A catalog of small proteins from the global microbiome
Small open reading frames (smORFs) shorter than 100 codons are widespread and perform essential roles in microorganisms, where they encode proteins active in several cell functions, including signal pathways, stress response, and antibacterial activities. However, the ecology, distribution and role of small proteins in the global microbiome remain unknown. Here, we construct a global microbial smORFs catalog (GMSC) derived from 63,410 publicly available metagenomes across 75 distinct habitats and 87,920 high-quality isolate genomes. GMSC contains 965 million non-redundant smORFs with comprehensive annotations. We find that archaea harbor more smORFs proportionally than bacteria. We moreover provide a tool called GMSC-mapper to identify and annotate small proteins from microbial (meta)genomes. Overall, this publicly-available resource demonstrates the immense and underexplored diversity of small proteins.
Authors
- Célio Dias Santos Júnior (ORCID: https://orcid.org/0000-0002-1974-1736)
- Anthony Fullam (ORCID: https://orcid.org/0000-0002-0884-8124)
- Xing‐Ming Zhao (ORCID: https://orcid.org/0000-0002-4531-3970)
- Thomas Schmidt (ORCID: https://orcid.org/0000-0001-8587-4177)
- Breno L. S. de Almeida (ORCID: https://orcid.org/0000-0002-2041-9170)
- Peer Bork (ORCID: https://orcid.org/0000-0002-2627-833X)
- Luís Pedro Coelho (ORCID: https://orcid.org/0000-0002-9280-7885)
- Michael Kuhn (ORCID: https://orcid.org/0000-0002-2841-872X)
- Yiqian Duan (ORCID: https://orcid.org/0000-0002-8046-9831)
- Chengkai Zhu (ORCID: https://orcid.org/0000-0002-8967-0531)
Institutions
- Translational Research Institute (AU)
- Shanghai Medical College of Fudan University (CN)
- Sun Yat-sen University (CN)
- Queensland University of Technology (AU)
- Universidade Federal de São Carlos (BR)
- Max Delbrück Center (DE)
- Fudan University (CN)
- University of Würzburg (DE)
- Shanghai Institute for Science of Science (CN)
- Zhongshan Hospital (CN)
- The First Affiliated Hospital, Sun Yat-sen University (CN)
- APC Microbiome Institute (IE)
- Obstetrics and Gynecology Hospital of Fudan University (CN)
- European Molecular Biology Laboratory (DE)
- Shanghai Center for Brain Science and Brain-Inspired Technology (CN)
Publication Details
- Journal
- Nature Communications
- Published
- 2024-08-30
- DOI
- https://doi.org/10.1038/s41467-024-51894-6
- Citations
- 20
- Primary Topic
- Genomics and Phylogenetic Studies
- Type
- article
- Field-Weighted Citation Impact
- 4.68
Funders
- National Key Laboratory of Human Factors Engineering
- Queensland University of Technology
- National Natural Science Foundation of China
- Science and Technology Commission of Shanghai Municipality