Protocol to study human gut bacterial communities and rhythmicity ex vivo using a chemostat system

Helena Heimes; Deborah Häcker; Hélène Omer; Daan R. van der Veen; Silke Kiessling; Dirk Haller

doi:10.1016/j.xpro.2024.103419

Protocol to study human gut bacterial communities and rhythmicity ex vivo using a chemostat system

Helena Heimes, Deborah Häcker, Hélène Omer, Daan R. van der Veen, Silke Kiessling, Dirk Haller

Chair of Nutrition and Immunology

Research output: Contribution to journal › Article › peer-review

Abstract

Chemostat systems can be used to cultivate complex intestinal microbial communities ex vivo. Here, we present a protocol to transfer bacteria from human fecal material into chemostat systems as well as settings to simulate infant or adult colonic conditions. We describe the experimental setup, media design, donor selection, 16S rRNA amplicon sequencing, and circadian analysis of bacterial abundance. This protocol enables the investigation of changes in microbial community composition and bacteria-derived metabolites upon exposure to different dietary components. For complete details on the use and execution of this protocol, please refer to Heppner et al.¹

Original language	English
Article number	103419
Journal	STAR Protocols
Volume	5
Issue number	4
DOIs	https://doi.org/10.1016/j.xpro.2024.103419
State	Published - 20 Dec 2024

Keywords

cell culture
health sciences
microbiology

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10.1016/j.xpro.2024.103419

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abstract = "Chemostat systems can be used to cultivate complex intestinal microbial communities ex vivo. Here, we present a protocol to transfer bacteria from human fecal material into chemostat systems as well as settings to simulate infant or adult colonic conditions. We describe the experimental setup, media design, donor selection, 16S rRNA amplicon sequencing, and circadian analysis of bacterial abundance. This protocol enables the investigation of changes in microbial community composition and bacteria-derived metabolites upon exposure to different dietary components. For complete details on the use and execution of this protocol, please refer to Heppner et al.1",

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AU - Heimes, Helena

AU - Häcker, Deborah

AU - Omer, Hélène

AU - van der Veen, Daan R.

AU - Kiessling, Silke

AU - Haller, Dirk

PY - 2024/12/20

Y1 - 2024/12/20

N2 - Chemostat systems can be used to cultivate complex intestinal microbial communities ex vivo. Here, we present a protocol to transfer bacteria from human fecal material into chemostat systems as well as settings to simulate infant or adult colonic conditions. We describe the experimental setup, media design, donor selection, 16S rRNA amplicon sequencing, and circadian analysis of bacterial abundance. This protocol enables the investigation of changes in microbial community composition and bacteria-derived metabolites upon exposure to different dietary components. For complete details on the use and execution of this protocol, please refer to Heppner et al.1

AB - Chemostat systems can be used to cultivate complex intestinal microbial communities ex vivo. Here, we present a protocol to transfer bacteria from human fecal material into chemostat systems as well as settings to simulate infant or adult colonic conditions. We describe the experimental setup, media design, donor selection, 16S rRNA amplicon sequencing, and circadian analysis of bacterial abundance. This protocol enables the investigation of changes in microbial community composition and bacteria-derived metabolites upon exposure to different dietary components. For complete details on the use and execution of this protocol, please refer to Heppner et al.1

KW - cell culture

KW - health sciences

KW - microbiology

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JO - STAR Protocols

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ER -

Protocol to study human gut bacterial communities and rhythmicity ex vivo using a chemostat system

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