A protocol combining breath testing and ex vivo fermentations to study the human gut microbiome

Laura Payling; Nicole C Roy; Karl Fraser; Simon M Loveday; Ian M Sims; Peter H Janssen; Stefan J Hill; Laura G Raymond; Warren C McNabb

doi:10.1016/j.xpro.2020.100227

A protocol combining breath testing and ex vivo fermentations to study the human gut microbiome

STAR Protoc. 2020 Dec 24;2(1):100227. doi: 10.1016/j.xpro.2020.100227. eCollection 2021 Mar 19.

Authors

Laura Payling^{1

2

3}, Nicole C Roy^{2

4

5

6}, Karl Fraser^{2

3

6}, Simon M Loveday^{2

3}, Ian M Sims⁷, Peter H Janssen³, Stefan J Hill⁸, Laura G Raymond⁸, Warren C McNabb^{2

6}

Affiliations

¹ School of Food and Advanced Technology, Massey University, Palmerston North 4410, New Zealand.
² Riddet Institute, Massey University, Palmerston North 4410, New Zealand.
³ Food and Bio-Based Products, AgResearch Limited, Tennent Drive, Palmerston North 4410, New Zealand.
⁴ Department of Nutrition, University of Otago, Dunedin 9016, New Zealand.
⁵ Liggins Institute, The University of Auckland, Auckland 1023, New Zealand.
⁶ High-Value Nutrition National Science Challenge, Auckland 1023, New Zealand.
⁷ Ferrier Research Institute, Victoria University of Wellington, Wellington 5010, New Zealand.
⁸ Advanced Chemical Characterisation, Scion, Te Papa Tipu Innovation Park, Rotorua 3010, 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.

Keywords: Cell Culture; Clinical Protocol; Genomics.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Breath Tests
Feces / microbiology*
Gastrointestinal Microbiome*
Humans