In the spirit of open access science, all de-identified American Gut data are made freely available to the public. This enables any researcher-or participant-to further explore American Gut data. The data are available in several forms:

  1. Sequences and metadata can be accessed from EBI (accession #ERP012803). *Note: the filter for blooming bacteria has not been applied to this data.
  2. Sequences, metadata, and OTU tables can be accessed on Qiita (qiita.ucsd.edu; study ID 10317). *Note: the filter for blooming bacteria has not been applied to this data.
  3. To produce participant results and prepare the data for other analyses, we have created a series of IPython notebooks. All outputs from the notebooks, including raw sequences, sequences that have been filtered for blooming bacteria, OTU tables, and alpha and beta diversity analyses outputs, can be found on our ftp site. The notebooks themselves can be found on GitHub.
  4. Additionally, all protocols for DNA extraction, PCR amplification, and sequencing can be found on the Earth Microbiome Project webpage.

If you have any questions about any of the data forms listed above, please email American Gut project manager Embriette Hyde at ehyde@ucsd.edu.