Accessible, curated metagenomic data through ExperimentHub

By Edoardo Pasolli, Lucas Schiffer, Paolo Manghi, Audrey Renson, Valerie Obenchain, Duy Tin Truong, F. Beghini, Faizan Malik, Marcel Ramos, J. Dowd and 4 more. Nature Methods, 2017

480 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/9526214b21a2acee1af70ed6a62e386306a98989

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Citations in the corpus

NetCoMi: network construction and comparison for microbiome data in R (2020, unknown): “A common exploratory analysis approach for microbiome survey data [13–17] is the estimation of microbe–microbe association networks [18–21], allowing for high-level insights into the global structure of microbial communities.”
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3 (2020, methodology): “The resulting integrated profiles are available for download ( Table S5 ) and included in the new release of curatedMetagenomicData (Pasolli et al., 2017) .”
Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, unknown): “This number of kSGBs is consistent with the 1,266 species we found at least once in the same set of metagenomes (Pasolli et al., 2017) at >0.”
Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome (2018, background): “, 2016) available for infants in curatedMetagenomicData (Pasolli et al., 2017) (Table S2B).”