Deyaert Stef, Moens Frédéric, Pirovano Walter, van den Bogert Bartholomeus, Klaassens Eline Suzanne, Marzorati Massimo, Van de Wiele Tom, Kleerebezem Michiel, Van den Abbeele Pieter
ProDigest BV, Gent, Belgium.
Baseclear, Leiden, Netherlands.
Front Microbiol. 2023 Mar 17;13:1054061. doi: 10.3389/fmicb.2022.1054061. eCollection 2022.
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 . This study therefore aimed to develop and validate a dynamic, long-term simulation of the ileal microbiota using the SHIME-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 ± 0.12 log (cells/ml)], composition and function. Indeed, the observed community mainly consisted of the genera , and (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 , 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® where it further increased the compositional relevance of the colonic community. This long-term 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 simulation increases the biological relevance of the current M-SHIME® technology.
人类胃肠道由不同区域组成，每个区域都有独特的生理学、解剖学和微生物群落特征。虽然结肠微生物群在最近的研究项目中受到了很多关注，但对于小肠微生物群及其与摄入化合物的相互作用却知之甚少，主要是因为该区域难以触及。因此，本研究旨在利用SHIME技术开发并验证一种动态、长期的回肠微生物群模拟方法。通过一项为期18天的筛选实验，测试不同的接种策略、营养培养基和环境参数，确定并优化了关键参数。将合成细菌群落置于选定条件下，得到了一个稳定的微生物群，其在丰度[8.81±0.12 log(细胞/ml)]、组成和功能方面具有代表性。事实上，观察到的群落主要由 属、 属和 属组成（定量聚合酶链反应和靶向16S rRNA基因的Illumina测序），而营养物质的添加促进了乳酸的产生，随后通过交叉喂养相互作用生成乙酸盐和丙酸盐。此外，与 情况类似，胆汁盐仅部分去结合，仅少量转化为次级胆汁盐。在确认小肠微生物群模型的可重复性后，将其整合到已建立的M-SHIME®中，这进一步提高了结肠群落组成的相关性。这个长期模型提供了回肠细菌群落的代表性模拟，便于研究回肠微生物群在补充微生物或饮食成分等情况下的动态变化和活性。此外，这种当前模拟的整合增加了当前M-SHIME®技术的生物学相关性。
