November 2013

NIH funds three projects focused on characterizing microbiota in disease

Body parts in the Human Microbiome Project healthy cohort study
The body sites that were sampled as part of the Human Microbiome Project healthy cohort study. Image credit: NIH

The Human Microbiome Project, funded by the National Institutes of Health Common Fund, is entering its second phase with three research projects focused on understanding changes in microbiomes in disease. Two members of the American Society for Biochemistry and Molecular Biology will lead one of the projects.
The first phase of the HMP started in 2007 and focused on characterizing microbial communities of different body sites, including skin, nasal and oral cavities, and gastrointestinal and urogenital tracts.
The new studies will harness the technological tools of the -omics revolution – genomics and metagenomics, transcriptomics, proteomics and metabolomics – to capture coordinated snapshots of the dynamic changes in the microbiome and in the individual during disease progression.
One project, led by Gregory Buck of Virginia Commonwealth University and funded by the Eunice Kennedy Shriver National Institute of Child Health and Human Development, will characterize urogenital tract bacteria in pregnant women and their babies to gain insights into preterm birth.
A second project, led by Ramnik Xavier of the Broad Institute of Massachusetts Institute of Technology and Harvard University and Curtis Huttenhower of Harvard School of Public Health, will assess populations and physiological activities of gut microbes in people with Crohn’s disease and ulcerative colitis, the two major forms of chronic inflammatory bowel disease. The project is funded by the National Institute of Diabetes and Digestive and Kidney Diseases.

Enterococcus faecalis
The bacterium Enterococcus faecalis is one of many commensal microbes that live in the human gut. Image credit: NIH

ASBMB members Michael Snyder of Stanford University and George Weinstock of Washington University at St. Louis will lead the third project, also funded by the NIDDK. They will examine changes in gut and nose microbial communities in a cohort over three years, sampling the same individual in periods of good health and during viral infections as well as other stresses. The study will focus on people at risk for diabetes, adding another dimension of analysis, and will include blood glucose measurements. In all, more than 1,080 different physiological states will be analyzed.
The project builds upon the expertise of the two teams. Snyder is a leader in the field of functional genomics and proteomics, having led one of seven research groups participating in the ENCODE project, which aimed to identify all functional elements in the human genome. Weinstock led one of the first bacterial genome sequencing projects and was an investigator in the HMP precursor project, the Human Gut Microbiome Initiative.

Soo Hee LeeSoo Hee Lee ( received a Ph.D. in biochemistry from the Johns Hopkins University School of Medicine and undertook a Jane Coffin Childs Memorial Fund postdoctoral fellowship at the Yale University School of Public Health.

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