A flexible high-throughput cultivation protocol to assess the response of individuals' gut microbiota to diet-, drug-, and host-related factors.

Autor:	Zünd JN; Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland., Plüss S; Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland., Mujezinovic D; Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland., Menzi C; Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland.; PharmaBiome AG, 8952 Schlieren, Switzerland., von Bieberstein PR; Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland.; PharmaBiome AG, 8952 Schlieren, Switzerland., de Wouters T; PharmaBiome AG, 8952 Schlieren, Switzerland., Lacroix C; Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland., Leventhal GE; PharmaBiome AG, 8952 Schlieren, Switzerland., Pugin B; Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland.
Jazyk:	angličtina
Zdroj:	ISME communications [ISME Commun] 2024 Mar 12; Vol. 4 (1), pp. ycae035. Date of Electronic Publication: 2024 Mar 12 (Print Publication: 2024).
DOI:	10.1093/ismeco/ycae035
Abstrakt:	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. Competing Interests: C.M., P.B., T.W., and G.L. are or were employees of PharmaBiome AG. T.W. and C.L. are founders of PharmaBiome AG. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.)
Databáze:	MEDLINE
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