Lars Barquist

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

Diagram illustrating early genome erosion during the transition from a free-living Sodalis bacterium to two host-associated endosymbionts inside the long-tailed mealybug. Circular genomes show intact genes in blue and pseudogenes in red, highlighting increased pseudogene accumulation in symbiotic forms. Caption asks: “What are the downstream molecular consequences of early genome erosion?”

Happy to share a preprint—the last chapter of my dissertation with @mcsymbiont.bsky.social and Co—on what happens when bacterial endosymbionts accumulate huge numbers of pseudogenes during early genome reduction.

www.biorxiv.org/content/10.6...

What a beautiful dream.

BackToBack #PhageSky in @nature.com

A pore-forming antiphage defence is activated by oligomeric phage proteins
-from Maxwell & Norris
www.nature.com/articles/s41...

Bacterial immune activation via supramolecular assembly with phage triggers
-from Laub & Ghanbarpour
www.nature.com/articles/s41...

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)

Still lots of time to apply for this exciting project with us. Please share and encourage interested students to get in touch.

Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...

Always good to start the year with a new preprint. We charted DNA methylation in Salmonella enterica: www.biorxiv.org/content/10.64898/2026.01.27.702048v1.

Microbial Primer: Ancientbiotics – making modern antimicrobials from historical infection remedies The modern antibiotic era began in the early twentieth century, but humans have long used materials from the natural world to attempt to treat the symptoms of infection. In this primer, we will discus...

Why should microbiologists be interested in historical infection remedies, and how can we best investigate them for antimicrobial discovery? Thoroughly enjoyed co-writing this Microbiology Primer with @tosinorababa.bsky.social www.microbiologyresearch.org/content/jour... #MicroSky #Ancientbiotics

Check out our new review in Nature Reviews Genetics on de novo emerged genes and proteins. How they emerge, are lost and persist - and how de novo emerged proteins relate to randomized proteins! @bornberglab.bsky.social www.nature.com/articles/s41...

We are looking for a junior group leader in RNA biology to join us in Würzburg at the @helmholtz-hiri.bsky.social !

A generous funding package, a great collaborative environment, and a beautiful city are all included :)

Deadline for application is Feb 15; more information below 👇

Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages Introduction. Klebsiella pneumoniae is an opportunistic pathogen that causes a wide spectrum of infections within healthcare settings and the community. Four K. pneumoniae sub-lineages, defined using ...

Our new paper on Insertion Sequences (IS) in #Klebsiella

- Lineages have vastly different IS loads and profiles
- An inverse relationship between IS load and metabolic capacity, in particular phosphorus use, consistent with early reductive evolution.

www.microbiologyresearch.org/content/jour...

📢 We are hiring 📢 1st round of recruiting for our ERC project BacImmune-Decode! @erc.europa.eu
We are looking for a postdoc for wet-lab work on regulation of phage defence systems in bacteria using high-throughput microbial genetics. Check it out: lnkd.in/es7AE968
#Hiring #Postdoc #Microbiology

prototyping co-drawing with Gemini Flash 3 at Google

in these demos "thinking" is disabled, which makes the model return tokens very quickly (all videos are realtime), and I find these rapid responses pretty good for the use-cases I'm experimenting with, like:

executing simple diagrams ...

SimUrine: a novel, fully defined artificial urinary medium for enhanced microbiological research of urinary bacteria

journals.asm.org/doi/10.1128/...

Uropathogenic Escherichia coli invade luminal prostate cells via FimH–PPAP receptor binding - Nature Microbiology Uropathogenic Escherichia coli infection of a murine prostate organoid model reveals a bacterial FimH–host prostatic acid phosphatase adhesin-receptor interaction enabling invasion and replication wit...

Our first paper is out today in @natmicrobiol.nature.com!

We introduce a prostate organoid model and show that UPEC invades prostate cells via FimH binding to the prostate-specific protein PAPP. A step toward targeted therapies against bacterial prostatitis. 🎉

#UTI #UPEC #Organoids #AMR

'Robust Aitchison PCA was not insensitive to uneven sequencing effort and did not perform as well as rarefaction. (...) Using the benchmarking framework from the original analysis, rarefaction outperformed robust Aitchison PCA, other compositional data analysis methods + other normalization methods'

3′UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages Abstract. Acid resistance is crucial for enterobacteria to withstand host acidic environments during infection, including the gastrointestinal tract and ma

3′UTR-derived small RNA couples acid resistance to metabolic reprogramming of Salmonella within macrophages url: academic.oup.com/nar/article/...

Highly, highly recommended for persons interested in Bayesian methods and for persons not interested in Bayesian methods who should be.

Just a few hours left to apply for this #PhD!!

Do you like phages, genomes & public health impact?🦠🧬🏥

Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?

🤔this could be just the project for you!!🧑‍🔬😎

Apply NOW before midnight

#PhDposition #academicsky

And we're live, Lecture A1 is online. Introduction to Bayesian workflow, generative models, estimands, estimators, estimates, error checking, beginnings of probability theory and Bayesian updating. www.youtube.com/watch?v=ztbY...

Enterococcus faecalis modulates phase variation in Clostridioides difficile | Journal of Bacteriology Clostridioides difficile is an enteric pathogen with critical implications for public health. The microbial ecosystem in which C. difficile resides shapes the behavior and fitness of C. difficile; however, the mechanisms underlying these interactions are not well defined. Here, we demonstrate that Enterococcus faecalis, an opportunistic pathogen known to co-colonize the gut with C. difficile, influences phase variation and downstream growth phenotypes in C. difficile. This phenomenon represents a new paradigm by which co-residing bacteria can modulate phase variation dynamics in C. difficile or other enteric pathogens. Understanding factors that influence C. difficile behavior may elucidate new therapeutic strategies, especially in complex polymicrobial infections.

Excited to share my publication, showing that co-residing bacteria in the gut alters population heterogeneity in C. difficile. Thank you to my co-author, Jilarie Santos-Santiago, and our collaborative team from the labs of @joeyzacks.bsky.social and @ritatamayo.bsky.social! 
doi.org/10.1128/jb.0...

Large-scale analysis of bacterial genomes reveals thousands of lytic phages - Nature Microbiology Diverse genomes of lytic phages are found in bacterial assemblies, challenging assumptions about the nature of the lytic lifestyle.

Large-scale analysis of bacterial genomes reveals thousands of lytic phages | Nature Microbiology https://www.nature.com/articles/s41564-025-02203-4

The sporulation phosphorelay protein Spo0B is membrane localized in Paenibacillus! The transmembrane domain appears to increase interaction with relay partners. Congrats to former lab undergrad @isabellalin.bsky.social and her grad mentor @cassidyprints.bsky.social

journals.asm.org/doi/10.1128/...

Available Postdoc position in my lab to advance ASO technology for biotechnology, food production, infectious diseases, environmental microbiology & more. Looking for specialists in these areas with an interest in RNA applications. Involves numerous national & international collaborations.

It's really too bad there's no antimemetics division to look into this for you.

Intramacrophage RIL-seq uncovers an RNA antagonist of the Salmonella virulence-associated small RNA PinT Abstract. Salmonella virulence chiefly relies upon two major pathogenicity islands, SPI-1 and SPI-2, which enable host cell invasion and intracellular surv

RIL-seq boosts the study of sRNAs. Here comes its first application to intracellular bacteria. Plus, 10 years after its characterization, we now present an RNA sponge of Salmonella PinT.
Congrats to @kooshapour.bsky.social & great collaboration w/ @jorg-vogel-lab.bsky.social!
doi.org/10.1093/nar/...

Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...

Our preprint on predicting drug resistance in bacteria is now out in @plosbiology.org. We show ignoring phylogenetic structure in genome collections leads to overly optimistic evaluations of machine learning methods for AMR prediction. Work from @yanyingyu.bsky.social with @nwheeler443.bsky.social.

@peterfineran.bsky.social and colleagues develop Tn-seq for phages by leveraging anti-CRISPR (Acr) as a positive
selectable marker in the presence of CRISPR-Cas counter-selection, and identify essential genes in phage from non model orgs
www.biorxiv.org/content/10.6...

Looking for a POSTDOC to work on jumbo phages (those with large genomes and fascinating cell biology), using our latest ASO technology (Gerovac M et al. 2025 Nature) to define RNA export mechanisms as well as to help to advance phage therapy. Here's the job ad.