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BacDive Genomes with Phenotype Annotations
This dataset bundles bacterial genomes downloaded from NCBI (linked to BacDive strain records) together with the BacDive phenotypic metadata — providing a paired genome ↔ phenotype resource for bacterial trait prediction.
Contents
| File | Size | Description |
|---|---|---|
genome_download.zip |
27.3 GB (~91 GB unzipped, 21,069 files) | NCBI Datasets package with 21,461 bacterial genomes in FASTA. Includes assembly_data_report.jsonl (NCBI metadata) and dataset_catalog.json |
gca_list.txt |
280 KB | List of all 20,486 GCA accessions submitted to NCBI download |
bacdive_merged.csv |
9.3 MB | 99,392 BacDive entries spanning 22,840 unique species with phenotypic features |
Genome Assembly Statistics
Computed from assembly_data_report.jsonl (21,461 genomes):
| Metric | Min | Median | Mean | Max |
|---|---|---|---|---|
| Total sequence length (bp) | 54,895 | 4,142,744 | 4,457,843 | 16,040,666 |
| Number of contigs | 1 | 37 | 104 | 11,539 |
| Contig N50 (bp) | 567 | 312,410 | 1,275,268 | 16,040,666 |
| GC content (%) | 22.5 | 56.0 | 53.0 | 77.0 |
Assembly level breakdown:
| Level | Count | % |
|---|---|---|
| Contig | 10,377 | 48% |
| Scaffold | 6,848 | 32% |
| Complete Genome | 3,836 | 18% |
| Chromosome | 400 | 2% |
Phenotype Feature Coverage (bacdive_merged.csv)
Coverage = fraction of the 99,392 BacDive entries that have a non-empty value.
| Feature | Coverage | Notes |
|---|---|---|
| is_type_strain_header | 100.0% | All entries flagged |
| Temperature | 49.8% | Growth temperature (range/single value) |
| Oxygen tolerance | 29.1% | aerobe / anaerobe / facultative / microaerophile |
| Gram stain | 22.8% | positive / negative / variable |
| Motility | 16.8% | 0/1 binary |
| Cell shape | 15.3% | rod / coccus / oval / filament / spiral |
| Ability of spore formation | 14.6% | 0/1 binary |
| pH | 6.8% | Growth pH |
| Cell length | 6.0% | μm |
| Cell width | 5.9% | μm |
| Pathogenicity (animal) | 2.3% | 0/1 binary |
| Pathogenicity (human) | 1.6% | 0/1 binary |
| Pathogenicity (plant) | 0.4% | 0/1 binary |
Top categorical values
Gram stain: negative (14,236) > positive (8,360) > variable (67) Cell shape: rod-shaped (11,928) > coccus-shaped (1,845) > oval (584) > ovoid (372) > filament (104) > spiral (67) Oxygen tolerance: aerobe (10,610) > obligate aerobe (5,360) > anaerobe (5,153) > microaerophile (3,785) > facultative anaerobe (3,769) Motility (1=motile): 0 = 11,076, 1 = 5,668 Spore formation (1=can form): 0 = 11,592, 1 = 2,957
Full column list (24 cols)
| Category | Features |
|---|---|
| Identity | ID (BacDive ID), species, designation_header, strain_number_header (DSM/ATCC/etc.), is_type_strain_header |
| Morphology | Cell shape, Gram stain, Motility, Cell length, Cell width |
| Growth conditions | Temperature, pH |
| Physiology | Oxygen tolerance (obligate aerobe / anaerobe / facultative / microaerophile), Ability of spore formation |
| Pathogenicity | Pathogenicity (human), Pathogenicity (animal), Pathogenicity (plant) |
Example row
| Field | Value |
|---|---|
| ID | 219 |
| species | Abiotrophia defectiva |
| strain_number_header | DSM 9849, ATCC 49176, CIP 103242, SC 10, CCUG 27639 |
| is_type_strain_header | 1 |
| Cell shape | coccus-shaped |
| Gram stain | positive |
| Motility | 0.0 |
| Temperature | 25-41 |
| Ability of spore formation | 0.0 |
| Oxygen tolerance | anaerobe |
Note: Some columns appear duplicated (Cell shape, Gram stain, Motility, Cell length, Cell width, Temperature) — this is an artifact of an upstream join. Either copy can be used.
Genome ↔ Phenotype Linkage
The CSV does not contain a direct GCA accession column. To link a genome to its BacDive entry, join via:
- Strain designation: match
strain_number_header(e.g. "DSM 9849") to the genome's strain inassembly_data_report.jsonl - Species name: match
speciesto NCBI organism (less precise — same species often has many strains) - NCBI taxonomy ID: BacDive entries include
NCBI tax id(in original BacDive JSON) → matchable against NCBI assembly metadata
Source
- Genomes: Downloaded from NCBI Datasets API (
ncbi datasets download genome accession ...) on 2025-04-11 - Phenotype data: BacDive (https://bacdive.dsmz.de/) — Bacterial Diversity Metadatabase, operated by DSMZ
- Genome list: Derived from BacDive strain records with available type-strain or representative NCBI assemblies
Citation
If you use this dataset, please cite BacDive:
Reimer, L.C., Sardà Carbasse, J., Koblitz, J., et al. BacDive in 2022: the bacterial diversity metadatabase in 2022. Nucleic Acids Research 50(D1): D741-D746 (2022). https://doi.org/10.1093/nar/gkab961
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