The human microbiota impacts a variety of diseases and responses to therapeutics. Due to a lack of robust in vitro models, detailed mechanistic explanations of host‐microbiota interactions cannot often be recapitulated. We describe the design and development of a novel, versatile and modular in vitro system that enables indirect coculture of human epithelial cells with anaerobic bacteria for the characterization of host‐microbe secreted metabolite interactions. This system was designed to compartmentalize anaerobes and human cells in separate chambers conducive to each organism's requisite cell growth conditions. Using perfusion, fluidic mixing, and automated sample collection, the cells continuously received fresh media, while in contact with their corresponding compartments conditioned supernatant. Supernatants from each chamber were collected in a cell‐free time‐resolved fashion. The system sustained low oxygen conditions in the anaerobic chamber, while also supporting the growth of a representative anaerobe (Bacteroides thetaiotaomicron) and a human colonic epithelial cell line (Caco‐2) in the aerobic chamber. Caco‐2 global gene expression changes in response to coculture with B. thetaiotaomicron was characterized using RNA sequencing. Extensive, targeted metabolomics analysis of over 150 central carbon metabolites was performed on the serially collected supernatants. We observed broad metabolite changes in host‐microbe coculture, compared to respective mono‐culture controls. These effects were dependent both on sampling time and the compartment probed (apical vs. basolateral). Coculturing resulted in the depletion of several important metabolites, including guanine, uridine 5'‐monophosphate, asparagine, and thiamine. Additionally, while Caco‐2 cells cultured alone predominantly affected the basolateral metabolite milieu, increased abundance of 2,3‐dihydroxyisovalerate and thymine on the basolateral side, occurred when the cells were cocultured with B. thetaiotaomicron. Thus, our system can capture the dynamic, competitive and cooperative processes between host cells and gut microbes.

中文翻译：

---

灌注宿主微生物生物反应器（HMB）系统，捕获与人肠道厌氧菌共培养的上皮细胞之间分泌代谢物的动态相互作用

人类微生物群影响多种疾病和对治疗的反应。由于缺乏可靠的体外模型，宿主-微生物群相互作用的详细机制解释通常无法概括。我们描述了一种新型、多功能和模块化体外系统的设计和开发，该系统能够将人类上皮细胞与厌氧细菌间接共培养，以表征宿主微生物分泌的代谢物相互作用。该系统旨在将厌氧菌和人类细胞分隔在有利于每种生物体所需细胞生长条件的单独室中。通过灌注、流体混合和自动样品收集，细胞不断接受新鲜培养基，同时与其相应的隔室条件上清液接触。以无细胞时间分辨方式收集每个室的上清液。该系统在厌氧室中维持低氧条件，同时也支持代表性厌氧菌的生长（多形拟杆菌）和需氧室中的人结肠上皮细胞系（Caco-2）。 Caco-2 响应共培养的全局基因表达变化B.thetaiotamicron使用 RNA 测序进行表征。对连续收集的上清液进行了超过 150 种中心碳代谢物的广泛、有针对性的代谢组学分析。与各自的单一培养对照相比，我们观察到宿主微生物共培养中广泛的代谢变化。这些影响取决于采样时间和探测的隔室（顶端与基底外侧）。共培养导致几种重要代谢物的消耗，包括鸟嘌呤、尿苷 5'-单磷酸、天冬酰胺和硫胺素。此外，虽然单独培养的 Caco-2 细胞主要影响基底外侧代谢环境，但当细胞与基底外侧共培养时，基底外侧 2,3-二羟基异戊酸和胸腺嘧啶的丰度增加。B.thetaiotamicron。因此，我们的系统可以捕获宿主细胞和肠道微生物之间的动态、竞争和合作过程。