{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T07:43:59Z","timestamp":1793087039150,"version":"4.5.0"},"reference-count":46,"publisher":"Springer Science and Business Media LLC","issue":"7","license":[{"start":{"date-parts":[[2024,12,4]],"date-time":"2024-12-04T00:00:00Z","timestamp":1733270400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,12,4]],"date-time":"2024-12-04T00:00:00Z","timestamp":1733270400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat. Biomed. Eng"],"DOI":"10.1038\/s41551-024-01313-4","type":"journal-article","created":{"date-parts":[[2024,12,4]],"date-time":"2024-12-04T05:04:13Z","timestamp":1733288653000},"page":"1075-1085","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Patterned gastrointestinal monolayers with bilateral access as observable models of parasite gut infection"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9714-0143","authenticated-orcid":false,"given":"Moritz","family":"Hofer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0567-0412","authenticated-orcid":false,"given":"Maria A.","family":"Duque-Correa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5898-305X","authenticated-orcid":false,"given":"Matthias P.","family":"Lutolf","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,12,4]]},"reference":[{"key":"1313_CR1","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1016\/j.cell.2016.05.082","volume":"165","author":"H Clevers","year":"2016","unstructured":"Clevers, H. Modeling development and disease with organoids. Cell 165, 1586\u20131597 (2016).","journal-title":"Cell"},{"key":"1313_CR2","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1038\/ncb3312","volume":"18","author":"A Fatehullah","year":"2016","unstructured":"Fatehullah, A., Tan, S. H. & Barker, N. Organoids as an in vitro model of human development and disease. Nat. Cell Biol. 18, 246\u2013254 (2016).","journal-title":"Nat. Cell Biol."},{"key":"1313_CR3","doi-asserted-by":"publisher","first-page":"1247125","DOI":"10.1126\/science.1247125","volume":"345","author":"MA Lancaster","year":"2014","unstructured":"Lancaster, M. A. & Knoblich, J. A. Organogenesisin a dish: modeling development and disease using organoid technologies. Science 345, 1247125 (2014).","journal-title":"Science"},{"key":"1313_CR4","doi-asserted-by":"publisher","first-page":"262","DOI":"10.1038\/nature07935","volume":"459","author":"T Sato","year":"2009","unstructured":"Sato, T. et al. Single Lgr5 stem cells build crypt\u2013villus structures in vitro without a mesenchymal niche. Nature 459, 262\u2013265 (2009).","journal-title":"Nature"},{"key":"1313_CR5","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1038\/s41578-021-00279-y","volume":"6","author":"M Hofer","year":"2021","unstructured":"Hofer, M. & Lutolf, M. P. Engineering organoids. Nat. Rev. Mater. 6, 402\u2013420 (2021).","journal-title":"Nat. Rev. Mater."},{"key":"1313_CR6","doi-asserted-by":"publisher","first-page":"400","DOI":"10.1136\/gutjnl-2017-314540","volume":"68","author":"F Boccellato","year":"2019","unstructured":"Boccellato, F. et al. Polarised epithelial monolayers of the gastric mucosa reveal insights into mucosal homeostasis and defence against infection. Gut 68, 400\u2013413 (2019).","journal-title":"Gut"},{"key":"1313_CR7","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1038\/s41421-018-0036-z","volume":"4","author":"Y Liu","year":"2018","unstructured":"Liu, Y., Qi, Z., Li, X., Du, Y. & Chen, Y. G. Monolayer culture of intestinal epithelium sustains Lgr5+ intestinal stem cells. Cell Discov. 4, 4\u20136 (2018).","journal-title":"Cell Discov."},{"key":"1313_CR8","doi-asserted-by":"publisher","first-page":"911","DOI":"10.1136\/gutjnl-2013-306651","volume":"64","author":"KL VanDussen","year":"2015","unstructured":"VanDussen, K. L. et al. Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays. Gut 64, 911\u2013920 (2015).","journal-title":"Gut"},{"key":"1313_CR9","doi-asserted-by":"publisher","first-page":"1144","DOI":"10.1016\/j.cell.2019.10.015","volume":"179","author":"Y Wang","year":"2019","unstructured":"Wang, Y. et al. Long-term culture captures injury\u2013repair cycles of colonic stem cells. Cell 179, 1144\u20131159.e15 (2019).","journal-title":"Cell"},{"key":"1313_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fcimb.2020.00272","volume":"10","author":"T Roodsant","year":"2020","unstructured":"Roodsant, T. et al. A human 2D primary organoid-derived epithelial monolayer model to study host\u2013pathogen interaction in the small intestine. Front. Cell Infect. Microbiol. 10, 1\u201314 (2020).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"1313_CR11","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1016\/j.devcel.2018.01.024","volume":"44","author":"CA Thorne","year":"2018","unstructured":"Thorne, C. A. et al. Enteroid monolayers reveal an autonomous WNT and BMP circuit controlling intestinal epithelial growth and organization. Dev. Cell 44, 624\u2013633.e4 (2018).","journal-title":"Dev. Cell"},{"key":"1313_CR12","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1089\/ten.tec.2012.0710","volume":"19","author":"Z Jabaji","year":"2013","unstructured":"Jabaji, Z. et al. Use of collagen gel as an alternative extracellular matrix for the in vitro and in vivo growth of murine small intestinal epithelium. Tissue Eng. Part C 19, 961\u2013969 (2013).","journal-title":"Tissue Eng. Part C"},{"key":"1313_CR13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-022-29334-0","volume":"13","author":"MA Duque-Correa","year":"2022","unstructured":"Duque-Correa, M. A. et al. Defining the early stages of intestinal colonisation by whipworms. Nat. Commun. 13, 1725 (2022).","journal-title":"Nat. Commun."},{"key":"1313_CR14","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.jcmgh.2017.10.007","volume":"5","author":"Y Wang","year":"2018","unstructured":"Wang, Y. et al. Formation of human colonic crypt array by application of chemical gradients across a shaped epithelial monolayer. Cell Mol. Gastroenterol. Hepatol. 5, 113\u2013130 (2018).","journal-title":"Cell Mol. Gastroenterol. Hepatol."},{"key":"1313_CR15","doi-asserted-by":"publisher","first-page":"2030","DOI":"10.1021\/mp5001422","volume":"11","author":"CM Costello","year":"2014","unstructured":"Costello, C. M. et al. 3-D intestinal scaffolds for evaluating the therapeutic potential of probiotics. Mol. Pharm. 11, 2030\u20132039 (2014).","journal-title":"Mol. Pharm."},{"key":"1313_CR16","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.biomaterials.2017.03.005","volume":"128","author":"Y Wang","year":"2017","unstructured":"Wang, Y. et al. A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium. Biomaterials 128, 44\u201355 (2017).","journal-title":"Biomaterials"},{"key":"1313_CR17","doi-asserted-by":"publisher","unstructured":"Creff, J. et al. Fabrication of 3D scaffolds reproducing intestinal epithelium topography by high-resolution 3D stereolithography. Biomaterials https:\/\/doi.org\/10.1016\/j.biomaterials.2019.119404 (2019).","DOI":"10.1016\/j.biomaterials.2019.119404"},{"key":"1313_CR18","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1039\/D0LC00672F","volume":"21","author":"M Verhulsel","year":"2021","unstructured":"Verhulsel, M. et al. Developing an advanced gut on chip model enabling the study of epithelial cell\/fibroblast interactions. Lab Chip 21, 365\u2013377 (2021).","journal-title":"Lab Chip"},{"key":"1313_CR19","doi-asserted-by":"publisher","unstructured":"Gjorevski, N. et al. Tissue geometry drives deterministic organoid patterning. Science https:\/\/doi.org\/10.1126\/science.aaw9021 (2022).","DOI":"10.1126\/science.aaw9021"},{"key":"1313_CR20","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1038\/s41586-020-2724-8","volume":"585","author":"M Nikolaev","year":"2020","unstructured":"Nikolaev, M. et al. Homeostatic mini-intestines through scaffold-guided organoid morphogenesis. Nature 585, 574\u2013578 (2020).","journal-title":"Nature"},{"key":"1313_CR21","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.stem.2009.11.013","volume":"6","author":"N Barker","year":"2010","unstructured":"Barker, N. et al. Lgr5+ve stem cells drive self-renewal in the stomach and build long-lived gastric units in vitro. Cell Stem Cell 6, 25\u201336 (2010).","journal-title":"Cell Stem Cell"},{"key":"1313_CR22","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13619-020-00061-5","volume":"10","author":"G Zhu","year":"2021","unstructured":"Zhu, G., Hu, J. & Xi, R. The cellular niche for intestinal stem cells: a team effort. Cell Regen. 10, 1\u201316 (2021).","journal-title":"Cell Regen."},{"key":"1313_CR23","doi-asserted-by":"publisher","first-page":"176","DOI":"10.1258\/la.2009.009112","volume":"44","author":"C Casteleyn","year":"2010","unstructured":"Casteleyn, C., Rekecki, A., Van Der Aa, A., Simoens, P. & Van Den Broeck, W. Surface area assessment of the murine intestinal tract as a prerequisite for oral dose translation from mouse to man. Lab Anim. 44, 176\u2013183 (2010).","journal-title":"Lab Anim."},{"key":"1313_CR24","doi-asserted-by":"publisher","first-page":"1711","DOI":"10.1136\/gutjnl-2013-305964","volume":"63","author":"E Choi","year":"2014","unstructured":"Choi, E. et al. Cell lineage distribution atlas of the human stomach reveals heterogeneous gland populations in the gastric antrum. Gut 63, 1711\u20131720 (2014).","journal-title":"Gut"},{"key":"1313_CR25","doi-asserted-by":"publisher","first-page":"741","DOI":"10.1006\/bbrc.2000.2673","volume":"271","author":"A Ootani","year":"2000","unstructured":"Ootani, A., Toda, S., Fujimoto, K. & Sugihara, H. An air\u2013liquid interface promotes the differentiation of gastric surface mucous cells (GSM06) in culture. Biochem. Biophys. Res. Commun. 271, 741\u2013746 (2000).","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"1313_CR26","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s13287-020-01941-y","volume":"11","author":"Y Zhang","year":"2020","unstructured":"Zhang, Y., Zeng, F., Han, X., Weng, J. & Gao, Y. Lineage tracing: technology tool for exploring the development, regeneration, and disease of the digestive system. Stem Cell Res. Ther. 11, 1\u201316 (2020).","journal-title":"Stem Cell Res. Ther."},{"key":"1313_CR27","doi-asserted-by":"publisher","first-page":"126","DOI":"10.1053\/j.gastro.2014.09.042","volume":"148","author":"S Bartfeld","year":"2015","unstructured":"Bartfeld, S. et al. In vitro expansion of human gastric epithelial stem cells and their responses to bacterial infection. Gastroenterology 148, 126\u2013136.e6 (2015).","journal-title":"Gastroenterology"},{"key":"1313_CR28","doi-asserted-by":"publisher","first-page":"2509","DOI":"10.1016\/j.celrep.2019.01.108","volume":"26","author":"JY Co","year":"2019","unstructured":"Co, J. Y. et al. Controlling epithelial polarity: a human enteroid model for host\u2013pathogen interactions. Cell Rep. 26, 2509\u20132520.e4 (2019).","journal-title":"Cell Rep."},{"key":"1313_CR29","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1016\/j.coi.2017.07.012","volume":"48","author":"D Dutta","year":"2017","unstructured":"Dutta, D. & Clevers, H. Organoid culture systems to study host\u2013pathogen interactions. Curr. Opin. Immunol. 48, 15\u201322 (2017).","journal-title":"Curr. Opin. Immunol."},{"key":"1313_CR30","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3389\/fcimb.2022.976017","volume":"12","author":"R White","year":"2022","unstructured":"White, R., Blow, F., Buck, A. H. & Duque-Correa, M. A. Organoids as tools to investigate gastrointestinal nematode development and host interactions. Front. Cell Infect. Microbiol. 12, 1\u20139 (2022).","journal-title":"Front. Cell Infect. Microbiol."},{"key":"1313_CR31","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1016\/j.pt.2019.10.013","volume":"36","author":"MA Duque-Correa","year":"2020","unstructured":"Duque-Correa, M. A., Maizels, R. M., Grencis, R. K. & Berriman, M. Organoids\u2014new models for host\u2013helminth interactions. Trends Parasitol. 36, 170\u2013181 (2020).","journal-title":"Trends Parasitol."},{"key":"1313_CR32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.3390\/pathogens10080925","volume":"10","author":"Y Yousefi","year":"2021","unstructured":"Yousefi, Y., Haq, S., Banskota, S., Kwon, Y. H. & Khan, W. I. Trichuris muris model: role in understanding intestinal immune response, inflammation and host defense. Pathogens 10, 1\u201321 (2021).","journal-title":"Pathogens"},{"key":"1313_CR33","doi-asserted-by":"crossref","unstructured":"Bancroft, A. J. et al. The major secreted protein of the whipworm parasite tethers to matrix and inhibits interleukin-13 function. Nat Commun. 10, 2344 (2019).","DOI":"10.1038\/s41467-019-09996-z"},{"key":"1313_CR34","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/0020-7519(80)90006-5","volume":"10","author":"TS Panesar","year":"1980","unstructured":"Panesar, T. S. & Croll, N. A. The location of parasites within their hosts: site selection by Trichuris muris in the laboratory mouse. Int J. Parasitol. 10, 261\u2013273 (1980).","journal-title":"Int J. Parasitol."},{"key":"1313_CR35","doi-asserted-by":"publisher","first-page":"560","DOI":"10.1038\/nature20168","volume":"539","author":"N Gjorevski","year":"2016","unstructured":"Gjorevski, N. et al. Designer matrices for intestinal stem cell and organoid culture. Nature 539, 560\u2013564 (2016).","journal-title":"Nature"},{"key":"1313_CR36","doi-asserted-by":"publisher","first-page":"1650","DOI":"10.1016\/S0006-3495(02)73933-7","volume":"83","author":"S Ramanujan","year":"2002","unstructured":"Ramanujan, S. et al. Diffusion and convection in collagen gels: implications for transport in the tumor interstitium. Biophys. J. 83, 1650\u20131660 (2002).","journal-title":"Biophys. J."},{"key":"1313_CR37","doi-asserted-by":"publisher","first-page":"2471","DOI":"10.1038\/nprot.2013.153","volume":"8","author":"H Miyoshi","year":"2013","unstructured":"Miyoshi, H. & Stappenbeck, T. S. In vitro expansion and genetic modification of gastrointestinal stem cells in spheroid culture. Nat. Protoc. 8, 2471\u20132482 (2013).","journal-title":"Nat. Protoc."},{"key":"1313_CR38","doi-asserted-by":"publisher","unstructured":"Bartfeld, S. & Clevers, H. Organoids as model for infectious diseases: culture of human and murine stomach organoids and microinjection of Helicobacter pylori. J. Vis. Exp. https:\/\/doi.org\/10.3791\/53359 (2015)","DOI":"10.3791\/53359"},{"key":"1313_CR39","doi-asserted-by":"publisher","first-page":"707","DOI":"10.1016\/j.ijpara.2020.06.001","volume":"50","author":"MA Duque-Correa","year":"2020","unstructured":"Duque-Correa, M. A. et al. Development of caecaloids to study host-pathogen interactions: new insights into immunoregulatory functions of Trichuris muris extracellular vesicles in the caecum. Int. J. Parasitol. 50, 707\u2013718 (2020).","journal-title":"Int. J. Parasitol."},{"key":"1313_CR40","doi-asserted-by":"publisher","first-page":"42","DOI":"10.2144\/000114055","volume":"55","author":"AM Nik","year":"2013","unstructured":"Nik, A. M. & Carlsson, P. Separation of intact intestinal epithelium from mesenchyme. Biotechniques 55, 42\u201344 (2013).","journal-title":"Biotechniques"},{"key":"1313_CR41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12859-021-04344-9","volume":"22","author":"DR Stirling","year":"2021","unstructured":"Stirling, D. R. et al. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinf. 22, 1\u201311 (2021).","journal-title":"BMC Bioinf."},{"key":"1313_CR42","doi-asserted-by":"publisher","first-page":"676","DOI":"10.1038\/nmeth.2019","volume":"9","author":"J Schindelin","year":"2012","unstructured":"Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676\u2013682 (2012).","journal-title":"Nat. Methods"},{"key":"1313_CR43","doi-asserted-by":"crossref","first-page":"1","DOI":"10.12688\/f1000research.7039.1","volume":"5","author":"Y Chen","year":"2016","unstructured":"Chen, Y., Lun, A. T. L. & Smyth, G. K. From reads to genes to pathways: differential expression analysis of RNA-seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Research. 5, 1\u201351 (2016).","journal-title":"F1000Research."},{"key":"1313_CR44","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1038\/s41592-022-01663-4","volume":"19","author":"M Pachitariu","year":"2022","unstructured":"Pachitariu, M. & Stringer, C. Cellpose 2.0: how to train your own model. Nat. Methods 19, 1634\u20131641 (2022).","journal-title":"Nat. Methods"},{"key":"1313_CR45","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1016\/j.ymeth.2016.09.016","volume":"115","author":"JY Tinevez","year":"2017","unstructured":"Tinevez, J. Y. et al. TrackMate: an open and extensible platform for single-particle tracking. Methods 115, 80\u201390 (2017).","journal-title":"Methods"},{"key":"1313_CR46","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1038\/s41592-019-0582-9","volume":"16","author":"S Berg","year":"2019","unstructured":"Berg, S. et al. ilastik: interactive machine learning for (bio)image analysis. Nat. Methods 16, 1226\u20131232 (2019).","journal-title":"Nat. Methods"}],"updated-by":[{"DOI":"10.1038\/s41551-025-01351-6","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2025,1,20]],"date-time":"2025-01-20T00:00:00Z","timestamp":1737331200000}}],"container-title":["Nature Biomedical Engineering"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41551-024-01313-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41551-024-01313-4","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41551-024-01313-4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,6]],"date-time":"2025-09-06T01:45:17Z","timestamp":1757123117000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41551-024-01313-4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,4]]},"references-count":46,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2025,7]]}},"alternative-id":["1313"],"URL":"https:\/\/doi.org\/10.1038\/s41551-024-01313-4","relation":{},"ISSN":["2157-846X"],"issn-type":[{"value":"2157-846X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,4]]},"assertion":[{"value":"17 August 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"1 November 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"4 December 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 January 2025","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Correction","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A Correction to this paper has been published:","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"https:\/\/doi.org\/10.1038\/s41551-025-01351-6","URL":"https:\/\/doi.org\/10.1038\/s41551-025-01351-6","order":7,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"M.P.L. is an employee of Hoffmann-La Roche. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}