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....

Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops @cp-cellhostmicrobe.bsky.social review by Dario X. Ramirez-Villacis, Antonio Leon-Reyes, @cornepieterse.bsky.social and Jos Raaijmakers @niooknaw.bsky.social www.sciencedirect.com/science/arti...

My team has updated our free database of POSTDOC fellowships. This database contains 286 entries. For each entry, we provide a link, short description, deadline, amount, and eligibility criteria. Download this updated and expanded database here: research.jhu.edu/rdt/funding-...

The microbiome of plant woody tissues is far more diverse than we thought 🤩

Great publication from Maggie Wagner (KU) and Manuel Kleiner (NCS) on how to design microbiome (+ other Omic) projects with downstream statistics in mind! A must read for trainees! www.nature.com/articles/s41...

#Perspective In this perspective, the authors propose research priorities necessary to facilitate the application of these ecological principles to improve microbiome functionality. #MicroSky #MicrobiomeSky 🦠 www.nature.com/articles/s41...

After many years in the making, here is our host range #phage paper with #ecology, #evolution and #biocontrol perspectives published in Molecular Ecology! @phimresearch.bsky.social‬ @inrae-pv.bsky.social‬ #PVBMT #JulianGarneau onlinelibrary.wiley.com/doi/10.1111/... These are our key findings:

Our latest super cool article! #endohyphalmicrobiome #mycovirus environmentalmicrobiome.biomedcentral.com/articles/10.... “Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes”

New in Mol. Ecol.: integrating multiple data and methods, we show how seasonal fluctuations in pathogen strain composition, diversity and their climate-influenced fitness play a significant role in shaping severity and variability of bacterial disease outbreaks doi.org/10.1111/mec.... #PlantHealth

T6SS-mediated competition by Stenotrophomonas rhizophila shapes seed-borne bacterial communities and seed-to-seedling transmission dynamics #mSystems from Alain Sarniguet @irhs-angers.bsky.social with @lmatthieul.bsky.social @microbialmarie.bsky.social journals.asm.org/doi/10.1128/...

Experimental evolution of plant rhizobacteria reveals emerging adaptive mutations -in #mBio Pseudomonas bijieensis ▶️ wheat rhizosphere ▶️ fleN mutations ▶️ increased flagella number ▶️ enhanced motility and colonization capacity in the wheat rhizosphere journals.asm.org/doi/10.1128/...

An effluent pump family distributed across plant commensal bacteria conditions host- and organ-specific glucosinolate detoxification

The July 2025 issue is now online! With the cover image representing the power of synthetic microbial communities in promoting plant growth. www.cell.com/issue/S0966-...

🌍🦠 World Microbiome Day shout-out: we’ve just unveiled the Microbiota Vault—a planetary backup for microbial diversity. Built on equitable, One Health values & linked to the new IUCN SSC Microbiomes. Read our Nature Comms piece: doi.org/10.1038/s414... #MicrobiotaVault #Conservation #WMD2025

Stepping out of the dark: How metabolomics shed light on fungal biology in @femsjournals.bsky.social Microbiology Reviews academic.oup.com/femsre/advan...

A new Consensus Statement led by @greening.bsky.social and @noahfierer.bsky.social in @natmicrobiol.nature.com Guidelines for preventing and reporting contamination in low-biomass microbiome studies ❗A must-read for anyone working in this field #microsky 🧪🦠 www.nature.com/articles/s41...

Amazing paper for chronomicrobiologists in @cp-cellhostmicrobe.bsky.social 👇🏼 Metatranscriptomics uncovers diurnal functional shifts in bacterial transgenes with profound metabolic effects www.cell.com/cell-host-mi...

Congratulations to our Phd student Kristin Hauschild to her first-author-paper no.3 🥳 Here we tested whether different soil amendment strategies (catch crops, microbial inoculants) can improve apple plant performance in replant disease-affected soil. academic.oup.com/femsec/artic...

Role of soil microbes in enhancing #crop heterosis #iMetaOmics onlinelibrary.wiley.com/doi/10.1002/... #microbiome #SoilHealth

Which model should be used? Which explanatory variables should be selected?... Let's use a model ensemble instead of a single model to characterize and predict spatio-temporal disease distributions. Read our ms in @phytopathology.bsky.social with application to virus yellows doi.org/10.1094/PHYT...

Do this first!

【EDITOR'S CHOICE】 #MicrobialCommunity structure in #Rice #Rhizosheaths🌾 under #Drought stress #Water-useEfficiency doi.org/10.1093/jpe/...

Thrilled to share our new paper in @science.org describing our discovery that bacteria can switch from competitors to bonafide predators when resources run dry—arming nanoscale “spears” (T6SS) to stab & consume neighbours. www.science.org/doi/10.1126/... #MicroSKy #Microbiology

#See#microbiome environmentalmicrobiome.biomedcentral.com/articles/10....

The new version of MetaPhlAn v4.2.2 released! 📌taxonomic profiling of long-read metagenomes for the first time 📌new version of the MetaPhlAn db (vJan25_202503) containing >21k new SGBs Try it out & @hutlab.bsky.social and we are looking forward to your feedback! forum.biobakery.org/t/metaphlan-...

The microbiome: An actor or stage for the beneficial action of probiotics, prebiotics, synbiotics, and postbiotics? Perspective by Sanders & Hill examining evidence that health benefits of “biotics” result from impacts on the microbiome. www.cell.com/cell-host-mi...

Peptides in plant–microbe interactions: Functional diversity and pharmacological applications -in The Cell Surface www.sciencedirect.com/science/arti...

(5/5) 🚨 It’s time to flood the zone. NIH scientists just took a huge risk speaking out. Now it’s our turn. 📜 Read the Bethesda Declaration ✍️ Sign the Public Letter of Support 👯‍♀️Follow NIHers doing the work: @nihvigils.bsky.social Read and sign here 👉 www.standupforscience.net/bethesda-dec...

The latest publication from our lab! The famous "glomalin" from arbuscular mycorrhizal (AM) fungi is not a protein but a polysaccharide from AM fungi, so we renamed it "glomalose". Glomalin-related proteins are bacterial proteins stuck in this glomalose. nph.onlinelibrary.wiley.com/doi/10.1111/...

How do dominant plants' functional traits affect biomass responses to global change? New paper by Mingyan Hu et al uses the large Manipulation Experiments Synthesis Initiative (MESI) database to find out. besjournals.onlinelibrary.wiley.com/doi/epdf/10....

One more week to apply for an open PhD position in my team at Utrecht University. Interested in genetics, genomics, bioinformatics, microorganisms and plant-microbiota interactions, don't hesitate and apply! www.uu.nl/en/organisat...

Coexistence ecology of pathogen-inhibiting microbes in the phytobiome #Pseudomonas "bacterial coexistence and interactions in host plant–microbe and microbe–microbe relationships" 🌱 @cp-trendsplantsci.bsky.social Review from Heribert Hirt www.cell.com/trends/plant...

📢 New #Colletotrichum #biocontrol study out, in collaboration with our colleagues at #Tec-Monterrey. "Control of avocado anthracnose by carposphere-associated Kosakonia cowanii VG1 for agricultural applications". Led by V. Gallardo-Camarena and C. Licona-Cassani. doi.org/10.1186/s135...

Successfully presented my exit seminar today! I’ve got some minor revisions to do, but then I submit my dissertation next week! @lmatthieul.bsky.social @ucdavis.bsky.social

New paper! led by Ruben Bernardo-Madrid "A general rule on the organization of biodiversity in Earth’s biogeographical regions" in NEE @natureportfolio.nature.com Read it here: doi.org/10.1038/s415...

📣 We have a postdoc position in fungus-microbiota interactions! Apply here: jobportal.uni-koeln.de/bewerben/2197 ⁩ For more details, visit: bewerbungsmanagement.uni-koeln.de/ausschreibun...

Scientists are nerds, so when a new transposable element was found to move big chunks of fungal genomes around & also between species (horizontal gene transfer), they called them 'Starships' and the enzyme that mobilized them are 'Captains'. To explore strange new worlds! 🍄🧬🖖