Ayush Valecha

Unlocking data in Klebsiella lysogens to predict capsular type-specificity of phage depolymerases - Nature Communications Here, the authors exploit the genetic information encoded in Klebsiella prophages to model the interplay between bacteria, prophages, and their depolymerases, using a directed acyclic graph-model and a sequence clustering-based model.

Can we exploit past phage infection events (prophages) to decipher the specificity of phage receptor-binding proteins such as depolymerases?🔎 Happy to share our recent work at @natcomms.nature.com 🔽 #microsky #phagesky

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

Is a healthy microbiome one that is rich in phages? 🦠 Excited to share our paper out in Lancet Microbe with @bkoskella.bsky.social & @dholtappels.bsky.social where we test whether virome diversity can be used a broad signature of microbiome health 📈

Schematic of P. chabaudi within-host infection dynamics and fitness optimization. Left: Flow diagram of model tracking the dynamics of red blood cells (R; RBCs), RBCs infected with asexual parasites (I), RBCs infected with sexual— but not yet mature — parasites ( ), asexually-committed merozoites (M), sexually-committed merozoites ( ), and gametocytes (G). Right: Temporal dynamics of cue perception. Cue perception occurs one day before the production of asexual/sexual merozoites, thereby introducing a delay between cue perception and the consequences of cue perception (i.e., production of more asexual infected RBCs or gametocytes). A further delay occurs in the sexual cycle since gametocytes of P. chabaudi take two days to mature. Dashed circles indicate the bursting/maturation of a particular cohort of iRBCs.

#Malaria parasites infecting a #RedBloodCell can either replicate asexually or produce a transmissible gametocyte, a plastic decision driven by environmental cues. This study uses math models to explore which cue(s) #parasites should sense to maximize fitness @plosbiology.org 🧪 plos.io/4q5a8aU

Trade-offs between phage resistance and conjugative ability shape the ecological and evolutionary response of a multidrug resistance plasmid to plasmid-dependent phage Phage therapy is a promising alternative to antibiotics to treat multidrug resistant infections. Plasmid dependent phages (PDPs) are particularly attractive as therapeutics because they can both kill ...

New pre-print www.biorxiv.org/content/10.1...
Plasmid-dependent phage (PDPs) are ubiquitous, but the selective pressures that they impose on plasmids are not well understood. Project led by Daniel Cazares in collaboration with @brockhurstlab.bsky.social!
#phagesky#microsky

Our opinion paper on embracing #disequilibrium dynamics to model #biodiversity trends is now published in the latest issue of Trends in Ecology & Evolution

🌳🌲🌴🪻🦔🦉🐜🪱

A very important work led by Étienne Lalechère ⬇️

@etiennelalechere.bsky.social
@cp-trendsecolevo.bsky.social

shorturl.at/QUWXm

YouTube video by TEDx Talks The social lives of viruses | Asher Leeks | TEDxNewEngland

I gave a talk last year at TEDxNewEngland aimed at introducing the idea of viral sociality to a general audience, including implications for evolution & virology. Video now available online below.

#socialviruses #evosky #virosky 🧪

Metabolic interplay drives population cycles in a cross-feeding microbial community - Nature Communications Here the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

Metabolic interplay drives population cycles in a cross-feeding microbial community

@natcomms.nature.com from @oventurelli2.bsky.social

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

Metabolic interplay drives population cycles in a cross-feeding microbial community - Nature Communications Here the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

Metabolic interplay drives population cycles in a cross-feeding microbial community www.nature.com/articles/s41... #jcampubs

Looking forward to this! A non-Elsevier alternative to Theoretical Population Biology / Journal of Theoretical Biology

Population Biology Modeling & Theory (PBMT) is a peer-reviewed journal reporting advances in modeling and theory within population biology. Its scope spans demography, ecology, epidemiology, evolutionary biology, population genetics, and phylogenetics. PBMT will be online soon.

mickey mouse is doing a handstand on the ground while wearing a hat and gloves . ALT: mickey mouse is doing a handstand on the ground while wearing a hat and gloves .

A very very #latepost, but super happy to kick-off my #bluesky profile by announcing the first couple of results from my PhD. Now, we have all grown up seeing our favourite cartoon float towards food, but can we mimic this behaviour in #activematter systems, which lack such a sense of smell? 1/

Bram van Dijk @bramvandijk.bsky.social (@utrechtuniversity.bsky.social): How mobile genes reshape the microbial arms race
#NIME2025

AI developed to read the “code” of bacterial viruses and design personalised phage therapies <p>A research team from the Institute of Integrative Systems Biology (I&sup2;SysBio), a joint centre of the University of Valencia and the CSIC, has developed an innovative artificial intelligence sys...

🧪💻 A research team from the #I2SysBio (@csic.es-@uv.es) has developed AI to read the “code” of bacterial viruses and design personalised phage treatments.

The study has been published in Nature Communications.

www.i2sysbio.es/communicatio...

New Article: "Ginger genome reveals the SMPED1 gene causing sex-phase synchrony and outcrossing in a flowering plant" rdcu.be/eJPdX

SMPED1, located in a dichogamy-determining region in Alpinia species, controls the timing of sex-organ synchrony.

Les phages à large spectre, omniprésents dans les écosystèmes Les phages, les virus des bactéries, représentent les entités génétiques les plus abondantes de notre environnement.

#ResultatScientifique 🔎| Et si les phages, ces virus des bactéries, pouvaient infecter plusieurs espèces à la fois et remodeler l’écologie microbienne ? 🦠
✍️ Martial Marbouty
📕 @natmicrobiol.nature.com | buff.ly/1R9kqjv

Does population size shape protein coevolution?
I explored this in my talk today at the MPI for Evolutionary Biology.
Our work in mammals suggests the answer is yes - genetic drift is a major determinant of compensatory mutations.

#evolution #genomics #proteinevolution @mpi-evolbio.bsky.social

Two full-time positions | Bioinformatician (m/f/d) + Applications Specialist (m/f/d) - Molecular Biology The Genome Facility at the Max Planck Institute for Evolutionary Biology in Plön is seeking to fill two positions (full time) to support and expand our core facility services.

Two new positions are available at the MPI for Evolutionary Biology to support development of our genomics facility. Both stand to become permanent. Both offer a ton of opportunity to engage in a wide range of creative science.

Pls repost 🙏

www.evolbio.mpg.de/3838377/job_...

Host constraints on viral recombination and emergence https://www.biorxiv.org/content/10.1101/2025.10.01.679867v1

How do mate-finding Allee effects affect evolutionary rescue? https://www.biorxiv.org/content/10.1101/2025.09.27.678992v1

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

www.biorxiv.org/content/10.1...

Thinking about a postdoc in microbiome science?
Our lab at the MPI for Biology (Tübingen) builds on the culture I established at Cornell: collaborative, creative, and internationally diverse. Postdocs lead their own projects with secure funding. Join us!
#PostdocJobs #HostMicrobe #AcademicJobs

absolutely wild, from the Small Molecules Considered (SMC) branch:
"...this work provides another piece in a complex biological puzzle aiming to understand the persistent and pervasive nature of 𝘞𝘰𝘭𝘣𝘢𝘤𝘩𝘪𝘢 endosymbionts." (doi.org/10.1016/j.ce...)
#MicroSky #SymbioSky

Filamentous cheater phages drive bacterial and phage populations to lower fitness Kubota et al. show that bacteria can use their filamentous phage to outcompete other bacteria, but increased phage production enables the evolution of cheater miniphages with truncated genomes. Miniph...

Filamentous cheater phages drive bacterial and phage populations to lower fitness

Pseudomonas aeruginosa VS Pf phage

@currentbiology.bsky.social by @nanamikubota.bsky.social, @shellyscrib.bsky.social and @vscooper.micropopbio.org

www.cell.com/current-biol...

#PhageSky

Luck can explain the positive link between fecundity and longevity: the Matthew effect in social insects and beyond Abstract. The universality of the trade-off between fecundity and longevity in life-history theory is sometimes contested. Social insects present the argua

Why is it so hard to detect fecundity-longevity #trade-offs in social insects? And what does this have to do with the Gospel of #Matthew??
Find out in our new paper with @kokkonut.bsky.social and Susanne Foitzik @mainzuniversity.bsky.social!

doi.org/10.1093/jeb/...

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.

Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...

We are thrilled to announce that our NEW Large Language Model will be released on 11.18.25.

A teal flyer for a PhD opportunity to investigate how warming may change antimicrobial resistance. The project will use experiments on Klebsiella bacteria to answer questions about how temperature affects their response to antibiotics, plasmid transfer, and fitness costs. The research involves microbiology lab work, bioinformatics, and mathematical modeling. The flyer includes contact details for Dr. Daniel Padfield and the logos of the sponsoring institutions.

I have an MRC-funded PhD project available (www.exeter.ac.uk/study/fundin...) on how warming will change the problem of AMR. Join a small and friendly group (padpadpadpad.netlify.app/about) in (sometimes) sunny Cornwall. 🧪🦠 #microsky

Please share the ad below with anyone who may be interested.

So happy to see my first first-author paper published! 🎈
A short thread on how Ectocarpus and its TE secrets have kept me busy lately:

rdcu.be/eITQH

Come and work with me and @ariannebabina.bsky.social on #Streptomyces evolution and antibiotic production

Origins of a tangled bank: Adaptation and evolution in antibiotic-producing Streptomyces

www.gla.ac.uk/postgraduate...

please repost

A commentary on Godfray 1990: The consequences of constrained sex allocation in diploids and haplodiploids under local mate competition

Chokechaipaisarn and @andygardner.bsky.social

doi.org/10.1093/jeb/...