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

16S rRNA gene sequencing anaerobic chamber ex vivo fecal microbiota fibers in vitro microbial ecology personalized microbiota response short-chain fatty acids xenobiotics

Journal

ISME communications
ISSN: 2730-6151
Titre abrégé: ISME Commun
Pays: England
ID NLM: 9918205372406676

Informations de publication

Date de publication:
Jan 2024
Historique:
received: 01 11 2023
revised: 13 11 2023
accepted: 08 03 2024
medline: 2 4 2024
pubmed: 2 4 2024
entrez: 2 4 2024
Statut: epublish

Résumé

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

Identifiants

DOI: 10.1093/ismeco/ycae035 PMID: 38562261 PMC: PMC10982853
pubmed: 38562261
doi: 10.1093/ismeco/ycae035
pii: ycae035
pmc: PMC10982853
doi:

Types de publication

Journal Article

Langues

eng

Pagination

ycae035

Informations de copyright

© The Author(s) 2024. Published by Oxford University Press on behalf of the International Society for Microbial Ecology.

Déclaration de conflit d'intérêts

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.

Auteurs

Janina N Zünd (JN)

Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland.

Serafina Plüss (S)

Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland.

Denisa Mujezinovic (D)

Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland.

Carmen 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.

Philipp R 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.

Tomas de Wouters (T)

PharmaBiome AG, 8952 Schlieren, Switzerland.

Christophe Lacroix (C)

Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland.

Gabriel E Leventhal (GE)

PharmaBiome AG, 8952 Schlieren, Switzerland.

Benoit Pugin (B)

Laboratory of Food Biotechnology, Institute of Food, Nutrition and Health, Department of Health Sciences and Technology, ETH Zürich, 8092 Zürich, Switzerland.

Classifications MeSH