Codon degeneracy contributes to divergent fitness effects of rare tRNAs with A-starting anticodons www.biorxiv.org/content/10.6... => why are tRNAs with adenine at the wobble position (tRNA_ANN) are almost universally absent in nature ? mistranslation-related fitness costs... 🦠

Amazing work! "In E coli, we achieved 142 kb insertions at >90% efficiency, megabase-scale inversions (2.3 Mb), and pathway-scale 50 kb excisions. With a single ortholog and bridge RNA (bRNA), we edited bacterial isolates spanning five phyla and diverse members of two human gut communities."

Genome editing of phylogenetically distinct bacteria using cross-species retron-mediated recombineering www.nature.com/articles/s41... #jcampubs

Planetary microbiome structure and generalist-driven gene flow across disparate habitats: Cell www.cell.com/cell/fulltex...

Studying DNA modification in microbes shouldn't be limited by methodology. 🧬 We’re excited to introduce MODIFI, our new scalable method for detecting DNA modifications in PacBio metagenomic data and estimating ECE-host linkage. Check out the preprint: www.biorxiv.org/content/10.6...

A paper published in Nature presents Evo 2: an artificial intelligence-based biological foundation model trained on 9 trillion DNA base pairs spanning all domains of life that predicts functional properties from genomic sequences and provides a rich generative model for researchers in biology. 🧪

Very happy to see this work from Fabian Rehm, Jason Chin, and team on the development of a high error-rate orthogonal DNA replication system in E. coli, thus supporting continuous hypermutation and evolution of target genes in vivo. www.nature.com/articles/s41...

📣new preprint from the phagefoundry.org team 🎉 Jessica Trinh and Catherine Mageeney (Sandia National Laboratories)!! Systematic analysis of prophages from ~1000 Acinetobacter baumannii isolates, induction & screening. We found this 😎 looking phage with bunch of 💍💍

New paper from my group in @science.org : "A small polymerase ribozyme that can synthesise itself and its complementary strand" www.science.org/doi/10.1126/... Outstanding work by @edogia.bsky.social

Just published: "Planetary microbiome structure and generalist-driven gene flow across disparate habitats" by @podlesny.bsky.social @chanyeong-kim.bsky.social and @jonas-bio.bsky.social www.cell.com/cell/fulltex... See the quoted post below for a thread on the preprint!

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)

Excited to share our discovery of archaeal circular, jumbo extrachromosomal elements (up to ~535 kb genomes). One related, 409-kb genome is integrated in CH4-eating Methanoperedens, representing the largest integrative element in Archaea so far! Curious about what they are doing? See the paper

A new extreme of meiotic evolution: ✔️ 𝗻𝗼 crossovers ✔️ 𝗻𝗼 gene conversion ✔️ 𝗻𝗼𝗿𝗺𝗮𝗹 meiosis & fertility Sex mimics clonality without becoming asexual, in the holocentric multicellular eukaryote 𝘙𝘩𝘺𝘯𝘤𝘩𝘰𝘴𝘱𝘰𝘳𝘢 𝘵𝘦𝘯𝘶𝘪𝘴. more about it: www.biorxiv.org/content/10.6...

A related study from Nandita’s group on gene-specific sweeps - a great idea to compare non-synonymous linkage disequilibrium (LD) vs synonymous LD! Gut microbiome show pervasive selective sweeps in carbohydrate metabolism - diet adaptation! #microsky #microbiomesky 🧪🦠 www.nature.com/articles/s41...

#microsky #synbiosky www.science.org/doi/10.1126/...

Born #OnThisDay in 1922, Esther Lederberg was the first to isolate the lambda phage in 1951. She characterised the lysogenic phase, whereby the phage are able to integrate into the bacterial genome, staying dormant. This discovery made them a model tool of study, leading to many more breakthroughs.

Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch Teaser: Increased proline in ΔputP #microsky #MEvoSky

Out now in Nature Communications: Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses www.nature.com/articles/s41... @luisvalentin.bsky.social @lingdong-shi.bsky.social @martianmicrobe.bsky.social @mschoelmerich.bsky.social

#microsky #phagesky Transposon mutagenesis of jumbo #phage using an anti-CRISPR factor as selectable marker www.biorxiv.org/content/10.1...

New paper out: An archaeal genetic code with all TAG codons as pyrrolysine: www.science.org/doi/10.1126/...

We are thrilled to announce our latest publication in the Microbiome journal in collaboration with @thehesslab.bsky.social Supplementation with red seaweed in cows reduces methane and induces previously uncharacterized hydrogenotropic bacteria. microbiomejournal.biomedcentral.com/articles/10....

Very happy to share our recent work @cultivarium.bsky.social on genetic tools for Ideonella sakaiensis, a (Betaproteo-)bacterium that degrades PET plastic. We identified a plasmid vector for the strain and generated a large RB-TnSeq library, screening for genes impacting plastic degradation.

We selected the laziest mouse at each round to inoculate the next batch of germfree mice: over rounds of selection and passaging, behavior shifted without changes to the mouse genome: rdcu.be/eM3rO 🦠🧫

Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫 We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠 Huge thanks to amazing co-authors and collaborators! @plos.org #rnasky #microsky #tRNAmodifications

How do spontaneous mutations arise? In this latest #GENETICS review, Susan Lovett and @thalia.bsky.social provide a detailed overview of bacterial genetics experiments instrumental in understanding how genomes change. buff.ly/CXJnTqn

VACANCY - Independent research fellowships leading to tenured positions We’re inviting applications from outstanding researchers who either hold, or wish to apply for, Independent Research Fellowships. APPLICATION DEADLINE: 10 November 2025 Click here to apply: jic.link/Fellows

Now online at @nature.com we show how the Panoptes defense system protects against viruses that attempt immune evasion - and expands our understanding of the role of oligonucleotides in immunity. Check out this work co-led with @benadler.bsky.social here: www.nature.com/articles/s41...

Most plasmids described in E. coli are small compared to the megaplasmids we identified here! Check out the preprint if you want to learn about these mysterious large elements and their potential functions 🧬. I’m very grateful to have had the opportunity to work on this in @banfieldlab.bsky.social

📢 New preprint on work by my first PhD student William Pallier. Recovery of microbial ecophysiology and carbon accrual functions in peatlands under restoration. We demonstrate that microbial ecophysiology predictably changes with peatland ecosystem health. www.biorxiv.org/content/10.1...

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range. @rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social www.nature.com/articles/s41...

The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word! jobs.colostate.edu/postings/165...

GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio www.nature.com/articles/s41...

Hexokinase 2 (HK2) is known for its metabolic role in #glycolysis. This study shows that it also functions as an #RNAbindingProtein that regulates mRNA translation, particularly of SOX10, promoting #melanoma cell proliferation independently of glycolysis @plosbiology.org 🧪 plos.io/3ViI1qL

Naiavirus: an enveloped giant virus with a pleomorphic, flexible tail nature.com/articles/s41467-025-63463-6

Nature research paper: Programmable antisense oligomers for phage functional genomics go.nature.com/46b1XAQ

Quantifying phage infectivity from characteristics of bacterial population dynamics www.pnas.org/doi/abs/10.1... #jcampubs

Our paper on model cyanobacterial communities by @andrejakust.bsky.social is finally typeset and looks beautiful, check it out: academic.oup.com/ismej/articl...

I was shocked when I first saw these results from standard climate models used in IPCC reports: for high emissions, the Atlantic overturning circulation #AMOC shuts down in all 9 models that ran past 2100, and is well on the way to shutdown by 2100. Our paper on that is out today.🧵

Widespread purine bias in bacterial genes driven by runaway transcription www.biorxiv.org/content/10.1... #jcampubs

New evidence of AI’s impact on the job market — Stanford economists found that early career employment has weakened in occupations vulnerable to AI automation (eg: software engineers and customer service reps)

Stoked to finally have a preprint out for Phold, our tool that uses protein structural information to enhance phage genome annotation #phagesky 1/n www.biorxiv.org/content/10.1...

Putting the Global South on the Microbiome research map - Really proud of Chilean PhD student @bvalderrama.bsky.social who championed this new important paper just out in ‪@natcomms.nature.com‬ "If microbiome science is to benefit everyone, it must include everyone." www.nature.com/articles/s41...

This preprint from Helen Sakharova is one of the coolest things to come out of my lab: “Protein language models reveal evolutionary constraints on synonymous codon choice.” Codon choice is a big puzzle in how information is encoded in genomes, and we have a new angle. www.biorxiv.org/content/10.1...

Outcome of soil microbiome transplants is controlled more by selective pressures of recipient soil environment (habitat filtering) than original composition of transplanted community, emphasising habitat’s characteristics, not microbiota origin, determine transplant success👇  doi.org/10.1093/isme...

‼️Diamond Lab is considering potential a new postdoctoral researcher. If you have strong interests in microbiomes, metagenomics, machine learning, or rumen biology drop us a line and shoot us a CV!

Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing "Here, we engineer phage λ with CRISPR-associated transposases to enable flexible bacterial genome manipulation, including in a mixed microbial community context." www.pnas.org/doi/10.1073/...

We (with Clement Coclet, not on Bsky) had the chance to work on a broad "state of viromics" review. We tried to use this to give an overview of how the field changed over the last ~ 15 years, and also what we think are some of the major remaining challenges. Full-text access at -> rdcu.be/excHt

New review article with @mmdesai.bsky.social is out today! Grateful for the opportunity to contribute something we hope will serve the community well

The Xue lab at UC Irvine is looking for a staff scientist to support our work investigating how microbes interact and evolve in the gut microbiome! Open to a wide range of previous experience levels, see ad for more. recruit.ap.uci.edu/JPF09601