by Geoffrey A. Preidis and Peter J. Hotez
Metagenomic analyses are most often undertaken by sequencing the bacterial 16S ribosomal RNA (rRNA) subunit or by whole metagenome shotgun sequencing, typically on a massively parallel pyrosequencing platform. These technologies have expanded the scope of traditional culture-dependent microbiological methods and have enhanced our understanding of the rich microbial communities that inhabit the intestine, skin, oral cavity, and genitourinary tract and how these commensal microbes interact with both pathogen and host.In parallel, the field of metabolomics emerged as the systematic, nonbiased analysis of all low-molecular-weight small molecules, or metabolites, produced by a system in response to an environmental stimulus. Metabolites are secreted into body fluids by host and microbial cells, measured by mass spectrometry–based approaches, and aligned against libraries of known biochemicals. These techniques have been used to gain insights into mechanisms of pathogenesis and to identify new biomarkers of disease. Metabolomics also offers clues to the presence and function of microbes living deep within the small bowel that are difficult to sample directly and highlights the complex relationship between resident microbes, host metabolism, pharmacotherapeutic action, and relative health or disease.