurately reproduce human gastrointestinal architecture and physiological conditions remains a major challenge. Gut-on-chip (GoC) systems, which integrate microfluidics with cell cultures, have emerged as a promising solution in the past decade. By recreating dynamic microenvironments that incorporate fluid flow, peristalsis-like mechanical stimulation and co-culture with microorganisms, GoC systems enable more physiologically relevant investigation of host\u2013microbe and host\u2013microbiome interactions. This systematic review provides a comprehensive overview of available GoC technology used in host\u2013microbe research, including their structural and cellular components. A systematic search of PubMed, Embase and Google Scholar databases up to May 2026 identified forty-eight studies evaluating interactions between the host and probiotic strains, postbiotics, commensal microorganisms, pathogenic bacteria, fungi, viruses, or faecal-derived microbiota using GoCs. Common features, distinctive characteristics and application for modelling host\u2013microbiome interactions and pathogenic infections are summarized. The available literature is characterized by heterogeneous study designs, variable microbiome compositions and analytical approaches, and limited cross-platform standardization, which should be considered when interpreting findings. Lastly, current limitations and future perspectives are discussed, highlighting the potential of GoC models to support biotic characterization and preclinical evaluation while underscoring the need for further validation and standardization.<\/jats:p>","DOI":"10.3390\/microorganisms14092059","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T11:57:34Z","timestamp":1789473454000},"page":"2059","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Gut-on-Chip Models for Host\u2013Microbiome Studies: A Systematic Review"],"prefix":"10.3390","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0009-0006-2241-840X","authenticated-orcid":false,"given":"Jennifer","family":"Redondo","sequence":"first","affiliation":[{"name":"Archer Daniels Midland, Microbiome Research Center, Biopolis S.L. Parc Cientific Universitat de Val\u00e8ncia, C\/Catedr\u00e1tico Agust\u00edn Escardino Benlloch, 9, 46980 Paterna, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1459-0702","authenticated-orcid":false,"given":"Guillermo","family":"Garcia-Lainez","sequence":"additional","affiliation":[{"name":"Archer Daniels Midland, Microbiome Research Center, Biopolis S.L. Parc Cientific Universitat de Val\u00e8ncia, C\/Catedr\u00e1tico Agust\u00edn Escardino Benlloch, 9, 46980 Paterna, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7068-0804","authenticated-orcid":false,"given":"Ver\u00f3nica","family":"Mart\u00ednez-R\u00edos","sequence":"additional","affiliation":[{"name":"Archer Daniels Midland, Microbiome Research Center, Biopolis S.L. Parc Cientific Universitat de Val\u00e8ncia, C\/Catedr\u00e1tico Agust\u00edn Escardino Benlloch, 9, 46980 Paterna, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6891-3573","authenticated-orcid":false,"given":"Empar","family":"Chenoll","sequence":"additional","affiliation":[{"name":"Archer Daniels Midland, Microbiome Research Center, Biopolis S.L. Parc Cientific Universitat de Val\u00e8ncia, C\/Catedr\u00e1tico Agust\u00edn Escardino Benlloch, 9, 46980 Paterna, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5689-8399","authenticated-orcid":false,"given":"Patricia","family":"Martorell","sequence":"additional","affiliation":[{"name":"Archer Daniels Midland, Microbiome Research Center, Biopolis S.L. 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Microbiol."},{"key":"ref_4","first-page":"1","article-title":"Gut microbiota as a source of novel antimicrobials","volume":"10","author":"Mayer","year":"2019","journal-title":"Gut Microbes"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00394-017-1445-8","article-title":"Gut microbiota functions: Metabolism of nutrients and other food components","volume":"57","author":"Rowland","year":"2018","journal-title":"Eur. J. Nutr."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1038\/nrmicro818","article-title":"Pathogenic Escherichia coli","volume":"2","author":"Kaper","year":"2004","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1016\/j.bbamem.2008.10.028","article-title":"Tight junctions as targets of infectious agents","volume":"1788","author":"Guttman","year":"2009","journal-title":"Biochim. Biophys. Acta"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/j.cgh.2018.09.028","article-title":"Prebiotics and Probiotics in Digestive Health","volume":"17","author":"Quigley","year":"2019","journal-title":"Clin. Gastroenterol. Hepatol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"2065","DOI":"10.1007\/s10068-024-01620-1","article-title":"Exploring the gut microbiome: Probiotics, prebiotics, synbiotics, and postbiotics as key players in human health and disease improvement","volume":"33","author":"Kim","year":"2024","journal-title":"Food Sci. Biotechnol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Nowicki, C., Ray, L., Engen, P., Madrigrano, A., Witt, T., Lad, T., Cobleigh, M., and Mutlu, E.A. (2023). Comparison of gut microbiome composition in colonic biopsies, endoscopically-collected and at-home-collected stool samples. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1148097"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1470","DOI":"10.1038\/s41467-024-45855-2","article-title":"Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease","volume":"15","author":"Hu","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2165","DOI":"10.1039\/c2lc40074j","article-title":"Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow","volume":"12","author":"Kim","year":"2012","journal-title":"Lab Chip"},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"14704","DOI":"10.1021\/acs.jafc.5c14263","article-title":"Intestinal Organoid Models as Emerging Tools to Investigate the Impact of Dietary Components on Gut Health","volume":"74","author":"Ye","year":"2026","journal-title":"J. Agric. Food Chem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"4295","DOI":"10.1016\/j.cell.2025.05.041","article-title":"Co-development of mesoderm and endoderm enables organotypic vascularization in lung and gut organoids","volume":"188","author":"Miao","year":"2025","journal-title":"Cell"},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"RP97860","DOI":"10.7554\/eLife.97860","article-title":"The gut contractile organoid for studying the gut motility regulated by coordinating signals between interstitial cells of Cajal and smooth muscles","volume":"13","author":"Yagasaki","year":"2025","journal-title":"eLife"},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Fofanova, T.Y., Karandikar, U.C., Auchtung, J.M., Wilson, R.L., Valentin, A.J., Britton, R.A., Grande-Allen, K.J., Estes, M.K., Hoffman, K., and Ramani, S. (2024). A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction. PLoS ONE, 19.","DOI":"10.1371\/journal.pone.0300666"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"1222","DOI":"10.1093\/ecco-jcc\/jjaa257","article-title":"Organoid-based Models to Study the Role of Host-microbiota Interactions in IBD","volume":"15","author":"Poletti","year":"2021","journal-title":"J. Crohn\u2019s Colitis"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Jing, B., Wang, Z.A., Zhang, C., Deng, Q., Wei, J., Luo, Y., Zhang, X., Li, J., and Du, Y. (2020). Establishment and Application of Peristaltic Human Gut-Vessel Microsystem for Studying Host-Microbial Interaction. Front. Bioeng. Biotechnol., 8.","DOI":"10.3389\/fbioe.2020.00272"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"783","DOI":"10.1016\/j.scib.2020.11.015","article-title":"SARS-CoV-2 induced intestinal responses with a biomimetic human gut-on-chip","volume":"66","author":"Guo","year":"2021","journal-title":"Sci. Bull."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s13619-024-00198-7","article-title":"Standard: Human intestine-on-a-chip","volume":"13","author":"Liu","year":"2024","journal-title":"Cell Regen."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"e146496","DOI":"10.1172\/jci.insight.146496","article-title":"Microfluidic device facilitates in vitro modeling of human neonatal necrotizing enterocolitis-on-a-chip","volume":"8","author":"Lanik","year":"2023","journal-title":"JCI Insight"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Morelli, M., Kurek, D., Ng, C.P., and Queiroz, K. (2023). Gut-on-a-Chip Models: Current and Future Perspectives for Host-Microbial Interactions Research. Biomedicines, 11.","DOI":"10.3390\/biomedicines11020619"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"101079","DOI":"10.1016\/j.mtbio.2024.101079","article-title":"Establishment and evaluation of on-chip intestinal barrier biosystems based on microfluidic techniques","volume":"26","author":"Wang","year":"2024","journal-title":"Mater. Today Bio"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"117322","DOI":"10.1016\/j.jpba.2025.117322","article-title":"Multidimensional development of gut-on-a-chip technology: From fabrication processes, models, gut microbiome to gut-organ axis","volume":"271","author":"Chai","year":"2026","journal-title":"J. Pharm. Biomed. Anal."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"n71","DOI":"10.1136\/bmj.n71","article-title":"The PRISMA 2020 statement: An updated guideline for reporting systematic reviews","volume":"372","author":"Page","year":"2021","journal-title":"BMJ"},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"De la Rosa Gonzalez, A., Guerra-Ojeda, S., Camacho-Villa, M.A., Valls, A., Alegre, E., Quintero-Bernal, R., Martorell, P., Chenoll, E., Serna-Garcia, M., and Mauricio, M.D. (2024). Effect of Probiotics on Gastrointestinal Health Through the Aryl Hydrocarbon Receptor Pathway: A Systematic Review. Foods, 13.","DOI":"10.3390\/foods13213479"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e2116197119","DOI":"10.1073\/pnas.2116197119","article-title":"Bacteriophages evolve enhanced persistence to a mucosal surface","volume":"119","author":"Chin","year":"2022","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1007\/s12257-021-0268-x","article-title":"Development of a Pumpless Microfluidic System to Study the Interaction between Gut Microbes and Intestinal Epithelial Cells","volume":"27","author":"Lee","year":"2022","journal-title":"Biotechnol. Bioprocess Eng."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"18","DOI":"10.20517\/mrr.2023.79","article-title":"A host-microbial metabolite interaction gut-on-a-chip model of the adult human intestine demonstrates beneficial effects upon inulin treatment of gut microbiome","volume":"3","author":"Donkers","year":"2024","journal-title":"Microbiome Res. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"967","DOI":"10.1038\/s41551-024-01318-z","article-title":"A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma","volume":"9","author":"Ballerini","year":"2025","journal-title":"Nat. Biomed. Eng."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Lange, T., Sprague, J.L., Vij, R., Alonso-Roman, R., Jablonowski, N., Radosa, S., Kruger, T., Kniemeyer, O., Hillmann, F., and Brakhage, A.A. (2025). \u201cPour some sugar on me\u201d-Environmental Candida albicans isolates and the evolution of increased pathogenicity and antifungal resistance through sugar adaptation. PLoS Pathog., 21.","DOI":"10.1371\/journal.ppat.1013542"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"wrag054","DOI":"10.1093\/ismejo\/wrag054","article-title":"Cellular membrane protein MipA from E.coli Nissle 1917 protects against Salmonella infection","volume":"20","author":"Xiang","year":"2026","journal-title":"ISME J."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"4396","DOI":"10.1039\/D5LC00147A","article-title":"Gut-on-chip methodology based on 3D-printed molds: A cost-effective and accessible approach","volume":"25","author":"Delannoy","year":"2025","journal-title":"Lab Chip"},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Villenave, R., Wales, S.Q., Hamkins-Indik, T., Papafragkou, E., Weaver, J.C., Ferrante, T.C., Bahinski, A., Elkins, C.A., Kulka, M., and Ingber, D.E. (2017). Human Gut-On-A-Chip Supports Polarized Infection of Coxsackie B1 Virus In Vitro. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0169412"},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/j.chom.2019.08.007","article-title":"Bioengineered Human Organ-on-Chip Reveals Intestinal Microenvironment and Mechanical Forces Impacting Shigella Infection","volume":"26","author":"Grassart","year":"2019","journal-title":"Cell Host Microbe"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"102517","DOI":"10.1016\/j.xcrm.2025.102517","article-title":"In mouse and in vitro models, bowel preparation promotes pathogen colonization, translocation, and exacerbation of inflammation","volume":"7","author":"Clayton","year":"2026","journal-title":"Cell Rep. Med."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"113992","DOI":"10.1016\/j.isci.2025.113992","article-title":"A review of organ-on-chip fabrication methods: From early developments to overcoming inert barriers","volume":"28","author":"Bayona","year":"2025","journal-title":"iScience"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Marzorati, M., Vanhoecke, B., De Ryck, T., Sadaghian Sadabad, M., Pinheiro, I., Possemiers, S., Van den Abbeele, P., Derycke, L., Bracke, M., and Pieters, J. (2014). The HMI module: A new tool to study the Host-Microbiota Interaction in the human gastrointestinal tract in vitro. BMC Microbiol., 14.","DOI":"10.1186\/1471-2180-14-133"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"11535","DOI":"10.1038\/ncomms11535","article-title":"A microfluidics-based in vitro model of the gastrointestinal human-microbe interface","volume":"7","author":"Shah","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_40","first-page":"E7","article-title":"Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip","volume":"113","author":"Kim","year":"2016","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"E10539","DOI":"10.1073\/pnas.1810819115","article-title":"Intestinal barrier dysfunction orchestrates the onset of inflammatory host-microbiome cross-talk in a human gut inflammation-on-a-chip","volume":"115","author":"Shin","year":"2018","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1016\/j.celrep.2019.04.001","article-title":"Integrated In Vitro and In Silico Modeling Delineates the Molecular Effects of a Synbiotic Regimen on Colorectal-Cancer-Derived Cells","volume":"27","author":"Greenhalgh","year":"2019","journal-title":"Cell Rep."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1038\/s41551-019-0397-0","article-title":"A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip","volume":"3","author":"Gazzaniga","year":"2019","journal-title":"Nat. Biomed. Eng."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"119396","DOI":"10.1016\/j.biomaterials.2019.119396","article-title":"A three-dimensional immunocompetent intestine-on-chip model as in vitro platform for functional and microbial interaction studies","volume":"220","author":"Maurer","year":"2019","journal-title":"Biomaterials"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"Shin, W., Wu, A., Massidda, M.W., Foster, C., Thomas, N., Lee, D.W., Koh, H., Ju, Y., Kim, J., and Kim, H.J. (2019). A Robust Longitudinal Co-culture of Obligate Anaerobic Gut Microbiome With Human Intestinal Epithelium in an Anoxic-Oxic Interface-on-a-Chip. Front. Bioeng. Biotechnol., 7.","DOI":"10.3389\/fbioe.2019.00013"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1186\/s40168-019-0650-5","article-title":"Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites","volume":"7","author":"Tovaglieri","year":"2019","journal-title":"Microbiome"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Shin, Y.C., Shin, W., Koh, D., Wu, A., Ambrosini, Y.M., Min, S., Eckhardt, S.G., Fleming, R.Y.D., Kim, S., and Park, S. (2020). Three-Dimensional Regeneration of Patient-Derived Intestinal Organoid Epithelium in a Physiodynamic Mucosal Interface-on-a-Chip. Micromachines, 11.","DOI":"10.3390\/mi11070663"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1211","DOI":"10.1017\/S143192762002454X","article-title":"Visualization of Bacterial Colonization and Cellular Layers in a Gut-on-a-Chip System Using Optical Coherence Tomography","volume":"26","author":"Yuan","year":"2020","journal-title":"Microsc. Microanal."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Gazzaniga, F.S., Camacho, D.M., Wu, M., Silva Palazzo, M.F., Dinis, A.L.M., Grafton, F.N., Cartwright, M.J., Super, M., Kasper, D.L., and Ingber, D.E. (2021). Harnessing Colon Chip Technology to Identify Commensal Bacteria That Promote Host Tolerance to Infection. Front. Cell. Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.638014"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"2805","DOI":"10.1038\/s41467-021-23072-5","article-title":"Characterization of an engineered live bacterial therapeutic for the treatment of phenylketonuria in a human gut-on-a-chip","volume":"12","author":"Nelson","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"121573","DOI":"10.1016\/j.biomaterials.2022.121573","article-title":"Immunoresponsive microbiota-gut-on-chip reproduces barrier dysfunction, stromal reshaping and probiotics translocation under inflammation","volume":"286","author":"Sgambato","year":"2022","journal-title":"Biomaterials"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s40580-022-00299-6","article-title":"Contributions of the microbiome to intestinal inflammation in a gut-on-a-chip","volume":"9","author":"Jeon","year":"2022","journal-title":"Nano Converg."},{"key":"ref_53","doi-asserted-by":"crossref","unstructured":"Jing, B., Xia, K., Zhang, C., Jiao, S., Zhu, L., Wei, J., Wang, Z.A., Chen, N., Tu, P., and Li, J. (2022). Chitosan Oligosaccharides Regulate the Occurrence and Development of Enteritis in a Human Gut-On-a-Chip. Front. Cell Dev. Biol., 10.","DOI":"10.3389\/fcell.2022.877892"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"22641","DOI":"10.1038\/s41598-022-27300-w","article-title":"Live probiotic bacteria administered in a pathomimetic Leaky Gut Chip ameliorate impaired epithelial barrier and mucosal inflammation","volume":"12","author":"Min","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Zhao, W., Yao, Y., Zhang, T., Lu, H., Zhang, X., Zhao, L., Chen, X., Zhu, J., Sui, G., and Zhao, W. (2022). Primary exploration of host-microorganism interaction and enteritis treatment with an embedded membrane microfluidic chip of the human intestinal-vascular microsystem. Front. Bioeng. Biotechnol., 10.","DOI":"10.3389\/fbioe.2022.1035647"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"2504","DOI":"10.1039\/D2BM01490D","article-title":"Establishment of a gut-on-a-chip device with controllable oxygen gradients to study the contribution of Bifidobacterium bifidum to inflammatory bowel disease","volume":"11","author":"Liu","year":"2023","journal-title":"Biomater. Sci."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"5136","DOI":"10.1021\/acsbiomaterials.2c00774","article-title":"Evaluation of Human Performance Aiding Live Synthetically Engineered Bacteria in a Gut-on-a-Chip","volume":"9","author":"Nelson","year":"2023","journal-title":"ACS Biomater. Sci. Eng."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"122525","DOI":"10.1016\/j.biomaterials.2024.122525","article-title":"Modeling of intravenous caspofungin administration using an intestine-on-chip reveals altered Candida albicans microcolonies and pathogenicity","volume":"307","author":"Kaden","year":"2024","journal-title":"Biomaterials"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e2302113","DOI":"10.1002\/advs.202302113","article-title":"Dissecting Gut-Microbial Community Interactions using a Gut Microbiome-on-a-Chip","volume":"11","author":"Lee","year":"2024","journal-title":"Adv. Sci."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"e2303943","DOI":"10.1002\/adhm.202303943","article-title":"An Organ-on-Chip Platform for Simulating Drug Metabolism Along the Gut-Liver Axis","volume":"13","author":"Lucchetti","year":"2024","journal-title":"Adv. Healthc. Mater."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Van Nieuwenhuyse, B., Merabishvili, M., Goeders, N., Vanneste, K., Bogaerts, B., de Jode, M., Ravau, J., Wagemans, J., Belkhir, L., and Van der Linden, D. (2024). Phage-Mediated Digestive Decolonization in a Gut-On-A-Chip Model: A Tale of Gut-Specific Bacterial Prosperity. Viruses, 16.","DOI":"10.3390\/v16071047"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"2537","DOI":"10.1039\/D3LC01052J","article-title":"A microfluidic-based gut-on-a-chip model containing the gut microbiota of patients with depression reveals physiological characteristics similar to depression","volume":"24","author":"Wang","year":"2024","journal-title":"Lab Chip"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"e2408485","DOI":"10.1002\/adma.202408485","article-title":"An Intelligent Intestine-on-a-Chip for Rapid Screening of Probiotics with Relief-Enteritis Function","volume":"36","author":"Wu","year":"2024","journal-title":"Adv. Mater."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"4764","DOI":"10.1038\/s41467-024-48560-2","article-title":"Bacteriophage defends murine gut from Escherichia coli invasion via mucosal adherence","volume":"15","author":"Wu","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Belotserkovsky, I., Vernochet, C., Roelens, M., Beitz, B., Ben Abdallah, B., Poissonnier, S., Bellais, S., Hesketh, A., Meza Torres, J., and Mouharib, M. (2025). Bifidobacterium longum subsp. infantis and Lacticaseibacillus Rhamnosus GG Protect Intestinal Epithelium Against Inflammation-Mediated Damage in an Immunocompetent In-Vitro Model. Appl. Microbiol., 5.","DOI":"10.20944\/preprints202509.0459.v1"},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Canourgues, N., Adic\u00e9am, E., Beitz, B., Atwell, S., Roelens, M., Rekiki, A., Vedrine, C., and Belotserkovsky, I. (2025). Immunocompetent High-Throughput Gut-on-Chip Model for Intestinal Microbes\u2014Host Interaction Studies. Appl. Microbiol., 5.","DOI":"10.20944\/preprints202509.1675.v1"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1816","DOI":"10.1002\/bit.28989","article-title":"Small Intestine on a Chip Demonstrates Physiologic Mucus Secretion in the Presence of Lacticaseibacillus rhamnosus Biofilm","volume":"122","author":"Dash","year":"2025","journal-title":"Biotechnol. Bioeng."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"e2410258","DOI":"10.1002\/smll.202410258","article-title":"Dynamics of Spatial Organization of Bacterial Communities in a Tunable Flow Gut Microbiome-on-a-Chip","volume":"21","author":"Lee","year":"2025","journal-title":"Small"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"2444411","DOI":"10.1080\/19490976.2024.2444411","article-title":"Clostridioides difficile binary toxin CDT induces biofilm-like persisting microcolonies","volume":"17","author":"Tinevez","year":"2025","journal-title":"Gut Microbes"},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"De Rudder, C., Greenhalgh, K., Baginska, J., Martin-Gallausiaux, C., Grandmougin, L., Villette, R., Lucchetti, M., Hansen, B., Ostaszewski, M., and Petrov, V.A. (2026). immunoHuMiX: A personalizable gut-on-chip model for unraveling human microbiome\u2013immune interactions. View, early view.","DOI":"10.1002\/VIW.20250213"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"101641","DOI":"10.1016\/j.jpha.2026.101641","article-title":"Enhancements of symbiotic adhesion and antibiotic efficacy observed by the metabolic crosstalk within cell-bacteria cocultured on a microfluidic gut chip","volume":"16","author":"Li","year":"2026","journal-title":"J. Pharm. Anal."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"2782","DOI":"10.1099\/ijsem.0.004107","article-title":"A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae","volume":"70","author":"Zheng","year":"2020","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_73","doi-asserted-by":"crossref","unstructured":"Hooijmans, C.R., Rovers, M.M., de Vries, R.B., Leenaars, M., Ritskes-Hoitinga, M., and Langendam, M.W. (2014). SYRCLE\u2019s risk of bias tool for animal studies. BMC Med. Res. Methodol., 14.","DOI":"10.1186\/1471-2288-14-43"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/9\/2059\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T12:08:51Z","timestamp":1789474131000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/9\/2059"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,15]]},"references-count":73,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["microorganisms14092059"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14092059","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,15]]}}}