Taxonomic Coverage Across Databases
This document describes what organisms and clades are covered by different databases
in the JGI and KBase lakehouses.
Overview
| Database |
Scope |
Organisms |
Focus |
| GOLD |
Universal |
598K |
All sequenced organisms (registry) |
| IMG |
Microbial |
287K |
Annotated microbial genomes |
| KBase Pangenome |
Bacteria/Archaea |
293K |
GTDB-classified prokaryotes |
| MycoCosm |
Fungi |
~2,500 |
Fungal comparative genomics |
| Phytozome |
Plants |
~250 |
Plant comparative genomics |
| IMG/VR |
Viruses |
22K+ |
Viral sequences |
Data Types
Databases contain a mix of:
| Type |
Description |
GOLD Count |
| Isolate genomes |
Cultured organisms |
518K (87%) |
| MAGs |
Metagenome-assembled genomes |
79K |
| SAGs |
Single-cell amplified genomes |
16K |
| Metagenomes |
Community DNA |
223K projects |
| Metatranscriptomes |
Community RNA |
40K projects |
GOLD: The Genome Registry
GOLD (Genomes OnLine Database) tracks all sequencing projects at JGI and beyond.
Domain Distribution
| Domain |
Organisms |
Percentage |
| Bacteria |
489,957 |
81.9% |
| Eukarya |
69,683 |
11.6% |
| Viruses |
17,496 |
2.9% |
| Archaea |
6,877 |
1.2% |
| Unknown |
14,048 |
2.4% |
Bacterial Coverage
Top phyla (using modern nomenclature):
| Phylum |
Count |
% of Bacteria |
| Pseudomonadota (Proteobacteria) |
211,920 |
43% |
| Bacillota (Firmicutes) |
139,789 |
29% |
| Actinomycetota (Actinobacteria) |
70,898 |
14% |
| Bacteroidota |
23,577 |
5% |
| Campylobacterota |
11,079 |
2% |
| Cyanobacteriota |
4,828 |
1% |
Top genera:
| Genus |
Count |
Notes |
| Pseudomonas |
24,177 |
Environmental/clinical |
| Escherichia |
22,452 |
Model organism, pathogens |
| Streptococcus |
22,083 |
Human pathogens |
| Staphylococcus |
19,825 |
Human pathogens |
| Salmonella |
16,301 |
Food safety |
| Bacillus |
12,960 |
Industrial/environmental |
| Streptomyces |
12,156 |
Natural products |
Bias note: Clinical and industrially-relevant genera are overrepresented.
Archaeal Coverage
| Kingdom |
Count |
Notes |
| Methanobacteriati |
4,358 |
Methanogens |
| Thermoproteati |
1,709 |
Thermophiles |
| Other |
~800 |
Various |
Archaea are underrepresented (1.2%) with roughly equal cultured/uncultured split,
unlike bacteria where cultured dominates.
Eukaryotic Coverage
| Kingdom |
Count |
Notes |
| Viridiplantae |
40,978 |
Plants (→ Phytozome) |
| Fungi |
21,298 |
Fungi (→ MycoCosm) |
| Metazoa |
4,934 |
Animals |
| Other protists |
~2,500 |
Various |
Viral Coverage
| Realm |
Count |
Notes |
| Orthornavirae |
5,255 |
RNA viruses |
| Shotokuvirae |
2,750 |
dsDNA viruses (phages) |
| Other |
~9,500 |
Various |
Cultured vs Uncultured
| Status |
Count |
Percentage |
| Cultured |
518,241 |
86.7% |
| Uncultured |
79,815 |
13.3% |
Uncultured breakdown:
| Type |
Count |
Description |
| Metagenomic |
63,270 |
Binned from metagenomes |
| Single Cell |
15,962 |
SAGs |
| Other |
~600 |
Enrichments, pooled |
Project Types
| Project Type |
Count |
| Genome Analysis (Isolate) |
286,643 |
| Metagenome Analysis |
152,545 |
| Metagenome-Assembled Genome |
78,813 |
| Metatranscriptome Analysis |
29,309 |
| Single Cell Analysis |
14,741 |
Ecosystem Classification
GOLD uses a hierarchical ecosystem classification:
Ecosystem (top level)
└── Ecosystem Category
└── Ecosystem Type
└── Ecosystem Subtype
└── Specific Ecosystem
Top-Level Ecosystems
| Ecosystem |
Count |
Examples |
| Host-associated |
153,878 |
Human gut, plant roots |
| Environmental |
80,581 |
Soil, ocean, freshwater |
| Engineered |
22,261 |
Bioreactors, wastewater |
Host-Associated Breakdown
| Category |
Count |
Notes |
| Human |
85,157 |
55% of host-associated |
| Other Mammals |
21,477 |
Livestock, wildlife |
| Plants |
22,816 |
Rhizosphere, phyllosphere |
| Birds |
4,804 |
Poultry, wildlife |
| Insects |
3,268 |
Pollinators, pests |
Human body sites:
| Site |
Count |
| Digestive system |
34,767 |
| Respiratory system |
14,679 |
| Circulatory system |
7,645 |
| Skin |
~5,000 |
| Oral cavity |
~4,000 |
Environmental Breakdown
| Type |
Count |
Examples |
| Soil |
31,563 |
Forest, agricultural, permafrost |
| Marine |
19,527 |
Pelagic, sediment, hydrothermal |
| Freshwater |
7,101 |
Lakes, rivers, wetlands |
| Other |
~22,000 |
Air, rock, ice |
Special categories:
- "Plant-associated metagenome" → Host-associated > Plants
- "Soil metagenome" → Environmental > Terrestrial > Soil
- "Human gut metagenome" → Host-associated > Human > Digestive system
IMG: Annotated Microbial Genomes
IMG focuses on microbial genomes with comprehensive functional annotation.
Total taxa: 286,758
Domain Distribution
| Domain |
Count |
Percentage |
| Bacteria |
167,336 |
58.5% |
| *Microbiome |
90,371 |
31.6% |
| Viruses |
21,818 |
7.6% |
| Archaea |
4,536 |
1.6% |
| Eukaryota |
1,192 |
0.4% |
| Plasmids |
~1,200 |
0.4% |
Note: "*Microbiome" entries are metagenomic assemblies, not isolate genomes.
Genome Types
IMG distinguishes:
- Isolate - Single organism genomes (~173K)
- Metagenome - Community assemblies (~90K)
- Plasmids - Mobile elements
- Genome Fragments - Partial sequences
KBase Pangenome: GTDB-Classified Prokaryotes
The KBase pangenome database contains 293,059 bacterial and archaeal genomes
classified using GTDB (Genome Taxonomy Database).
Coverage
| Domain |
Genomes |
Species Clades |
| Bacteria |
~280K |
~80K |
| Archaea |
~13K |
~5K |
GTDB vs NCBI Taxonomy
GTDB provides standardized, rank-normalized taxonomy that often differs from NCBI:
| NCBI Name |
GTDB Name |
Notes |
| Proteobacteria |
Pseudomonadota |
Renamed |
| Firmicutes |
Bacillota |
Renamed |
| "Candidatus X" |
X |
Standardized |
MycoCosm: Fungal Genomes
JGI's fungal genome portal with ~2,500+ genomes across three MySQL servers.
Taxonomic Coverage
| Phylum |
Genomes |
Examples |
| Ascomycota |
~1,500 |
Aspergillus, Neurospora, yeasts |
| Basidiomycota |
~800 |
Agaricus, Coprinopsis, Laccaria |
| Mucoromycota |
~100 |
Mucor, Rhizopus |
| Chytridiomycota |
~50 |
Batrachochytrium |
| Other |
~50 |
Microsporidia, etc. |
Database Structure
Each fungal genome has its own schema in Dremio:
- myco-db-1 mysql.Aspni7 (Aspergillus niger)
- myco-db-1 mysql.Copci1 (Coprinopsis cinerea)
- myco-db-2 mysql.Lacbi2 (Laccaria bicolor)
Tables per genome: 100-250, including:
| Table |
Description |
FilteredModels1 |
Curated gene models (primary gene set) |
GeneCatalog1 |
Gene catalog entries |
InterPro1 |
InterPro domain annotations |
blastp1 |
BLASTP hits |
SM_cluster1 |
Secondary metabolite clusters |
KOG1 |
KOG functional categories |
Naming Convention
Genome schema names follow pattern: {Genus3}{species3}{version}
- Aspni7 = Aspergillus niger v7
- Copci1 = Coprinopsis cinerea v1
- Agabi_varbisH97_2 = Agaricus bisporus var. bisporus H97 v2
Phytozome: Plant Genomes
JGI's plant comparative genomics portal using GMOD Chado schema.
Database: plant-db-7 postgresql.public (306 tables)
Coverage
| Clade |
Genomes |
Examples |
| Angiosperms |
~200 |
Arabidopsis, rice, maize, soybean |
| Gymnosperms |
~10 |
Pine, spruce |
| Ferns/Lycophytes |
~5 |
Selaginella |
| Bryophytes |
~10 |
Physcomitrella, Marchantia |
| Algae |
~30 |
Chlamydomonas, Volvox, Ostreococcus |
Database Structure
Unlike MycoCosm (schema-per-genome), Phytozome uses a unified Chado schema:
| Table |
Description |
feature |
All genomic features (genes, mRNAs, exons) |
featureloc |
Feature coordinates |
organism |
Species metadata |
analysis |
Annotation pipeline metadata |
featureprop |
Feature properties/attributes |
Key Features
- Gene family clustering across all plant genomes
- Expression atlas data
- Synteny and whole-genome duplication analysis
- PFAM/InterPro domain annotations
IMG/VR: Viral Genomes
Database: img-db-1 mysql.imgvr_prod
Total UViGs: 15.7 million viral sequences
Sources
| Source |
Count |
Description |
| Metagenome |
14.2M (90.6%) |
Predicted from metagenomes |
| Metatranscriptome |
1.2M (7.3%) |
RNA viruses from metatranscriptomes |
| Isolate |
294K (1.9%) |
Cultured phages and viruses |
| RefSeq |
14K |
Curated reference sequences |
| MAG |
13.5K |
From metagenome-assembled genomes |
| SAG |
1.6K |
Single amplified genomes |
Viral Realm Distribution
| Realm |
Count |
Description |
| Duplodnaviria |
13.5M (86%) |
dsDNA viruses (mostly bacteriophages) |
| Varidnaviria |
1.0M (6.7%) |
Large/giant DNA viruses |
| Riboviria |
531K (3.4%) |
RNA viruses |
| Unclassified |
521K (3.3%) |
No realm assigned |
| Monodnaviria |
72K (0.5%) |
ssDNA viruses |
| Adnaviria |
3.7K |
Archaeal filamentous viruses |
Key Tables
| Table |
Rows |
Description |
uvig |
15.7M |
Main viral sequences |
uvig_lineage |
15.7M |
ICTV taxonomy |
uvig_hosts |
1.1M |
Predicted hosts |
uvig_domain |
118.7M |
Protein domains |
uvig_pfams |
50.4M |
PFAM annotations |
Cross-Database Organism Lookup
By NCBI Taxonomy ID
Most databases link via NCBI taxonomy:
-- Find organism across databases
SELECT 'GOLD' as db, organism_name
FROM "gold-db-2 postgresql".gold.organism_v2
WHERE ncbi_taxon_id = 562 -- E. coli
UNION ALL
SELECT 'IMG' as db, taxon_display_name
FROM "img-db-2 postgresql".img_core_v400.taxon
WHERE ncbi_taxon_id = 562
By Assembly Accession
For genome-level matching:
-- Match KBase to GOLD via assembly accession
SELECT kb.genome_id, gold.organism_name
FROM kbase_ke_pangenome.genome kb
JOIN "gold-db-2 postgresql".gold.ncbi_assembly gold
ON SUBSTRING(kb.genome_id FROM 4) = gold.assembly_accession
Coverage Gaps and Biases
Overrepresented
| Category |
Reason |
| Human pathogens |
Clinical relevance, surveillance |
| Model organisms |
Research investment |
| Industrial microbes |
Biotechnology applications |
| Human gut microbiome |
Health research funding |
Underrepresented
| Category |
Reason |
| Environmental Archaea |
Difficult to culture |
| Deep-sea organisms |
Sampling challenges |
| Protists |
Genome complexity |
| Non-human host microbiomes |
Less funding |
| Rare biosphere |
Low abundance |
Data Type Biases
| Bias |
Impact |
| Isolate bias (87%) |
Missing unculturable diversity |
| Short-read assemblies |
Fragmented genomes, missing repeats |
| Reference genome focus |
Strain diversity undersampled |
Recommendations
- For prokaryotic diversity: Use KBase pangenome with GTDB taxonomy
- For metagenome context: Use GOLD ecosystem classification
- For fungi: Use MycoCosm (clade-specific annotations)
- For plants: Use Phytozome (clade-specific annotations)
- For viruses: Use IMG/VR
- For cross-database queries: Join on NCBI taxonomy ID or assembly accession
Key Tables
GOLD
| Table |
Description |
organism_v2 |
Organism metadata with taxonomy |
project |
Sequencing project metadata |
ncbi_taxonomy |
Full NCBI taxonomy |
ncbi_assembly |
Assembly accessions |
IMG
| Table |
Description |
taxon |
Genome metadata |
taxon_stats |
Genome statistics |
KBase
| Table |
Description |
genome |
GTDB-classified genomes |
gtdb_species_clade |
Species-level groupings |