A review on human fecal metabolomics: Methods, applications and the human fecal metabolome database

Anal Chim Acta. 2018 Nov 7;1030:1-24. doi: 10.1016/j.aca.2018.05.031. Epub 2018 May 12.


Metabolomic analysis of human biospecimens had progressed quickly over the past decade. Technological and methodological advances have led to the comprehensive characterization of human serum, urine, cerebrospinal fluid and saliva metabolomes, and the creation of freely available metabolome reference databases. Unfortunately, the characterization of the human fecal metabolome still lags behind these other metabolomes in terms of the availability of standardized methods and freely available resources. The purpose of this review is to bring the knowledge of the human fecal metabolome, and the methods to characterize it, to the same level as most other human biofluid metabolomes. More specifically, this review is intended to critically assess the field of fecal metabolomics and to provide a comprehensive review of the current state of knowledge with regard to the protocols, technologies and remaining challenges in fecal metabolite analysis. In addition to providing an overview of fecal metabolomics and some consensus recommendations, we also present the human fecal metabolome database (HFMDB - http://www.fecalmetabolome.ca), a freely available, manually curated resource that currently contains over 6000 identified human fecal metabolites. Each entry in the HFMDB includes extensive chemical information, metabolite descriptions and reference data in the same format as the Human Metabolome Database (HMDB).

Keywords: Chromatography; Feces; Human; Metabolome; Metabolomics; Stool.

Publication types

  • Review

MeSH terms

  • Databases, Factual*
  • Feces*
  • Humans
  • Metabolomics*