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Peer Inside the American Gut

By Bio-IT World Staff

July 11, 2014 | This Wednesday, American Gut, the crowdsourced project spearheaded by Rob Knight of the University of Colorado that has now sequenced gut microbiota samples from over 3,000 volunteers, released both a round of results and its own analytical pipeline. In addition to comparing the microbiota of different cohorts within American Gut, researchers can now access the raw sequencing data (stripped of identifying information), and the IPython Notebooks that American Gut used to analyze that data. This makes American Gut, which has sequenced samples from 13 times as many subjects as the similar Human Microbiome Project, the first major microbiome initiative to make its pipeline completely transparent, reproducible and modifiable. American Gut has also promised to release more Notebooks as new analyses are performed.

The American Gut population is notable not only for the number of participants, but also for having much greater representation than previous projects of key groups like the elderly and very young, and people with extreme BMIs. The preliminary results released this week include interesting observations such as: getting more sleep, exercising outdoors, and drinking alcohol are all associated with great microbial diversity; and differences between seemingly significant groups, such as vegans vs. omnivores, those on antibiotics vs. those not on antibiotics, or the elderly vs. babies, all pale in comparison to differences between individuals.

The release by American Gut, including links to the IPython Notebooks, can be found at

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