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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 Access | | 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

Research

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 Access | | 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 Access | | 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 Access | | 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 National Institutes of Health Human Microbiome Project, published in 2012, provided a broad overview of the baseline microbiome in healthy individuals using samples from 18 different body sites. In this second installment, the authors expand this dataset with new whole-metagenome sequences and additional time points to assess the diversity and spatiotemporal distributions of the microbiota at six of these body sites. Using a combination of strain profiling, species-level metagenomic functional profiling and longitudinal analyses, this study delivers deeper insights into human microbial communities and provides an important resource for understanding what constitutes a 'healthy' microbiota.

Article | Open Access | | Nature

The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.

Article | Open Access | | Nature

The Human Microbiome Project (HMP), supported by the National Institutes of Health Common Fund, has the goal of characterizing the microbial communities that inhabit and interact with the human body in sickness and in health. In two Articles in this issue of Nature, the HMP Consortium presents the first population-scale details of the organismal and functional composition of the microbiota across five areas of the body. An associated News & Views discusses the initial results — which, along with those of a series of co-publications, already constitute the most extensive catalogue of organisms and genes related to the human microbiome yet published — and highlights some of the major questions that the project will tackle in the next few years.

Article | Open Access | | Nature