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Fantin Mesny

@mesny.bsky.social
730 followers 494 following 81 posts

Post-doctoral researcher at ETH Zürich (@usyseth.bsky.social) Fungal biology, ecology & evolution ✹ Plant pathology ✹ Genomics ✹ Microbiomes

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Fantin Mesny @mesny.bsky.social · 01/10/2026
5 years ago, @hacquardst.bsky.social and I became very interested in 𝑃𝑙𝑒𝑐𝑡𝑜𝑠𝑝ℎ𝑎𝑒𝑟𝑒𝑙𝑙𝑎 𝑐𝑢𝑐𝑢𝑚𝑒𝑟𝑖𝑛𝑎, an emerging fungal pathogen that colonizes the roots of many plants 🌱 🍅 🌾 🆕📝 Final result of a huge team effort to uncover the bases of its multi-host compatibility👇 www.nature.com/articles/s41...
nature.com
Carbohydrate-active enzymes from a core root mycobiota member enable infection of multiple plant hosts - Nature Microbiology
Host-induced fungal CAZymes act as disease determinants and drive multihost compatibility.
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Tonni Andersen @tonnigrubeandersen.bsky.social · 29/09/2026
Do you want to know more about plant barriers? Read our new review, here is probably more than you ever wanted :-) . A very fun writing experience with Gwyneth Ingram: Welcome to The Junction: Polymeric extracellular interfaces and barriers in plant life academic.oup.com/jxb/article/...
academic.oup.com
Validate User
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Andrew Urquhart @starships-andrew.bsky.social · 24/09/2026
Another step in the #Starship story - they move via a circular intermediate. Helps explain how these elements horizontally transfer and means that we can modify them into transformation vectors (starmids). www.biorxiv.org/content/10.6...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 30/08/2026
Run AlphaFold2 locally in your browser via WebGPU, no installation needed, it's just a static webpage using your own GPU or CPU. Short proteins run in seconds. Larger ones are still slow: a 291-aa protein takes ~7 minutes on my M4 Pro. ❗It's just a PoC. 🌐 martin-steinegger.github.io/alphafold2-w...
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Max Planck Institute for Plant Breeding Research @mpipz.bsky.social · 18/08/2026
🔬Big news🥳 We’re excited to welcome Prof. Dr. Rosa Lozano-Durán as new Director and head of the Department of Plant Virology @mpipz.bsky.social Her research focuses on how plant viruses interact with their hosts. 🎉Welcome to MPIPZ, Rosa 🌿🌱 www.mpipz.mpg.de/5842514/loza...
mpipz.mpg.de
The Max Planck Institute for Plant Breeding Research welcomes Prof. Dr. Rosa Lozano-Durán as new director
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PM Delaux @pierremarcdelaux.bsky.social · 18/08/2026
Finally online! It took ut 9 yars from formulating the hypothesis to actually finalizing the last experiments... but there it is!
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Gulnara Tagirdzhanova @metalichen.bsky.social · 11/08/2026
Our study on giant transposons Starship 🚀🧬 in the genome of the lichen fungus Xanthoria is now out in @pnas.org! What did we find out about Starships in #lichen fungi? 👇Updated thread below 🖥️ 🧪 🦠 🧫 #SymbioSky 1/6 www.pnas.org/doi/10.1073/...
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Genome Biology and Evolution @genomebiolevol.bsky.social · 11/08/2026
@loreament.bsky.social & Saupe suggest that fungal NOD-like receptors evolve under diversity-enhancing mechanisms and display selective signatures consistent with a general immune function. 🔗 doi.org/10.1093/gbe/... #societyjournal #genome #evolution
doi.org
NOD-Like Receptor Genes Undergo Diversity-Enhancing Evolution in a Fungal Species Complex
Abstract. Fungi harbor diverse arrays of genes encoding NOD-like receptors (NLRs), key intracellular immune proteins found in plants, animals, and bacteria
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Lorenz Oberkofler @oberkoflerlorenz.bsky.social · 10/08/2026
Super happy to finally share our preprint with the community! 🎉 Fungal extracellular vesicles deliver RNA cargo into host cells - but how do they get through the plant cell wall? This question puzzled us and the field for years… 🧵 1/6
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Ákos T Kovács @evolvedbiofilm.bsky.social · 01/08/2026
Virulent strains of Pseudomonas aeruginosa are more disruptive during invasion of a microbial model community #THoR #SynCom FEMS Microbiology Letter by Emil Burman, Mikkel Anbo, @larsjelsbak.bsky.social and Johan Bengtsson-Palme academic.oup.com/femsle/advan...
academic.oup.com
Virulent strains of Pseudomonas aeruginosa are more disruptive during invasion of a microbial model community
Abstract. Pseudomonas aeruginosa, a major opportunistic pathogen involved in cystic fibrosis and many nosocomial infections, exhibits strong competitive ab
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Carl T. Bergstrom @carlbergstrom.com · 31/07/2026
Nature did a short piece on our preprint about how LLMs will affect the practice of science; my more detailed thread is below.
nature.com
Scientists using LLMs will ‘do more, less well’, modelling study predicts
Research suggests that the combination of incentives to publish and the use of large language models will lead to more papers, but they will be less refined.
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GreenRobust @greenrobust.de · 29/07/2026
New GreenRobust publication by the group of Eric Kemen on using machine learning to identify beneficial microbiota: www.nature.com/articles/s41...
nature.com
Machine learning reveals biocontrol agents shaping disease outcome in natural Arabidopsis populations - Nature Communications
Plants can recruit beneficial microbes to suppress pathogens, offering a route to rational biocontrol beyond empirical screening. Here, the authors use machine learning to identify disease-associated ...
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Team Thomma @teamthomma.bsky.social · 28/07/2026
📣 New preprint! 🧵 Fantastic work led by @antonkraege.bsky.social Fact: Cerato-platanins are everywhere in fungi. Found across the fungal kingdom, implicated in everything from development to virulence to immune activation. But what do they *actually* do? We finally found the answer 👇
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Ákos T Kovács @evolvedbiofilm.bsky.social · 15/07/2026
How do bacteria recognize fungal competitors? @cp-trendsmicrobiol.bsky.social by Lingfang Zhu (朱玲芳), Changfu Li (李长富), Xihui Shen (沈锡辉) www.cell.com/trends/micro...
cell.com
How do bacteria recognize fungal competitors?
Bacterial–fungal interactions (BFIs) are central to microbial community dynamics in diverse ecosystems, with profound implications for medicine, agriculture, and environmental microbiology. A critical...
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Team_Zuccaro @algazuccaro.bsky.social · 12/07/2026
Microbial chitinases perform functions beyond antagonism, including facilitating host colonization by interfering with chitin-triggered immunity. We review evidence that their diversification reflects adaptation to distinct host-associated ecological niches. academic.oup.com/femsre/artic...
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Gitta Coaker @gittacoaker.bsky.social · 29/06/2026
I'm getting more requests for gift authorship lately. Complete with a written MS and a request to just add my name or to provide minor comments to add me as a co-author. Please don't do this. Authorship should reflect substantial intellectual contributions and shared responsibility for the work.
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Fantin Mesny @mesny.bsky.social · 25/06/2026
Happy to see that AMAPEC helps to get novel insights into lichen biology and evolution!
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Diana Gómez De La Cruz @dianagdlc.bsky.social · 05/06/2026
So proud to see this story finally out!🎉 We added new data since our previous preprint—transgenic barley plants with an engineered immune receptor that fights off two fungal pathogens at once. Short 🧵 and link to the original preprint thread on X👇 www.science.org/doi/10.1126/...
science.org
Molecular mimicry of a pathogen virulence target by a plant immune receptor
Plants and animals respond to pathogen attack by mounting innate immune responses that require intracellular nucleotide-binding leucine-rich repeat (NLR) proteins. These immune receptors detect pathog...
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Gabriella Petti @gabriellapetti.bsky.social · 28/05/2026
Excited to share our latest study with @nicksnelders.bsky.social and @teamthomma.bsky.social! We uncover the mode of action of the V. dahliae antimicrobial effector Ave1 and show that it binds LTA and disrupts bacterial membranes 🦠 www.biorxiv.org/cgi/content/...
biorxiv.org
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bioRxivpreprint @biorxivpreprint.bsky.social · 21/05/2026
geneML: Gene annotation across diverse fungal species using deep learning www.biorxiv.org/content/10.64898/20…
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Matthias C. Rillig @mrillig.bsky.social · 21/05/2026
"Academic science is not only about productivity, it is also about deep understanding, exploring creative solutions and training critical thinkers to be the next generation of researchers. Now is the time for the scientific community to evaluate whether AI products help or hinder these endeavours."
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bioRxivpreprint @biorxivpreprint.bsky.social · 21/05/2026
The model alga Chlamydomonas reinhardtii forms mutualistic interactions with Verticillium fungi www.biorxiv.org/content/10.64898/20…
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Christine Faulkner @pdchristine.bsky.social · 19/05/2026
Emma Turley started her PhD expecting the effector ChEC108 would aid Colletotrichum establish infection, but she instead discovered that when it makes it's way to plasmodesmata it's bound by host HIPP6, triggering PD closure and impeding infection. #PlantScience
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Riccardo Baroncelli @riccardobaroncelli.bsky.social · 15/05/2026
Thrilled to see this finally out!! Our new work suggests #Starships helped #Colletotrichum acquire the genes needed to infect lupin. A glimpse into how fungal pathogens emerge through horizontal transfer and genome reshaping. biorxiv.org/content/10.6... #Fungi #Genomics #Pathogenicity #evolution
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Fantin Mesny @mesny.bsky.social · 10/05/2026
Bacteria evolving to survive the soil battleground 🦠🛡️ Super glad I got to be part of this fascinating study, led by my friend @jinyi-zhu.bsky.social, who’s equally impressive in the lab and at the gym 💪
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Jinyi Zhu @jinyi-zhu.bsky.social · 10/05/2026
Fungi deploy antimicrobial proteins (AMPs) to compete with microbes, including bacteria. But can bacteria fight back? We @teamthomma.bsky.social found that some AMP-sensitive bacteria can repress AMP deployment, suggesting an unrecognized bacterial–fungal arms race. www.biorxiv.org/content/10.6...
biorxiv.org
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einatmen.bsky.social @einatmen.bsky.social · 30/04/2026
🌱 A research team led by @teamthomma.bsky.social has discovered the surprising evolutionary origin of fungal "effector proteins": molecules that pathogens use today to infect their hosts appear to have evolved from ancient antimicrobial proteins.
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Universität zu Köln @unicologne.bsky.social · 30/04/2026
🍂🌱 An international research team led by @teamthomma.bsky.social has discovered the surprising evolutionary origin of fungal effector proteins: molecules that pathogens use today to infect their hosts appear to have evolved from ancient antimicrobial proteins. More: ➡️ uni.koeln/UCMWQ #UniCologne
uni.koeln
Fungi utilize ancient antimicrobial proteins to attack hosts and their microbiomes
A team of plant researchers at the University of Cologne decodes a key infection strategy of fungal pathogens. Significant findings for disease control, plant protection and food security as well as f...
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Fantin Mesny @mesny.bsky.social · 29/04/2026
🎉 📰 Very happy to share the journal publication of our manuscript "Plant-associated fungi co-opt ancient antimicrobials for host manipulation"! #ScienceAdvancesResearch @science.org @teamthomma.bsky.social www.science.org/doi/10.1126/...
science.org
Plant-associated fungi co-opt ancient antimicrobials for host manipulation
Fungal effectors may have evolved from ancient antimicrobials, shaping plant microbiota and immunity during infection.
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Eva Stukenbrock @estukenbrock.bsky.social · 13/04/2026
So diverse and yet conserved. Check out opinion paper by Leonhard Pachinger @leopach.bsky.social on antimicrobial effectors produced by fungal pathogens: www.sciencedirect.com/science/arti...
sciencedirect.com
Antimicrobial effectors of plant-associated fungi: multipurpose proteins with fast-evolving surfaces and structurally conserved cores
Plants are exposed to a variety of devastating pathogens, causing significant yearly yield losses. In order to facilitate infections, plant pathogens …
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Cecile Lorrain @ccilelorrain.bsky.social · 15/04/2026
Thrilled to share our paper now out in Nature Plants 🎉 We developed a genome-host association (GHA) approach to study pathogen adaptation directly from field metadata by using the originating host cultivar as phenotype. www.nature.com/articles/s41...
nature.com
Genome–host association mapping reveals wheat pathogen genes involved in host specialization - Nature Plants
This study introduces genome–host association (GHA), leveraging natural epidemics to map the genetic landscape of host adaptation in the pathogen Zymoseptoria tritici. Applied to 832 wheat fungal stra...
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Michael Habig @michaelhabig.bsky.social · 25/03/2026
Now out! We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus. www.nature.com/articles/s41... @oggenfussursula.bsky.social #TEsky
nature.com
Transposable elements hitchhike on Starships across fungal genomes - Nature Communications
Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...
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Ákos T Kovács @evolvedbiofilm.bsky.social · 24/03/2026
Drought drives elevated antibiotic resistance across soils @natmicrobiol.nature.com from Dianne Newman with @hannahjeckel.bsky.social www.nature.com/articles/s41...
nature.com
Drought drives elevated antibiotic resistance across soils - Nature Microbiology
Drought conditions in soil systems lead to elevated concentrations of natural antibiotics, as well as the enrichment of antibiotic-resistant microorganisms, highlighting a link between climate and the...
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Nature @nature.com · 15/03/2026
The finding could offer hope that gut-targeted therapies could reverse cognitive decline go.nature.com/40vgODK
go.nature.com
Memory loss is fuelled by gut microbes in ageing mice
Nature - If confirmed in people, the finding might lead to gut-targeted therapies that could reverse cognitive decline.
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Mark A. Hanson @hansonmark.bsky.social · 06/03/2026
Pleased to finally share this fun collab that began at #Ento23 @cedricaumont.bsky.social presented & I had seen NCBI annotated some cockroach genomes as "contaminated." Turns out NCBI & I were wrong (much more fun). Horizontal transfer of an #AntimicrobialPeptide across insects bit.ly/DrsHGT 1/🧵
A phylogenetic tree of insects is shown annotating the presence or absence of a an antimicrobial peptide gene across winged insectsVarious phylogenetic secondary loss events are mapped to a tree of insects to explain the parsimony calculations necessary to explain the diversity of insect Drosomycin antimicrobial peptide genesAntimicrobial peptides (AMPs) are key defence molecules of the innate immune system of plants and animals. Understanding the evolutionary origins of AMPs can help to explain how immune systems acquire novelty and vary in their defensive capabilities. However, AMPs evolve rapidly, and so the origins of similar AMPs across organisms is often unclear. Furthermore, false negatives due to low search sensitivity are common and can hinder confident annotations about true absences. Due to these difficulties, understanding whether similar AMP genes found in diverse organisms represent ancestral molecules or evolutionary novelties has been challenging. In this report, we present evidence of
horizontal gene transfer (HGT) of the antifungal peptide gene Drosomycin across insects. We show that in Diptera, the presence of Drosomycin is restricted to the Melanogaster group and additionally the
distant relative Drosophila busckii. We go on to recover Drosomycin genes in cockroaches (Blattodea), mantises (Mantodea), one katydid (Orthoptera), various beetles (Coleoptera), and a recently acquired
pseudogenized Drosomycin locus in Liposcelis booklice (Psocodea), but no other insects. Explaining this diversity through shared ancestry requires at least 50 independent loss events, or just seven HGT
events. Previous studies have suggested that similar AMPs found across divergent species reflect conservation from a common ancestor, or due to their small size, that they arose via convergent evolution resulting from pathogen-imposed selection. Our findings suggest horizontal gene transfer can be responsible for the presence of some AMP genes found scattered across the tree of life. By presenting a mechanism through which immune systems can acquire novelty, our study also suggests a possible explanation for certain lineage-specific competencies for defence against infectious disease. While loss of AMP genes is common in certain lineages, here we suggest gain of AMPs can occur just as suddenly.
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Andre Cornman @ancornman1.bsky.social · 03/03/2026
Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required. We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵
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Trends in Ecology & Evolution @cp-trendsecolevo.bsky.social · 18/12/2025
Online now: Deconstructing host quality offers insight into disease ecology
dlvr.it
Deconstructing host quality offers insight into disease ecology
Disease risk varies among ecological communities because species differ in their host quality, that is, their contribution to parasite fitness. We propose a four-component framework of host quality that harmonizes terminology across plant and animal domains. Using this framework, we demonstrate how the host defense strategies of resistance and tolerance relate to distinct components of host quality. Easily extendable to multi-parasite systems, the framework also helps to identify new ways of examining the continuum between specialist and generalist parasites. Ultimately, breaking down and formalizing the components of host quality helps with synthesizing disease ecology across domains and unlocking relationships between biodiversity and disease risk.
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Carl T. Bergstrom @carlbergstrom.com · 16/12/2025
Just decline the peer review invitation. What are you people even doing?
nature.com
More than half of researchers now use AI for peer review — often against guidance
A survey of 1,600 academics found that more than 50% have used artificial-intelligence tools while peer reviewing manuscripts.
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Cecile Lorrain @ccilelorrain.bsky.social · 28/11/2025
Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social link.springer.com/article/10.1...
link.springer.com
Three-dimensional genome architecture connects chromatin structure and function in a major wheat pathogen - BMC Biology
Background Genome spatial organization plays a fundamental role in biological function across all domains of life. While the principles of nuclear architecture have been well-characterized in animals ...
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Megan McDonald @mcdonaldmeganc.bsky.social · 18/11/2025
Our latest pre-print on TE-mediated tandem duplication of the ToxB effector is now online...still a puzzle for us but we think it is in a Helitron! Together with amazing collaborators, Reem Aboukhaddour and Ryan Gourlie #TE #fungi www.biorxiv.org/content/10.1...
biorxiv.org
The virulence gene ToxB is both amplified and disrupted by transposons in the wheat pathogen Pyrenophora tritici-repentis
### Competing Interest Statement The authors have declared no competing interest. Agriculture and Agri-Food Canada, https://ror.org/051dzs374 Alberta Grain Saskatchewan Wheat Development Commissio...
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Luzia Stalder @luzia-stalder.bsky.social · 30/10/2025
Still using 16S/ITS profiling? You might want to reconsider👀 Our new paper presents pangenome-informed amplicons that provide up to 10× higher phylogenetic resolution than full-length ribosomal markers- while remaining cost effective and scalable! microbiomejournal.biomedcentral.com/articles/10....
microbiomejournal.biomedcentral.com
High-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons - Microbiome
Background High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Results...
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Team Thomma @teamthomma.bsky.social · 30/10/2025
📣 Now announcing the journal publication 📄 of our work in @newphyt.bsky.social on how Verticillium undermines the plant's 🌱 "cry for help": terrific work by @antonkraege.bsky.social & @wolki95.bsky.social doi.org/10.1111/nph....
doi.org
Undermining the cry for help: the phytopathogenic fungus Verticillium dahliae secretes an antimicrobial effector protein to undermine host recruitment of antagonistic Pseudomonas bacteria
During pathogen attack, plants recruit beneficial microbes in a ‘cry for help’ to mitigate disease development. Simultaneously, pathogens secrete effectors to promote host colonisation through vario...
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Stephen Turner @stephenturner.us · 25/09/2025
Apple is entering the protein folding arena. SimpleFold: Folding Proteins is Simpler than You Think arxiv.org/abs/2509.18480 🧬🖥️🧪 github.com/apple/ml-sim...
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John M. Drake @jdrakephd.bsky.social · 21/08/2025
Given the tremendous diversity of microorganisms in the world, why do only a small fraction cause disease? My essay in #PLOSBiology argues that the answer is lack of opportunity and that humans encounter only one new bacterial pathogen for every 1.4b years lived. journals.plos.org/plosbiology/...
journals.plos.org
Why are there so few pathogens? Ecology and evolution in pathogen emergence
Why are there so few pathogens, and what determines their emergence? This Perspective argues that ecological and evolutionary forces (host availability, geographic exposure and microbial innovation) w...
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MPI for Evolutionary Biology @mpi-evolbio.bsky.social · 11/09/2025
Could humans and AI one day form a single “evolutionary individual”? Researchers at the Max Planck Institute for Evolutionary Biology raise this question in a new publication exploring human–AI interdependence. www.evolbio.mpg.de/3836073/news...
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Alexandre Almeida @alexmsalmeida.bsky.social · 10/09/2025
🚨 New pre-print from the lab! We performed a large-scale meta-analysis of the uncultured gut #microbiome in >10,000 metagenomes enabling us to identify a new candidate biomarker of health. www.biorxiv.org/content/10.1...
biorxiv.org
Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a new candidate biomarker of health
The human gut microbiome plays an important biological role in host health, yet over 60% of gut species remain uncultured and hence inaccessible to experimental manipulation. Here we analysed 11,115 h...
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Daniel Croll @danielcroll.bsky.social · 03/09/2025
Reproduction in ants 🐜 just keeps blowing my mind 🤯 But this here is the crown for sure... for now. www.nature.com/articles/s41... (go also check out obligate chimerism, social chromosomes, clonal production of females and males, and much more...)
nature.com
One mother for two species via obligate cross-species cloning in ants - Nature
In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same moth...
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Rayan Chikhi @rayanchikhi.bsky.social · 03/09/2025
🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...
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Lara Van Dijck @laravdijck.bsky.social · 21/08/2025
Super excited to share that my PhD research paper is finally out! @newphyt.bsky.social doi.org/10.1111/nph.... @parkergroup.bsky.social
doi.org
Cooperation between a root fungal endophyte and host‐derived coumarin scopoletin mediates Arabidopsis iron nutrition
Iron acquisition is a critical challenge for plants, especially in iron-deficient soils. Recent research underscores the importance of root-exuded coumarins in modulating the root microbiome communi.....
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Zamin Iqbal @zaminiqbal.bsky.social · 17/08/2025
"We show that unrelated proteins have a universal tendency towards convergent evolution of secondary and tertiary motifs, causing an excess of high-scoring FP alignment... previous methods routinely overestimate significance by up to six orders of magnitude." www.biorxiv.org/content/10.1...
biorxiv.org
Protein structure alignment significance is often exaggerated
Machine learning has generated millions of high-quality predicted protein structures, creating a need for computationally efficient structure search algorithms and robust estimates of statistical sign...
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