Table 1.
Databases and Repositories.
| Database Name | Description | Data Types | Accessibility | User Submission |
|---|---|---|---|---|
| GenBank | Archive for sequencing data | Genomes, Metagenomes, Metatranscriptomes, Amplicons | Publicly accessible | Yes |
| Sequence Read Archive (SRA) | Archive for sequencing data | Raw sequencing data | Publicly accessible | Yes |
| European Nucleotide Archive (ENA) | Archive for all publicly available nucleotide sequences | Genomes, Metagenomes, Metatranscriptomes, Amplicons | Publicly accessible | Yes |
| DOE Systems Biology Knowledgebase (KBase) | A platform for sharing, integrating, and analyzing microbial, plant, and community data | Genomes, Metagenomes, Metatranscriptomes, Amplicons | Publicly accessible | Yes |
| Genomes OnLine Database (GOLD) | Repository for genome projects and metadata (ecosystems) | Ecosystems | Publicly accessible | Yes |
| Integrated Microbial Genomes & Microbiomes (IMG/M) | Community-driven repository hosting genomes of cultivated and uncultivated microbial taxa, metagenomes, metatranscriptomes, amplicons, plasmids, and genome fragments | Metagenomes, Metatranscriptomes, Amplicons, Genomes | Publicly accessible | Yes |
| MGnify | Archive for exploration, and analysis, of microbiome sequencing datasets | Metagenomes, Metatranscriptomes, Amplicons, MAGs | Publicly accessible | Yes |
| Metagenome RAST (MG-RAST) | Microbiome repository with a unified pipeline for automated analysis of metagenomic samples | Metagenomes | Registered users | Yes |
| Integrated Microbial Viral Genomes (IMG/VR) |
Viral genomes and metagenomes | Viral Genomes, Viral Metagenomes | Publicly accessible | Yes |
| NMPFamsDB | Novel protein families from IMG’s metagenomes and metatranscriptomes | Protein Families | Publicly accessible | No |
| FESnov catalog | Catalog reporting functionally unannotated proteins derived from MAGs | Proteins | Publicly accessible | No |
| NIH Human Microbiome Project | Metagenomes from human host-associated systems, such as the gut microbiome | Human Microbiome Metagenomes | Publicly accessible | No |
| TerrestrialMetagenomeDB | Annotation of metagenomes obtained from soil samples | Soil Metagenomes | Publicly accessible | Yes |
| MarineMetagenomeDB | Annotation of metagenomes obtained from marine samples | Marine Metagenomes | Publicly accessible | Yes |
| HumanMetagenomeDB | Annotation of metagenomes obtained from human microbiome samples | Human Microbiome Metagenomes | Publicly accessible | Yes |
| SPIRE | Searchable resource of ecosystem metadata obtained from MAGs | Ecosystem Metadata | Publicly accessible | No |
| Marine Metagenomics Portal (MMP) | Collection of databases annotating marine-oriented metagenomic datasets | Marine Metagenomes | Publicly accessible | No |
| National Microbiome Data Collaborative (NMDC) | A platform for collaboration and data sharing among researchers studying microbiomes across diverse ecosystems | Microbiome Data | Publicly accessible | Yes |