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Updated: Nov 11, 2025

Analysis of Interactions between Endobiotics and Human Gut Microbiota Using In Vitro Bath Fermentation Systems
Published on: August 23, 2019
A protocol combining breath testing and ex vivo fermentations to study the human gut microbiome
Laura Payling1,2,3, Nicole C Roy2,4,5,6, Karl Fraser2,3,6
1School of Food and Advanced Technology, Massey University, Palmerston North 4410, New Zealand.
Abstract:
This protocol describes the application of breath testing and ex vivo fermentations to study the association between breath methane and the composition and functionality of the gut microbiome. The protocol provides a useful systems biology approach for studying the gut microbiome in humans, which combines standardized methods in human breath testing and fecal sampling. The model described is accessible and easy to repeat, but its relative simplicity means that it can deviate from human physiological conditions.
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