Source coverage

Species, strains, deposits and assemblies are different kinds of records. These catalogs retain source identifiers and assertions even when they cannot be attached to an NCBI taxon.

“Complete” describes the named snapshot. Crosslinks and external resources have narrower coverage, shown below. Catalog counts must not be added together as counts of distinct organisms.

Coverage and refresh guide · Download the source manifest

Catalogs

Source	Records	Coverage	Downloads
AllTheBacteria full catalog	3,227,665	Every source sample/assembly row, including all unavailable statuses 2025-05	1 file(s) allthebacteria.tsv.xz (3,227,665 records)
BacDive	101,417	Every strain in the captured public census; original identity and sequence projection 2026-09-13T17:17:21.092811+00:00	1 file(s) records.jsonl.gz (101,417 records)
BacDive deposit crosswalk	101,417	Every current strain and its reported culture-collection identifiers 2026-09-13T17:50:44Z	1 file(s) bacdive_strains.tsv (101,417 records)
BV-BRC / PATRIC	1,419,549	Complete public bacterial and archaeal genome census and identity metadata 2026-09-13T17:42:47.000815+00:00	29 file(s) bvbrc-0000.jsonl.gz (50,000 records) bvbrc-0001.jsonl.gz (50,000 records) bvbrc-0002.jsonl.gz (50,000 records) bvbrc-0003.jsonl.gz (50,000 records) bvbrc-0004.jsonl.gz (50,000 records) bvbrc-0005.jsonl.gz (50,000 records) bvbrc-0006.jsonl.gz (50,000 records) bvbrc-0007.jsonl.gz (50,000 records) bvbrc-0008.jsonl.gz (50,000 records) bvbrc-0009.jsonl.gz (50,000 records) bvbrc-0010.jsonl.gz (50,000 records) bvbrc-0011.jsonl.gz (50,000 records) bvbrc-0012.jsonl.gz (50,000 records) bvbrc-0013.jsonl.gz (50,000 records) bvbrc-0014.jsonl.gz (50,000 records) bvbrc-0015.jsonl.gz (50,000 records) bvbrc-0016.jsonl.gz (50,000 records) bvbrc-0017.jsonl.gz (50,000 records) bvbrc-0018.jsonl.gz (50,000 records) bvbrc-0019.jsonl.gz (50,000 records) bvbrc-0020.jsonl.gz (50,000 records) bvbrc-0021.jsonl.gz (50,000 records) bvbrc-0022.jsonl.gz (50,000 records) bvbrc-0023.jsonl.gz (50,000 records) bvbrc-0024.jsonl.gz (50,000 records) bvbrc-0025.jsonl.gz (50,000 records) bvbrc-0026.jsonl.gz (50,000 records) bvbrc-0027.jsonl.gz (50,000 records) bvbrc-0028.jsonl.gz (19,549 records)
GOLD Analysis Project	459,542	Every public workbook row; original identity, strain and genome/project fields 7d22ea3f2c9ac40d513cd4af1410f7d19f3525347eb272787ba1c20525340370	1 file(s) analyses.jsonl.gz (459,542 records)
GOLD Organism	531,961	Every public workbook row; original identity, strain and genome/project fields 7d22ea3f2c9ac40d513cd4af1410f7d19f3525347eb272787ba1c20525340370	1 file(s) organisms.jsonl.gz (531,961 records)
GOLD Sequencing Project	636,630	Every public workbook row; original identity, strain and genome/project fields 7d22ea3f2c9ac40d513cd4af1410f7d19f3525347eb272787ba1c20525340370	1 file(s) projects.jsonl.gz (636,630 records)
GTDB genomes	901,341	Every bacterial and archaeal genome in RS232 RS232	19 file(s) gtdb_genomes-0000.jsonl.gz (50,000 records) gtdb_genomes-0001.jsonl.gz (50,000 records) gtdb_genomes-0002.jsonl.gz (50,000 records) gtdb_genomes-0003.jsonl.gz (50,000 records) gtdb_genomes-0004.jsonl.gz (50,000 records) gtdb_genomes-0005.jsonl.gz (50,000 records) gtdb_genomes-0006.jsonl.gz (50,000 records) gtdb_genomes-0007.jsonl.gz (50,000 records) gtdb_genomes-0008.jsonl.gz (50,000 records) gtdb_genomes-0009.jsonl.gz (50,000 records) gtdb_genomes-0010.jsonl.gz (50,000 records) gtdb_genomes-0011.jsonl.gz (50,000 records) gtdb_genomes-0012.jsonl.gz (50,000 records) gtdb_genomes-0013.jsonl.gz (50,000 records) gtdb_genomes-0014.jsonl.gz (50,000 records) gtdb_genomes-0015.jsonl.gz (50,000 records) gtdb_genomes-0016.jsonl.gz (50,000 records) gtdb_genomes-0017.jsonl.gz (50,000 records) gtdb_genomes-0018.jsonl.gz (1,341 records)
GTDB NCBI mappings	322,327	Every supplied species-to-NCBI mapping 2026-09-13T17:50:44Z	1 file(s) gtdb_mappings.tsv (322,327 records)
GTDB species	199,923	Every species cluster, including unmapped clusters 2026-09-13T17:50:44Z	1 file(s) gtdb_species.tsv (199,923 records)
LPSN names	34,301	Every name in the pinned kg-microbe transform, including unmapped names 2026-09-13T17:50:44Z	1 file(s) lpsn_names.tsv (34,301 records)
NCBI Assembly genbank	3,365,719	All bacterial/archaeal rows and unresolved taxon IDs; all original columns and statuses 2026-09-13	68 file(s) ncbi_genbank-0000.jsonl.gz (50,000 records) ncbi_genbank-0001.jsonl.gz (50,000 records) ncbi_genbank-0002.jsonl.gz (50,000 records) ncbi_genbank-0003.jsonl.gz (50,000 records) ncbi_genbank-0004.jsonl.gz (50,000 records) ncbi_genbank-0005.jsonl.gz (50,000 records) ncbi_genbank-0006.jsonl.gz (50,000 records) ncbi_genbank-0007.jsonl.gz (50,000 records) ncbi_genbank-0008.jsonl.gz (50,000 records) ncbi_genbank-0009.jsonl.gz (50,000 records) ncbi_genbank-0010.jsonl.gz (50,000 records) ncbi_genbank-0011.jsonl.gz (50,000 records) ncbi_genbank-0012.jsonl.gz (50,000 records) ncbi_genbank-0013.jsonl.gz (50,000 records) ncbi_genbank-0014.jsonl.gz (50,000 records) ncbi_genbank-0015.jsonl.gz (50,000 records) ncbi_genbank-0016.jsonl.gz (50,000 records) ncbi_genbank-0017.jsonl.gz (50,000 records) ncbi_genbank-0018.jsonl.gz (50,000 records) ncbi_genbank-0019.jsonl.gz (50,000 records) ncbi_genbank-0020.jsonl.gz (50,000 records) ncbi_genbank-0021.jsonl.gz (50,000 records) ncbi_genbank-0022.jsonl.gz (50,000 records) ncbi_genbank-0023.jsonl.gz (50,000 records) ncbi_genbank-0024.jsonl.gz (50,000 records) ncbi_genbank-0025.jsonl.gz (50,000 records) ncbi_genbank-0026.jsonl.gz (50,000 records) ncbi_genbank-0027.jsonl.gz (50,000 records) ncbi_genbank-0028.jsonl.gz (50,000 records) ncbi_genbank-0029.jsonl.gz (50,000 records) ncbi_genbank-0030.jsonl.gz (50,000 records) ncbi_genbank-0031.jsonl.gz (50,000 records) ncbi_genbank-0032.jsonl.gz (50,000 records) ncbi_genbank-0033.jsonl.gz (50,000 records) ncbi_genbank-0034.jsonl.gz (50,000 records) ncbi_genbank-0035.jsonl.gz (50,000 records) ncbi_genbank-0036.jsonl.gz (50,000 records) ncbi_genbank-0037.jsonl.gz (50,000 records) ncbi_genbank-0038.jsonl.gz (50,000 records) ncbi_genbank-0039.jsonl.gz (50,000 records) ncbi_genbank-0040.jsonl.gz (50,000 records) ncbi_genbank-0041.jsonl.gz (50,000 records) ncbi_genbank-0042.jsonl.gz (50,000 records) ncbi_genbank-0043.jsonl.gz (50,000 records) ncbi_genbank-0044.jsonl.gz (50,000 records) ncbi_genbank-0045.jsonl.gz (50,000 records) ncbi_genbank-0046.jsonl.gz (50,000 records) ncbi_genbank-0047.jsonl.gz (50,000 records) ncbi_genbank-0048.jsonl.gz (50,000 records) ncbi_genbank-0049.jsonl.gz (50,000 records) ncbi_genbank-0050.jsonl.gz (50,000 records) ncbi_genbank-0051.jsonl.gz (50,000 records) ncbi_genbank-0052.jsonl.gz (50,000 records) ncbi_genbank-0053.jsonl.gz (50,000 records) ncbi_genbank-0054.jsonl.gz (50,000 records) ncbi_genbank-0055.jsonl.gz (50,000 records) ncbi_genbank-0056.jsonl.gz (50,000 records) ncbi_genbank-0057.jsonl.gz (50,000 records) ncbi_genbank-0058.jsonl.gz (50,000 records) ncbi_genbank-0059.jsonl.gz (50,000 records) ncbi_genbank-0060.jsonl.gz (50,000 records) ncbi_genbank-0061.jsonl.gz (50,000 records) ncbi_genbank-0062.jsonl.gz (50,000 records) ncbi_genbank-0063.jsonl.gz (50,000 records) ncbi_genbank-0064.jsonl.gz (50,000 records) ncbi_genbank-0065.jsonl.gz (50,000 records) ncbi_genbank-0066.jsonl.gz (50,000 records) ncbi_genbank-0067.jsonl.gz (15,719 records)
NCBI Assembly genbank historical	101,100	All bacterial/archaeal rows and unresolved taxon IDs; all original columns and statuses 2026-09-13	3 file(s) ncbi_genbank_historical-0000.jsonl.gz (50,000 records) ncbi_genbank_historical-0001.jsonl.gz (50,000 records) ncbi_genbank_historical-0002.jsonl.gz (1,100 records)
NCBI merged taxon IDs	101,006	Every source merged-ID assertion 2026-09-13T17:50:44Z	1 file(s) ncbi_merged_ids.tsv (101,006 records)
NCBI Taxonomy names	783,107	Every bacterial/archaeal name class 2026-09-13	16 file(s) ncbi_names-0000.jsonl.gz (50,000 records) ncbi_names-0001.jsonl.gz (50,000 records) ncbi_names-0002.jsonl.gz (50,000 records) ncbi_names-0003.jsonl.gz (50,000 records) ncbi_names-0004.jsonl.gz (50,000 records) ncbi_names-0005.jsonl.gz (50,000 records) ncbi_names-0006.jsonl.gz (50,000 records) ncbi_names-0007.jsonl.gz (50,000 records) ncbi_names-0008.jsonl.gz (50,000 records) ncbi_names-0009.jsonl.gz (50,000 records) ncbi_names-0010.jsonl.gz (50,000 records) ncbi_names-0011.jsonl.gz (50,000 records) ncbi_names-0012.jsonl.gz (50,000 records) ncbi_names-0013.jsonl.gz (50,000 records) ncbi_names-0014.jsonl.gz (50,000 records) ncbi_names-0015.jsonl.gz (33,107 records)
NCBI Assembly refseq	532,797	All bacterial/archaeal rows and unresolved taxon IDs; all original columns and statuses 2026-09-13	11 file(s) ncbi_refseq-0000.jsonl.gz (50,000 records) ncbi_refseq-0001.jsonl.gz (50,000 records) ncbi_refseq-0002.jsonl.gz (50,000 records) ncbi_refseq-0003.jsonl.gz (50,000 records) ncbi_refseq-0004.jsonl.gz (50,000 records) ncbi_refseq-0005.jsonl.gz (50,000 records) ncbi_refseq-0006.jsonl.gz (50,000 records) ncbi_refseq-0007.jsonl.gz (50,000 records) ncbi_refseq-0008.jsonl.gz (50,000 records) ncbi_refseq-0009.jsonl.gz (50,000 records) ncbi_refseq-0010.jsonl.gz (32,797 records)
NCBI Assembly refseq historical	112,178	All bacterial/archaeal rows and unresolved taxon IDs; all original columns and statuses 2026-09-13	3 file(s) ncbi_refseq_historical-0000.jsonl.gz (50,000 records) ncbi_refseq_historical-0001.jsonl.gz (50,000 records) ncbi_refseq_historical-0002.jsonl.gz (12,178 records)
NCBI Taxonomy	650,767	Complete prokaryote backbone plus other attested taxa and ancestors 2026-09-13T17:50:44Z	1 file(s) ncbitaxon_taxa.tsv (650,767 records)
NCBI type material	277,306	Type and excluded-from-type assertions; no inferred equivalence 2026-09-13T17:50:44Z	1 file(s) ncbi_type_material.tsv (277,306 records)
SeqCode names	48,392	Every public name (discovery census) 2026-09-13T17:18:13.485769+00:00	1 file(s) names.jsonl.gz (48,392 records)
SeqCode type-genomes	1,808	Every returned type-genome name, preserving rank, status and classification 2026-09-13T17:18:13.485769+00:00	1 file(s) type-genomes.jsonl.gz (1,808 records)
StrainInfo	314,470	Every strain in the captured public census; original identity and sequence projection 2026-09-13T17:29:00Z	1 file(s) records.jsonl.gz (314,470 records)

Coverage boundaries and other resources

Source audit: 2026-09-13.

Resource	Included	Boundary
NCBI Taxonomy complete snapshot	Full bacterial and archaeal backbone, original name classes, type-material assertions and merged IDs.	Species and below become taxon records; higher ranks remain lineage. Names are not proof of strain identity.
NCBI GenBank and RefSeq assemblies complete snapshot	Current and historical prokaryotic assembly metadata; unresolved taxonomy retained; all supplied columns.	Only latest assemblies with an explicit registered culture identifier supply direct strain links.
GTDB complete snapshot	All RS232 species clusters and bacterial/archaeal genomes, including clusters without an NCBI mapping.	MAGs and species clusters are not physical strain deposits; GTDB taxonomy remains a separate assertion.
LPSN complete pinned transform	All names and available API annotations in the pinned kg-microbe transform, including unmapped names.	This is the recorded upstream extraction, not a claim to the live authenticated LPSN service.
BacDive complete snapshot	Complete public ID census and current v2 identity, deposit and sequence records.	One wholly empty census export row has no source ID and is reported separately.
StrainInfo complete snapshot	Every captured public strain, its own deposits, taxon assertions and sequence records, independent of BacDive overlap.	SI-ID, SI-DP and DOI versions remain distinct; only explicitly named eligible deposits supply genome links.
SeqCode Registry complete snapshot	Complete public name census and type-genome endpoint, including uncultivated species names.	Discovery names are not all validly published; source statuses and genome types are retained independently.
JGI GOLD and IMG complete gold snapshot with img crosslinks	Every public workbook organism, sequencing project and analysis, including supplied IMG identifiers and GenBank accessions.	This is complete for the pinned GOLD workbook, not for every IMG database or private genome.
AllTheBacteria complete snapshot	Complete 2025-05 source metadata, all statuses, samples, runs, analysis accessions, checksums and supplied download URLs.	Evidenced strain/genome crosslinks are a subset of the full catalog; shared BioSample is not assembly equivalence.
BV-BRC / PATRIC complete snapshot	Complete public bacterial and archaeal genome census with identity, culture, taxonomy, assembly, sample and project metadata.	Strain links require whole registered culture identifiers; private genomes and non-prokaryotic records are excluded.
ENA and DDBJ / INSDC source crosslinks	Exchanged GenBank assembly accessions and supplied sample, project, sequence, run and ENA analysis identifiers.	No claim that every ENA or DDBJ metadata field or unassembled sequence is locally mirrored.
Culture collections and CAFI source crosslinks	All reported culture-collection accessions in captured BacDive and StrainInfo; pinned CAFI validates join authorities and formats.	ATCC, DSMZ, JCM, NBRC, CIP, CECT, CCUG, LMG, KCTC and other collections retain their source deposit identities; no claim of independent complete collection crawls.
MediaDive, Madin et al. and BactoTraits supporting evidence	Existing growth-media and phenotypic evidence from the pinned upstream transforms remains in taxon records.	These evidence sources do not define complete species or strain censuses.
TYGS external index	Type-strain genome classification resource, linked in the source directory; related LPSN and BacDive assertions are retained.	The documented API retrieves analysis-job results. No direct complete TYGS genome-table capture is asserted.
WDCM GCM, gcType and reference strains external index	Global culture-catalog and reference-strain discovery resources, linked in the source directory.	No independent full WDCM bulk snapshot is committed; overlapping deposits are retained only as asserted by captured sources.
SILVA and Living Tree Project external index	Ribosomal sequence taxonomy and type-strain reference resources, linked in the source directory.	Ribosomal accessions are sequence records, not genome assemblies; no complete SILVA sequence catalog is claimed.
EnteroBase and PubMLST external index	Specialist isolate and typing catalogs; BacDive-supplied EnteroBase references are preserved in its primary projection.	No independent full isolate census or MLST-to-genome equivalence is inferred.