Diversity-generating retroelements for programmable targeted hypermutagenesis - Nature Biotechnology Diversity-generating retroelements are engineered for directed evolution in E.coli.

Diversity-generating retroelements for programmable targeted hypermutagenesis - @dbikard.bsky.social @institutpasteur.bsky.social go.nature.com/3OG2nKN

Machine learning models by the Bernheim and Laub labs vastly expand the predicted space of bacterial immunity, demonstrating that we are still at the beginning of our exploration 🔎

Congrats @mdmlab.bsky.social and @pdeweirdt.bsky.social et al!

I am excited to share our latest paper, Uniform bacterial genetic diversity along the gut, now out in Nature Communications! www.nature.com/articles/s41.... (1/n)

Horizontal gene transfer is often depicted as a process distributing pre-existing functions to novel genetic backgrounds. Yet HGT can also increase the rate of functional innovation after transfer. Here's a brief review on the topic: ecoevorxiv.org/repository/v... #evosky #microsky

New preprint where @lbobay.bsky.social and I were motivated by the fact that non-synonymous substitutions are commonly analyzed in molecular evolution studies, but the similarity of the amino acids being substituted is an understudied area.
doi.org/10.64898/202...

Although it was a small part of our analyses, @gmdouglas.bsky.social and I just released a preprint where we compared some of these methods to general exchangeability matrices: www.biorxiv.org/content/10.6...

New paper showing that much of the apparent success of protein language models in predicting mutational effects is a mirage: These models mostly memorize sites. 1/
www.biorxiv.org/content/10.6...

➡️ preprint from the lab! Bacteria have loads of antiviral defences in their mobile genetic elements (MGEs). So when MGEs move between bacteria, the defences move with them, generating a fast turnover of defences in bacteria. But what about the antiviral defence turnover in the MGEs themselves? 🤔

🧵👇

If you are interested in investigating horizontal gene transfer by phages and virus-like particles using computational approaches, this postdoc position in the Callahan Lab could be for you

jobs.ncsu.edu/postings/226...

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Prevalence and Evolutionary Implications of Genome Rearrangements in Bacteria Abstract. The genetic material of bacteria and archaea is organized into various structures and setups, attesting that genome architecture is dynamic in th

@carolinamicro.bsky.social Huang & @lbobay.bsky.social investigated genomic rearrangements across 121 microbial species, showing that rearrangements occur at a variable pace across bacteria and archaea, pointing to different selective constraints.

🔗 doi.org/10.1093/gbe/evag002

#genome #evolution

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

The paradox of immune systems conservation between prokaryotes and eukaryotes - Nature Reviews Microbiology The widespread prokaryotic immune systems, in particular restriction–modification, CRISPR–Cas and defensive toxin–antitoxin systems, are absent in eukaryotes, whereas relatively rare ones, such as Arg...

Aude Bernheim @audeber.bsky.social and Eugene Koonin discuss one of most interesting questions in the field connecting bacterial and animal immunity!

www.nature.com/articles/s41...

My book is available for pre-order!
www.routledge.com/Quantitative...

Or you can request an inspection copy here:
www.routledge.com/textbooks/ev...

Postdoctoral position - Synthetic Biology / Bacterial Immunity - Research The Bikard lab at Institut Pasteur in Paris is seeking to hire postdoctoral researchers. We are investigating bacteria / bacteriophages interactions, and the genetic innovation that happens at this in...

🚨 Hiring Alert! 🚨My lab at Institut Pasteur is recruiting several Postdocs! We have exciting open projects in: 🦠 Synthetic Biology and🛡️ Bacterial Immunity. Come do great science with us in the middle of Paris! 🇫🇷🥐 research.pasteur.fr/en/job/postd...

My pleasure! Those were busy times for you indeed! Congrats on all these accomplishments.

Congrats to @carolinamicro.bsky.social for leading this study! We looked at genome rearrangements over short evolutionary timescales. Among other things, we found that genomes are highly syntenic within most species. However, several bacteria experienced sudden and massive genome rearrangements.

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

🥁 NEW

Our study on infant gut microbiome and #straintransmission is now published in @nature.com:

doi.org/10.1038/s415...

1/10

Characterizing a novel Symbiopectobacterium purcellii MEX strain at the early stages of establishing a symbiotic relationship Abstract. Insects ally with microbial symbionts for a diversity of services. The range of these interactions is wide, spanning from beneficial to pathogeni

I’m excited to share a new paper by a super talented graduate-student-now-postdoc. Grateful to work with old and new collaborators!

Characterizing a novel Symbiopectobacterium MEX strain at the early stages of establishing a symbiotic relationship url: academic.oup.com/gbe/article/...

Deadline is approaching (Feb 9) to apply for a PI position at Institut Pasteur. Come join us and contribute to an amazing scientific environment!!!

a quick reminder!

Une opportunité unique de former des étudiants talentueux à la biologie des bactéries à l'ENS Lyon et mener des recherches sur les phages, l'immunité bactérienne, le transfert génétique horizontal (HGT) et/ou les éléments génétiques mobiles au sein du département de bactériologie du CIRI.

Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change
doi.org/10.64898/202...

The distinction between virulent & temperate phages gets fuzzier if one can find so many virulent phages in the sequences of bacterial genomes coming from standard lab "pure" cultures. Check Peter's thread on our work and the N&V by Carson & Hynes: doi.org/10.1038/s415...
#phagesky #microsky

Congratulations! Amazing work!

If you are interested in this work and are looking for a postdoc position, please get in touch -- we are actively looking for someone to join our group at UCLA!

Recombination between strains fuels pervasive adaptive evolution among human gut commensal bacteria, and strongly implicate host diet and lifestyle as critical selection pressures @nature.com @nanditagarud.bsky.social
www.nature.com/articles/s41...

Looking for a postdoc in 2026? The Ewel fellowship at UF provides $70K salary and $20K research support for 2 yrs. I'm happy to sponsor a postdoc interested in microbial ecology of Florida coastal ecosystems (seagrass, coral, mangroves, springs). 🦠 Due 1/11/26

postdoc.aa.ufl.edu/current-post...

We are recruiting a Lab Manager/Research Specialist
jobs.ncsu.edu/postings/225...
Please re-post, thank you

Screenshot from GRC portal confirming microbial population biology meeting June 27, 2027 in Andover, New Hampshire.

It’s officially happening folks! The Microbial Population Biology Gordon Research Conference is back in Andover, New Hampshire starting June 27th of 2027!
See you there!!

@wcratcliff.bsky.social @ksbakes.bsky.social @surtlab.bsky.social

#microsky #mevosky