Downloads

You can download metadata in long or wide format and taxonomic profiles. This database is made available under the Open Database License. This means that you can build upon this database, but have to attribute this website and share-alike according to the terms of the license. Any rights in individual contents of the database are licensed under the Database Contents License.

The majority of samples in Metalog are available at ENA/SRA/DDBJ, although some are from MG-RAST and CNSA. Mappings of Metalog identifiers to samples, runs, and experiments are available in this mapping file. An external sample accession can actually correspond to several biological samples, and vice versa sometimes sequences belonging to the same actual sample have been submitted under multiple sample accessions. For this reason, we use our own sample identifiers throughout Metalog.

We have prepared an R script as an usage example that downloads data from Metalog and looks for associations between bacteria and medication in the gut microbiome of adults.


Metadata in long format

Metadata in long format with one row per sample and metadata item.

Human
104495 samples
Core metadata 11.2 MB Including partially harmonized metadata 12.5 MB Including all study-specific metadata 19.3 MB
Animal
11218 samples
Core metadata 1.3 MB Including partially harmonized metadata 1.5 MB Including all study-specific metadata 1.7 MB
Ocean
5608 samples
Core metadata 0.52 MB Including partially harmonized metadata 0.65 MB Including all study-specific metadata 0.87 MB
Environmental
26823 samples
Core metadata 2.5 MB Including partially harmonized metadata 3.1 MB Including all study-specific metadata 3.7 MB

Metadata in wide format

Metadata in wide (matrix-like) format with one row per sample. As this contains many partially empty columns, we do not generate the download file containing all study-specific metadata fields in this format.

Human
104495 samples
Core metadata 2.0 MB Including partially harmonized metadata 2.5 MB
Animal
11218 samples
Core metadata 0.3 MB Including partially harmonized metadata 0.37 MB
Ocean
5608 samples
Core metadata 0.13 MB Including partially harmonized metadata 0.22 MB
Environmental
26823 samples
Core metadata 0.88 MB Including partially harmonized metadata 1.3 MB

Taxonomic Profiles

Taxonomic profiles can be downloaded for these profilers: mOTUs 3.0, MetaPhlAn 4.0 (database version: vJun23_202307; mapping between clade names and full lineages and NCBI Taxonomy identifiers), and mOTUs based on the species in the SPIRE database. For adult human fecal samples, enterotype predictions (including the Enterotype Dysbiosis Score) are available. We will also add the predicted fecal microbial load as soon as possible.

Human
mOTUs 3.0 157.3 MB, 71716 samples MetaPhlAn 4.0 (all levels) 311.3 MB, 79428 samples MetaPhlAn 4.0 (species only) 106.8 MB, 79428 samples SPIRE mOTUs 140.1 MB, 49866 samples Enterotype predictions (only for fecal samples from adults) 1.6 MB, 47809 samples
Animal
mOTUs 3.0 27.1 MB, 9959 samples MetaPhlAn 4.0 (all levels) 21.4 MB, 10177 samples MetaPhlAn 4.0 (species only) 21.4 MB, 10177 samples SPIRE mOTUs 46.3 MB, 9122 samples
Ocean
mOTUs 3.0 18.7 MB, 5046 samples MetaPhlAn 4.0 (all levels) 41.1 MB, 5210 samples MetaPhlAn 4.0 (species only) 13.4 MB, 5210 samples SPIRE mOTUs 21.6 MB, 4147 samples
Environmental
mOTUs 3.0 30.3 MB, 18045 samples MetaPhlAn 4.0 (all levels) 52.1 MB, 21715 samples MetaPhlAn 4.0 (species only) 18.8 MB, 21715 samples SPIRE mOTUs 49.6 MB, 16356 samples

Taxonomic profiles may be unavailable for a number of reasons, e.g. missing or empty sequencing data, but also delays in processing after metadata curation. We are aware that some studies are missing a large number of taxonomic profiles and are working on adding these. Known to be missing are mOTUs 3 profiles for: