The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease: Cell Host & Microbe
Figure 1
Integrative Multi-Omic Analysis of the Vaginal and Related Microbiomes in Pregnancy: Sample Collection, Assays, and Data Generation Workflow
Samples from pregnant women and neonates will be collected at clinics associated with Virginia Commonwealth University and the Global Alliance to Prevent Prematurity and Stillbirth (GAPPS). Health questionnaires will be administered and samples collected from multiple body sites over multiple visits throughout pregnancy, at delivery, at discharge, and at follow-up visits. Neonates will be sampled at delivery, discharge, and follow-up visits. A multi-omic approach will probe properties of the host and microbial communities to generate an integrative, longitudinal, and comprehensive data set of 16S rRNA gene surveys, mass spectrometry-based lipidomic profiles, and cytokine assays. A subset of samples will be subjected to whole metagenome and metatranscriptome sequencin for cultivation and isolation of bacterial strains for genome sequencing, and for generation of interactome maps.
The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease
The human microbiome is important for human health, behavior, and disease, yet its function and dynamics during healthy and disease states are only partially understood. Studies of the microbiome to date have indicated impacts on personalized medicine ranging from inactivation of pharmaceuticals in some individuals (Haiser et al., 2013) to increased risk of cardiovascular disease due to microbial metabolic byproducts (Koeth et al., 2013). These findings show particular promise given that they have already come to light early in the field's transition from high-throughput discovery to detailed mechanistic studies, a process still ongoing after more than a decade of human omics. The first phase of the NIH Human Microbiome Project (HMP, fiscal years 2008–2012,http://www.commonfund.nih.gov/hmp) examined the diversity and composition of the human microbiome to evaluate (1) common patterns of microbial diversity associated with health and (2) whether taxonomic or functional features of the microbiome correlated with diseases by analyzing a large healthy cohort and a set of demonstration projects. These efforts revealed the vast microbial diversity associated with humans and provided new insights into the ecology of the host-microbiome supraorganism (Human Microbiome Project Consortium, 2012a,Human Microbiome Project Consortium, 2012b).
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