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...

Clustering proteins using DIAMOND is out now @natmethods.nature.com www.nature.com/articles/s41...

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...

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

New paper out! Here's a puzzle: phototrophy, the ability to use light for energy, is one of life's great innovations. It evolved early and transformed the biosphere. But it evolved 2x. Why not just once, why not more? Our work suggests the answer is priority effects. www.nature.com/articles/s44...

LAUNCH DAY🎙️ We're thrilled to share the very first episode of #MVIFconversations w/ Jack Gilbert 💫 Stefanie Malan-Müller & @cpavloud.bsky.social talked with @gilbertjacka.bsky.social about how microbes shape our health and the invisible living world around us. Give it a listen & spread the word!

DISCOVER ZOONIVERSE PROJECTS IN A WHOLE NEW WAY We’re happy to introduce an updated Projects page on Zooniverse, designed to make it easier, faster, and more enjoyable to find projects that match your interests. The new page brings together improved navigation, long-requested features like sorting…

It's Friday! ...and a new #MVIF program is out! 🤩 Free registration: cassyni.com/s/mvif-46 Highlights: 🇺🇸 Rebecca L. Knoll 🇯🇵 Akito Sakanaka Keynote: 🇺🇸 @simrouxvirus.bsky.social ⭐️ Talks: 🇦🇺 @jeremyjbarr.bsky.social 🇨🇦 @erikbakkeren.bsky.social 🇨🇳 Guanxiang Liang

The ISME Early Career Scientist Committee is glad to begin the year by spotlighting @aroneys.bsky.social, a Postdoctoral Researcher at QUT, and his paper, “Bin Chicken: targeted metagenomic coassembly for the efficient recovery of novel genomes.” doi.org/10.1038/s415... (1/2)

Present your research at the 20th International Symposium on Microbial Ecology in Auckland, from 16 - 21 August 2026! When submitting your abstract, make sure to check whether you are eligible for one of the travel grants. isme-microbes.org/call-for-abs... #microbialecology #isme20

🚨vConTACT3 now in Nature Biotechnology: - >95% agreement with ICTV for known viruses - Classifies both prokaryotic and eukaryotic viruses - Extends beyond genus → subfamily, family & order - Systematically assigns taxonomy to tens of thousands of previously unclassified viruses

New paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods. www.biorxiv.org/content/10.6...

Really important read for people working with long-read MAGs. www.nature.com/articles/s41...

A free, open-access library of high-quality organism illustrations for science communication

Landmark study in @Nature! 🇩🇰 The "Microflora Danica" project has created the first-ever national microbiome atlas. Led by Aalborg University, @fwf-at.bsky.social CoE Microplanet's Director @michiwagner4.bsky.social, and @daanspeth.bsky.social, Andrew Giguere @cemess.bsky.social analyzed nitrifiers.

New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga). 🔗 DOI: www.biorxiv.org/content/10.6...

Our Review article is now featured in the January issue of @natrevgenet.nature.com, check it out!

🎉 The #SeqCode has reached a significant milestone: with the validation of the genus Skiveiella, a total of 1,000 #names have now been validly published under the SeqCode. This achievement marks a major step forward in the adoption and impact of the SeqCode within the scientific community.

GTDB is now cross-referenced from ENA genome assembly pages. Check it out: www.ebi.ac.uk/ena/browser/.... Thank you to @ebi.embl.org for support with setting up these links!

From @jhcepas.bsky.social and colleagues in the @narjournal.bsky.social #NARDatabaseIssue | eggNOG v7: phylogeny-based orthology predictions and functional annotations | #Bioinformatics #ProteinCentric #Database #OpenScience 🧬 🖥️🧪🇨🇭🇪🇸🇩🇪🔓 ⬇️ academic.oup.com/nar/advance-...

A lucky year in 2025, and now I've a QUT Faculty of Health Researcher of the Year to prove it. Thank you to the many non-myself people who made it happen.

Some archaea—an ancient group of microorganisms—have an entirely novel genetic code, according to a new study in Science. The findings expand our understanding of how alternative genetic codes evolve and hint at new molecular tools for biotechnology applications. https://scim.ag/4omApQ7

An Asgard Archaeon (Lokiarchaeum ossiferum) growing and retracting its arms

Microflora Danica: What can you learn from collecting and sequencing 10,000+ samples from a single country? Check out our new paper in @nature.com to find out. Incredible work led by Caitlin Singleton, Thomas B. N. Jensen, and Mads Albertsen from @aau.dk. 🦠🧫🧬 www.nature.com/articles/s41...

Happy December! Join #MVIF 44 – we will discuss diverse #microbiome topics: human urinary, gut, oral and nasal microbiomes, extreme environments, and a new sequence alignment tool.

metaTraits: a large-scale integration of microbial phenotypic trait information academic.oup.com/nar/advance-...

Out after peer-review: www.science.org/doi/full/10.... Our bottom line stayed: never use leave-one-out cross-validation as it has inherent train-test leakage. Consider our Rebalanced version instead! We now also account for regression and nested cross-validation, with more extensive benchmarking.

🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.”  Explore the full study: https://doi.org/10.1093/bioadv/vbaf280

Celebrating Excellence at the Centre for Microbiome Research! We’re thrilled to share that Gene Tyson, @benjwoodcroft.bsky.social and @luispedrocoelho.bsky.social have once again been named Highly Cited Researchers for 2025 by Clarivate! #HighlyCited2025

Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠

Congrats @fullam.bsky.social @pangenomics.bsky.social @borklab.bsky.social & team(s). Great to see this published! proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes: academic.oup.com/nar/article/...

Soils contain an amazing diversity of functions encoded in plasmids. The Global Soil Plasmidome Resource: 98,728 soil plasmids from 6,860 samples. Led by @mattlabguy.bsky.social and @apcamargo.bsky.social at @jgi.doe.gov @biosci.lbl.gov @berkeleylab.lbl.gov www.nature.com/articles/s41...

SingleM v0.20.2 - ONT/PacBio input reads now supported (if somewhat inefficiently), plus improved Lyrebird database for phage profiling. Microbial fraction is now prokaryotic fraction, easier to specify input genomes.

Curious about plasmid biology? Our latest paper is out now in Nature Communications! 🚨 doi.org/10.1038/s414... We analyzed thousands of diverse bacterial plasmids to shed light for the first time on a key aspect of plasmid biology: plasmid copy number. 1/7 👇

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6