TIC Seminar - Microbiome Datasets at Scale

Dr Daniel McDonald, Department of Pediatrics, University of California San Diego, CA, USA

The American Gut is an Earth Microbiome Project study, and is the largest crowdfunded science project to date which seeks to bring the technologies developed for the Human Microbiome Project to the general public. Through the use of crowdfunding, we have successfully raised over $1,500,000 USD from over 10,000 members of the general public and key donations from industry partners. In exchange for a donation, individuals can choose to receive a sample kit and in return, they receive an analysis of their sample, how they compare to the rest of the population, how they compare to the Human Microbiome Project and a taxonomy summary. Individuals who choose to receive a sample are consented and presented a voluntary survey according to protocols approved by the Institutional Review Board of the University of California San Diego. All samples in the American Gut Project are processed using the standard Earth Microbiome Project 16S protocol, sequencing the V4 region on the Illumina MiSeq platform. 
The American Gut is itself a substudy within the Earth Microbiome Project which spans over 40,000 samples from a range of environment types on our planet. Critically, the Earth Microbiome Project is composed of individual studies from a network of collaborators who abide by metadata and sample handling standards to facilitate meta-analysis. In addition, one key tenant of these projects is that they are aggressively open-access. In this talk, I will outline present findings within the largest microbiome efforts to date, and discuss some of the key challenges faced while operating at unprecedented scales.

Date & time

2–3pm 12 December 2016


Slatyer Seminar room, DA Brown building


 Marcin Adamski

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