All you want for christmas is.... transposon mutagenesis! Our new work at @cultivarium.bsky.social screening lots of transposon vectors in lots of bacteria, from @charliegilbert.bsky.social and team. Transposon and promoter modular parts available on Addgene (pooled library will be there soon too)

⭐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

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.

Nature research paper: The Microflora Danica atlas of Danish environmental microbiomes go.nature.com/4oT9ZG1

🦠 New #symbionts in #wastewater: #denitrifying #protist #endosymbionts are found in #sewage plants all over the world. One common species releases #nitrousoxide. Our now @isme-microbes.bsky.social mpi-bremen.de/en/Page6579.... doi.org/10.1093/isme... @daanspeth.bsky.social @einzeller.bsky.social

Nice new review on my favorite topic. www.cell.com/trends/ecolo...

💾 Prokka 1.15.6 is released! This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to. #bioinformatics #microbiology #genomics github.com/tseemann/pro...

DNA is the best kind of time machine - really feels like we’re in a golden age of big data studies like this. Can’t wait to read!

“Cultivation of Methanonezhaarchaeia, the third class of methanogens within the phylum Thermoproteota” by @kohtzarchaeota.bsky.social, Sylvia Nupp, and myself is out in Science Advances. 90% enriched culture of a methyl-dismutating thermoproteotal methanogen. #Microsky 🧪 tinyurl.com/bdcc3uzs

Denmark just mapped its entire environmental microbiome. More than 10,000 samples revealing hidden, dominant nitrifiers that shape fertilizer use, water quality, and climate impact. A national microbiome atlas could transform sustainable agriculture across Europe. #AMR www.nature.com/articles/s41...

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-...

Phages are full of genes of unknown function that are likely adaptive in specific conditions. New preprint: Phage TnSeq identifies essential genes rapidly and knocks all non-essentials. We would like to send a pool of phiKZ mutants to anyone wanting it! Reach out tinyurl.com/bdcfrejh

After years of struggling with how to cryopreserve one of our endosymbiotic bacteria, we found something that worked! 🦠☃️ We crowd-sourced suggestions and then @ruthwright.bsky.social tried the most common ones (like 🥛...). Want to do the same? Here is how we did it: www.biorxiv.org/content/10.6...

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!

New review on the structure and function of bacterial amyloids. My PhD student @andersohd.bsky.social did a great job with the bioinformatic analysis of both curli and Fap amyloids. advanced.onlinelibrary.wiley.com/doi/epdf/10....

seems that protists were way ahead of us with the invention of the circular economy 😊 great to hear of 'holobionts' again 👍 #SymnioSky #MicroSky #ProtistsOnSky

Respiratory endosymbionts, that allow their ciliate hosts to breathe nitrate instead of (or in addition to) oxygen are frequent members of the wastewater microbiome. 🦠 🖥️🧬 Great to see this work by @louison-nicolas.bsky.social published in ISME coummuncations! doi.org/10.1093/isme...

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

Protist–bacteria partnerships are more common in wastewater treatment plants than we thought. In this ISME communications paper, we uncovered widespread denitrifying endosymbionts inside ciliates, their global distribution, and their temporal dynamics across WWTPs.🦠 academic.oup.com/ismecommun/a...

New #MicrobiomeDigest is OUT microbiomedigest.com/2025/12/04/d... • urinary biochem ecology / @mikeneugent.bsky.social • Microflora Danica atlas / @mkddueholm.bsky.social • gut lumen -> hypothalamus / ‪@pipethero.bsky.social See you next week at #MVIF 44 (@microbiomevif.bsky.social)!

Excited to share our new @natecoevo.nature.com paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8) 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...

Forskere fra Aalborg Universitet har navngivet over 1.000 hidtil ukendte mikroorganismer, fundet i dansk jord, efter danske byer som Hadersleviella, Glyngoereum og Rungstediana. Projektet Microflora Danica kortlægger Danmarks mikrobielle diversitet.

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...

Identification of Previously Unknown DNA-Binding Proteins Using DNA Affinity/Pull-Down Methods Followed by Mass Spectrometry Jutras, Babb, Jusufovic, Krusenstjerna, Saylor, Verma, and Stevenson Current Protocols 2025, 5:e70264 doi: 10.1002/cpz1.70264 #MicroSky

I had a master student who used the same technique to identify transcription factors associated with functional amyloids in Pseudomonas several years ago. We did not have the man power to confirm our hits using knock out mutants, so we never published the results, but cool technique 😎

We are organizing a conference on environmental biofilms and EPS in Aalborg, Denmark in April 2026 🦠🧫🧬 All biofilm and EPS enthusiasts should consider to join.👩‍🔬👨‍🔬 Please share this invitation with your scientific networks and here! Abstract submission is open until December 8. www.eps26.bio.aau.dk

www.nature.com/articles/s41... #protistsonsky

Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...

rdcu.be/eRxNf here our new study on the characterization of the lipopolysaccharide holotranslocon, LptDE and the newly identified subunits LptM and LptY. Great collaboration with @fronzeslab.bsky.social @pstansfeld.bsky.social @JulienMarcoux @YvesQuentin

High-throughput cultivation and isolation of environmental anaerobes using selectively permeable hydrogel capsules. academic.oup.com/ismecommun/a...

We are hiring! If you're interested in exploring the #biogeography of #prokaryotes using #genomics and #metagenomics, are interested in biology and geographic information systems, and are passionate about #OpenScience, this is for you! New PhD and PostDoc positions in my lab at Aalborg University

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 🖥️🧬🦠

🧬🖥️SILVA in 2026: a global core biodata resource for rRNA within the DSMZ digital diversity 📑The new publication about the #SILVA database for the #NAR database issue is now online. 👉 academic.oup.com/nar/article/...

Clone-FISH paper out: Manuscript/resource alert #microsky 🦠 We present a collection of 30 E. coli (CloneFISH) cultures, each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from one of 30 lineages of archaea, including 17 yet uncultured ones.

Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes Very cool paper and method. I was looking forward to this coming out of preprint (short thread below on why) www.nature.com/articles/s41...

Version 5.1.1 of the PR2 database has been released. The major novelty is the inclusion of the recently published eKOI database (coi gene- doi.org/10.1093/data...) in the web interface. The 18S rRNA database is not changed so you can use 5.1.0 or 5.1.1 for metabarcode annotations

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-...

Nice work by @ryanziels.bsky.social lab that combines BONCAT, FACS, and genome-resolved metaproteomics using affinity capture of newly made proteins.

I’m very happy this is finally out! Here, we showcase the combination of BONCAT and SIP metaproteomics to uncover rare and active microbes driving anaerobic acetate turnover. We are excited to see what other microbial metabolisms and ecosystems this approach can help to illuminate! 🦠

OUT NOW Activity-targeted metaproteomics uncovers rare syntrophic bacteria central to anaerobic community metabolism by @ryanziels.bsky.social www.nature.com/articles/s41...

Now published: EnVhogDB, a large database of viral protein family HMM profiles to help functional annotation of new phage genomes - peercommunityjournal.org/articles/10....

Fascinating Evo mechanism: diversity-generating retroelements (DGRs)! Highly abundant and frequently horizontally transferred - diversifying ligand-binding domains in gut Bacteroides! 🧪🦠 #microsky #microbiomesky www.science.org/doi/10.1126/...

Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation www.nature.com/articles/s41...

metaPR2 version 3.0 has just been released. Here are the major changes: - Metabarcodes (ASVs) are now annotated with the latest version of the PR2 reference sequence database (5.1.0). - 8 new published datasets have been added from the Arctic and from the South West Pacific. app.metapr2.org

New preprint! Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠 Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare! An epic effort by Rosanna Wright www.biorxiv.org/content/10.1...

#microsky www.nature.com/articles/s41...

Structural basis of Pseudomonas biofilm-forming functional amyloid FapC formation -in Science Advances from Ümit Akbey with @mkddueholm.bsky.social www.science.org/doi/10.1126/...

www.nature.com/articles/s44... #microsky #phagesky #synbio

Congratulations to #YuzeLi and all co-authors with the publication of rhizoSMASH: a new tool to identify catabolic gene clusters involved in the metabolism of plant root exudates, thus driving rhizosphere colonization. 1/4 rdcu.be/eH8tr