MiCoDa: Microbial Community Database

Search, select, and download curated and processed 16S rRNA gene microbiome data

MiCoDa is a searchable database that hosts curated and processed 16S rRNA gene amplicon sequences from all environments and spans the entire globe. All samples in MiCoDa resulted from amplicon sequencing of the 16S rRNA gene from base pair position 515, and have been re-processed for increased comparability. All sequenced data in MiCoDa is linked to a publication or project, and we have included additional technical metadata (e.g. sequencer, DNA extraction kit) directly from the literature to facilitate re-analysis. Raw files for all samples in MiCoDa are available in INSDC databases, and MiCoDA metadata includes INSDC accession numbers. MiCoDa includes data from hundreds of microbiome studies as well as data collections including the Earth Microbiome Project and µSudAqua datasets in ready-to-use CSV formats. Our aim is to encourage the reuse of microbiome data across regions and disciplines.

Filters

Source

Location

Realm

Environment - broad scale

Environment - local scale

Host

Animal Gut

Host Kingdom

Host Phylum

Host Class

Host Order

Host Family

Host Genus

Host Species

Methodology

Sequencing Platform

DNA Extraction Method

Experimental

Collection

Source

Host

Methodology

Location

Realm

Environment - broad scale

Environment - local scale

Collection

Download file detailing the numbers of reads preserved after each step of processing (i.e., processing metadata), for all samples

How to cite MiCoDa?

To cite the whole database:

Jurburg et al. (2024) Microbial Community Database (MiCoDa). v2 [Database]. German Centre for Integrative Biodiversity Research. https://doi.org/10.25829/8d64 [Accessed: 18-10-2024].

To cite subsets of the database:

Please check our how-to page here.