Excited to share our new paper out today in @science.org 🎉
We show that HGT via natural competence drives diversification of chromosomal integrons in V. cholerae 🤩
Below a 🧵 on key findings incl. background on natural competence in V. cholerae 1/
#microsky #phagesky
www.science.org/doi/10.1126/...
Latest from the lab!
Between clinical S. aureus, most gene transfer mechanisms are blocked, yet lateral transduction remains highly efficient.
Restriction modification-defective strains act as gateways for horizontal gene transfer, enabling DNA flow across populations. rdcu.be/fbNQK
🔥Preprint fresh off the press🔥
Hello Bluesky!
I'm delighted to share the story I have been working on for the past 3y in @vivekmutalik.bsky.social's lab at LBNL and Adam Arkin's lab @ucberkeleyofficial.bsky.social.
It's a wild story about 255 phages & 1,000+ HT genetic screens, are you ready? 🧵
This paper started as an idea @albertomarina.bsky.social had many years ago… which of course means he was right all along 😄. Some of us just needed a few years (and a lot of experiments) to catch up.
Grateful (and slightly humbled) to be part of this. Thanks Alberto!
www.cell.com/cell/fulltex...
Congrats, Angus! That seems like a very important work.
The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements www.biorxiv.org/content/10.64898/2026.03...
So happy to see this finally published in @plosbiology.org!
This is the first chapter of @julielebris.bsky.social PhD thesis demonstrating how capsules are exchanged by plug-and-play dynamics
w/ @epcrocha.bsky.social
#microsky @klebclub.bsky.social
Link below-
Check out her 🧵 for more details!
We are pleased to share our last article rdcu.be/fabhM. It offers the most comprehensive analysis so far of Ab+non-Ab resistance genes in human gut microbiome, using an Indigenous population (low industrialization, chronic Hg exposure from gold mining) 6/6👇
Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years
www.sciencedirect.com/science/arti...
Thanks so much for having me! I had a fantastic time! The audience was very engaged and asked great questions!
Here is a photo I really like from that day
#PlasmidsAreCool
Plasmid conjugation from a heteroplasmic donor
New preprint! We show that conjugation accelerates the segregation of #plasmid alleles -> horizontal transfer is a route for allele segregation in MGE evolution. Led by Lisa Hartmann, with @mariosanter.bsky.social &Nils Hülter. Naturally, reviewed by @qedscience.bsky.social!
doi.org/10.64898/202...
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
Glad to see our latest work out in Nature Microbiology!!
Extremely grateful to everyone involved in the project.
Check it out!! 👇🏻👇🏻
New preprint on the limits of detecting higher-order interactions in microbial communities.
www.biorxiv.org/content/10.6...
We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.
Fantastic collaboration w/ @dbikard.bsky.social @audeber.bsky.social @rayanchikhi.bsky.social labs led by @jmouradesousa.bsky.social : We assessed the rates of variation of anti-phage systems in P4-like satellites and P2 helper phages. Quick conclusion: Huge variation! We focus on 4 key questions/5
How do evolutionary forces shape bacterial adaptation to the plant environment? 🌱🦠
Curious? Read our new review in @femsjournals.bsky.social Microbiology Reviews.
#PlantMicrobiome #MicrobialEvolution #HostMicrobeInteractions #Rhizosphere #Microbiome
🔗 doi.org/10.1093/fems...
➡️ 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? 🤔
🧵👇
Congrats Pedro et al!! Beautiful story!
New preprint out on bioRxiv!
www.biorxiv.org/content/10.6...
Can conjugative plasmids be used to control plasmid and pathogen spread?
Follow me down the rabbit hole that led to this story 🧵
A distinct class of conjugative megaplasmids includes potential vehicles for prophage dissemination www.biorxiv.org/content/10.64898/2026.02...
BRIG v1.0.0 Released — BLAST Ring Image Generator
This is dedicated to Joe Healey Who asked me many years ago to round up the version number to v1.
BRIG creates circular comparison images showing sequence similarity between a reference genome and multiple query sequences as concentric rings — […]
Cancer therapies exploit DNA repair defects to kill tumours. We asked whether the same logic could constrain antibiotic resistance evolution...
www.biorxiv.org/content/10.6...
🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here:
www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)
How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…
New pre-print with @wtmatlock.bsky.social!!!
www.biorxiv.org/content/10.6...
What shapes the distribution of plasmids across bacteria? Our paper shows that conjugative plasmids actually have a very narrow distribution compared to mobilizable plasmids. Conjugative systems restrict plasmid transfer!
Conjugation structures plasmid populations through host-lineage restriction www.biorxiv.org/content/10.64898/2026.02...
CRISPR-Cas is beneficial in plasmid competition, but limited by competitor toxin–antitoxin activity when horizontally transferred | PLOS Biology journals.plos.org/plosbiology/article
SFI’s Santiago Elena has been elected a fellow of the American Academy of Microbiology.
He joins 62 fellows in the 2026 class. His work explores how RNA viruses adapt to hosts and manipulate cellular resources. Since joining SFI in 2008, he has organized several working groups on virus evolution.
