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Human Microbiome Project, part 2

The second phase of the 10-year NIH-funded Human Microbiome Project (HMP2) has reached its fruition in the form of a collection of studies addressing the role of the microbiota in inflammatory bowel disease, the onset of type 2 diabetes and in pregnancy and preterm birth. Through the power of multi-omic technologies and clinical analyses, these studies provide the most comprehensive analysis of both the host and the microbiota to date, revealing important insights into the complex interplay between these partners and how this changes over time. The work of the HMP has generated vital resources and analytical tools that continue to fuel progress in the field, and has set a precedent for future human multi-omic studies that strive to integrate basic and clinical science.

We are pleased to present this Nature collection of commentary and research publications from across Nature journals and related publications from HMP2.

Perspective & Commentary

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.

Perspective | open | | Nature

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.

News & Views | | Nature

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.

Editorial | | Nature Medicine

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.

News & Views | | Nature Medicine


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.

Article | open | | Nature

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.

Article | open | | Nature

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.

Article | open | | Nature Medicine

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.

Brief Communication | | Nature Methods

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.

Article | open | | Nature

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.

Article | open | | Nature