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This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...

18d

Researchers say the Trump administration is finding new ways to punish science

www.npr.org

Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.

Zamin Iqbal

Our study describing `microntology` and annotations for >300k metagenomes is now online in Bioinformatics @academic.oup.com : academic.oup.com/bioinformati... Congratulations to @fullam.bsky.social @vishnuprasoodanan.bsky.social & @biocs.bsky.social ! See the thread below for more details.

15d

AbstractMotivation. Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and

academic.oup.com

Sebastian Schmidt

microntology: a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats

We’re excited to announce our keynote speakers for the JAMS 15 Symposium – Brisbane 2026! 🧬✨ This year, JAMS 15 will feature an incredible lineup of researchers and leaders in microbiology, infectious diseases, and antimicrobial resistance research.

15d

New version of OrfM, a simple and not slow open reading frame (ORF) caller, is out. Still simple, but a port from C to Rust gained ~25% on runtime. Now with an API too. github.com/wwood/OrfM

2mo

Today marks 30 years since we identified the apicoplast, a relict plastid in human and animal parasites (PMID 8632819). Apicoplasts are the target of the widely used antimalarial prophylactic doxycycline, which has saved many thousands of malaria infections.

We now provide environmental metadata for the GlobDB genomes! 🖥️🧬🦠 More info here: globdb.org/news 🧵

2mo

GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.

simple and not slow ORF caller. Contribute to wwood/OrfM development by creating an account on GitHub.

github.com

1mo

GitHub - wwood/OrfM: simple and not slow ORF caller

gtdb.ecogenomic.org

The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

GTDB - Genome Taxonomy Database

JAMS Brisbane

We just released a @biorxivpreprint.bsky.social describing the *microntology*, a lightweight controlled vocabulary that we have been using for a while to tag metagenomes with contextual data. Study by @fullam.bsky.social @vishnuprasoodanan.bsky.social et al: 1/ www.biorxiv.org/content/10.6...

5mo

Sebastian Schmidt

Summary. We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k m...

www.biorxiv.org

microntology: a lightweight, data-driven controlled vocabulary to describe Earth's microbial habitats

Geoff McFadden

Ben J Woodcroft

#microsky

Daan Speth

ace-gtdb.bsky.social

2mo

Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social

SingleM 0.21 is go - @ace-gtdb.bsky.social R232 reference database, less verbose logging, fixes, etc. Thanks @thepatientwait.bsky.social @aroneys.bsky.social @rossenzhao.bsky.social and on GitHun @EisenRa @magicprotoss @MCeciC

17d

Ben J Woodcroft

24d