AllTheBacteria/BacCorpus-prot-90

BacCorpus Protein 90

BacCorpus Protein 90 is a large-scale, sequence-level clustered dataset of bacterial protein sequences. It contains representative protein sequences clustered at 90% sequence identity and 90% coverage, derived from BacCorpus, a uniformly processed bacterial genome resource spanning millions of quality-controlled isolate genomes and metagenome-assembled genomes.

This dataset is intended for training and evaluating protein language models and bacterial genomic language models. Protein sequences capture much of the conserved functional signal in bacterial genomes and are useful for modelling gene function, protein composition, and genome-scale bacterial phenotypes.

BacCorpus Protein 90 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], annotating the genomes, extracting predicted protein-coding sequences, and clustering them with MMSeqs2 (version 18.8cc5c).

Intended Uses

This dataset is intended for:

• pretraining protein language models on bacterial proteins;
• training bacterial genomic language models;
• studying bacterial protein sequence diversity;
• sampling representative bacterial proteins for downstream model training;
• evaluating sequence redundancy reduction strategies for bacterial genomics.

How to Use

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

from datasets import load_dataset

ds = load_dataset(
    "AllTheBacteria/BacCorpus-prot-90",
    split="train",
    streaming=True,
)

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

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