Secret life of prophages: template-directed synthesis of DNA superstructures via prophage activation and rolling circle replication in bacterial biofilms bioRxiv by Gabriel Antonio S. Minero et al with @thethormannden.bsky.social, Rikke Louise Meyer www.biorxiv.org/content/10.6...

And the poster is up at #microbio26! Come and find me at A037 to talk all things biofilm :) @microbiologysociety.org

Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky

I made a map of 3.4 million Bluesky users - see if you can find yourself! bluesky-map.theo.io I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail

Want to convert old relative abundance ocean amplicon data into absolute abundances? Williams et al. show a flow cytometry "anchor" can provide reasonable absolute abundances, validated by internal-standard corrected metagenomics with single copy genes, and amplicons academic.oup.com/ismecommun/a...

On the architecture and evolution of prokaryotic multicellularity Preprint from @escolizzi.bsky.social www.authorea.com/doi/full/10....

New online! Leveraging microbial phylogeny for computational efficiency

Moore, Gitai and colleagues report "CauloKO:an ordered transposon mutant library in Caulobacter crescentus", and use my favorite assay - a crystal violet screen for biofilm mutants, validating the libray and identifying new mutants. journals.asm.org/doi/10.1128/... @asm.org #JBacteriology

Now published! 'Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli' www.nature.com/articles/s41... insights below.....

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

If we're going to solve this we need to have an honest and informed conversation about the true costs of doing things 2/2 journals.plos.org/plosbiology/...

One of the biggest challenges in microbial biotechnology? Unlocking the potential of non-model microbes and synthetic communities! Glad to share our review @sonjablasche.bsky.social @simonemozzachiodi.bsky.social @kiranrpatil.bsky.social @cambridgebiosci.bsky.social🧵(1/7) doi.org/10.1016/j.co...

A new era for #ONT amplicon sequencing? We show that #ONT #amplicon sequencing now achieves accuracy sufficient for #ASV resolution using standard Illumina-based pipelines. We validated this by sequencing identical amplicons on #ONT and #PacBio. @nanoporetech.com www.biorxiv.org/content/10.6...

New preprint alert! We conducted a long-term evolution experiment to ask: How do species interactions shape adaptive evolution in microbial biofilms? #biofilm #LTEE www.biorxiv.org/content/10.6... 1/5

Now out in @natcomms.nature.com : versions 2.0 of both BiG-SCAPE and BiG-SLiCE! With significant speed and accuracy increases, as well as new interactive functionalities. Read the full paper here #openaccess: www.nature.com/articles/s41...

“Many of the planet’s microbiomes are under serious threat, with untold numbers of species & ecosystems flickering silently out of existence.” — @moiradonovan.bsky.social #microbes #microbiome #conservation #environment

🔖 kucharski AI and science research

Kids: “Dad that car cut you off!” Me: “He’s harmless.”

This is a major issue is that the incentives are to output false positives in your tools If you need to survive on having many citations to your tools, it is better if your tool gives users lots of results so that they cite it! open.substack.com/pub/luispedr...

The house that Kocuria built: A potential role for functional amyloid in the unique cube-based structure of K. varians biofilms. 🦠🧫 www.sciencedirect.com/science/arti...

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others academic.oup.com/femsre/artic... 🧵👇

He may have only barely known about bacteria, and not at all about viruses, but Darwin was right about hating an ill-defined species concept

A national baseline for methane sink habitats and methanotroph diversity https://www.biorxiv.org/content/10.64898/2026.02.02.703227v1

More microbiologists need to think about goop! We only found 31 studies to compare our results to, mostly clinical gammaproteobacteria. Erin Gloag's review is a great starting point pubmed.ncbi.nlm.nih.gov/33447803/

Such a cool exopolysaccharide, and a really fascinating story! Also happy to report that epsSMASH detects the Ralstonia EPS-I gene cluster 🙌 🧫🦠🧬🖥

Dust looks dead but it is, in fact, alive, teeming with hardy microbes traveling around the world. How are they surviving the trip? Scientists think biofilm formation may play a role. Watch Microbial Minutes for the full story! 🦠 youtu.be/3q-rhw17h2o

Ever wondered if your favorite bacteria 🧫🦠 produce exopolysaccharides? You can now easily check that with epsSMASH, our new bioinformatic tool built on the antiSMASH framework. It detects both known and novel exoPS BGCs. Check out and share the preprint! www.biorxiv.org/content/10.6...

Welcome to another member of the antiSMASH ecosystem of tools. When @marnixmedema.bsky.social and I were putting together antiSMASH version 1.0 15 years ago, I don't think our wildest dreams would have predicted where our little tool would go.

Merry X-SMASH! My first first author paper is out on bioRxiv! 🖥 We present epsSMASH, a comprehensive and high-throughput tool for predicting exopolysaccharide (exoPS) biosynthetic gene clusters (BGCs) in bacterial genomes 🦠🧬🧫 1/8

⭐NAR Breakthrough! ⭐ 🧬 A synthetic RNA forms a #G-quadruplex without a G-rich sequence, using a complex 3D fold and GTP as a ligand. This suggests G-quadruplexes may be far more widespread in biologically important RNAs. Read more: doi.org/10.1093/nar/... #NARBreaktrhough #RNA #StructuralBiology

Now available online: the new 2.0 version of gutSMASH, with capabilities to detect 12 new types of catabolic gene clusters relevant to gut microbiome ecology, as well as predictions of their regulation through transcription factor binding site detection. www.sciencedirect.com/science/arti...

New @fwf-at.bsky.social CoE Microplanet study introduces GlobDB globdb.org, a comprehensive database integrating 14 genomic catalogues providing consistent taxonomy for microbial species. academic.oup.com/bioinformati...

Another fruitful collaboration with the Otzen group 🦠🧫🧬 We looked for curli and Fap operons across the bacterial tree of life (GTDB v226), and found that while Fap operon synteny and FapC repeat numbers are remarkably conserved, the opposite is true for curli operons and csgA!

People working with #protists and #fungi might be interested to hear that we in this study sequenced 13.4 mio. eukaryotic rRNA operons from 450 representative samples. #ProtistsOnSky #Metabarcoding

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...

#Resource HRGM2 - a catalogue of 155,211 high-quality metagenome-assembled genomes spanning 41 countries that allows improved genome-scale metabolic modelling and functional characterization of human gut microbes. #MicroSky #MicrobiomeSky 🦠💻 www.nature.com/articles/s41...

Via the REThiNk project we are organising a conference on Environmental biofilms and flocs: matrix composition, properties and applications" at the beautiful waterfront in Aalborg, Denmark in April 2026 🦠🧫🧬 Abstract submission is open, check out the link below! www.eps26.bio.aau.dk

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 🖥️🧬🦠

Let me use this as an opportunity to talk about Jordi et al's very cool paper, now out in PNAS 🧪: pmc.ncbi.nlm.nih.gov/articles/PMC... You can read our news and views here: www.pnas.org/doi/10.1073/...

“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

Opinion: Chaos is coming for scholarly publishing. Buckling of commercial models alongside maturing of community-led efforts promises major shifts, says Caroline Edwards (@theblochian.bsky.social). www.researchprofessionalnews.com/rr-news-uk-v...

gut fauna

DMS 2025 is a wrap! 🧫 I had a lot of great discussions with people about biofilms and EPS 🦠 Thomas Bjarnsholt's keynote about rediscovering the drivers of chronic infections was a highlight 🧬 A lot of interest in epsSMASH, so now I am even more motivated to get our preprint out ASAP! 🖥

1/ Working with big data in R? Your wrangling just got a massive upgrade. duckplyr is now in the tidyverse—and it’s fast. Really fast. 🧵

note, gliding is not comparable to sliding the here described spreading is very similar to sliding (=spreading by growth and facilitating compounds, like polysaccharides), which was known for Salmonella - the authors are not fully correct stating that sliding always depends on surfactant

Cellulose biosynthesis and function in Streptomyces @cp-trendsmicrobiol.bsky.social by Chennan Yang, @xiaobozhong.bsky.social and Dennis Claessen www.cell.com/trends/micro...

Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...

Ultra-deep long-read metagenomics captures diverse taxonomic and biosynthetic potential of soil microbes. #Long-read #Sequencing #Metagenomics #SoilMicrobiome #Genomics #Bioinformatics @biorxivpreprint.bsky.social 🧪🧬 🖥️ www.biorxiv.org/content/10.1...

Diverse biofilm-forming Sphingomonadaceae represent twelve novel species isolated from glaciers on the Tibetan Plateau. Published Open Access and fee-free in IJSEM using a Publish and Read agreement: doi.org/10.1099/ijse... #IJSEM #PublishAndRead

PhD opportunity in my lab: exploring how commensals and pathogens build biofilm communities on endotracheal (ventilator) tubes. Microbial ecology, medical microbiology and fancy imaging! Co-supervised with the fabulous Saskia Bakker and Jeremy Webb warwick.ac.uk/fac/cross_fa... #MicroSky