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The aim of this study was to investigate differences in the molecular phenotype of organoids derived from pigs divergent for FE as well as their responses to challenge with adherent and invasive\n                      <jats:italic>Escherichia coli<\/jats:italic>\n                      (\n                      <jats:italic>E. coli<\/jats:italic>\n                      ).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Colon and ileum tissue from low and high FE pigs was used to generate 3D organoids and two dimensional (2D) monolayers of organoid cells for\n                      <jats:italic>E. coli<\/jats:italic>\n                      challenge. Genome-wide gene expression was used to investigate molecular differences between pigs that were phenotypically divergent for FE and to study the difference in gene expression after challenge with\n                      <jats:italic>E. coli<\/jats:italic>\n                      . We showed, (1) minor differences in gene expression of colon organoids from pigs with low and high FE phenotypes, (2) that an\n                      <jats:italic>E. coli<\/jats:italic>\n                      challenge results in a strong innate immune gene response in both colon and ileum organoids, (3) that the immune response seems to be less pronounced in the colon organoids of high FE pigs and (4) a slightly stronger immune response was observed in ileum than in colon organoids.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>These findings demonstrate the potential for using organoids to gain insights into complex biological mechanisms such as FE.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-024-10064-0","type":"journal-article","created":{"date-parts":[[2024,2,13]],"date-time":"2024-02-13T07:02:35Z","timestamp":1707807755000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Transcriptomic analysis of intestinal organoids, derived from pigs divergent in feed efficiency, and their response to Escherichia coli"],"prefix":"10.1186","volume":"25","author":[{"given":"Ole","family":"Madsen","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roxann S.C.","family":"Rikkers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jerry M.","family":"Wells","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rob","family":"Bergsma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Soumya K.","family":"Kar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nico","family":"Taverne","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anja J.","family":"Taverne-Thiele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esther D.","family":"Ellen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henri","family":"Woelders","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,2,13]]},"reference":[{"key":"10064_CR1","doi-asserted-by":"publisher","DOI":"10.1186\/s13567-021-00904-2","author":"SK Kar","year":"2021","unstructured":"Kar SK, Wells JM, Ellen ED, Te Pas MFW, Madsen O, Groenen MAM, et al. 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