The human microbiome is large and complex. It is thought that there are as many indigenous microbes in your body as there are other cells. The only way to understand how the microbiome’s presence affects the body at any given time is through studying the comprehensive or global metabolome—the collection of metabolites that the microbiome and host produces and interacts with. Metabolites are the microbiome’s language.
In short, trying to resolve the link between the microbiome and human health without looking at the metabolome is like trying to predict a married couple’s compatibility without observing how they communicate with each other.
Since a metabolomics approach allows scientists to examine all the small molecules in our body, including hormones, amino acids, co-factors, neurotransmitters, and other compounds, it gives us a shot at understanding every step of disease etiology, from gene to phenotype.