The Newest “Omics”—Metagenomics and Metabolomics—Enter the Battle against the Neglected Tropical Diseases

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.

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Reflections on feces and its synonyms

As medical parasitologists we tend not to be too squeamish when discussing human feces. They represent one of the “five F’s” of parasitology – feces, fingers, flies, food, fomites – and indeed, most of the world’s poor living below the World Bank poverty level lives with intestinal worms and consequently parasitic helminth eggs in their feces.

Still, we were caught a bit off guard when one of the staff at PLOS Neglected Tropical Diseases telephoned to give us a heads up that we were about to publish “An In-Depth Analysis of a Piece of Shit: Distribution of Schistosoma mansoni and Hookworm Eggs in Human Stool” by Krauth et al. The voice on the other line said the article had gone through extensive peer review as well as reviews by both Associate and Deputy Editors, and it was to go live in a couple of days. They called because we should know that as the Editors-in-Chief we still had the prerogative to change the title.

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