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

Dynamic visualization of extracellular matrix components in S. aureus colony biofilms reveals functional amyloids leading to the formation of cap-like structures @biofilmjournal.bsky.social from Agneta Richter-Dahlfors www.sciencedirect.com/science/arti...

Confused writing is usually a symptom of confused thinking. As we struggle to clarify writing, we clarify our thoughts. AI writing aids rob us of that struggle, leaving clean-looking text and thoughts still confused for lack of inspection. Writing is not just a product; it is a diagnostic tool.

I’m excited to share our effort to obtain one of the first estimates of the net rate, in physical time, of lateral gene transfer (LGT) – nature’s own genetic engineering - across a complex, global microbiome: doi.org/10.1093/isme...

“Writing an essay is hard because it forces you to use your brain in ways you haven't before…Your job is not to turn in completed assignments; it's to learn how to think. Turning in completed assignments can help you learn how to think, but only if you're the one who completed them.”

Really liked the explanation about human understanding, and what we miss when we use black box models. This has always been my gripe with prediction models for eg AMR - I want to know why that feature is associated with resistance!

I frequently meet ppl who tell me about medieval German, or fen art, or alchemy, muons, human language processing, or extremely specific sorts of religious scholarship. Occasionally inventors of extraordinary things. I love how all these diverse specialties can be in one place (a university canteen)

schaechter.asmblog.org/schaechter/2... #MicroSky

#ResearchBriefing Deep, long-read metagenome sequencing expands knowledge of prokaryotic phylogenetic diversity #MicroSky www.nature.com/articles/s41...

Gaza has recorded the most health-care worker deaths (over 1400 deaths), UN deaths (295) & journalist deaths (212) than in any recent conflict zone. Life expectancy at birth dropped 35 yrs in 2024. From Oct '23-May '25, there were 720 attacks on healthcare targets www.thelancet.com/journals/lan...

What is the role of extracellular polymeric substances (EPS) in carbon exchange among microbial species? @sammy-pontrelli.bsky.social &co show that #EPS, formed via #chitin degradation, drives #MicrobialDiversity by acting as a sequentially degraded #CarbonSource @plosbiology.org 🧪 plos.io/3J9kbuu

Someone on here compared AI produced material as "digital asbestos " which in a few decades' time we will have to work out how to eradicate from the fabric of research.

Was talking to a student who wasn't sure about why one would get a PhD. So I wrote up a list of reasons! www.eugenevinitsky.com/posts/reason...

knowablemagazine.org/content/arti... My favorite advice piece. I compile this and other useful advice articles on my lab website: lowepowerlab.ucdavis.edu/resources

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1... and GH repo: github.com/refresh-bio/...

Genome-resolved long-read sequencing expands known microbial diversity across terrestrial habitats www.nature.com/articles/s41... #jcampubs

New pre-print from my group - project led by PhD student Michael Hoffert. We set out on a daunting mission to generate a 'periodic table' of bacterial diversity (1/6) www.biorxiv.org/content/10.1...

well this is kinda cool 🦠✨

Awesome story, biofilms are so fascinating! 🦠🧬🧫

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/... www.biorxiv.org/content/10.1...

piqtree: A Python Package for Seamless Phylogenetic Inference with IQ-TREE www.biorxiv.org/content/10.1... #jcampubs

If you are an R user and want to use python This blog is for you www.emilyriederer.com/post/py-rgo/

Congrats to @margotbligh.bsky.social 🎉 terrific work on a complex problem in mass spectrometry - See her new GlycoAnnotateR tool for De Novo #Glycan Annotation of Mass Spectrometry Data // it works for all, #LCMS #MSI pubs.acs.org/doi/10.1021/... @mpimarinemicrobio.bsky.social

GATOR-GC is out at @narjournal.bsky.social!! Check out our new targeted genome mining tool featuring a novel similarity metric to efficiently compare and deduplicate gene clusters. We uncover biosynthetic diversity missed by other genome mining tools academic.oup.com/nar/article/...

Very excited to share the first paper out of my Postdoc @CMR: GenomeFISH: genome-based fluorescence in situ hybridisation for strain-level visualisation of microbial communities. @sjmcilroy.bsky.social @jamesvolmer.bsky.social @benjwoodcroft.bsky.social doi.org/10.1093/isme... 🧵1/7

The 3-decade-old competition that enabled the emergence and evaluate of AlphaFold has run out of NIH funding. The program will be terminated in weeks. This is terminating success. www.science.org/content/arti...

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 👇