BDB-Lab September Updates
Small proteins still have a lot to tell us
Looking forward
Sep 24 (today!): Luis will be presenting online at APBioNet on using machine learning to find antimicrobial peptides in the global microbiome. The talk will be at 5am UTC (1pm SGT). [Learn more and register]
Oct 14-22: Luis will be visiting Shanghai
Nov 4-6: Luis will be at ABACBS 2024 and presenting in the SBEI event
Nov 11-15: Luis will be co-teaching a 1-week course on state-of-the-art bioinformatic approaches to analyze metagenomic data. [Learn more and register]
Nov 7-Dec 15: Yiqian visiting Brisbane
Dec 10 & 12: Open office hours. Two sessions at different times of the day, so it works for all timezones. Attendance is free, but registration is required:
Dec 10 @ 9.30am UTC (find your local time): Register now
Dec 12 @ 9.30pm UTC (find your local time): Register now
Feel free to get in touch with Luis or Yiqian if you will be at any of these events!
Focus of the quarter: Yiqian’s paper
Since 2018, we have been working on understanding small proteins from the global microbiome (and we’ve featured results on the newsletter throughout the years). At the end of August, we published another milestone, a global catalog, the GMSC:
Duan, Y., Santos-Júnior, C.D., Schmidt, T.S. et al. A catalog of small proteins from the global microbiome. Nature Communications (2024). doi:10.1038/s41467-024-51894-6
Small proteins, which we operationally defined as those up to 100 amino acids, are encoded by small open reading frames (smORFs). They are widespread and perform essential roles in microorganisms, such as participating in signal pathways, stabilizing large protein complexes, and exhibiting antibacterial activities. The GMSC (global microbiome smORF catalog) is an integrated catalog, combining >63k publicly available metagenomes from the SPIRE database and >87k high-quality isolated microbial genomes from the Progenomes2 database.
Even conserved small protein families that are conserved across phyla and present in multiple habitats still lack functional domain annotation! Trying to assign functions to these will be one of the areas of focus for the lab in the future.
Updates of the quarter
People
Claudine Cainghog joined as an undergraduate work-experience student
Anil (@anpokhrel on X/Twitter) joined the group as an MSc student
Conferences/Presentations
Anna gave a talk at the Oxford Nanopore event within ASM Microbe in Atlanta, USA. You can watch it on YouTube:
Anna gave a talk at the Applied Hologenomics conference in Copenhaguen. It was also posted on YouTube:
Luis attended ISMB and had two talks, one on AMPphere and another one on sustainable software (based on a perspective piece in PLoS CB). If you missed it, you can watch a version on YouTube:
Luis visited the JGI in San Francisco and gave a general lab talk
Luis gave a talk on AMPSphere at the Australian Society of Microbiology conference
Both Anna and Luis were in Cape Town for ISME19. Anna presented a poster and Luis presented at the "Night of the Microbes" event (an outreach event that was open to the public).
Tools
Macrel v1.4.0 and v1.5.0 released. This tool now a new subcommand for query-ampsphere to match against the AMPSphere database (v1.5.0 added the
--localflag which enables querying the database locally after an initial download)argNorm has had a lot of development, with versions 0.4.0, 0.5.0, and 0.6.0 released. In particular, it now supports GROOT, performs better drug categorization, and includes more manual curation. A manuscript describing all of these features is forthcoming.
argNorm is now included in nf-core/funcscan (part of the git version, will included in next release)
Other updates
The Extremely Open Science project continues with updates on YouTube and on the mailing-list
Luis and Célio did a Reddit r/askscience AMA on AMPSphere: https://www.reddit.com/r/askscience/comments/1ess914/askscience_ama_series_we_have_discovered/
Luis talked about AMPSphere paper on Portuguese radio: https://www.rtp.pt/play/p6406/e786289/holofote