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Short answer
The Human Microbiome Project (HMP) was a ten-year, two-phase NIH program that built resources, methods and data to link interactions between humans and their microbiomes to health-related outcomes. Phase one characterised microbial communities in healthy people; the second phase, the Integrative Human Microbiome Project (iHMP), followed microbiome and host changes over time in three conditions.
General information for researchers and laboratory staff. It is not medical advice and the microbiome findings described here are not a clinical test.
Definition and scope
The HMP is the NIH research program that set out to describe the microbial communities living on and in the human body and to make that description reusable. The consortium’s flagship 2012 paper states the aim as characterising the ecology of human-associated microbial communities, noting that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin and vagina, and that much of this diversity remains unexplained (Human Microbiome Project Consortium, Nature 2012).
The 2019 summary paper describes the whole program as “carried out over ten years and two phases to provide resources, methods, and discoveries” (Integrative HMP Research Network Consortium, Nature 2019). The microbiome itself is a broader subject within microbiology; the HMP is one specific, named program within it.
How the project worked in practice
Phase one: healthy-population characterisation
The first phase analysed what the 2012 paper calls “the largest cohort and set of distinct, clinically relevant body habitats so far.” Its reported findings, taken from the paper’s abstract:
- The diversity and abundance of each habitat’s signature microbes varied widely even among healthy subjects, with strong niche specialisation both within and among individuals.
- The project encountered an estimated 81-99% of the genera, enzyme families and community configurations occupied by the healthy Western microbiome.
- Metagenomic carriage of metabolic pathways was stable among individuals despite variation in community structure.
- Ethnic/racial background was one of the strongest associations of both pathways and microbes with clinical metadata.
Phase two: the Integrative Human Microbiome Project (iHMP)
The iHMP is described as the second phase of the NIH HMP. It analysed microbiome and host activities in longitudinal studies of disease-specific cohorts and created integrated data sets of microbiome and host functional properties (Integrative HMP Research Network Consortium, Cell Host Microbe 2014). The three models were preterm birth, inflammatory bowel disease and type 2 diabetes; the completed work, reported in 2019, covered pregnancy and preterm birth, inflammatory bowel diseases, and stressors affecting individuals with prediabetes.
Types or related concepts: HMP phase one and the iHMP
| Feature | HMP phase one (2012 paper) | iHMP (2014 and 2019 papers) |
|---|---|---|
| Population studied | Healthy subjects | Disease-specific cohorts |
| Question | What is the range of normal microbial structure and function across body habitats? | How do the microbiome and host interact and change over time? |
| Conditions | None (healthy baseline) | Preterm birth, inflammatory bowel disease, type 2 diabetes / prediabetes |
| Design emphasis | Many body habitats, including gut, skin and vagina | Longitudinal studies with integrated multi-omic data |
| Data resource | Consortium data and metagenomic analyses | Data resources at the HMP Data Coordination Center |
This comparison is our own side-by-side of statements in the three cited papers; the cells are drawn from their abstracts.
Where it matters for labs and clinics
- Reference data. The iHMP paper states that its data resources are held at the HMP Data Coordination Center, and the 2014 paper describes the data sets as experimental test beds to evaluate new models, methods and analyses. Labs developing microbiome pipelines can therefore benchmark against shared public data. Functional profiling tools such as HUMAnN are typical of the downstream analysis used with such metagenomic data.
- Variability as a design input. Because healthy individuals vary widely, a single sample or small control group may not represent “normal”; the 2012 paper’s range-of-normal framing is the reason baseline cohorts are described rather than assumed.
- Population coverage. The 81-99% coverage estimate refers specifically to the healthy Western microbiome, so it should not be quoted as coverage of all populations.
- Model organisms. Studies that test human-derived communities in animals rely on controlled colonisation status; see gnotobiotic mice and specific-pathogen-free (SPF) mice.
Checklist before reusing HMP-derived data or methods
- Identify which phase the data set comes from (healthy baseline or a disease-specific iHMP cohort).
- Record the body habitat and whether samples are longitudinal.
- Check that your comparison population is compatible with a Western cohort before using the 81-99% coverage figure.
- Cite the originating consortium paper and the data resource, not a secondary summary.
Common misunderstandings
- “The HMP defined one healthy microbiome.” The 2012 results emphasise wide variation among healthy subjects and describe a range of normal configurations, not a single profile.
- “The HMP produced a diagnostic test.” The papers cited describe characterisation, mechanisms and data resources. They do not present a clinical test.
- “The HMP ended with the 2012 paper.” The 2012 paper reports phase one; the program continued as the iHMP and was reported as completed in 2019.
FAQ
What was the Human Microbiome Project?
An NIH program run over ten years and two phases to provide resources, methods and discoveries linking human-microbiome interactions to health-related outcomes.
What is the iHMP?
The Integrative Human Microbiome Project, the second phase of the HMP, which studied dynamic microbiome and host changes in pregnancy and preterm birth, inflammatory bowel diseases, and prediabetes-related stressors.
Where are the data?
The 2019 paper places the data resources at the HMP Data Coordination Center.
Sources
- Human Microbiome Project Consortium. Structure, function and diversity of the healthy human microbiome. Nature 2012;486(7402):207-214. PMID 22699609. Read 2026-11-08.
- Integrative HMP (iHMP) Research Network Consortium. The Integrative Human Microbiome Project. Nature 2019;569(7758):641-648. PMID 31142853. Read 2026-11-08.
- Integrative HMP Research Network Consortium. The Integrative Human Microbiome Project: dynamic analysis of microbiome-host omics profiles during periods of human health and disease. Cell Host Microbe 2014. PMID 25211071. Read 2026-11-08.
