BacCorpus100

BacCorpus100 is a large-scale bacterial genome corpus for training and evaluating genome-aware genomic language models. It contains quality-controlled bacterial genomes represented at the genome level, with predicted protein-coding sequences stored as protein translations and intergenic regions stored as DNA sequences. Genomes were deduplicated at 100% identity using genome sketching.

BacCorpus100 spans approximately 7 million genomes, 20 billion protein-coding features, 16 billion intergenic regions, more than 150,000 species, and over 10,000 environments. The dataset is intended for large-scale pretraining and analysis of bacterial genomic language models.

BacCorpus was built by combining genomes from several public bacterial genome resources, including MGnify [1], SPIRE [2], HRGM [3], GTDB [4], mOTUs DB [5], and AllTheBacteria [6]. Genomes were uniformly quality controlled and annotated.

Intended Uses

This dataset is intended for:

• pretraining bacterial genomic language models;
• studying bacterial genome organisation;
• building protein, DNA, mixed-modality, or genome-aware models;
• extracting protein or intergenic DNA sequences for representation learning;
• benchmarking model architectures that use genome context.

How to Use

Because BacCorpus100 is large, we recommend streaming the dataset rather than downloading it locally.

from datasets import load_dataset

ds = load_dataset(
    "AllTheBacteria/BacCorpus100",
    split="train",
    streaming=True,
)

example = next(iter(ds))
print(example.keys())

Schema

BacCorpus100 stores one row per genome. Each row contains aligned list-valued fields describing the features extracted from that genome.

Column	Type	Description
genome_id	string	Genome identifier.
contig_id	list<int64>	Contig index for each feature.
feature_id	list<int64>	Feature index within a contig.
molecule	list<string>	Feature type: AA for translated CDS, DNA for intergenic region.
start	list<int64>	Feature start coordinate.
end	list<int64>	Feature end coordinate.
strand	list<int64>	Feature strand, typically 1 or -1.
sequence	list<string>	Protein or DNA sequence for the feature.
source	string	Source database or resource.

The list-valued columns are aligned by position, so index i across contig_id, feature_id, molecule, start, end, strand, and sequence refers to the same genomic feature.

Other resources

For deduplicated and clustered DNA and protein sequence datasets, see:

• Protein sequences: https://huggingface.co/datasets/AllTheBacteria/BacCorpus-prot-90
• Intergenic regions (DNA): https://huggingface.co/datasets/AllTheBacteria/BacCorpus-intergenic-dna-90

Citation:

TBD

References

[1] Richardson, L. et al. MGnify: the microbiome sequence data analysis resource in 2023. Nucleic Acids Research 51(D1), D753–D759 (2023). doi:10.1093/nar/gkac1080

[2] Schmidt, T. S. B. et al. SPIRE: a Searchable, Planetary-scale mIcrobiome REsource. Nucleic Acids Research 52(D1), D777–D783 (2024). doi:10.1093/nar/gkad943

[3] Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nature Biotechnology 39, 105–114 (2021). doi:10.1038/s41587-020-0603-3

[4] Parks, D. H. et al. GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research 50(D1), D785–D794 (2022). doi:10.1093/nar/gkab776

[5] Dmitrijeva, M. et al. The mOTUs online database provides web-accessible genomic context to taxonomic profiling of microbial communities. Nucleic Acids Research 53(D1), D797–D805 (2025). doi:10.1093/nar/gkae1004

[6] Hunt, M. et al. AllTheBacteria – all bacterial genomes assembled, available, and searchable. bioRxiv (2024). doi:10.1101/2024.03.08.584059