Marie Simonin
@microbialmarie.bsky.social
Ecologist studying plant microbiota assembly and microbiome engineering / Seeds / SynComs 🦠/ Sustainable agriculture 🌾
Researcher at INRAE, France
http://mariesimonin.com/
Researcher at INRAE, France
http://mariesimonin.com/
Pinned
Marie Simonin
@microbialmarie.bsky.social
· Sep 12
www.sciencedirect.com
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...
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...
Reposted by Marie Simonin
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/...
nph.onlinelibrary.wiley.com/doi/10.1002/...
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...
nph.onlinelibrary.wiley.com
November 14, 2025 at 5:05 PM
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/...
nph.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Marie Simonin
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/...
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
November 14, 2025 at 3:36 AM
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/...
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Marie Simonin
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.
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.
Transgenerational decline through insidious effects of drought memory
Click on the article title to read more.
buff.ly
November 11, 2025 at 7:15 PM
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.
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.
Reposted by Marie Simonin
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...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Marie Simonin
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...
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 ...
www.nature.com
November 11, 2025 at 5:15 PM
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...
Reposted by Marie Simonin
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...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
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...
www.cell.com
November 9, 2025 at 9:39 AM
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...
@cp-trendsmicrobiol.bsky.social Spotlight by Kotaro Kiga and Rodrigo Ibarra-Chávez
www.cell.com/trends/micro...
Reposted by Marie Simonin
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...
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...
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.
www.nature.com
November 7, 2025 at 2:19 PM
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...
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
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
November 6, 2025 at 1:43 PM
#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
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
Some results from the SUCSEED project on culturomics and SynComs 🫘🧫🌱 #PMS2025
@emersys-irhs.bsky.social
November 4, 2025 at 8:10 AM
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
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
We will present results from the SUCSEED project on culturomics and seed microbiome engineering using multi-kingdom SynComs 🫘🧫
@emersys-irhs.bsky.social
November 2, 2025 at 10:28 PM
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
We will present results from the SUCSEED project on culturomics and seed microbiome engineering using multi-kingdom SynComs 🫘🧫
@emersys-irhs.bsky.social
Reposted by Marie Simonin
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
Looking forward to seeing you in Antequera (Malaga) on 3-7 November!
Final program at: 6thplantmicrobiomesymposium2025.com/programme/
#Plantscience #MicrobiomeResearch #Bioinformatics
October 30, 2025 at 6:03 PM
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
Looking forward to seeing you in Antequera (Malaga) on 3-7 November!
Final program at: 6thplantmicrobiomesymposium2025.com/programme/
#Plantscience #MicrobiomeResearch #Bioinformatics
Reposted by Marie Simonin
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....
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....
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...
microbiomejournal.biomedcentral.com
October 30, 2025 at 1:32 PM
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....
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....
Reposted by Marie Simonin
Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome
Ricks et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
Ricks et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
October 30, 2025 at 11:17 PM
Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome
Ricks et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
Ricks et al.
nph.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Marie Simonin
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...
To simplify things, I've attached a visual abstract.
Comments on the preprint are welcome!
#microsky #microbesky
www.biorxiv.org/content/10.1...
October 30, 2025 at 7:35 PM
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...
To simplify things, I've attached a visual abstract.
Comments on the preprint are welcome!
#microsky #microbesky
www.biorxiv.org/content/10.1...
Reposted by Marie Simonin
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
October 21, 2025 at 4:55 PM
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
Reposted by Marie Simonin
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
📖 doi.org/10.1111/nph....
#mycorrhiza #PlantScience
October 17, 2025 at 5:09 PM
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
📖 doi.org/10.1111/nph....
#mycorrhiza #PlantScience
Reposted by Marie Simonin
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...
More details below. The position will start next year.
Please circulate and repost.
jobs.smartrecruiters.com/WesternSydne...
October 2, 2025 at 4:32 AM
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...
More details below. The position will start next year.
Please circulate and repost.
jobs.smartrecruiters.com/WesternSydne...
Reposted by Marie Simonin
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/...
Paper here: www.science.org/doi/10.1126/...
Perspective here: www.science.org/doi/10.1126/...
October 7, 2025 at 9:52 AM
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/...
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
I enjoyed chatting about our research on seed microbiota, holobionts and alternatives to pesticides 🦠👩💻🌱
@emersys-irhs.bsky.social @irhs-angers.bsky.social
October 2, 2025 at 9:23 PM
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
I enjoyed chatting about our research on seed microbiota, holobionts and alternatives to pesticides 🦠👩💻🌱
@emersys-irhs.bsky.social @irhs-angers.bsky.social
Reposted by Marie Simonin
"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...
Nutritional endosymbionts are prevalent with a new 7,783 bacterial genomes from 1,373 bacterial species. @holobiontbiology.bsky.social
www.nature.com/articles/s41...
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.
www.nature.com
September 29, 2025 at 7:14 PM
"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...
Nutritional endosymbionts are prevalent with a new 7,783 bacterial genomes from 1,373 bacterial species. @holobiontbiology.bsky.social
www.nature.com/articles/s41...
Reposted by Marie Simonin
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...
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
doi.org
September 24, 2025 at 1:22 PM
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 🤓
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 🤓
September 26, 2025 at 8:16 AM
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 🤓
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 🤓
Reposted by Marie Simonin
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
June 12, 2025 at 8:16 PM
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
Reposted by Marie Simonin
👩🔬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 !
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 !
September 23, 2025 at 2:22 PM
👩🔬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 !
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 !
Reposted by Marie Simonin
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
Save the Date!
Join us for SeedCon 2026 – The First International Seed Microbiome Conference in Potsdam, Germany.
📅 May 5–7, 2026
More details coming soon: seedcon.org
#SeedCon2026 #SeedMicrobiome #MicrobialInheritance #PlantMicrobiome #Conference
Join us for SeedCon 2026 – The First International Seed Microbiome Conference in Potsdam, Germany.
📅 May 5–7, 2026
More details coming soon: seedcon.org
#SeedCon2026 #SeedMicrobiome #MicrobialInheritance #PlantMicrobiome #Conference
September 19, 2025 at 2:30 PM
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