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Microbial Isolate Data Across Lakehouses

This document summarizes the availability and structure of microbial isolate data across JGI, KBase, and NMDC lakehouses.

Overview

Microbial isolates—cultured, single-strain organisms—are fundamental to genomics research. Each lakehouse captures isolate data differently, with JGI's GOLD and IMG databases providing the richest isolate coverage.

JGI Lakehouse

GOLD Database - Organism Records

The GOLD database tracks 598,061 organisms in the gold_master_organism table, with culture status as a key attribute.

Culture Status Distribution

Cultured Count
Yes 518,241
No 79,815
Unknown 5

Culture Types

Culture Type Count
Isolate 518,172
Co-Culture 134

Cultured Organisms by Domain

Domain Cultured Count
Bacteria 427,450
Eukarya 69,020
Viruses 11,880
Unknown 6,425
Archaea 3,466

Key Query

SELECT domain, cultured, COUNT(*) as cnt
FROM "gold-db-2 postgresql".gold.gold_master_organism
WHERE cultured = 'Yes'
GROUP BY domain, cultured
ORDER BY cnt DESC

GOLD Biosample Ecosystem Types

Biosamples are classified by ecosystem. Lab cultures represent direct isolate work:

Ecosystem Category Type Count
Engineered Lab culture Culture media 7,850
Environmental Terrestrial Soil 57,083
Host-associated Mammals: Human Digestive system 43,958
Environmental Aquatic Marine 35,287
Environmental Aquatic Freshwater 28,082

IMG Database - Genome Types

IMG's taxon table distinguishes isolate genomes from metagenomes:

Genome Type Count
isolate 196,379
metagenome 90,241

IMG Taxon Domain Distribution

Domain Count
Bacteria 167,336
*Microbiome 90,233
Viruses 21,818
Archaea 4,536
Eukaryota 1,192

Key Query

SELECT genome_type, COUNT(*) as cnt
FROM "img-db-2 postgresql".img_core_v400.taxon
WHERE genome_type IS NOT NULL
GROUP BY genome_type
ORDER BY cnt DESC
Schema Table Column Description
gold gold_master_organism cultured Yes/No/Unknown
gold gold_master_organism culture_type Isolate or Co-Culture
gold dw_samples sample_isolated_from Isolation source
gold ncbi_assembly isolate NCBI isolate field
img_core_v400 taxon genome_type "isolate" or "metagenome"
img_core_v400 img_funcs_info isolates Isolate count
imgsg_dev project_info isolate_selected HMP selection flag
imgsg_dev project_info hmp_isolate_selection_source HMP source

KBase/BERDL

KBase databases likely contain isolate genome data in:

  • kbase_genomes - General genome collection
  • kbase_ke_pangenome - Pangenomic data with GTDB taxonomy

Note: Direct queries require valid authentication token.

NMDC

NMDC focuses primarily on environmental metagenomes rather than isolates. However, lab culture samples exist as controls:

Lab Culture Samples

nmdc biosample --filter "ecosystem: Engineered" --filter "ecosystem_category: Lab culture"

Example record: - Organism: Vibrio fischeri ES114 - Purpose: Positive control for metagenome analysis - Ecosystem classification: Engineered > Lab culture > Culture media > Bacteria

NMDC lab culture samples are linked to GOLD via gold_biosample_identifiers.

Cross-Database Summary

Lakehouse Isolate Records Primary Use Key Tables
JGI GOLD ~518,000 organisms Genome project metadata, culture tracking gold_master_organism, biosample
JGI IMG ~196,000 genomes Annotated isolate genomes with functional data taxon, gene, gene_function
NMDC ~4 samples Environmental focus; isolates as controls biosample
KBase Unknown Genome analysis platform kbase_genomes

Join Points for Isolate Data

graph LR GOLD_ORG[GOLD Organism
organism_id] --> GOLD_PROJ[GOLD Project
project_id] GOLD_PROJ --> IMG_TAXON[IMG Taxon
taxon_oid] GOLD_ORG --> NCBI[NCBI Taxonomy
ncbi_taxon_id] IMG_TAXON --> IMG_GENE[IMG Gene
gene_oid] NMDC_BSM[NMDC Biosample] -->|gold_biosample_identifiers| GOLD_BSM[GOLD Biosample]

Key Join Fields

Source Target Join Field
GOLD organism NCBI ncbi_taxonomy_id
GOLD project IMG taxon gold_id / sequencing_gold_id
NMDC biosample GOLD biosample gold_biosample_identifiers
IMG taxon GOLD sample_gold_id, study_gold_id

Recommendations

  1. For isolate genome analysis: Start with JGI IMG taxon table filtered by genome_type = 'isolate'
  2. For culture metadata: Query GOLD gold_master_organism with cultured = 'Yes'
  3. For cross-linking to NCBI: Use ncbi_taxonomy_id from GOLD organism records
  4. For environmental context of isolates: Join GOLD organism to biosample via project

Example Queries

Find all cultured bacteria with complete genomes in IMG

SELECT t.taxon_display_name, t.domain, t.phylum, t.genus, t.species
FROM "img-db-2 postgresql".img_core_v400.taxon t
WHERE t.genome_type = 'isolate'
  AND t.domain = 'Bacteria'
  AND t.seq_status = 'Finished'
LIMIT 100

Find GOLD organisms with isolation source metadata

SELECT o.ncbi_genus, o.ncbi_species, o.strain, o.sample_collection_site
FROM "gold-db-2 postgresql".gold.gold_master_organism o
WHERE o.cultured = 'Yes'
  AND o.sample_collection_site IS NOT NULL
LIMIT 50