Nazir & @bramvandijk.bsky.social demonstrate how phage lifecycle dynamics and spatial heterogeneity drive mobile genetic element–gene associations, providing new insights into the evolution of phage-encoded virulence. 🔗 doi.org/10.1093/gbe/evag181 #societyjournal #virus

Viral Lifecycle Dynamics and Spatial Structure Explain Why Accessory Genes Are Associated With Temperate Phages

Abstract. Genes encoding for virulence factors are frequently found on prophages, yet the evolutionary forces driving this association remain unclear. The

doi.org

It’s not the backlash I worry about, I think a lot of people are generally done sharing opinions on the internet. After two decades it’s perhaps time to realise: it’s not doing anything. Just my opinion, ironically ;)

Maxim Greenberg@maxvcg.bsky.social · 2d ago

I have a pet theory about bluesky: there's actually a silent majority of people with concern, but ultimately a nuanced opinion on AI. But this crowd is generally too hesitant to express any excitement or wonder bc there will be a hard-and-fast backlash from the vocal anti-AI contingent. Kinda sucks

Why do conferences always specify that it's a "social" diner. As apposed to what, exactly?

Epic Food Fight Chaos

ALT: Epic Food Fight Chaos

static.klipy.com

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

Cool! pubmed.ncbi.nlm.nih.gov/42244712/

Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono? - PubMed

Analysis of our model shows that the key determinant of the evolution and spread of defense systems in MGEs is the strength of cross-MGE interference. Weakly interfering MGEs would serve as 'MGE banks...

pubmed.ncbi.nlm.nih.gov

portlandpress.com/essaysbioche...

Very excited with the online publication of our modeling work on the evolution of sexual reproduction during obligate endosymbiosis: doi.org/10.1098/rstb.... The first publication of Alkmini Zania 🎉; together with Paulien Hogeweg.

Phd Position alert 🚨 Join our project ASTRAfun (Adaptation and Starship Traffic in Root-Associated fungi), in which we will use computational models to unveil the hidden dynamics of fungal evolution. It’s not going to be just regular fun. It’s going to ASTRAfun. 🤓 www.uu.nl/en/organisat...

PhD Position in Computational Modelling of Fungal Evolution

How do giant mobile elements called ‘Starships’ reshape fungal plant pathogens? Help us computationally model their spread and impact in nature and agriculture!

uu.nl

ecoevorxiv.org/repository/v...

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...

Microbes grow in spatially structured communities. Bäcker et al. comprehensively synthesize evidence that spatial organization drives microbial ecological and evolutionary processes across scales. #FEMSMicrobiolRev buff.ly/wceLoPr @bramvandijk.bsky.social

Computational modelling at it’s finest, with videos 💜

Enrico Sandro Colizzi@escolizzi.bsky.social · 5mo ago

Curious about the origin of development during the transition to multicellularity? A very belated preprint alert: bit.ly/4rr2mHU Reproduction emerges from ecological interactions at the onset of multicellularity. A short 🧵 with lots of videos...

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨 Let me hit you with some highlights on why spatial structure matters. (and why you should care!) Sharing is appreciated 🙏 🧵👇 doi.org/10.1093/fems...

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor www.nature.com/articles/s41... #jcampubs

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor - Nature

Sequencing of marine sediments finds 136 newly identified Heimdallarchaeia and several novel lineages, and indicates that Heimdallarchaeia evolved distinct metabolic capabilities from other Asgar...

nature.com

Phage–host interactions are a key driver of microbial ecology, but observing them in nature is hard! With metaHi-C, we detect freshwater phage–host pairs and link their infection dynamics to evolution. Together with @nadal-molero.bsky.social & Ana Martin-Cuadrado www.biorxiv.org/content/10.6...

Last year, we proposed a model of plasmid evolution via fusion and fragmentation (via mge mediated recombination) generating mosaics, by studying historical isolates. Excited to see a MASSIVE paper from @jrpenades.bsky.social , @epcrocha.bsky.social expanding on this www.biorxiv.org/content/10.6...

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

Genomic and physiological signatures of adaptation in pathogenic fungi - Nature Communications

Emerging fungal pathogens have detrimental impacts on crops, animals, and humans, however little is known about their transition to a pathogenic lifestyle. This study demonstrates that the transition ...

nature.com

Please check out our review on the impact of spatial structure in microbial ecosystems! In it, we discuss how spatial patterns impact microbial ecology and evolution, eventually impacting everything we see around us! See @marcelbaecker.bsky.social's amazing summary below :) 🦠 𝚂𝙿𝙰𝙲𝙴 𝙼𝙰𝚃𝚃𝙴𝚁𝚂 ! 🦠

Marcel Bäcker@marcelbaecker.bsky.social · 6mo ago

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others academic.oup.com/femsre/artic... 🧵👇

Everyone knows that space and spatial structure is super important in shaping the Microverse 🌎🌍🌏 Check out this amazing review where @marcelbaecker.bsky.social and @bramvandijk.bsky.social et al bring together a huge body of knowledge @microverse.bsky.social @binfutrecht.bsky.social

Marcel Bäcker@marcelbaecker.bsky.social · 6mo ago

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others academic.oup.com/femsre/artic... 🧵👇

...not in shaking flasks, not in microtiter plates either 😉

Most microbes don't live in shaking flasks; spatial structure shapes how microbes interact and evolve at every scale, as we discuss in our recent review @jeroenmeijer.bsky.social @simonvanvliet.bsky.social @bedutilh.bsky.social @bramvandijk.bsky.social and others academic.oup.com/femsre/artic... 🧵👇

Spatial structure: shaping the ecology and evolution of microbial communities

Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up

academic.oup.com

@bramvandijk.bsky.social (and many other)'s new paper covered insights in microbial ecology, evolution and theoretical biology.

Simon van Vliet@simonvanvliet.bsky.social · 6mo ago

Wrapping up a productive week: very glad to have contributed to this review on how spatial structure shapes microbial ecology and evolution, led by @marcelbaecker.bsky.social, @bedutilh.bsky.social, @bramvandijk.bsky.social and many others. doi.org/10.1093/fems...

Wrapping up a productive week: very glad to have contributed to this review on how spatial structure shapes microbial ecology and evolution, led by @marcelbaecker.bsky.social, @bedutilh.bsky.social, @bramvandijk.bsky.social and many others. doi.org/10.1093/fems...

Spatial structure: shaping the ecology and evolution of microbial communities

Spatial structure naturally emerges in microbial communities, shaping growth, interactions, and evolution, and revealing how microscale processes scale up

doi.org

Spatial structure: Shaping the ecology and evolution of microbial communities @femsjournals.bsky.social Microbiology Review by @marcelbaecker.bsky.social et al from @bedutilh.bsky.social @bramvandijk.bsky.social academic.oup.com/femsre/advan...

Spatial structure: Shaping the ecology and evolution of microbial communities

Abstract. Most microbes grow in spatially structured communities, and this profoundly shapes their ecology and evolution. At the microscale, short interact

academic.oup.com

This is fine. www.nature.com/articles/s41...

Training large language models on narrow tasks can lead to broad misalignment - Nature

Finetuning a large language model on a narrow task of writing insecure code causes a broad range of concerning behaviours unrelated to coding.

nature.com

"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT

The changing roles of Escherichia coli

Nature Microbiology - Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

rdcu.be

Less than two 2 weeks to apply for this PhD position in my group. Please do not miss the opportunity to apply if the topic is of interest to you 👇

Christian Kost@kostchristian.bsky.social · 8mo ago

I am very excited to announce that a fully funded PhD position is available in my group. Topic: Synergistic coevolution in mono-specific and multi-species microbial consortia Please RT or forward this information to interested candidates. Deadline: 11.01.26 More info: shorturl.at/f1TuF

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky journals.plos.org/plosbiology/...

Bacterial immune systems as causes and consequences of microbiome structure

Bacterial immune systems have evolved in response to diverse molecular "parasites", yet their ecological roles remain poorly understood. This Essay explores how interactions between mobile genetic ele...

journals.plos.org

Great work by @prczhaoyansong.bsky.social, once again elucidating how much flow of information there is in complex microbial ecosystems.

Paul Rainey@paulbrainey.bsky.social · 9mo ago

@prczhaoyansong.bsky.social’s deep dive into the dark matter of compost communities is now out 🎉 Genomic islands hijack jumbo phages—whose capsids enable transfer of large tracts of DNA—shedding new light on the scale & scope of phage-mediated gene flow 😎 www.pnas.org/doi/10.1073/...

Getting old means going to your own Google Scholar and seeing "if you wrote a paper about something"