What this entity is
Canonical name: ENIGMA Genome Depot
Known aliases: ENIGMA genome-depot; genome-depot
Stable external identifier: No stable external identifier was reported in the source. 1
ENIGMA Genome Depot is a genome resource used in the ENIGMA Carbon Census to connect compound-utilization predictions with genome annotations and ENIGMA-isolate records. 1 The newer genotype-to-phenotype study supports this role by integrating the Depot with ENIGMA growth curves, pangenome data, Fitness Browser RB-TnSeq data, Web of Microbes exometabolomics, Carbon Source Phenotypes, and global 16S environmental data for genome-by-condition phenotype modeling. 2
Key facts from the ENIGMA Carbon Census
The census integrated ENIGMA Genome Depot with PubChem, KEGG, ModelSEED, the Fitness Browser, GTDB, SSO, NMDC, and Planet Microbe in a tiered compound-to-environment workflow. 1
The analysis evaluated 83 enrichment compounds across 3109 genomes and identified 8 compounds with ENIGMA-isolate utilization calls. 1
The ENIGMA-isolate deliverable contained 569 utilization-prediction rows across the 8 ENIGMA-isolate-callable compounds. 1
The utilization predictions included 129 strains for salicylic acid, 127 for 3-hydroxybenzoic acid, 125 for 4-hydroxybenzaldehyde, 36 for phthalic acid, 34 for terephthalic acid, 28 for phenylethylamine, 13 for xanthine, and 2 for abscisic acid. 1
The census placed 494 strain records representing 359 distinct strains on GTDB taxonomy, including 64 high-certainty records based on gene-complete Tier-2 pathways, 387 medium-certainty records based on Tier-2 pathways, and 43 medium-certainty records based on Tier-3 signature enzymes. 1
Utilizer predictions were concentrated in Pseudomonadota and Burkholderiales, with additional compound-specific contributions from Pseudomonadales and Sphingomonadales; 47 Sphingomonadales strains were associated with 4-hydroxybenzaldehyde. 1
Terephthalic acid had 34/34 high-certainty records, although the source identified this as a possible single-reaction-signature artifact rather than evidence of complete pathway coverage. 1
The source cautioned that certainty was calculated from the raw number of carried signature reactions divided by required reactions and was not directly comparable across compounds with different signature lengths. 1
Integration and linkage validation
The new study refines the Depot’s cross-resource role by placing its genome and annotation records in a combined modeling corpus of 46,389 genome-by-condition pairs spanning 727 genomes, 363 conditions, and 4,293 shared kegg orthologs (KOs). 2
It also identifies a data-integration hazard: matching ENIGMA strains to the KBase Data Lakehouse pangenome through short identifiers such as MT20 caused 12 of 32 genus-level mismatches, including a Rhodanobacter glycinis–streptococcus-pneumoniae collision that introduced 1,751 spurious clinical genomes into environmental profiles. 2 Using CORAL brick 522 GTDB-Tk assignments and genus-consistency checks reduced verified linkages from 32 to 20 and eliminated all false matches, supporting stricter identity validation for Depot-linked analyses. 2
Related pages
The dataset contributes to pangenome-integration by linking genome annotations across 3109 genomes to isolate-level utilization predictions and GTDB strain placements. 1
It participates in cross-tenant-data-bridging alongside gtdb, kescience-fitnessbrowser, modelseed, and other cross-resource datasets. 1 The genotype-to-phenotype study strengthens this connection by documenting both multi-tenant phenotype integration and the strain-name collision risk. 2
The source documents are ENIGMA Carbon Census — Tiered Knowledge Census of 83 Enrichment Compounds and Genotype × Condition to Phenotype Prediction from ENIGMA Growth Curves.