The latest American Gut results are out and we’re very excited to share them with the American Gut community.  We now have sequencing and analysis data from 3,238 participants, and as of today, this data equates to 101 million DNA sequences and 27 gigabytes of sequencing information.

The latest results can be viewed here, and the IPython Notebook demonstrating the analyses performed on the American Gut dataset can be accessed here.  Notably, the notebook has some pre-run analyses that interested individuals can practice on to get a taste of the American Gut pipeline and how it works.

A few noteworthy patterns observed in the data that we wish to highlight are:

  • How much of the microbial diversity participants shared with other participants depended greatly on how recently they had taken antibiotics. Those participants who had taken antibiotics within the last year tended to have less shared diversity with other participants.
  • Alcohol imbibers tended to have greater microbial diversity than those that don’t drink alcohol at all.
  • Spikes in microbiome populations seem to occur around holidays: in July, and in November through January.
  • There is no single organism that is found in every person, but some are more common across the population than others.
  • People who sleep more and who exercise outdoors have more diverse microbiomes.
  • The microbiomes of the elderly resemble those of infants in certain respects, as seen in other studies


Of these results, Dr. Rob Knight says “These patterns are certainly interesting, and we are hoping that the American Gut data provides other researchers a foundation to further study the effects of diet and lifestyle on the human microbiome.”  He adds, “This isn’t a diagnostic tool to detect disease, but it may lead to the development of many tools that doctors can use to diagnose and treat a wide variety of diseases that are influenced by the microbiome.”

According to Daniel McDonald, a graduate student in Knight’s lab, “Any researcher who is looking into the human microbiome will benefit from the American Gut data and the new processing pipeline we are releasing.  Researchers will be able to frame their own data against the American Gut data for context or additional insight.”  This emphasis on “reproducible computing” is a first for any major microbiome initiative.

American Gut is particularly exciting and unique because it gives citizens the opportunity to participate in real science. The project is built on the open-source and open-access principles of the Earth Microbiome Project, with its (de-identified) data available for use for any purpose and available to the general public through the International Nucleotide Sequence Database Collaboration (INSDC).  Using the IPython Notebook pages referred to above, anyone can analyze American Gut data, exploring a countless number of questions about human health, disease, and the microbiome.