Cooperation is a universal feature of complex systems, from the origins of life and microbiomes to societies. What universal patterns can be found in these systems? Here's our new @pnas.org paper. @jordipinero.bsky.social @artemyte.bsky.social @sfiscience.bsky.social www.pnas.org/doi/epdf/10....

Transformer-based Prediction of Microbial Growth Rates from Genomic Data doi.org/10.1145/3765...

Check our new perspective paper exploring how the seed holobiont goes to sleep 😴 and reactivate for germination. A lot of exciting research to be done to understand dormancy mechanisms in microbes and plants ☘️ @emersys-irhs.bsky.social @irhs-angers.bsky.social

Excited to share our new @natecoevo.nature.com paper. We identified microbes found across nearly all ruminants that act as the functional backbone of both the rumen ecosystem and the host, with major implications for food security and climate change mitigation. (1/8) www.nature.com/articles/s41...

We are delighted to announce Marie Simonin @microbialmarie.bsky.social as a speaker at SeedCon 2026! seedcon.org 👉 Join us for Marie's talk at the upcoming #Seed #Microbiome Conference (May 5–7, 2026) in Potsdam, Germany!

The @kiranrpatil.bsky.social Group have published a paper in Nature Microbiology that identifies over 150 common industrial chemicals, from pesticides to flame retardants, that have a toxic effect on bacteria found in the healthy human gut microbiome. Read more: www.bioc.cam.ac.uk/news/patil-g...

Very excited to share a big part of my dissertation work with the Deutschbauer lab at LBNL and @ucberkeleyofficial.bsky.social! BarTn7: A method for bacterial lineage tracking at sub-species resolution in population, ecological, and evolutionary experiments. www.biorxiv.org/content/10.1...

🧫 Just out in Bioinformatics Advances: “GlobDB: A comprehensive species-dereplicated microbial genome resource.”  Explore the full study: https://doi.org/10.1093/bioadv/vbaf280

Excited to bring to your attention 2-year work by @sylvain-vicente.bsky.social and collaborators #BIOSP #MathNum @inrae-dpt-spe.bsky.social. A re-evaluation of STAMP modelling, introducing a much needed time-resolution. Works also on Animal-bacterial infection models. www.biorxiv.org/content/10.1...

🎉 Check out the latest from Qin Gu’s team at Nanjing Agricultural University: “Keystone Pseudomonas species in the wheat phyllosphere” (Cell Host & Microbe) 👉 www.cell.com/cell-host-mi...

Un poste d’IE en bioinformatique est actuellement ouvert au CEFE à Montpellier pour travailler dans le cadre de l'ERC RegEvol. Détails ici: emploi.cnrs.fr/Offres/CDD/U... Début 01/01/2026 pour 18 mois potentiellement renouvelable. candidature jusqu'au 29/11 N’hésitez pas à diffuser largement

New work in @newphyt.bsky.social: fruit isn’t not only for #seed dispersal, it filters and redirects #microbiome assembly in the next plant generation. This should change how we think about inheritance beyond #seeds. nph.onlinelibrary.wiley.com/doi/10.1111/...

We are delighted to let you know that your Plants, People, Planet article 'Demystifying Fungal Systematics: A Gateway to Fungal Literacy and Societal/Ecological Relevance Through Familiar Species' has been published on Early View. nph.onlinelibrary.wiley.com/doi/10.1002/...

A gene-editing approach enables modification of bacteria within the mouse gut @science.org @harriswang.bsky.social @columbiauniversity.bsky.social @shsternberg.bsky.social www.science.org/doi/10.1126/... www.science.org/doi/10.1126/...

Long term deleterious effects of drought memory buff.ly/0sNZeWs A 5-year long experiment, super impressive! I wonder whether the offspring of the final generation would have retained the performance difference, esp. after controlling for seed size/maternal investment.

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

However, these findings are consistent with recent ecological theory by my amazing labmate @johndmcenany.bsky.social which suggested that conspecific strains may coexist in saturated communities even when new strains displace other species. (15/n) www.nature.com/articles/s41...

The hitchhiker’s guide to cross-species DNA delivery @cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez www.cell.com/trends/micro...

Strain displacement in microbiomes via ecological competition Cool @natmicrobiol.nature.com publication by @erikbakkeren.bsky.social @vit-pi.bsky.social @meganleeny.bsky.social @microscape.bsky.social & Kevin Foster www.nature.com/articles/s41...

#PMS2025 Check the posters of my 2 wonderful PhD students @logansuteau.bsky.social & Louna Colaert-Sentenac! Results on multi-kingdom SynCom experiments inoculated on seeds to perform plant microbiome engineering & promote pathogen resistance on rapeseed & common bean 🫘 🌱 @emersys-irhs.bsky.social

Come check my poster 137 "Seed Microbiota: Core diversity, Transmission and Legacy effects on Plant Microbiome Assembly" Some results from the SUCSEED project on culturomics and SynComs 🫘🧫🌱 #PMS2025 @emersys-irhs.bsky.social

Very happy to be in Antequera, Spain for #PMS2025 with my 2 PhD students @logansuteau.bsky.social and Louna Coleart-Sentenac We will present results from the SUCSEED project on culturomics and seed microbiome engineering using multi-kingdom SynComs 🫘🧫 @emersys-irhs.bsky.social

Final countdown before the start of the #PMS2025!!! 🪴 Looking forward to seeing you in Antequera (Malaga) on 3-7 November! Final program at: 6thplantmicrobiomesymposium2025.com/programme/ #Plantscience #MicrobiomeResearch #Bioinformatics

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....

Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome Ricks et al. nph.onlinelibrary.wiley.com/doi/10.1111/...

ICYMI: Our latest shows what happens to transcriptional and metabolic profiles in a desiccated soil bacterium. To simplify things, I've attached a visual abstract. Comments on the preprint are welcome! #microsky #microbesky www.biorxiv.org/content/10.1...

Léa Ninzatti, Marie-Françoise Jardinaud, and Aurélien Carlier review current knowledge of hereditary leaf symbiosis in tropical plants and explore hypotheses regarding mechanisms that enable these highly specific interactions: https://doi.org/10.1094/PBIOMES-11-24-0111-RVW

Martin Zobel is the corresponding author of the recently published #TansleyReview ‘#Symbiont plasticity as a driver of plant success.’ 📖 doi.org/10.1111/nph.... #mycorrhiza #PlantScience

We are searching for a 4- year postdoctoral fellow to work us on Microbial Ecology and Crop Disease Management. More details below. The position will start next year. Please circulate and repost. jobs.smartrecruiters.com/WesternSydne...

Wonderful to see this beautiful image on the cover of Science this week highlighting a paper that uses high resolution imaging to show the spatial patterns of bacterial attraction to glutamine from roots. Paper here: www.science.org/doi/10.1126/... Perspective here: www.science.org/doi/10.1126/...

Great night for the Fête de la Science at the stunning Digital Floralia exhibition (Miguel Chevalier)-Musée des Beaux Arts Angers I enjoyed chatting about our research on seed microbiota, holobionts and alternatives to pesticides 🦠👩‍💻🌱 @emersys-irhs.bsky.social @irhs-angers.bsky.social

"Tick–pathogen–microbiome interactions based on #hologenome-wide analysis" from 16,000 ticks, 48 species, and 8 genera. 👀 Nutritional endosymbionts are prevalent with a new 7,783 bacterial genomes from 1,373 bacterial species. @holobiontbiology.bsky.social www.nature.com/articles/s41...

The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...

Had a fantastic time in the jardin du col du Lautaret (Alpes) for a machine learning in ecology training 🏔️👩‍💻 Thanks to @anaeefrance.bsky.social and @symbioticworld1.bsky.social for the organization! I have so many ideas on how to test ML on our microbiota datasets 🤓

How 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

👩‍🔬J'ai commencé un kit de démarrage "chercheuses en France" go.bsky.app/TBEzKC #FemmesEnScience J'ai besoin de votre aide pour le remplir et donner de la visibilité aux chercheuses que vous connaissez et qui sont sur Bluesky ! ▶️Taguez celles que vous connaissez, je les ajoute !

We are very excited to make the first announcement of SeedCon 2026. Please mark your calendars and look out for further updates on seedcon.org #SeedCon2026 #SeedMicrobiome #MicrobialInheritance #PlantMicrobiome #Conference

Transient microbial architects: tracing the legacy effects of ephemeral taxa during plant microbiome assembly Current Opinion in Microbiology by @logansuteau.bsky.social et al from @microbialmarie.bsky.social www.sciencedirect.com/science/arti...

New Paper! Machine learning models that attempt to predict microbial load collapse outside of their training context with an R2<0! In contrast, our Bayesian Partially Identified Models embrace uncertainty in unmeasured microbial load and consistently outpreform. www.biorxiv.org/content/10.1...

Excited to summarize our most recent paper, "Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2" on controlling the false discovery rate (FDR) when analyzing high throughput sequencing (HTS) data. This has been an open problem since the dawn of HTS.

Pleased to share our new article in Cell Host & Microbe, a collaboration with the group of Zhong Wei at NJAU Common mycorrhizal networks facilitate plant disease resistance by altering rhizosphere microbiome assembly Free share link: authors.elsevier.com/c/1lnTD6t8JE...

Happy to see our paper out in Current Op in Microbiology! We show how transient microbes can play key roles in plant fitness & microbiota assembly 🦠 The 1st 1st author article for my 2 fantastic PhD students @logansuteau.bsky.social & Louna Coleart-Sentenac 🎉 www.sciencedirect.com/science/arti...

Super awesome new paper in #MEE describing #causal #detection of shifts in #biodiversity! So many great insights here—a must read for those interested in #causalinference And love Fig 3! Congrats team! @lsantinieco.bsky.social doi.org/10.1111/2041...

Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change @femsjournals.bsky.social Microbiol Ecology by @williampearman.bsky.social et al academic.oup.com/femsec/advan...

Reproducibility in #plant #microbiome experiments. This collaborative effort involving 5 labs achieved consistent, inoculum-dependent results, providing detailed protocols, datasets & best practices to promote #reproducibility in #PlantMicrobiome studies @plosbiology.org 🧪https://plos.io/41IVzzk

Interested in exploring prophages in your (meta)genomes, but don't know how and where to start? We've put together a beginners guide to exploring viral diversity in prokaryotes @marievasse.bsky.social @sebwielgoss.bsky.social @oxunipress.bsky.social

Pig breeds reared on the same farm exhibit rippling waves of #phylosymbiosis with their bacterial communities, viruses, mobile genetic elements, and antibiotic resistance genes (ARGs). ARGs is a first. 👀 www.sciencedirect.com/science/arti...

Revisiting the cry-for-help hypothesis in plant–microbe interactions @cp-trendsplantsci.bsky.social Forum from @fdiniandreote.bsky.social www.cell.com/trends/plant...

I did an interview with the In Defense of Plants podcast about my journey into researching seed microbiota, some of what we currently know and what remains to be explored! You can check it out here: www.indefenseofplants.com/podcast/2025...

It’s simply the right way. A hologenome approach increases predictive accuracy: “Likewise, when using the OTU abundance to predict the pea resistant phenotype, significantly higher prediction abilities were observed than all SNP marker-based approaches” bmcplantbiol.biomedcentral.com/articles/10....