I am so excited to share our new findings with you! We provide the structural evidence for a direct protein-to-DNA information pathway, showing how a bacterial enzyme 'reads' its own structure to 'write' DNA. www.science.org/doi/10.1126/...
🦠🧬🖥️
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.
🧬🖥️🦠
Excited to share our new paper out today in @science.org 🎉
We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩
Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...
We stumbled upon an unusual gene called 'rqua' in the genome of some freshwater sponges. In microbes, this gene confers the ability to make a ubiquinone analog - rhodoquinone - which can help the respiratory chain run without oxygen.
Notice for users submitting MAGs to INSDC
Issue: MAGs submitted to INSDC without taxonomic annotations, typically listed as ‘metagenome’, are not included in GTDB. Examples: www.ncbi.nlm.nih.gov/datasets/gen...
What to do: Provide at least a domain-level taxonomic affiliation in the Taxon field.
I'm hiring my first postdoc! Apply by 20/4/26, position #20443. Seeking an environmental microbiologist with experience in metagenomics (preferably viromics) and molecular biology. Experience with targeted metabolomics is a plus.
international.au.dk/about/profil...
gbdraw v0.9.1 is out now on Bioconda!
Easily visualize microbial genomes and enjoy the #gbdraw web app completely offline.
📦 Install via Bioconda: bioconda.github.io/recipes/gbdr...
🌐 Try the online app: gbdraw.app
#bioinformatics #genomics #microbiology #visualization
Out Now! Advancing microbiology through foundational science #MicroSky
"The struggle of figuring out the right analysis approach, wrestling with an unexpected result, or trying to turn a messy set of findings into a coherent story is not an obstacle to learning. It _is_ the learning".
Required reading for AI in the lab:
blekhman.substack.com/p/you-need-t...
We tested the efficacy of semi-permeable capsules to capture protists from cultures and environmental samples using the Onyx from @atrandi.bsky.social. Tremendous effort from everyone in the lab and led by Marco Fantini and Nik Brask - check out the videos here: www.biorxiv.org/content/10.6...
Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com :
www.nature.com/articles/s41...
See the linked threads for more details!
Incredible footage from a United Airlines flight of the Artemis II launch.
Phage receptor prediction from genome sequencing alone. Bacterial receptor (blue) interacting with phage proteins (purple) is shown here
📣Huge preprint 🔔
Today we share something our group has been working toward for a long time, led by @lucasmoriniere.bsky.social We asked can we predict which receptor a phage targets from its genome sequence alone? For most phages, we couldn’t. So Lucas set out to do something I had only dreamed of.
How diverse is bacterial immunity ?
We report in @science.org how language models allowed us to predict 2.4M antiphage proteins spanning >23K novel potential systems.
👏 @emordret.bsky.social, @alexhv.bsky.social & al doi.org/10.1126/scie...
Explore them here defensefinder.mdmlab.fr/wiki/refseq_...
If preparing figures please consider "colorblind friendly" approaches (www.nature.com/articles/d41...). I am missing the long-wave opsin, which manifests in strange ways: I can't discern red vs. black. This dichromacy is rare and severe, but ~300 million have more common forms addressed in link.
Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀
I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵
seqeralabs.github.io/RustQC/
Figure 1
Figure 2
Figure 3
Figure 4
Baktfold: Sensitive protein functional annotation across the microbial tree of life using structural information [new]
Annotates microbial proteins via struct info, converts seqs to 3Di tokens for DB searches to ID hypothetical ones.
ROCKET 🚀 inference-time optimization of AlphaFold to fit structural data is published! rdcu.be/fa9YH
Since our preprint, we’ve pushed it to regimes where other methods break: low resolution, weak signal, real experimental edge cases. Here’s what we learned: 1/15
A scale illustration of the Earth and the Moon, with the Earth on the far left, lots of black, and then the Moon on the far right, about 30 Earth diameters away.
In honor of (hopefully) today's launch of NASA's Artemis II mission, the first crewed mission to orbit the Moon in more than 50 years, here is a to-scale graphic of exactly how far away the Moon actually is. (Click image to expand.) You could fit about 30 Earths between the Earth and the Moon!
Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social
Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback.
rdcu.be/famFj
ggCaller v1.5.0 is out! We've removed the integrated clustering to enable users to benefit from new Panaroo features. Now, ggCaller generates GFFs that can be used with any clustering method. But for fans of an integrated ggCaller pangenome workflow read on...
github.com/bacpop/ggCal...
📢 New paper 🚨
☘️🌿🌱🐄💨🦠🔬🧫🧬
#sulfoquinovose #microbiome
#microsky #microbiomesky
academic.oup.com/ismej/articl...
On the architecture and evolution of prokaryotic multicellularity
Preprint from @escolizzi.bsky.social
www.authorea.com/doi/full/10....
Sulfur disproportionation occurs globally across anoxic habitats and has multiple mechanisms of independent evolutionary origin
#microbiology #sulfur #MicroSky
@isme-microbes.bsky.social
doi.org/10.1093/isme...
Found out today that @kyclark.bsky.social has made their great 'Mastering Python for Bioinformatics' book into a YouTube series.
youtube.com/playlist?lis...
LLM agents for biological intelligence across genomics, proteomics, spatial biology, and biomedicine academic.oup.com/bib/article/... 🧬💻🧪
The pre-print for Slorado and openfish is out. biorxiv.org/content/10.6...
You can do @nanoporetech.com basecalling with not just NVIDIA GPU, but also using a range of AMD GPU.
Would be useful since popular GPUs are now 💸💸💸💸(& hard to buy),
Work by @bonson-wong.bsky.social
