Frequently Asked Questions
Q: Can I volunteer to be part of the Human Microbiome Project?
A: The HMP is no longer accepting volunteers to be sequenced. For more information about how participants were recruited please see a full list of study inclusion/exclusion criteria. If you would like to have your own microbiome sampled, see the American Gut Project
Q: Do I need permission to use the HMP/iHMP data in my own scientific research?
A: No. The HMP is designated as a community resource project to accelerate access to, and use of HMP data by the entire scientific community. Please cite the HMP consortium papers.
Q: Do I need a password to access HMP data and resources?
A: All the HMP data and resources are freely available for browsing, however a password is required in order to add data files to the Advanced Query cart for download.
Q: How can I access the metadata for HMP1 metagenomic samples?
A: Metadata for all samples is available through the project catalog. Additional metadata (such as age, medical history, dietary habits, etc.) is kept confidential by the NIH and accessible only to authorized users through NCBI dbGAP. Researchers can request access to this data through this page. Click on the link to request authorized access.
Q: Can I perform a BLAST search against the HMP data sets?
A: We do not provide a BLAST server against HMP data, however Entrez BLAST submissions can be limited to HMP data by including "43021[BioProject]" in the Entrez Query field..
Q: How can I obtain an HMP reference strain?
A: Reference strains are available through strain repositories such as ATCC and BEI. Details for each strain are available in the project catalog (Strain Repository ID column).
Q: Can I get a list of organisms that make up the human microbiome?
A: We used a variety of methods to analyze the 16S and shotgun metagenomic reads in order to determine organism abundance in each sample. The results are available on the community profiling pages:
HMMCP - 16S mothur community profiling
HMQCP - 16S Qiime community profiling
HMSCP - Shotgun community profiling
HMSMCP - Shotgun MetaPHlAn community profiling
Q: Can I get the protocols that were used for the HMP?
A: All software, online resources and standard operating protocols used in, or developed as part of the HMP, are accessible on the Tools & Technology page. If you have a protocol or software package that you would like to post on this site, or would like more information on the currently available content, please contact us via the feedback form.
Q: Can you show me how to reproduce HMP analyses on my dataset?
A: We have put together walkthroughs, step-by-step tutorials taking users through typical HMP analysis paths, complete with sample datasets, details steps, screenshots and example output. These are designed for researchers without extensive bioinformatics infrastructure or experience so they can reproduce HMP analyses on any relevant dataset.
Q: How do I cite the Human Microbiome Project?
A: When citing the Human Microbiome Project in general please use the HMP consortium publications:
- A framework for human microbiome research. Human Microbiome Project Consortium, Nature, 486 (2012), pp. 215-221
- Structure, function and diversity of the healthy human microbiome. Human Microbiome Project Consortium, Nature, 486 (2012), pp. 207–214
When citing the integrative Human Microbiome Project please use the iHMP marker paper, or search our Publications page for project specific publications:
Q: How do I contact you?
A: If you want to ask us a question or send us comments, please use the feedback form.