Single-cell genomics reveals opportunistic Enterobacterales carrying putative cationic antimicrobial peptide resistance genes in red crown rot-affected soybean rhizoplanes www.biorxiv.org/content/10.64898/2026.04...

the sensitivity of "tagIMseq" will be broadly useful for CRISPR-associated transposon work. Ruling out off-target insertions in resuspended colonies with minimal effort and cost investment is critical because targeting isn't always perfect.

A quick thread summarizing our new bioRxiv preprint on using CASTs for DNA barcoding to tell "look-alike" bacteria apart (Sphingomonas edition)!! Enjoy the read! ✨

When organisms look similar, you can use a tag to tell them apart. We wanted to tag our collection of diverse Sphingomonas bacteria with DNA barcodes to distinguish them. We planned to use Tn7, until we saw new reports about CRISPR-associated transposons (CASTs).

Unveiling hidden variables in stressed bacteria Noise in bacterial stress responses is often dismissed as mere randomness. While true stochasticity exists, much variation reflects hidden variables—cell state, history, and microenvironment—that are only now becoming measurable. Choudhary and Vincent review emerging tools that disentangle chance from determinism, moving microbiology toward more mechanistic and predictive frameworks.

Unveiling hidden variables in stressed bacteria

Programmed strain tagging and gene disruption throughout a diverse bacterial genus www.biorxiv.org/content/10.64898/2026.02...

Sharing our lab’s first publication! Probing clinical isolates of Cryptococcus, a disease-causing fungus of the lungs and brain, we found multiple heat-mobile elements that ‘jump’ in the genome at body temperature (!) with the ability to drive adaptive changes. journals.plos.org/plosgenetics...

Integrative mobilizable elements are pervasive throughout Pseudomonadota www.biorxiv.org/content/10.64898/2026.01...

Replicon family of Vibrionaceae plasmids as a reservoir of antimicrobial and phage resistance genes in marine ecosystems Abstract. Plasmids are mobile genetic elements that drive horizontal gene transfer among bacteria, influencing microbial community composition and function

Replicon family of Vibrionaceae plasmids as a reservoir of antimicrobial and phage resistance genes in marine ecosystems | The ISME Journal | Oxford Academic academic.oup.com/ismej/article/19/1/wraf2...

🚀 Excited to share SMART-PTA (miniaturized Primary Template Amplification) a high-throughput single-cell whole-genome amplification method that preserves clonal lineage information while enabling deep genomic and transcriptomic profiling.

www.sciencedirect.com/science/arti...

How much environmental chaos to embrace in plant-microbe research, and to what end? A commentary on setting (with all choices OK as long as all options considered) w/ bergelsonlab.org, @fabriceroux7.bsky.social,
@plantevolution.bsky.social, tkarasovlab.org

Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes Abstract. Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities—shedding light on cell-to-cell va

New Review Out!
We explore how droplet microfluidics is opening new doors in microbial ecology - enabling single-cell functional insights into growth, metabolism & interactions.
🔗 doi.org/10.1093/fems...
#MicrobialEcology #DropletMicrofluidics #Microbiology

Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

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 👇

Thanks to everyone who came by my poster today for discussion! #2025ISMPMI

If you weren’t able to make it but still interested in the potential role native plasmids play within Sphingomonas-plant interactions. Can check it out now on Zenodo zenodo.org/records/1591...

A major trade-off between growth and defense in Arabidopsis thaliana can vanish in field conditions In controlled greenhouse conditions, Arabidopsis thaliana plants with a hyperactive allele of the ACD6 gene have stronger pathogen defenses but are smaller and make fewer seeds, in a classic fitness t...

This work started nearly 10 years ago and was once my main postdoctoral project at @plantevolution.bsky.social before I slowed work on it to a trickle because it became confusing. But it always remained extremely interesting.

journals.plos.org/plosbiology/...

Last week, I had a great time at the New Phytologist EiC Symposium: “Microbes as hidden or prominent players in plant life” in Tartu, Estonia!

Honored and very happy to receive the Best Poster Award! ✨
Big thanks to the organizers and all the inspiring scientists I met! 🌱 @newphyt.bsky.social