Metabolic phenotyping of the human microbiome

Wiley Barton; Orla O'Sullivan; Paul D Cotter

doi:10.12688/f1000research.19481.1

Metabolic phenotyping of the human microbiome

F1000Res. 2019 Nov 22:8:F1000 Faculty Rev-1956. doi: 10.12688/f1000research.19481.1. eCollection 2019.

Authors

Wiley Barton^{1

2

3}, Orla O'Sullivan^{1

2

3}, Paul D Cotter^{1

2

3}

Affiliations

¹ Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61C996, Ireland.
² APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, T12YT20, Ireland.
³ VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, P61C996, Ireland.

Abstract

The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.

Keywords: bile acids; metabolomics; metagenomics; microbiome; short chain fatty acids.

Publication types

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

MeSH terms

Humans
Metabolomics
Microbiota*

Grants and funding

This work was funded by Science Foundation Ireland (SFI) in the form of a centre grant (APC Microbiome Institute Grant Number SFI/12/RC/2273). Research in the PDC laboratory is funded through a principal investigator award, ‘Obesibiotics’ (11/PI/1137). OOS is funded by the SFI starting investigator research grant (13/SIRG/2160). WB is currently supported by a joint research centre grant from SFI and the Department of Agriculture, Food and Marine on behalf of the government of Ireland (VistaMilk, 16/RC/3835)