Publication Details

Category Text Publication
Reference Category Journals
DOI 10.1093/nar/gkaa1031
Licence creative commons licence
Title (Primary) HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes
Author Kasmanas, J.C.; Bartholomäus, A.; Borim Corrêa, F.; Tal, T.; Jehmlich, N. ORCID logo ; Herberth, G. ORCID logo ; von Bergen, M.; Stadler, P.F.; de Carvalho, A.C.P.L.F.; Nunes da Rocha, U.
Source Titel Nucleic Acids Research
Year 2021
Volume 49
Issue D1
Page From D743
Page To D750
Language englisch
Topic T7 Bioeconomy
T9 Healthy Planet
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
Persistent UFZ Identifier
Kasmanas, J.C., Bartholomäus, A., Borim Corrêa, F., Tal, T., Jehmlich, N., Herberth, G., von Bergen, M., Stadler, P.F., de Carvalho, A.C.P.L.F., Nunes da Rocha, U. (2021):
HumanMetagenomeDB: a public repository of curated and standardized metadata for human metagenomes
Nucleic Acids Res. 49 (D1), D743 - D750 10.1093/nar/gkaa1031