Dr James Volmer receiving his LINC grant award
Associate Professor Luis Pedro Coelho receiving his TRI Translation Fellowship
🎉 Big congratulations to Dr James Volmer and @luispedrocoelho !
James has been awarded a TRI LINC Grant, and Luis has received a TRI Translation Fellowship. Both are fantastic opportunities to translate their research into clinical applications and drive real-world impact.👏🚀
3 million volunteers!
Congratulations, Zooniverse! Today we have reached an extraordinary milestone: 3 million volunteers contributing to people-powered research around the world. From classifying galaxies and discovering exoplanets to tracking wildlife, transcribing historical records, and…
mvif 48
#MVIF 48 starts next week!
Free registration: cassyni.com/s/mvif-48
⭐️ Highlights:
🇺🇸 Rachel R. Rock
🇺🇸 @pamferretti.bsky.social
⭐️ Keynote:
🇦🇺 @pam-engelberts.bsky.social and @jamesvolmer.bsky.social
⭐️ Talks:
🇨🇳 Linxing Chen
🇨🇳 Zhemin Zhou
🇦🇺 Hoai-An Nguyen
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.
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.
🧬🖥️🦠
Genomic and evolutionary factors influencing the prediction accuracy of optimal growth temperature in prokaryotes
#microbiology #prokaryotes #MicroSky
@asm.org
doi.org/10.1128/msys...
We all know #fungi are the dominant microbial #eukaryotes in #forest #soils… or are they really?
In our new paper, we revisited 51 forest metatranscriptomes from 4 European and North American forest regions - and found that protistan predators outshine fungi in activity!
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...
MVIF 48 program
We have a new #MVIF program to share with you! 🤩
Free registration: cassyni.com/s/mvif-48
⭐️ Highlights:
🇺🇸 Rachel R. Rock
🇺🇸 @pamferretti.bsky.social
⭐️ Keynote:
🇦🇺 Gene Tyson
⭐️ Talks:
🇨🇳 Linxing Chen
🇨🇳 Zhemin Zhou
🇦🇺 Hoai-An Nguyen
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
Myloasm - long-read metagenomics assembler 🦠
Open preprint: www.biorxiv.org/content/10.1...
Publication: www.nature.com/articles/s41...
GitHub: github.com/bluenote-157...
Join the next #MVIF!
In April 2026 Gene Tyson will give a keynote talk,
the May 2026 event will be with Georg Zeller as a keynote,
and
in June 2026 we will welcome Julie Huber @julesdeep.bsky.social
Dates and details here: www.microbiome-vif.org/en-US/-/futu...
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
Urban soils are a small part of the world and lack the glamour of the wilderness or the economic importance of agriculture, but as most people live in cities, they are very important
Our latest preprint using long-read metagenomics reveals massive hidden diversity and function in city soils
🧵
The smallest bacterial genome, further blurring the bacteria-organelle boundary!
Convergent extreme reductive evolution in ancient planthopper symbioses
www.nature.com/articles/s41...
SPF of 4655 soil metagenomes
In soil, the difficulty of recovering microbial genomes is NOT primarily because eukaryotic DNA dominates the samples. 88% of soil metagenomes had >50% prokaryotic reads.
But, the consistent ~30% non-prokaryotic reads suggests there might be a lot of euk DNA in soil metagenomes.
New paper in mSystems! 🧵 - how much of your metagenome is actually bacterial/archaeal DNA? For many samples, nobody knows.
We built SingleM prokaryotic_fraction (SPF) to answer this, then ran it on >100,000 public metagenomes. 🧬🖥️🦠
Here's what we found 👇
doi.org/10.1128/msystems.01062-25
Similar microbes, different outcomes. Why do some rhizobial bacteroids fix nitrogen in legumes better than others? Check out the online version of our latest work by @poolelaboxford.bsky.social, an historical lab project showing how this comes down to differentiation 😉 ➡️ doi.org/10.1093/plph...
Jug 2.5.0 is out! Jug is a Python framework for parallel & reproducible computation. Write plain Python, run it across many processes or machines with no message-passing code.
pip install jug --upgrade
(Or use the conda-forge packages with conda/pixi)
We're pulling together the genomes for GlobDB release 232, which will be based on the upcoming GTDB release. We will also add new sources of genomes not in INSDC. Here's an overview of the data that will be included in the next GlobDB: globdb.org/news
Please contact me if we've missed something!🦠🖥️🧬
Interested in microbial proteins and their diversity? 🖥️🧬🦠
We have recently released the Amino Acid Sequence Toolkit (AASTK). AASTK is designed to work with the GlobDB to create and work with datasets of protein sequences.
AASTK currently consists of 4 tools:
- CASM
- PASR
- CUGO
- Meta
1/
Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this
www.biorxiv.org/content/10.6...
graph showing number of each community profiling type (amplicon, shotgun-nanopore and shotgun-illumina). Amplicon and shotgun-illumina are in the millions of runs, while shotgun-nanopore is in the tens of thousands of runs.
There was a 34% increase in shotgun metagenomes in 2025 vs 2024 (64% increase for nanopore, now ~15,000), but amplicons are still king.
We’re kicking off 2026 with an exciting lineup of speakers at BRISJAMS this February!
📅 Wednesday, 25 February 2026
⏰ 6:00–7:30pm
📍 The Burrow (Beer Garden Room), West End
🍕 Free pizza provided!
👉 Register via the QR code on the poster.
We look forward to seeing you there!
The ISME20 abstract submission deadline has been extended to 22 February. Microbial ecologists worldwide are invited to submit abstracts for oral, short talk, or poster presentations and contribute to the ISME20 programme.
isme-microbes.org/isme20-abstr...
#ISME20 #MicrobialEcology
Cross reactive antibodies produced by people with rare genetic variants explain the very rare clotting disorders in people receiving adenovirus-based COVID vaccines Gift🔗 www.theatlantic.com/science/2026...
Introducing ** Incendiamoeba **, a eukaryote that can live at temperatures well beyond what we thought possible. 63C!!
Read @hbrappap.bsky.social thread to see what we’ve already started to learn from this amazing organism!
doi.org/10.1101/2025...
#MicroSky #protistsonsky 🧪 #evobio
