Jake Barber
Evolutionary Biologist
Using Experimental Evolution to look at mutational biases in bacteria!
Research Gate Profile: t.co/xhw63knBCj
email: jakebarber42@gmail.com
- Reposted by Jake BarberNew paper by Saskia Wilmsen and me just came out BioEssays: A new classification framework to understand evolutionary transitions in individuality Please find the OA paper here: onlinelibrary.wiley.com/doi/10.1002/...
- Reposted by Jake BarberYou have heard of the gut microbiome but what do we know about plant microbiomes? Christopher Blake & colleagues examined the bacteria in the rhizosphere of Canola and suggest scope for better design interventions that support sustainable crop production. doi.org/10.1016/j.bc...
- Reposted by Jake BarberFresh news on de novo genes! Happy to present our latest work published in Nature communications: www.nature.com/articles/s41... Keywords not in specific order: intergenic ORFs, de novo genes, GC content, foldability, genetic code, ancestral sequence reconstruction and more :)
- Reposted by Jake BarberNew preprint from our lab www.biorxiv.org/content/10.1...! Andrea Dos Santos and Clément Vulin combine experiments and models showing how adding glucose can strengthen negative interactions between microbial species. This can be used in tandem with antibiotic treatment to inhibit pathogens!
- Reposted by Jake BarberVery cool paper by Jyotsna Kalathera et al. from @iamsamayp.bsky.social 's-lab on Bottleneck size drives the evolution of cooperative traits in an aggregative multicellular myxobacterium just out @plosbiology.org Congratulations to all coauthors. journals.plos.org/plosbiology/...
- Reposted by Jake BarberNew preprint from my lab (with Arya Kaul, @fernpizza.bsky.social, and @brinda.eu), in which we explore new genes hitchhiking on the beneficial deletion that fused them together, and find them in the LTEE, M. Tb/bovis, and across the bacterial tree of life
- Novel genes arise from genomic deletions across the bacterial tree of life biorxiv.org/content/10.64898/20…
- Reposted by Jake BarberAs we close the year, the ISME Early Career Scientist Committee is glad to spotlight @duhitasant.bsky.social , Postdoctoral Researcher at Rutgers University, and her paper “Eco-evolutionary robustness of wild bacterial communities to experimental perturbation”. doi.org/10.1093/isme... (1/2)
- Reposted by Jake BarberThis is totally worth 5 minutes of your time and probably should be in every biology class. Nature is awesome. neal.fun/size-of-life/
- Reposted by Jake BarberHey, fellow evolutionary biologists: If you support trans rights, like, comment, or repost this. I want to show that transphobes like Richard Dawkins are a loud minority that does not represent our community
- Reposted by Jake Barber"The changing roles of Escherichia coli" -- a short essay by yours truly. rdcu.be/eVtXT
- Reposted by Jake BarberHyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community in a spatially structured environment #ISMEJournal by @mlaenoc.bsky.social et al academic.oup.com/ismej/advanc...
- Reposted by Jake BarberHow do bacteria deal with double costs? And how costly are unusual levels of mistranslation anyway? In short - antibiotics are more of an issue than less/more mistranslation, but the latter changes how populations deal with antibiotics. For the long story, check out our new paper!
- So happy that this work simultaneously measuring the costs of antibiotic exposure and mistranslation is finally out in MBE! Work from @deepaagashe.bsky.social (who was ultra patient!) and my labs. Do see the research highlight here, with Nishant's lovely graphic. academic.oup.com/mbe/article/...
- Reposted by Jake BarberNature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
- Reposted by Jake Barber🗞️ New preprint from the lab, led by our postdoc Ana Garoña (not on here) in collab with @andreagiometto.bsky.social: “Experimental evolution of cellular miniaturization reveals a mechanism for cell size evolution”, aka: “honey, we shrank the yeasts!” 🎥 www.biorxiv.org/content/10.6...
- Reposted by Jake BarberImpact of fluctuating environments on the fitness and robustness of evolving laboratory and industrial Saccharomyces cerevisiae strains biorxiv.org/content/10.64898/20…
- Reposted by Jake BarberStrong genotype-by-genotype and genotype-by-environment interactions induced by antibiotic resistance mutations biorxiv.org/content/10.64898/20…
- Reposted by Jake BarberCompetition between Pseudomonas species constrains ecological diversification in polymicrobial biofilms NPJ Biofilms and Microbiomes from Henriette Lyng Røder and @vscooper.micropopbio.org www.nature.com/articles/s41...
- Reposted by Jake BarberOur new collaborative work led by @taliamycota.bsky.social Jiajun Cui & Emma Caullireau between my lab @ucllifesciences.bsky.social @cloeucl.bsky.social & the Karasov Lab (tkarasovlab.org) @uofubiology.bsky.social and collaborators: @plantricia.bsky.social et al. tinyurl.com/5yx2wmz5 (1/n)
- Reposted by Jake BarberAnother new preprint from former PhD student Daniel Wong (now @ ENS) has been a long time in the making, and builds on our recent efforts to model eco-evolutionary feedbacks in rapidly evolving microbial populations that compete for different resources (1/n)
- Reposted by Jake BarberHappy to share our new review on oligonucleotide chemical evolution on early Earth. We discuss how iterative sequence selection and diversification could have shaped RNA pools, facilitating sequence exploration and the emergence of ribozymes. www.jstage.jst.go.jp/article/biop...
- Reposted by Jake BarberNew online! Microbial genomics for antimicrobial resistance ecology and action
- Reposted by Jake BarberOut now at @plosbiology.org we evaluate the potential for antibiotic efflux and cell wall biogenesis as targets for reversing drug resistance and preventing its de novo evolution in Escherichia coli. Link below: journals.plos.org/plosbiology/...
- Reposted by Jake BarberNew in JB: Black and Wakeman review the challenges of treating polymicrobial infections in various body sites, a topic near and dear to my heart. journals.asm.org/doi/10.1128/... @asm.org #JBacteriology
- Reposted by Jake BarberEvolution of One Species Increases Resistance to Invasion in a Simple Synthetic Community Microbial Ecology link.springer.com/article/10.1...
- Reposted by Jake BarberA fun little side project I've been working on with @stepadenisov.bsky.social , Mato Lagator, and Andreas Wagner: "Strong promoters are mutationally robust". Briefly... www.biorxiv.org/content/10.1...
- Reposted by Jake BarberMassive undertaking with @teppo-h.bsky.social and others out. We studied 4 years (!!!) of synthetic 23 microbial species community evolution with/without antibiotic. Resistance mutations occurring over years led to stepwise restructuring and ultimately recovery of undisturbed community composition.
- Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...
- Reposted by Jake Barber
- Reposted by Jake BarberMetabolic interplay drives population cycles in a cross-feeding microbial community @natcomms.nature.com from @oventurelli2.bsky.social www.nature.com/articles/s41...
- Reposted by Jake BarberPseudomonas aeruginosa lasR is a keystone gene in polymicrobial cultures biorxiv.org/content/10.1101/202…
- Reposted by Jake Barber#PaperCBGP 🆕📰‼️ Can we predict which bacteria will turn into #superbugs? 🦠 A study led by Dr. Alejandro Couce and published in PLoS Genetics (@plos.org) shows that a single DNA change can open “bridges” to modern resistances. 🔗 Read more here: shorturl.at/TRRwD
- Reposted by Jake Barber#PaperCBGP 🆕📰‼️ 🧬 Led by Alejandro Couce, researchers of the CBGP used experimental evolution to predict how the superbug enzyme KPC-2 could outsmart antibiotics ⚔️The study, published at @natecoevo.nature.com, lets us block it and protect our antibiotics 📎 shorturl.at/F7oOa
- Reposted by Jake BarberSo this came online over the weekend: My dive into the "definition" of coevolution is online ahead of publication in @journal-evo.bsky.social! Don’t ask "when is it coevolution?" — ask "how?" doi.org/10.1093/evol...
- Reposted by Jake BarberNow peer-reviewed, improved and published in @microbiologysociety.org Microbiology - thanks to editor and reviewers! www.microbiologyresearch.org/content/jour...
- New preprint with nice detective work by PhD student Khadija Hanga: gain of pOXA MDR plasmid is facilitated by chromosomal mutations affecting OmpF which act synergistically with the plasmid’s carbapenamase to give high level resistance. Led by @mbottery.bsky.social www.biorxiv.org/content/10.1...
- Reposted by Jake BarberDelighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols. Thread 1/n
- Reposted by Jake BarberHow can we build a general theory of mutualistic communities? After five years, we finally completed a new Neutral Theory of Cooperation that is fully solved analytically and displays remarkable properties @jordipinero.bsky.social @artemyte.bsky.social @manlius.bsky.social arxiv.org/abs/2506.09737
- Reposted by Jake BarberMutation bias is a key predictor of adaptation rate biorxiv.org/content/10.1101/202…
- Reposted by Jake BarberWe have a new paper out in Molecular Ecology, led by @devinbendixsen.bsky.social ! Reproductive isolation due to divergent ecological selection is accompanied by vast genomic instability in experimentally evolved yeast populations onlinelibrary.wiley.com/doi/10.1111/...
- Reposted by Jake BarberNew in Evolution: Historical effects during experimental evolution of multicellularity in Saccharomyces cerevisiae, by Joleen Khey and Mike Travisano academic.oup.com/evolut/artic...
- Reposted by Jake BarberEcological diversification in rapidly evolving populations biorxiv.org/content/10.1101/202…
- Reposted by Jake BarberOur new paper @asn-amnat.bsky.social develops a Grand Unified Theory including both exploitative and interference competition doi.org/10.1086/737628. The R* rule of ecology (that 2 species cannot coexist on a single resource), is widely broken, including via a new trade-off we describe. 1/9
- Reposted by Jake BarberCancer is an evolutionary disease, but does knowing a cancer’s evolutionary past help predict its future? Out today in @nature, we learnt the evolution of 2000 lymphoid cancers and found it was highly correlated with clinical outcomes! (1/7) rdcu.be/eFrrc
- Reposted by Jake BarberParallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution biorxiv.org/content/10.1101/202…
- Reposted by Jake BarberNature research paper: Commensal yeast promotes Salmonella Typhimurium virulence go.nature.com/4mTnRzG
- Reposted by Jake BarberNEW PAPER! Some kinds of genetic mutations are more likely to arise than others. Such "biases" in mutation vary between species. Analyzing data from 14 species, we show that this variation explains species differences in the genetics of adaptation! (1/3) www.biorxiv.org/content/10.1...
- Reposted by Jake BarberMutational Biases and Selection in Mitochondrial Genomes: Insights from a Comparative Analysis of Natural and Experimental Populations of Caenorhabditis elegans biorxiv.org/content/10.1101/202…
- Reposted by Jake BarberI’m super happy to present the first discoveries of the RIKEN-Cambridge Joint Crop Symbiosis Research Team, based in Japan 🇯🇵 doi.org/10.1101/2025... A thread 👇
- Reposted by Jake BarberMolecular adaptation reflects taxon-specific mutational biases biorxiv.org/content/10.1101/202…
- Reposted by Jake BarberExcited to share our new publication, out today in Nature! www.nature.com/articles/s41.... @kanchanj.bsky.social led this fascinating fungal-bacterial interaction project. We are grateful for our wonderful collaborators Brian Peters and David Underhill.
- Reposted by Jake BarberExcited with two new preprints on evolution of molecular structure, in RNA (doi.org/10.1101/2025..., @n-martin.bsky.social) and proteins (doi.org/10.1101/2025...). Both RNA and protein structures are often conserved across evolution, but the underlying reasons are very different.
- Reposted by Jake BarberNatural protein structures have evolved exceptional robustness to mutations biorxiv.org/content/10.1101/202…
