Table 1 Examples of public databases for microbial community analysis. Prevalent microbial sequence databases are listed below with indications of their omics integration and functional assignment integration where applicable
From: Ecosystem-specific microbiota and microbiome databases in the era of big data
Database name | Data type | Meta-omics approach included | Target organisms | URL | References |
|---|---|---|---|---|---|
China National GeneBank (CNGB) | rRNA subunits Genomes Transcriptomes Proteomes Environmental/ contextual data | Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Environmental measurements | All microorganisms | [185] | |
ConsensusPathDB | rRNA subunits Genomes Transcriptomes Proteomes Environmental/ contextual data | Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics | Animal (human, mouse), fungi (yeast) | ||
DNA DataBank of Japan (DDBJ) | rRNA subunits Genomes Transcriptomes Proteomes Environmental/ contextual data | Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics | All microorganisms | ||
European Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI) European Life-Science Infrastructure (ELIXIR) | rRNA subunits Genomes Transcriptomes Proteomes Metabolomes Environmental/ contextual data | Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics Environmental measurements | All microorganisms | ||
EzBioCloud | rRNA subunits Genomes Environmental/ contextual data | Sanger sequencing Metabarcoding Metagenomics Environmental measurements | Bacteria and Archaea | [198] | |
International Nucleotide Sequence Database Collaboration (INSDC) | rRNA subunits Genomes | Sanger sequencing Metabarcoding Metagenomics | All microorganisms | ||
Joint Genomic Institute Integrated Microbial Genomes (JGI- IMG) | rRNA subunits Genomes Transcriptomes Proteomes | Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics | All microorganisms | [201] | |
Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) | rRNA subunits Genomes Transcriptomes | Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics | All microorganisms | ||
National Center for Biotechnology Information collections (NCBI RefSeq, NCBI BLAST, NCBI Entrez, NCBI GenBank) | rRNA subunits Genomes Transcriptomes Proteomes Metabolomes Environmental/ contextual data | Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics Environmental measurements | All microorganisms | https://www.ncbi.nlm.nih.gov/refseq/ https://www.ncbi.nlm.nih.gov/refseq/ | |
Protist ribosomal reference database (PR2) | rRNA subunits | Sanger sequencing Metabarcoding | All eukaryotes | [208] | |
SILVA | rRNA subunits | Sanger sequencing Metabarcoding | All microorganisms | [209] | |
University of California, Santa Cruz Genome Browser | rRNA subunits Genomes Transcriptomes | Sanger sequencing Metabarcoding Metagenomics | All microorganisms | [210] | |
Ribosomal RNA operon copy number database (rrnDB) | rRNA subunits | Sanger sequencing Metabarcoding | Bacteria and Archaea | [211] | |
The Microbe Directory (TMD) | rRNA subunits Genomes Environmental/ contextual data | Sanger sequencing Metabarcoding Metagenomics Environmental measurements | Microbial prokaryotes and eukaryotes | [212] | |
Vienna Metabolomics Center (VIME) | rRNA subunits Genomes Transcriptomes Proteomes Metabolomes | Sanger sequencing Metabarcoding Metatranscriptomics Metaproteomics Metabolomics | All microorganisms | [213] |