Stéphane Hacquard

Genetic factors driving multi-host infection in a core member of the root mycobiota https://www.biorxiv.org/content/10.1101/2025.12.01.690973v1

Super excited and honoured to have been awarded an ERC Starting Grant for CooPAIRation!

How do plant immune receptors work together to trigger an immune response? Can we modulate immune responses for disease resistance? We will tackle these questions in CooPAIRation

Positions to be announced soon!

Plant-associated fungi co-opt ancient antimicrobials for host manipulation Evolutionary histories of effector proteins secreted by fungal pathogens to mediate plant colonization remain largely elusive. While most functionally characterized effectors modulate plant immunity, ...

📣 NEW PREPRINT 📝

We identified evolutionary origins of many fungal effectors!
We show that fungi secrete lots of antimicrobial proteins, and that some of them were repurposed by plant pathogens for host immune suppression.
www.biorxiv.org/content/10.1...

cc @teamthomma.bsky.social

Coming back from 5 days of great science at #2025ISMPMI, I wanted to share some of my highlights, and particularly to mention my favourite presentations by early career researchers.

A thread 🧵 ⬇️

Emergence of isochorismate-based salicylic acid biosynthesis within Brassicales | PNAS Salicylic acid (SA) is a major defense phytohormone. In Arabidopsis thaliana, the isochorismate (IC) pathway is the primary route for pathogen-indu...

I'm very happy that this paper is now published in PNAS!

Isochorismate-based salicylic acid biosynthesis appears to have emerged in the Brassicales after the divergence of C. papaya, likely within the timeframe between the divergence of B. maritima and R. odorata.

www.pnas.org/doi/10.1073/...

Pseudomonas intra-genus competition determines the protective function of synthetic bacterial communities in Arabidopsis thaliana The plant microbiome can protect its host against detrimental bacterial strains. This study shows that competition among Pseudomonas bacteria in synthetic bacterial communities determines how well the...

Our paper on Pseudomonas intra-genus competition in SynComs on Arabidopsis roots is now out @plosbiology.org ! 🎉
If you want to chat about the story, visit poster 374 tomorrow, Thursday #2025ISMPMI

journals.plos.org/plosbiology/...

The post shows a picture of Ram after successfully passing her viva on a green background with words congratulating him on acquiring the PhD title.

Celebrating a new PhD at @mpipz.bsky.social! 🎓 Dr. Ram Sevak Raja Kumar defended her thesis in @hacquardst.bsky.social’s lab. Congrats, and all the best for what’s next! 🌟 #PhDone #PlantScience

Thanks Ute!

MetaFlowTrain: a highly parallelized and modular fluidic system for studying exometabolite-mediated inter-organismal interactions - Nature Communications Metabolic interactions shape ecosystems but remain hard to study. Here, authors present MetaFlowTrain, a modular, low-cost fluidic system controlling metabolic fluxes between microbes, and show its va...

📣Paper Alert! 📣New publication out by @hacquardst.bsky.social and his team on the development of MetaFlowTrain – a new tool to study metabolic exchange and interactions within microbial communities @naturecomms.bsky.social 👏🥳Congratulations! 👉https://bit.ly/44jnM1H
www.nature.com/articles/s41...

Very clever design and nicely presented. 👍

Thanks very much Johana!

New post doc opportunity in our team at Kiel University in the north of Germany. We are looking for a motivated molecular biologists to unravel plant-microbe interactions in grasses. Please see: www.uni-kiel.de/personal/de/...

More to our research and group here: www.environmental-genomics.de

Come and work with me!

The Nature Micro team is expanding and we're looking for someone to champion microbial ecology, plant micro & related areas for the journal

Knowledge of microbial ecology/plant micro is desirable but we're open to applications from all microbiologists

Link below 👇

Would you like to study metabolite-based microbe-microbe or plant-microbe interactions but do not have the tools to?
@chesneau-g.bsky.social came up with a simple solution with great potential! Check out our new publication in @naturecomms.bsky.social and Guillaume’s 🧵 below for details👇

5/5. MetaFlowTrain confirms that specific bacterial exometabolites, not media depletion, drive microbial antagonism.
🦠 Pseudomonas R401 WT suppresses SynCom growth via known inhibitory exometabolites.
❌ A triple mutant loses inhibitory power.

4/5. MetaFlowTrain dissects inter-kingdom microbial interactions via directional exometabolite flow.
🦠 Bacterial SynComs strongly inhibit fungal growth, even without physical contact.
🚫 Up to 82% growth suppression via exometabolites.

3/5. MetaFlowTrain reveals how soil conditioning alters microbial assembly/exometabolite output.
🦠 SynComs exposed to plant-conditioned peat undergo major community shifts & consume key metabolites (α-KG, fumarate).
🌱 BF SynCom-derived exometabolites impact Arabidopsis germination & root growth.

2/5. MetaFlowTrain cultivates diverse microbes & collects their exometabolites under continuous nutrient flow.
🌱 Using sterile peat extract, we grew 11 bacterial & 4 fungal strains from the Arabidopsis root microbiota.
💥 Exometabolite profiles differed significantly by strain.

📝 Paper: www.nature.com/articles/s41...
1/5. 🚂 MetaFlowTrain = 4 modular components:
a. Variety of liquid inputs
b. 24-channel pump enabling parallel metabolic trains
c. 3D-printed gnotobiotic microchambers
d. Multi-layered outputs for cell/metabolite analysis
🔗 protocols.io/view/36wgqd68ovk5/v3

YouTube video by Guillaume Chesneau MetaFlowTrain : A Highly-Parallelized and Modular Fluidic System.

🚨Excited to share our new publication! MetaFlowTrain, a highly parallelized and modular fluidic system to study exometabolite interactions between microbes-microbes-plants 🌱
@hacquardst.bsky.social @herpell.bsky.social S.Wolf S.Perin @mpipz.bsky.social
www.youtube.com/watch?v=gNUf...
🧵Thread 5/5:

Hi Ken! Thanks!!!

Thanks! Let’s hope this system will be useful to the community.

🙏🙏🙏

Thanks! We will be happy to help you to set it up.

Many thanks Fantin!!!

We present MetaFlowTrain, an easy-to-build, highly parallelized, and cost-effective fluidic system for studying microbial exometabolites and their roles in modulating microbe–microbe–host interactions. Kudos to @chesneau-g.bsky.social @mpipz.bsky.social
Give it a try: www.nature.com/articles/s41...

New paper from lab- in
@newphyt.bsky.social

Integrating ecological and evolutionary frameworks for SynCom success.

Led by @manudelbaq.bsky.social with Singh, Liu, Sáez-Sandino, Coleine, Muñoz-Rojas, Bastida, Trivedi
@microsky.bsky.social

nph.onlinelibrary.wiley.com/doi/full/10....

👏👏👏

Apoplastic barriers are essential for nodule formation and nitrogen fixation in Lotus japonicus Establishment of the apoplastic root barrier known as the Casparian strip occurs early in root development. In legumes, this area overlaps with nitrogen-fixing nodule formation, which raises the possi...

Finally!
Im so excited to present to culmination of many years of work from the fantastic Defeng Shen and some great collaborators. For details, I have made a digested thread below, but if you are more interested feel free to reach out (and read the paper of course).
www.science.org/doi/10.1126/...

POSTDOC POSITION AVAILABLE, UV-B Perception and Signalling, Geneva, Switzerland. Deadline approaching: 24.02.2025