HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes. Issue Volume 49:Issue D1(2021) (22nd November 2020)

• Record Type: Journal Article
• Authors: Kasmanas, Jonas Coelho; Bartholomäus, Alexander; Corrêa, Felipe Borim; Tal, Tamara; Jehmlich, Nico; Herberth, Gunda; von Bergen, Martin; Stadler, Peter F; Carvalho, André Carlos Ponce de Leon Ferreira de; Nunes da Rocha, Ulisses
• Is Part Of: Nucleic acids research. Volume 49:Issue D1(2021)
• Page Start: D743
• Page End: D750
• Publication Date: 2020-11-22
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkaa1031
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Metagenomics became a standard strategy to comprehend the functional potential of microbial communities, including the human microbiome. Currently, the number of metagenomes in public repositories is increasing exponentially. The Sequence Read Archive (SRA) and the MG-RAST are the two main repositories for metagenomic data. These databases allow scientists to reanalyze samples and explore new hypotheses. However, mining samples from them can be a limiting factor, since the metadata available in these repositories is often misannotated, misleading, and decentralized, creating an overly complex environment for sample reanalysis. The main goal of the HumanMetagenomeDB is to simplify the identification and use of public human metagenomes of interest. HumanMetagenomeDB version 1.0 contains metadata of 69 822 metagenomes. We standardized 203 attributes, based on standardized ontologies, describing host characteristics (e.g. sex, age and body mass index), diagnosis information (e.g. cancer, Crohn's disease and Parkinson), location (e.g. country, longitude and latitude), sampling site (e.g. gut, lung and skin) and sequencing attributes (e.g. sequencing platform, average length and sequence quality). Further, HumanMetagenomeDB version 1.0 metagenomes encompass 58 countries, 9 main sample sites (i.e. body parts), 58 diagnoses and multiple ages, ranging from just born to 91 years old. The HumanMetagenomeDB is publicly available at https://webapp.ufz.de/hmgdb/ .