The American Gut Project is a subset of the Earth Microbiome Project (EMP) [19], which has been instrumental in advocating for adherence to the standards of the Genomics Standards Consortium, including minimum information about a marker gene sequence (MIMARKS) [55]—a suite of standards defining variables to be collected within a marker gene survey for virtually any environment imaginable. The EMP and American Gut also follow published sequencing protocols [56] that aim to normalize technical bias for microbiome studies and employ the Biological Observation Matrix (BIOM) [44] specification as a standard and computationally efficient means to represent the resulting large, sparse-omics datasets and their sample and observation metadata. All data are de-identified and deposited into the public domain as quickly as possible via the European Bioinformatics Institute (EBI), which is part of the International Nucleotide Sequence Database Consortium (INSDC). American Gut has taken a further step by providing executable IPython [57] Notebooks allow others to reproduce and modify the analyses being performed on the data. All code for the project is hosted on Github in the “biocore” organization and is available under the BSD license, and all code and binaries used by the project are open-source.
