Dear microbiome enthusiasts: I'm excited to be moving my lab to New York University this fall (& the NYU Institute for Engineering Health); with joint-appointment @isbscience.org I'm hiring a postdoc @ NYU to look at diet-driven evolution in the gut: apply.interfolio.com/189980 Please share! 🦠🤓

I know we are not ordinarily AI fans here, but I make an exception for Web of Microbes, which is an AI agent designed to help you design microbial consortia designed by Trent Northen’s group at LBNL and Mingxun Wang’s group at UCR. webofmicrobes.org

New preprint led by @logansuteau.bsky.social ! What really drives the success of seed-applied multi-kingdom SynComs ? -> Strain selection matters more than assembly strategy -> SynComs can reshape native bacterial communities via recruitment from soil and network integration doi.org/10.64898/202...

Seed-applied multi-kingdom synthetic communities selectively reshape bacterial communities and highlight key criteria for strain selection

Defined microbial communities (also known as synthetic communities) are showing promising results for plant health but are lacking an efficient lab to field transition. This is the due to limited know...

doi.org

Just in time for the weekend: our latest paper is out in Plant Biology! Anthocyanins and betalains in evolution: Why mutual exclusion remains the best-supported model doi.org/10.1111/plb.... #PlantBiology #Evolution #Anthocyanins #Betalains @puckerlab.bsky.social @unibonn.bsky.social

Anthocyanins and betalains in evolution: Why mutual exclusion remains the best‐supported model

Anthocyanins and betalains are plant pigments produced through different biosynthetic pathways and are generally considered mutually exclusive. We examine claims of their co-occurrence, arguing that ...

doi.org

I’m happy to share our review on the evolution of root systems in land plants @currentbiology.bsky.social @rootdevelopment.bsky.social @psb-vib.bsky.social www.cell.com/current-biol...

Evolution of root systems in land plants

In this review, Lakehal et al. chart the evolution of root systems, discussing key innovations in root morphology and the regulatory mechanisms that enabled land plants to adapt. They argue that crop ...

cell.com

Current Biology@currentbiology.bsky.social · 2mo ago

Our latest issue just dropped! It's green & special! And super meaty, even though it is about #plants #evolution! 🌵🌿🫛🍃🌱 This is all you need to read this week! www.cell.com/issue/S0960-...

📆 Save The Date! The Plant-Bacteria Interaction Meeting (18th RPB) in Aussois, Savoie will take place from January 11 to 15th, 2027 👉 More info on the keynote speakers & sessions: plants-bacteria-2027.symposium.inrae.fr Deadline: September 25th @inrae-dpt-spe.bsky.social @sfp-france.bsky.social

A comment in @natcomms.nature.com for the use of defined microbial communities for microbial applications I was glad to be involved in this highly collaborative discussions during online workshops last year, the thought from which are now published www.nature.com/articles/s41...

Ever wanted to use metagenomic data to infer oxygen levels (or the oxygen preferences of whole bacterial communities)? We have the tool for you: journals.asm.org/eprint/9GUIR...

Predicting oxygen levels in microbial habitats using a metagenome-based approach | mSystems

Oxygen is one of the most important environmental variables affecting microbial activity and composition, but is often difficult to measure in situ. We developed a tool, OxyMetaG, that leverages diffe...

journals.asm.org

Can we use ecological principles to increase coexistence in synthetic bacterial communities? Our new paper is now out in @isme-microbes.bsky.social: "Environmental complexity shapes maintenance of bacterial diversity through context-dependent interactions among niche axes" doi.org/10.1093/isme...

Environmental complexity shapes maintenance of bacterial diversity through context-dependent interactions among niche axes

Abstract. Microbial communities are often more species-rich than predicted from classical ecological models. The high levels of coexistence observed in nat

academic.oup.com

Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology Step 1: Determine whether machine learning is necessary or even worth doing journals.asm.org/doi/10.1128/...

Nine (not so simple) steps: a practical guide to using machine learning in microbial ecology | mBio

Microbial ecologists are increasingly turning to machine learning (ML) models to better identify and predict meaningful biological patterns and relationships in molecular microbial community data (inc...

journals.asm.org

HoloUI: A web application to fetch holobiont data from a RDF database cnrs.hal.science/hal-05651546/

Check this new paper of the team led by @bobytaillefer.bsky.social on Stenotrophomonas T6SS and its specific or broad spectrum antibacterial effectors targeting a diversity of strains from the seed microbiota 💉 🦠 @inrae-dpt-spe.bsky.social @irhs-angers.bsky.social

Boris Taillefer@bobytaillefer.bsky.social · 2mo ago

Happy to share this one as a post-doc fellow, attempting to describe the T6SS biology in Stenotrophomonas and the role of its effectors. Work under the supervision of the great Alain Sarniguet at @emersys-irhs.bsky.social @irhs-angers.bsky.social

The new OrthoFinder paper is out now! In this new work, we introduce major advances in accuracy and scalability, allowing analysis on much larger datasets www.nature.com/articles/s41... github.com/OrthoFinder/...

OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability - Nature Methods

The updated OrthoFinder v3 software boosts accuracy and scalability in phylogenetic orthology inference with massive and diverse datasets.

nature.com

📢 New paper from the lab! "Phytophthora root rot induces compositional and functional changes in avocado rhizosphere bacterial communities" We analyzed through metabarcoding and metatranscriptomic analyses the shifts in the 🥑 microbiota induced by #Phytophthora academic.oup.com/femsmicrobes...

Phytophthora root rot induces compositional and functional changes in avocado rhizosphere bacterial communities

Compositional and functional readjustments of the rhizobacterial community in avocado induced by Phytophthora root rot.

academic.oup.com

What determines who wins in bacterial competition? We review how the environment can influence bacterial warfare! Hopefully interesting for anyone who likes Bacteriocins (my favorite), T6SS, or CDIs! portlandpress.com/essaysbioche...

Here we show that low intra-microbiota antagonism underlies stable, protective barley root microbiota. Microbiota function cannot be predicted from beneficial traits of individual strains alone, but depends on compatibility among community members. #Microbiome #Plant www.biorxiv.org/content/10.6...

C'était une super expérience! Un grand merci aux organisateurs de @pintofscience.fr Angers et l'Echappée Belle Et regardez ces magnifiques notes visuelles qui résument mon intervention par Marion Dehay (Infographie) 🤩 @inrae-dpt-spe.bsky.social @irhs-angers.bsky.social

Marie Simonin @microbialmarie.bsky.social · 3mo ago

Très heureuse de participer au Pint of Science Angers, lundi prochain à L'échappée Belle 🍺🧫🌾 @pintofscience.fr @irhs-angers.bsky.social pintofscience.fr/event/graine...

Phages as ecosystem engineers of plant microbiomes: Cell Host & Microbe www.cell.com/cell-host-mi...

Phages as ecosystem engineers of plant microbiomes

Phages modulate plant microbiomes through bacterial lysis and by equipping bacteria with auxiliary genes through lysogeny. In this Forum, we highlight the underappreciated role of phages in plant heal...

cell.com

Xylem Endophytes of Salicaceae: potential role in mitigating disease symptoms from Xylella fastidiosa or Brenneria salicis 📖 nph.onlinelibrary.wiley.com/doi/10.1111/... by Pesenti et al. @WileyPlantSci #PlantScience

Cool experimental system for phyllosphere microbial ecology from @mitjare.bsky.social in bioRxiv👇🏼

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 3mo ago

Developing permeable polydimethylsiloxane-based biomimetic leaf surfaces to study phyllosphere microbial ecology. https://www.biorxiv.org/content/10.64898/2026.05.12.724494v1

📣 New preprint on @biorxivpreprint.bsky.social: Bacteria rewire fungal antimicrobial gene expression in microbial arms races www.biorxiv.org/cgi/content/... This work, led by outstanding @jinyi-zhu.bsky.social, shows that bacteria suppress fungal antimicrobial protein expression to evade antagonism

The common symbiosis pathway controls plant root microbiomes in a host-specific manner https://www.biorxiv.org/content/10.64898/2026.05.08.723321v1

Très heureuse de participer au Pint of Science Angers, lundi prochain à L'échappée Belle 🍺🧫🌾 @pintofscience.fr @irhs-angers.bsky.social pintofscience.fr/event/graine...

Graines de savoir, histoires de transmission

Découvrez le voyage fascinant du microbiote des graines : et si ce monde invisible était la clé pour remplacer les pesticides ? Puis, interrogeons nous sur…

pintofscience.fr

Save the date for #miCROPe2027 International Symposium Microbe-assisted Crop Production - Opportunities, Challenges & Needs June 1-3, 2027 Vienna, Austria www.micrope.org

Really useful paper explaining why richness/diversity metrics are rarely informative when applied to microbial community sequencing data: enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Rethinking Alpha Diversity in Marker‐Gene Microbiome Studies: Dominance Matters More Than Richness

Marker-gene microbiome surveys systematically under-sample rare taxa, causing alpha diversity metrics to reflect dominance rather than true richness. This conceptual mismatch can lead to misleading e...

enviromicro-journals.onlinelibrary.wiley.com

We had a great time in Potsdam, great science and people! Many thanks to @seed-con.bsky.social organizing committee We are happy to announce that we will host the 2nd SeedCon in Angers, Spring 2028 🎉 @irhs-angers.bsky.social Looking forward to welcoming you all 🫘

My PhD student Louna Colaert-Sentenac presented her cool work on the impact of SynComs on plant metabolome and microbiote assembly during bean seedling emergence 🫘🌱 From the SUCSEED project @irhs-angers.bsky.social

And now @thomas-chadelaud.bsky.social presenting the results of his PhD in the SUCSEED project Amazing experiments on the transmission routes of bacteria to the seeds during plant development. A really challenging topic to study, but so important! #SeedCon2026

Now the boss is on stage! @lmatthieul.bsky.social synthesizing his research on the genetic factors involved in the transmission of microbes to seeds Some cool dual transcriptomics during seed development and SynCom experiments to show the role T6SS in microbiota assembly #SeedCon2026

#SeedCon2026 Now Muriel Marchi from the FungiSem team @irhs-angers.bsky.social presenting a large yeast collection isolated from seeds & their effects on bean emergence in presence of soil borne pathogen Globisporangium ultimum So much we still don't know on their transmission and role for plants!