灵活的高通量培养方案,用于评估个体肠道微生物群对饮食、药物和宿主相关因素的反应。

IF 5.1 Q1 ECOLOGY ISME communications Pub Date : 2024-03-12 eCollection Date: 2024-01-01 DOI:10.1093/ismeco/ycae035
Janina N Zünd, Serafina Plüss, Denisa Mujezinovic, Carmen Menzi, Philipp R von Bieberstein, Tomas de Wouters, Christophe Lacroix, Gabriel E Leventhal, Benoit Pugin
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引用次数: 0

摘要

厌氧培养粪便微生物群是研究肠道微生物群落如何对特定肠道条件和干扰做出反应的一种很有前景的方法。在此,我们介绍一种使用 96 深孔板培养粪便衍生肠道微生物群的灵活方案。我们的方案旨在弥补厌氧室高通量培养的不足。我们描述了气相对培养基化学和微生物生理学的影响,并引入了模块化培养基制备流程,以便同时测试多种条件。此外,我们还确定了一种培养基配方,既能最大限度地提高体内外培养物和供体微生物群的成分相似性,又能限制肠杆菌的繁殖。最后,我们验证了该方案,证明培养的粪便微生物群对膳食纤维(抗性糊精、可溶性淀粉)和药物(环丙沙星、5-氟尿嘧啶)的反应与体内报道的相似。这种高通量培养方案有望促进依赖培养的研究,加快发现肠道微生物群-饮食-药物-宿主之间的相互作用,并为以微生物群为中心的个性化干预铺平道路。
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A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.

The anaerobic cultivation of fecal microbiota is a promising approach to investigating how gut microbial communities respond to specific intestinal conditions and perturbations. Here, we describe a flexible protocol using 96-deepwell plates to cultivate stool-derived gut microbiota. Our protocol aims to address gaps in high-throughput culturing in an anaerobic chamber. We characterized the influence of the gas phase on the medium chemistry and microbial physiology and introduced a modular medium preparation process to enable the testing of several conditions simultaneously. Furthermore, we identified a medium formulation that maximized the compositional similarity of ex vivo cultures and donor microbiota while limiting the bloom of Enterobacteriaceae. Lastly, we validated the protocol by demonstrating that cultivated fecal microbiota responded similarly to dietary fibers (resistant dextrin, soluble starch) and drugs (ciprofloxacin, 5-fluorouracil) as reported in vivo. This high-throughput cultivation protocol has the potential to facilitate culture-dependent studies, accelerate the discovery of gut microbiota-diet-drug-host interactions, and pave the way to personalized microbiota-centered interventions.

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