New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws, making microbial communities far more predictable than one might expect.

New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect

Canonically minimal RNA-guided insertion sequences expand into large elements that disseminate antimicrobial resistance https://www.biorxiv.org/content/10.64898/2026.08.14.744561v1

La evolución bacteriana no siempre sigue el camino más ventajoso, sino el más fácil.  Más info: https://f.mtr.cool/tsurwbxhks Artículo en @natcomms.nature.com  https://f.mtr.cool/tyxydaxyna

📢 We have an open PhD position to study the evolution of antibiotic resistance plasmids! Ad and Application (English below): jobs.uni-kiel.de/jobposting/8... Candidates who read the recommended papers (see ad) will be well positioned to prepare a strong application. Deadline: 6. Septermber 2026.

Schulenburg Lab Kiel@schulenburglab.bsky.social · 5mo ago

Funding for new Leibniz ScienceCampus on AMR evolution at FZB Borstel and Kiel, with several open PhD positions! Incl @daganlab.bsky.social @bramkamplab.bsky.social @fzborstel.bsky.social @uni-kiel.de www.uni-kiel.de/de/detailans...

The latent simplicity of microbial ecological interactions https://www.biorxiv.org/content/10.64898/2026.07.30.741683v1

🚨 New preprint with @annadewar.bsky.social 🚨 Do plasmids “ameliorate” towards their hosts? Maybe… We show that the classic plasmid-host GC correlation is confounded by population structure, and argue that plasmid mobility shapes the opportunity for host-associated compositional evolution.

Mobility shapes plasmid GC content evolution

Plasmids are frequently AT-rich relative to their bacterial hosts. Despite this tendency towards lower GC content, plasmid and host chromosome GC content are positively correlated across diverse collections of plasmid-host pairs. However, the evolutionary processes underlying this pattern remain unclear. The classic model of amelioration predicts that horizontally acquired DNA gradually converges on host nucleotide composition. However, because plasmids can repeatedly transfer between bacterial hosts, the opportunity for such host-associated evolution may depend on their transmission dynamics. Using 50,936 plasmid-host pairs from a public sequence database, we found that the apparent global correlation between plasmid and host chromosome GC content was largely driven by differences between bacterial species rather than within species. We therefore accounted for plasmid and host population structure when testing how plasmid mobility shaped host-associated compositional evolution. We compared two contrasting regimes: a population of 3,682 Enterobacterales plasmids distributed across diverse host backgrounds, and six long-term host-associated plasmids from a Rhizobium leguminosarum lineage with INSeq-determined gene essentiality data. In the Enterobacterales population, GC content variation was overwhelmingly explained by plasmid lineage rather than host phylogeny, and conjugative plasmids showed greater similarity to their host chromosomes than mobilisable or non-mobilisable plasmids. In the Rhizobium leguminosarum plasmids, synonymous-site composition was more similar to the host chromosome among genes required across multiple host life stages. Together, these results support a model in which plasmid mobility influences the opportunity for host-associated evolutionary processes to alter nucleotide composition. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 319534/Z/24/Z St. John's College, University of Oxford, UK

doi.org

Significant update to the AllTheBacteria paper, including discovering new antimicrobial peptides and testing in vitro and vivo. This has grown into a fantastic collaboration!

César de la Fuente@delafuentelab.bsky.social · 2mo ago

Biology has plenty of data—the challenge is making it usable. AllTheBacteria transforms 2.44 million public bacterial and archaeal genomes into an open, uniformly processed, searchable, AI-ready resource. www.biorxiv.org/content/10.1...

1/10 🚨Preprint! One RING to rule them all (phages)👑💍⚔️ Bacteria build giant DNA-scaffolded RNase rings (larger than the ribosome!) to shut down viral infection🧬🧵👇 biorxiv.org/content/10.6...

New Essay: 'Resistance potentiators: Evolutionary catalysts of antibiotic resistance' To understand the evolutionary drivers of #AMR we need to move beyond resistance genes to thinking about the ability of genomes to generate AMR variants. #microsky journals.plos.org/plosbiology/...

Resistance potentiators: Evolutionary catalysts of antibiotic resistance

How do bacteria evolve resistance to antibiotics? Drawing on evidence from experimental evolution, pathogen genomics, and molecular microbiology, this Essay argues that the evolution of antibiotic res...

journals.plos.org

Spain's largest research organization confronts its dark past | Science | AAAS “This was a historical debt of the institution,” Ana Crespo, president of the Royal Academy of Sciences of Spain www.science.org/content/arti...

🧬 I'm looking for a Researcher (2 years) in Molecular Biology and Antimicrobial Resistance at UiT The ❄️Arctic University of Norway (Tromsø). 🔬 If you have experience building and screening enzyme libraries and characterising the variants that come out, get in touch.

Fresh out of the lab! Our new preprint is now up on BioRxiv, exploring how the beneficial bacterium Pseudomonas putida controls its T6SS nanoweapon. It turns out the Gac/Rsm pathway acts as a strict molecular brake on the system. 👇 (1/4) Read the full preprint here: doi.org/10.64898/202...

#microsky New preprint from the lab! Widespread immune systems protect bacteria against conjugative plasmids www.biorxiv.org/content/10.6... Kudos to the extremely talented lead author Ludovic Poiré! Key contributions by @francoisrousset.bsky.social and also help from C. Lesterlin/TacC lab. 🧵⬇️

Widespread immune systems protect bacteria against conjugative plasmids

Conjugative plasmids are a class of mobile genetic elements capable of efficient transfer between bacterial cells. Although they can introduce beneficial traits such as antibiotic resistance to recipi...

biorxiv.org

How do #bacteria evolve resistance to antibiotics ? This Essay by @craigmaclean.bskyb.social &co argues that the evolution of #AntibioticResistance is catalyzed by ‘resistance potentiators’ that accelerate evolution in a trait-specific manner. 🧪 #AcademicSky @biology.ox.ac.uk plos.io/4flYKnF

Widespread immune systems protect bacteria against conjugative plasmids https://www.biorxiv.org/content/10.64898/2026.07.06.735840v1

New preprint from our lab Statistical learning of bacterial growth in combinatorially constructed environments, led by brilliant PhD student Andrea Arrabal. www.biorxiv.org/content/10.6... We systematically study nutrient-nutrient interactions in bacterial growth under carbon-limiting conditions.

Bacterial Mercury Resistance Reveals a Robust Species-Structured Human Antimicrobial Mobilome https://www.biorxiv.org/content/10.64898/2026.06.26.734528v1

New #microsky#AMR Perspective paper with @penamiller.bsky.social rdcu.be/fqBJo ANTIBIOTIC RESISTANCE (IE MIC) AND TOLERANCE ARE NOT BACTERIAL TRAITS! Please read on if you want an explanation for this provocative claim.

Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells

Nature Communications - Beyond resistance and tolerance: rethinking evolutionary responses to antibiotics from the perspective of individual bacterial cells

rdcu.be

Latest work from my lab, in which @amycrobes.bsky.social probes the evolutionary consequences of prophages potentiating death at otherwise sublethal antibiotic doses

Amy Zamora@amycrobes.bsky.social · 2mo ago

We're excited to share our work on how prophages influence the evolution of resistance against DNA-damaging antibiotics! This has been a fun project with @sianowen.bsky.social, @baym.lol, @theshreyaspai.bsky.social, @kepatitis-c.bsky.social, & @fernpizza.bsky.social biorxiv.org/content/10.6... 1/

Evolutionary rescue in a phage community! New paper from former PhD student, Sam Greenrod, with brilliant colleague @craigmaclean.bsky.social : academic.oup.com/ismej/advanc...

Rapid adaptation accelerates competitive suppression in a parasite community

Abstract. Environmental stress leads to changes in community composition by altering competitive hierarchies and pushing taxa towards extinction. Parasites

academic.oup.com

New preprint from our lab, in collaboration with the Santiago/Ruiz-Perez group at UVA. We found a plasmid-encoded DNA-binding protein that preferentially binds its own plasmid! www.biorxiv.org/content/10.6... Thread:

A plasmid-encoded H-NS protein selectively binds its own plasmid

H-NS is an abundant nucleoid-associated protein found in Enterobacterales species. Some conjugative plasmids encode H-NS homologues, which are thought to facilitate plasmid maintenance and reduce the ...

biorxiv.org

New Perspective out co-led with Lisa Pagani! We look at how microbiome ecology and evolution shape AMR across scales, from within-host communities to hospitals and environments, and how mathematical models can help us understand them. @natmicrobiol.nature.com www.nature.com/articles/s41...

Modelling the role of the microbiome in antimicrobial resistance across scales - Nature Microbiology

The microbiome plays a significant yet underexplored role in antimicrobial resistance by influencing ecological and evolutionary processes. This Perspective proposes a framework to integrate microbiom...

nature.com

Spotlight on our recent work by @emmajbanks.bsky.social @pavol.bsky.social and team!!! @johninnescentre.bsky.social Thank you very much, @fnobrega.bsky.social, for this great piece!!!

Cell Chemical Biology@cp-cellchembiol.bsky.social · 3mo ago

A defense-like route to gene transfer agent release

We studied the causes of #collateralsensitivity from a single enzyme perspective using and how stable such #tradeoffs are during #coselection. In short, resistance evolution can cause strong but migigatable trade-offs. Preproof is now available on @JMB: www.sciencedirect.com/science/arti...

Mechanistic origins and evolutionary erosion of collateral sensitivity in a β-lactamase

As antibiotic discovery stalls, exploiting collateral sensitivity, where resistance to one drug increases sensitivity to another, offers a promising r…

sciencedirect.com

Excited to share this new paper from the lab: academic.oup.com/ismej/articl...! See thread below

Eco-evolutionary responses to plasmid-dependent phage constrain the spread of multidrug-resistance plasmids

Abstract. Phage therapy offers an alternative to antibiotics for treating multidrug-resistant infections. Plasmid-dependent phages (PDPs) are promising the

academic.oup.com

Molecular pet or parasite? Exploring selection for vertical and horizontal plasmid transfer https://www.biorxiv.org/content/10.64898/2026.06.02.729688v1

Our study comparing promoter existence and emergence in random vs genomic DNA is finally published!!! TLDR: the E. coli genome has more promoters than random DNA (even in intergenic regions), and promoters emerge ~3x more readily from random DNA than genomic DNA. (1/2)

De novo promoters emerge more readily from random DNA than from genomic DNA

Promoters emerge three times more readily from random DNA than from genomic DNA.

science.org

"Function-specific epistasis shapes evolutionary trajectories towards antibiotic resistance". Huge parallel experimental evolution effort in E. coli under antimicrobial pressure by @gabypetrungaro.bsky.social at Bollenbach Lab at University of Cologne. doi.org/10.1101/2025...

A livestream of a volcano in the Philippines captured a meteor crashing to Earth today. What are the odds? Mayon Volcano, Location: Albay, Luzon, Philippines