Example data in this directory comes from the following five papers:

Bokulich, N. A., et al., ``Antibiotics, birth mode, and diet shape
microbiome maturation during early life'', Science
Translational Medicine 8(343): 343ra82 (2016)

David, L. A., et al., ``Diet rapidly and reproducibly alters the human
gut microbiome'', Nature 505(7484): 559–63 (2014)

DiGiulio, D. B., et al., ``Temporal and spatial variation of the human
microbiota during pregnancy'', PNAS 112(35): 11060–5 (2015)

Vatanen, T., et al., ``Variation in Microbiome LPS Immunogenicity
Contributes to Autoimmunity in Humans'', Cell 165(4):842–853 (2016)

Kostic, A., et al., ``The Dynamics of the Human Infant Gut Microbiome
in Development and in Progression toward Type 1 Diabetes.'', Cell Host
& Microbe (2015). doi:10.1016/j.chom.2015.01.001

Data from the first four papers has been reprocessed as described in
the MITRE manuscript.  Metaphlan results and WGS sample metadata from
Kostic et al were downloaded from the DIABIMMUNE website
(https://pubs.broadinstitute.org/diabimmune/t1d-cohort)
and the metadata Excel sheet exported to CSV format and reprocessed as
shown in t1d/process_t1d_wgs.py.
