Kescience Bacdive
kescience_bacdive
Tenant: KE Science · Snapshot 2026-04-29T21:35:53.838483+00:00
Schema status
discoveredCuration status
discoveredSource
berdl-spark-connect://metrics.berdl.kbase.us:443Citation & Attribution
Provider: KE Science
Schema Browser
Tables (8)
culture_condition enzyme isolation metabolite_utilization physiology sequence_info strain taxonomy
metabolite_utilization
| Column | Type | Description |
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Projects Using This Collection
BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergies
What data is available in BERDL (across tenants, agencies, and programs), what biological topics does it cover, and wher...
Annotation-Gap Discovery via Phenotype-Fitness-Pangenome-Gapfilling Integration
Can we systematically identify and resolve metabolic annotation gaps in bacterial genomes by integrating experimental gr...
T4SS-CAZy Environmental HGT: Cross-Phylum Transfer of Carbohydrate-Active Enzyme Cassettes
Do Type IV secretion systems (T4SS) in environmental bacteria physically co-localise with carbohydrate-active enzyme (CA...
Lanthanide Methylotrophy Atlas
Across BERDL's 293K-genome pangenome, what is the phylogenomic distribution and cassette-completeness of the lanthanide-...
Self-Sufficiency, Anaerobic Toolkit, and Cultivation Bias in Clay-Confined Cultured Bacterial Genomes
Do BERDL's cultured bacterial genomes from clay-confined deep-subsurface environments recapitulate the genomic signature...
Subsurface Bacillota_B Specialization
Within the Bacillota_B phylum (Desulfosporosinus, BRH-c8a Peptococcaceae, BRH-c4a Desulfotomaculales, and other obligate...
Gene Function Ecological Agora
Across the prokaryotic tree (GTDB r214; 293,059 genomes / 27,690 species), build a multi-resolution **innovation + acqui...
Gene-Resolution Metal Cross-Resistance Across Diverse Bacteria
Is the genetic architecture of metal cross-resistance conserved across phylogenetically diverse bacteria, or is it rewir...
Metagenome-Prioritized Phage Cocktails for Crohn's Disease and IBD
Which bacterial pathobionts are **enriched, ubiquitous, and non-protective** in IBD, UC, and Crohn's disease patients — ...
Plant Microbiome Ecotypes
What is the genomic basis for plant-microbe associations across different plant compartments (rhizosphere, root, phyllos...
CF Protective Microbiome Formulation Design
Can we build a multi-criterion framework that explains measured *P. aeruginosa* PA14 inhibition from metabolic competiti...
BacDive Phenotype Signatures of Metal Tolerance
Can BacDive-measured bacterial phenotypes (Gram stain, oxygen tolerance, metabolite utilization, enzyme activities) pred...
Metabolic Consistency of Pseudomonas FW300-N2E3
For *Pseudomonas fluorescens* FW300-N2E3 (ENIGMA groundwater isolate), how consistent are exometabolomic outputs (Web of...
Atlas Pages
Lanthanide-dependent methylotrophy is widespread and soil-linked
XoxF markers are far more common than canonical MxaF markers across the BERDL pangenome, with strong soil/sediment enrichment and important marker-calibration caveats.
data typeExperimental Phenotypes, Traits, and Assays
Measured organism and gene behavior across laboratory conditions, including mutant fitness, growth phenotypes, utilization traits, and exometabolomic observations.
data typeHost, Clinical, Pathogen, and Isolate Data
Collections organized around host-associated samples, pathogen isolates, clinical context, or strain-level interpretation.
derived productFunctional Innovation KO Atlas
Reusable clade-level functional innovation and acquisition-depth outputs from the ecological agora project.
data collectionBacDive
Bacterial diversity metadatabase: phenotypes, growth conditions, isolation source, metabolite utilization (DSMZ)
opportunityRare-Earth RB-TnSeq Design
Design the first rare-earth fitness experiment by ranking candidate genes from cross-metal specificity, conservation, annotation, and structure evidence.
opportunityLab-to-Field Fitness Transfer Audit
Audit where laboratory fitness effects predict field ecology and where geochemistry, taxonomy, or metadata completeness blocks transfer.
opportunityLow-Confidence Collection Curation
Reduce Atlas caveat load by upgrading high-value low-confidence collection pages with schemas, reuse examples, and missing-data labels.