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Am J Epidemiol. 2019 Jan 10. doi: 10.1093/aje/kwz006. [Epub ahead of print]

HMP16SData: Efficient Access to the Human Microbiome Project through Bioconductor.

Author information

1
Graduate School of Public Health and Health Policy, City University of New York, New York, NY.
2
Institute for Implementation Science in Population Health, City University of New York, New York, NY.
3
Roswell Park Cancer Institute, University of Buffalo, Buffalo, NY.
4
Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA.
5
The Broad Institute of MIT and Harvard, Cambridge, MA.
6
Department of Global Health and Social Medicine, King's College London, London, UK.
7
The Centre for Integrative Biology, University of Trento, Trento, Italy.

Abstract

Phase 1 of the Human Microbiome Project (HMP) investigated 18 body subsites of 239 healthy American adults, to produce the first comprehensive reference for the composition and variation of the "healthy" human microbiome. Publicly-available data sets from amplicon sequencing of two 16S ribosomal RNA variable regions, with extensive controlled-access participant data, provide a reference for ongoing microbiome studies. However, utilization of these data sets can be hindered by the complex bioinformatic steps required to access, import, decrypt, and merge the various components in formats suitable for ecological and statistical analysis. The HMP16SData package provides count data for both 16S ribosomal RNA variable regions, integrated with phylogeny, taxonomy, public participant data, and controlled participant data for authorized researchers, using standard integrative Bioconductor data objects. By removing bioinformatic hurdles of data access and management, HMP16SData enables epidemiologists with only basic R skills to quickly analyze HMP data.

PMID:
30649166
DOI:
10.1093/aje/kwz006

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