Accessible, curated metagenomic data through ExperimentHub

Abstract

We present curatedMetagenomicData, a Bioconductor and command-line resource providing thousands of metagenomic profiles from the Human Microbiome Project and other publicly available datasets, and ExperimentHub, for convenient cloud-based distribution of data to the R desktop. curatedMetagenomicData provides standardized per-participant metadata linked to bacterial, fungal, archaeal, and viral taxonomic abundances, as well as quantitative metabolic functional profiles, generated by the HUMAnN2 and MetaPhlAn2 pipelines. The resulting datasets can be immediately analyzed with a wide range of statistical methods, requiring a minimum of bioinformatic expertise and no preprocessing of data. We demonstrate exploratory data analysis, an investigation of gut "enterotypes", and a comparison of the accuracy of disease classification from different data types. These documented analyses can be reproduced efficiently on a laptop, without the barriers of working with large-scale, raw sequencing data. The development of curatedMetagenomicData will continue with the addition, curation, and analysis of further microbiome datasets.