Disease risk and treatment response are determined, at the individual level, by a complex history
of genetic and environmental interactions, including those with our endogenous microbiomes. Personalized
health care requires a deep understanding of patient biology that can now be measured using a range of
‘‑omics’ technologies. Patient stratification involves the identification of genetic and/or phenotypic disease
subclasses that require different therapeutic strategies. Stratified medicine approaches to disease diagnosis,
prognosis and therapeutic response monitoring herald a new dimension in patient care. Here, we explore the
potential value of metabolic profiling as applied to unmet clinical needs in gastroenterology and hepatology.
We describe potential applications in a number of diseases, with emphasis on large-scale population studies
as well as metabolic profiling on the individual level, using spectrometric and imaging technologies that will
leverage the discovery of mechanistic information and deliver novel health care solutions to improve clinical
pathway management.