Marie Simonin

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...

BarTn7: Optimizing Bacterial Lineage Tracking at Sub-Species Resolution for Population Dynamics in Ecological and Evolutionary Studies Communities of bacteria undergo population bottlenecks which are crucial to their population, ecological, and evolutionary dynamics. However, conventional amplicon sequencing cannot distinguish such d...

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...

Keystone Pseudomonas species in the wheat phyllosphere microbiome mitigate Fusarium head blight by altering host pH Fusarium graminearum (F. graminearum) pathogen induces wheat phyllosphere alkalinization, promoting the development of Fusarium head blight (FHB). Xu et al. show that host-acidifying Pseudomonas, sele...

🎉 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

Impact of fruit decomposition on soil and plant microbiomes. (a) Fruits harbor their own microbiome, which is released into the soil upon decomposition. (b) Fruit decomposition changes the soil microbiome by introducing fruit-associated microbes and altering microbial interactions. (c) As seeds germinate, the enriched soil microbiome colonizes the emerging plant, influencing the microbial assembly in roots and shoots. This interplay between fruit decomposition, soil microbial dynamics, and plant colonization suggests that fruits may play an active role in shaping the microbiome of the next plant generation beyond seed dispersal. This figure was created in BioRender (https://BioRender.com/tw7zbn6).

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/...

Demystifying fungal systematics: A gateway to fungal literacy and societal/ecological relevance through familiar species Fungal systematics can feel overwhelming given the vast species diversity within this kingdom, with numerous subgroups at every taxonomic rank. This often creates a disconnect between the undertsnidn...

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/...

Transgenerational decline through insidious effects of drought memory Click on the article title to read more.

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...

Predicting the first steps of evolution in randomly assembled communities - Nature Communications Evolution often occurs within complex communities, but the way this context controls the rate and impact of evolution is poorly understood. The authors employ a model of resource competition to study ...

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 Microbial hitchhikers are rewriting the rules of horizontal gene transfer. He, Patkowski, et al. reveal how phage satellites assemble chimeric infective particles that deliver DNA across species bound...

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 - Nature Microbiology Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

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

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...

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....

Expectations for adaptive recruitment in the microbiome.

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...

Fig. 1. Diversity of leaf symbiotic structures.

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

Manifestation of symbiont plasticity, expressed as root mutualist flexibility.

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

Genome-resolved metagenomics reveals microbiome diversity across 48 tick species - Nature Microbiology Sequencing the genome and microbiome of about 1,500 tick samples from regions across China revealed host–microbe associations in ticks that could have implications for controlling ticks and tick-borne diseases.

"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...

Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies Abstract. Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynCom

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...