This page provides information regarding major databases providing raw data of microbiome studies along with links to their websites.
| Database Name | Description | PubMed ID |
|---|---|---|
| NCBI Sequence Read Archive (SRA) | Stores raw sequencing data and alignment information | 34850094 |
| EMBL-EBI European Nucleotide Archive (ENA) | Includes raw sequence data, sequence information | 39558171 |
| DDBJ Sequence Read Archive (DRA) | Stores raw sequencing data and alignment information | 36420889 |
| China National GeneBank DataBase | Built for biological big data sharing and application services | 32952115 |
| Database Name | Description | PubMed ID |
|---|---|---|
| MicrobiomeDB | Discovery tool empowering researchers to leverage metadata to interrogate microbiome datasets. | 29106667 |
| GMrepo | Curated database of consistently annotated human gut metagenomes | 34788838 |
| QIITA | Provides database and compute resources to the global community | 30275573 |
| Indian Microbiome Database | Comprehensive database documenting microbiome research in India. | NA |
| MGnify | Facilitates assembly, analysis, and archiving of microbiome-derived nucleic acid sequences. | 36477304 |
| MicrobiomeHD | Standardized database of human gut microbiome studies in health and disease | 29209090 |
| IBDMDB | An integrated resource for analyzing the gut microbial ecosystem in the context of IBD | 31142855 |
| Human Gut Microbiome Atlas | Global shotgun metagenomics of normal human gut microbiome from 20 countries are presented with species abundance, gene richness and enterotypes | NA |
| curatedMetagenomicData | It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. | 29088129 |
| Human Microbiome Compendium | This dataset includes over 1.6L samples of publicly available 16S rRNA amplicon sequencing data, all processed using the same pipeline and reference database | 37873416 |
| NIH Human Microbiome Project | Contains studies of dynamic changes in the microbiome and host under three conditions: pregnancy and preterm birth; inflammatory bowel diseases; and prediabetes. | 31142853 |
| H3Africa | Expanding the human gut microbiome atlas of Africa. | 39880958 |
| curatedMetagenomicData | The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. | 29088129 |
| microbiomap | 168,000 public 16S gut microbiome samples processed and integrated at microbiomap.org. | 39848248 |
| Database Name | Description | PubMed ID |
|---|---|---|
| NCBI RefSeq | Comprehensive, curated collection of reference sequences, including genomes for taxonomy. | 39526381 |
| MARMICRODB | Database for taxonomic classification of (marine) metagenomes. | zenodo |
| MGnify Database | Database for microbiome-derived sequences with taxonomic annotations and analysis tools. | 36477304 |
| IMG | Integrated genome and metagenome database. | 22194640 |
| IMG/PR | A database of plasmids from genomes and metagenomes with rich annotations and metadata. | 37930866 |
| IMG/VR | An expanded database of uncultivated virus genomes. | 36399502 |
| Kraken2 Database | Database tailored for use with Kraken2, optimized for fast and accurate metagenomic assignments. | 31779668 |
| NMPFamsDB | A database of novel protein families from microbial metagenomes and metatranscriptomes. | 37811892 |
| SILVA | Ribosomal RNA database for taxonomy and phylogenetics, widely used for microbial studies. | 23193283 |
| RDP (Ribosomal Database Project) | High-quality ribosomal RNA sequences for taxonomy and functional annotations. | 24288368 |
| Greengenes | 16S rRNA database for microbial taxonomy and phylogeny (limited updates). | 16820507 |
| GTDB | A standardized bacterial and archaeal taxonomy based on phylogenomics. | 34520557 |
| UniProtKB | Protein sequence and functional information database, supports taxonomy-based analysis. | 36408920 |
| EggNOG | Functional and phylogenomic annotation of genes, including taxonomic classifications. | 36399505 |
| KEGG | Comprehensive resource for biological pathways and genomes, with taxonomy support. | 36300620 |
| PROKKA Database | Specialized annotation database for bacterial genomes, used in taxonomy assignments. | 24642063 |
| MarFERReT | An open-source, version-controlled reference library of marine microbial eukaryote functional genes. | 38129449 |
| MetaCyc | Database of metabolic pathways and enzymes. | 31586394 |
| CAZy | The carbohydrate-active enzyme database. | 34850161 |
| MEROPS | A database for peptidases and their inhibitors, providing a comprehensive resource for the study of proteolytic enzymes. | 29145643 |
| SEED | A framework for genome annotation, providing curated subsystems and facilitating comparative genomics and metabolic reconstruction. | 24293654 |
| TIGRFAMs | A collection of protein families featuring curated multiple sequence alignments, Hidden Markov Models (HMMs), and associated annotation, useful for protein function prediction. | 23197656 |
| COG (Clusters of Orthologous Groups) | A database of orthologous gene families, facilitating functional annotation of proteins and genome evolution studies. | 39494517 |
| CARD (Comprehensive Antibiotic Resistance Database) | Curated database for AMR genes and associated resistance mechanisms. | 36263822 |
| MEGARes | Provides resistance gene annotations tailored for metagenomic data. | 31722416 |
| VFDB (Virulence Factor Database) | Comprehensive database of virulence factors in bacterial pathogens. | 15608208 |
| MvirDB | Broad repository for virulence and AMR genes, including toxins and pathogenicity islands. | 17090593 |
| PATRIC | Integrative resource for AMR, virulence factors, and pathogen genomes. | 21896772 |
| T3DB (Toxin and Toxin Target Database) | Contains detailed information about toxins, toxicants, and their effects on genes and proteins. | 19897546 |
| ISfinder | A database of bacterial insertion sequences, often linked to resistance gene mobilization. | 16381877 |
| CyanoBase | The genome database for cyanobacteria. | 27899668 |
| Database Name | Description | PubMed ID |
|---|---|---|
| ELGG | A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome | 36050292 |
| UHGG | A unified catalog of 204,938 reference genomes from the human gut microbiome | 32690973 |
| VMGC | A multi-kingdom collection of 33,804 reference genomes for the human vaginal microbiome | 38907008 |
| IMGG | A high-quality genome compendium of the human gut microbiome of Inner Mongolians | 36604505 |
| GMMC | The multi-kingdom microbiome of the goat gastrointestinal tract | 37779211 |
| GKGMC | Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids | 38365259 |
| RUG | Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery | 31375809 |
| African Boran MAGs | 1200 high-quality metagenome-assembled genomes from the rumen of African cattle and their relevance in the context of sub-optimal feeding | 32883364 |
| Japan RUGs | Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan | 36273894 |
| iMGMC | An Integrated Metagenome Catalog Reveals New Insights into the Murine Gut Microbiome | 32130896 |
| Murine MAGs | Metagenome-Assembled Genomes from Murine Fecal Microbiomes Dominated by Uncharacterized Bacteria | 36779794 |
| CMMG | Comprehensive mouse microbiota genome catalog reveals major difference to its human counterpart | 35259160 |
| Chicken Gut MAGs | Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes | 34795385 |
| GIT | Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition | 39135685 |
| Horse MAGs | Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse | 36631912 |
| PIG MAGs | A reference gene catalogue of the pig gut microbiome | 27643971 |
| HRGM2 | A human gut metagenome-assembled genome catalogue spanning 41 countries supports genome-scale metabolic models | 41345261 |
| MAGIC | A reference gene catalogue of the pig gut microbiome | 39591974 |
| PIGC | Expanded catalog of microbial genes and metagenome-assembled genomes from the pig gut microbiome | 33597514 |