Human Microbiome Project, part 2

The latest phase of this ambitious undertaking has provided important insights into inflammatory bowel disease, the onset of type 2 diabetes and preterm birth. But fully integrated multidisciplinary collaborations are now needed to convert knowledge of the microbiome into clinical applications.

Over ten years, the Human Microbiome Project has provided resources for studying the microbiome and its relationship to disease; this Perspective summarizes the key achievements and findings of the project and its relationship to the broader field.

The dream of microbiome-based medicine requires a fresh approach — an ecological and evolutionary understanding of host-microbe interactions — argues Lita Proctor.

The Human Microbiome Project put the health-associated microbes found in humans on centre stage. The project’s second phase shows how microbial disturbance in disease is linked to host processes.

The National Institutes of Health Human Microbiome Project is coming to a close, offering an opportunity to reflect on its legacy and the urgent need to understand the microbiome of underrepresented populations.

Using the principles of community ecology in microbiome research will help to interpret these dynamic ecosystems and their relevance to health and disease.

The diversity of the vaginal microbiome is linked to ethnicity, preterm birth and transitions to a healthier profile upon pregnancy.

Multi-omics longitudinal profiling of individuals can detect subtle changes in health status at the earliest possible time point, allowing preemptive initiation of mechanism-appropriate disease-prevention strategies.

The Inflammatory Bowel Disease Multi’omics Database includes longitudinal data encompassing a multitude of analyses of stool, blood and biopsies of more than 100 individuals, and provides a comprehensive description of host and microbial activities in inflammatory bowel diseases.

Deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, alongside changes in the microbiome, in samples from individuals with and without prediabetes reveal insights into inter-individual variability and associations between changes in the microbiome and other factors.

As part of the second phase of Human Microbiome Project, the Multi-Omic Microbiome Study: Pregnancy Initiative presents a community resource to help better understand how microbiome and host profiles change throughout pregnancy as well as to identify new opportunities for assessment of the risk of preterm birth.

Ancestry and socioeconomic factors influence predictable changes in the vaginal microbiome that occur early in pregnancy in women who experience normal term birth.

Personalized omics profiling can lead to actionable health discoveries and stimulate lifestyle changes.

Using metabolomics and shotgun metagenomics on stool samples from individuals with and without inflammatory bowel disease, metabolites, microbial species and genes associated with disease were identified and validated in an independent cohort.

Analysis of paired metagenomes and metatranscriptomes associated with patients with inflammatory bowel disease (IBD) and non-IBD controls over time provides some insights into microbial community variation and potential pathways influencing IBD symptoms.

The Qiita web platform provides access to large amounts of public microbial multi-omic data and enables easy analysis and meta-analysis of standardized private and public data.

HUMAnN2 uses a tiered sequence search to provide rapid and accurate species-level functional profiles of microbial communities from metagenomic and metatranscriptomic data.

Updates from the Human Microbiome Project analyse the largest known body-wide metagenomic profile of human microbiome personalization.

The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

The Human Microbiome Project Consortium has established a population-scale framework to study a variety of microbial communities that exist throughout the human body, enabling the generation of a range of quality-controlled data as well as community resources.