{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T17:47:17Z","timestamp":1792000037406,"version":"4.4.0"},"reference-count":77,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,3,17]],"date-time":"2023-03-17T00:00:00Z","timestamp":1679011200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100013297","name":"Eurostars","doi-asserted-by":"publisher","award":["E12091"],"award-info":[{"award-number":["E12091"]}],"id":[{"id":"10.13039\/100013297","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>\n                    The human gastrointestinal tract consists of different regions, each characterized by a distinct physiology, anatomy, and microbial community. While the colonic microbiota has received a lot of attention in recent research projects, little is known about the small intestinal microbiota and its interactions with ingested compounds, primarily due to the inaccessibility of this region\n                    <jats:italic>in vivo<\/jats:italic>\n                    . This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME\n                    <jats:sup>\u00ae<\/jats:sup>\n                    -technology. Essential parameters were identified and optimized from a screening experiment testing different inoculation strategies, nutritional media, and environmental parameters over an 18-day period. Subjecting a synthetic bacterial consortium to the selected conditions resulted in a stable microbiota that was representative in terms of abundance [8.81\u2009\u00b1\u20090.12 log (cells\/ml)], composition and function. Indeed, the observed community mainly consisted of the genera\n                    <jats:italic>Streptococcus, Veillonella, Enterococcus, Lactobacillus<\/jats:italic>\n                    , and\n                    <jats:italic>Clostridium<\/jats:italic>\n                    (qPCR and 16S rRNA gene targeted Illumina sequencing), while nutrient administration boosted lactate production followed by cross-feeding interactions towards acetate and propionate. Furthermore, similarly as\n                    <jats:italic>in vivo<\/jats:italic>\n                    , bile salts were only partially deconjugated and only marginally converted into secondary bile salts. After confirming reproducibility of the small intestinal microbiota model, it was integrated into the established M-SHIME\u00ae where it further increased the compositional relevance of the colonic community. This long-term\n                    <jats:italic>in vitro<\/jats:italic>\n                    model provides a representative simulation of the ileal bacterial community, facilitating research of the ileum microbiota dynamics and activity when, for example, supplemented with microbial or diet components. Furthermore, integration of this present\n                    <jats:italic>in vitro<\/jats:italic>\n                    simulation increases the biological relevance of the current M-SHIME\u00ae technology.\n                  <\/jats:p>","DOI":"10.3389\/fmicb.2022.1054061","type":"journal-article","created":{"date-parts":[[2023,3,17]],"date-time":"2023-03-17T01:22:22Z","timestamp":1679016142000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":24,"title":["Development of a reproducible small intestinal microbiota model and its integration into the SHIME\u00ae-system, a dynamic in vitro gut model"],"prefix":"10.3389","volume":"13","author":[{"given":"Stef","family":"Deyaert","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fr\u00e9d\u00e9ric","family":"Moens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter","family":"Pirovano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bartholomeus","family":"van den Bogert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eline Suzanne","family":"Klaassens","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Massimo","family":"Marzorati","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom","family":"Van de Wiele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michiel","family":"Kleerebezem","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pieter","family":"Van den Abbeele","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,3,17]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1007\/BF02605761","article-title":"Segmental colonic transit time","volume":"24","author":"Arhan","year":"1981","journal-title":"Dis. 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