Our ms on re-sampling 4 years apart vibrio phage in natural environments is now out with some improvements. First, clearer evidence of cryptic population dynamics between phage and vibrio, presumably because of genetic diversity. www.nature.com/articles/s41...

Local agricultural transition, crisis and migration in the Southern Andes - Nature In the Uspallata Valley, agriculture was adopted by local populations, as evidenced by genetic continuity from earlier hunter-gatherers to farmers; maize-dependent groups from the same regional p...

How did farming reach the Southern Andes? Through migration or cultural transmission? Our new paper in @nature.com combines ancient DNA, isotopes, archaeology & paleoclimate to reconstruct 2,000+ years of history in Uspallata, Mendoza.
www.nature.com/articles/s41...
A Thread🧵 (1/25+)

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

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

Here, we find that many Genomic islands have origins of transfer (oriT) mobilisable by conjugation, incl. known Pathogenicity & defense islands. iOriT use only an oriT for transfer by hitching on conjugative elements: they make abundant, diverse, ancient families of mobile genetic elements. See🧵

🧬🛡️How are new immune mechanisms created?

We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!

doi.org/10.1073/pnas...

The multifaceted roles of NAD+ in bacterial immunity In this review, Vaysset and Bernheim examine how nicotinamide adenine dinucleotide (NAD+) is a key player in diverse and widespread bacterial antiphage defense systems and phage counterdefense. The au...

Many antiphage systems use NAD+, in many ways.
@hugovaysset.bsky.social reviewed them all!

Read to know more about all their molecular mechanisms, how phages counteract them, their distribution in bacteria and their conservation in eukaryotic immunity!
www.cell.com/molecular-ce...

We're so excited to share our newest ancient DNA findings on hunter-gatherers and pastoralists in Kazakhstan!

www.science.org/doi/10.1126/...

Two intensive sampling periods of oyster-associated vibrio and their phage, 4 years apart, and many surprises. Despite being washed by the Atlantic, wide tides, and vibrio (almost?) disappearing most of the year, we can find the exact same virulent phages 4 years later (down to 0 SNP)! preprint👇

Ecological constraints foster both extreme viral-host lineage stability and mobile element diversity in a marine community Phages are typically viewed as very rapidly evolving biological entities. Little is known, however, about whether and how phages can establish long-term genetic stability. We addressed this eco-evolut...

Phages evolve fast, or do they?
In oysters, some stay identical for years.
With >1,200 phages & 600 Vibrio genomes, we reveal long-term stability and new mobile elements.
Proud of this collaborative work across our teams (Roscoff-UdeM and @epcrocha.bsky.social www.biorxiv.org/cgi/content/...

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵

Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open.

doi.org/10.1101/2024...

SPAAM Summer School (2025): Introduction to Ancient Metagenomics Share your videos with friends, family, and the world

Interested in learning more about how researchers analyze ancient DNA? Here you can find the free lectures from the SPAAM Summer School 2025 - Introduction to Ancient Metagenomics: tinyurl.com/3u9mhmd2
Slides: tinyurl.com/mkfrvru4
Feel free to ask questions in the comments!
#ancientDNA #SPAAM

I am still wrapping my head around the amazing week that I had first at our @spaam-community.bsky.social conference #SPAAM7 followed by 3 days of @isba11.bsky.social in Torino.
A conference that ended with a prestigious award. I am very grateful and honoured @isbarchaeology.bsky.social

Oh boy - we opened this year’s ISBA meetings in a Roman amphitheater!

The Warinner Group and collaborators having fun at ISBA11 in Torino, Italy!

Very happy to see this one out: doi.org/10.1093/molbev/msaf192
Here, we assessed the contribution of natural transformation to the acquisition of novel genes. See preprint thread. @molbioevol.bsky.social #microsky #evobio

🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

www.science.org/doi/10.1126/...

graphical abstract of the article the extended mobility of plasmids

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

NSF halts grant awards while staff do second review Action comes after DOGE team arrives at science agency

I learned today that the NSF SBE conference I’m co-organizing in DC in eleven days has been cancelled. This seems to be related to he return of DOGE at the NSF: www.science.org/content/arti...

Phage satellites are now known to be very diverse, numerous and ancient. They pose many evolutionary, ecological and mechanistic questions. Lots of fun in perspective!
Great pleasure to write this review to show it, with @jrpenades.bsky.social @dbikard.bsky.social Kim Seed & John Chen.

taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level | PHAGE Background: Bacteriophages are classified into genera and species based on genomic similarity, a process regulated by the International Committee on the Taxonomy of Viruses. With the rapid increase in...

🚀 Excited to share our new paper: taxMyPhage: Automated Taxonomy of dsDNA Phage Genomes at the Genus and Species Level 🦠🔬!

Big thanks to all collaborators, especially @milja001.bsky.social & Thomas Sicheritz-Pontén! 🙌

📄 www.liebertpub.com/doi/10.1089/...

New version of DefenseFinder available defensefinder.mdmlab.fr (& cli)

Now encompassing 263 systems (+111 this year..!).

Thanks @ftesson.bsky.social, DefenseFinder grandmaster. Full list of systems here: defense-finder-models/List_system_article.md at master · mdmparis/defense-finder-models

Check out our new research in NPJ Biofilms and Microbiomes on the surprising patterns of oral streptococci variation in humans and the clues they encode for understanding human evolution and the recent impacts of oral hygiene. A big congratulations to Irina Velsko! www.nature.com/articles/s41...

Exploring the potential of dental calculus to shed light on past human migrations in Oceania - Nature Communications Preservation of oral microbiome ancient DNA from Oceania is much better than human ancient DNA. The authors leverage this to demonstrate that oral microbial community composition in Oceania is not onl...

And another big study from our lab out this month on exploring the potential of dental calculus to shed light on past human migrations! A huge thank you to all of our collaborators throughout Oceania and Island Southeast Asia who made this research possible! www.nature.com/articles/s41...