Marie Simonin

La conférence de presse se déroulera au Collège de France, 11, place Marcelin Berthelot, 75005 à Paris, de 16h à 18h30, avec accès à partir de 15h30. Elle est ouverte au public mais les questions seront réservées aux journalistes. Elle comprendra des interventions sur la situation de l’Université et de la recherche aux Etats-Unis et en France : Yasmine Belkaid, Directrice générale de l’Institut Pasteur Michel Feher, philosophe et co-fondateur de la maison d'édition ZoneBooks Julien Gossa, chercheur au Laboratoire Sociétés, acteurs, gouvernement en Europe, Université de Strasbourg Valérie Masson-Delmotte, chercheuse au Laboratoire des sciences du climat et de l'environnement, CEA Nonna Mayer, chercheuse au Centre d'études européennes et de politique comparée, Sciences Po

📣 Conférence Stand Up for Science
Vendredi 6 mars 2026｜16h-18h30｜Collège de France

Attaques contre les sciences et l’Université aux États-Unis et en France: comprendre les stratégies, cibles et effets et lancer des les mobilisations à venir en France, en écho à celles prévues aux États-Unis.

Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials Prebiotic and probiotic interventions can induce therapeutically relevant shifts in the human microbiome, but their effects are variable across individuals. This study shows that metabolic models can ...

Our latest is out today in @plosbiology.org:

"Metabolic modeling reveals determinants of prebiotic and probiotic treatment efficacy across multiple human intervention trials"

@isbscience.org @uwbioe.bsky.social @uwgenome.bsky.social

doi.org/10.1371/jour...

#transgenerational transmission of a core #microbiome that protects against downy mildew from soil to #phyllosphere

Fantastic and important study by @jellespooren.bsky.social @rlberendsen.bsky.social
@cornepieterse.bsky.social
academic.oup.com/ismej/advanc...
#plantscience

New paper from lab-@natecoevo.nature.com

Abiotic and biotic controls of non-native perennial plant success in drylands

Non-native plant success in drylands is facilitated by high grazing pressure & resource availability.

Led by Rahmanian and @ftmaestre.bsky.social

www.nature.com/articles/s41...

A Bayesian approach to differential prevalence analysis with applications in microbiome studies Recent evidence suggests that analyzing the presence/absence of taxonomic features can offer a compelling alternative to differential abundance analysis in microbiome studies. However, standard approa...

A Bayesian approach to differential prevalence analysis with applications in microbiome studies ("DiPPER") arxiv.org/abs/2602.05938

Check out our new preprint using 30 SynComs covering a phylogenetic diversity gradient, we uncover many interesting strain and community features involved in seed to seedling bacterial transmission 🧫🌱
@emersys-irhs.bsky.social in the SUCSEED project @inrae-dpt-spe.bsky.social

A permanent position as a research scientist is opened in our team! We look for a plant physiologist with expertise in plant / microorganism interactions to identify plant susceptibility factors to fungal disease. Please forward!

Pleased to share our article in @nature.com

'Pesticide mixtures harm soil biodiversity'.

Along with Alex Pedrinho, we highlight policy implications& future research of new pub from @mvanderheijden.bsky.social group to support pesticide regulations & soil biodiversity protection
rdcu.be/e1aHs

Happy to share my solo-authored Perspective "An Interpretation, Survey, and Outlook of Microbial Macroecology"! Making time these last few months to take stock of the patterns us microbial ecologists examine + models we invoke has been invaluable. Feedback welcome!

ecoevorxiv.org/repository/v...

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

🥁 NEW

Our study on infant gut microbiome and #straintransmission is now published in @nature.com:

doi.org/10.1038/s415...

1/10

Community conservatism is widespread across microbial phyla and environments - Nature Ecology & Evolution This study reveals that closely related microorganisms tend to inhabit similar communities across all major environments and phyla. The authors term this phenomenon ‘community conservatism’, extending...

Community conservatism is widespread across microbial phyla and environments
#microbiology #microbes #MicroSky
@natecoevo.nature.com
www.nature.com/articles/s41...

Assembly of the infant gut microbiome and resistome are linked to bacterial strains in mother’s milk - Nature Communications Here, with metagenomic analyses on longitudinal samples collected from 195 mother-infant pairs, the authors show that the breast milk microbiome contributes to infant gut assembly through bacterial st...

Breast milk isn't just nutrition – it delivers live bacterial strains that colonize the infant gut and persist for months.

Happy to share our new paper, where we used metagenomics to track bacterial strains between 195 mother-infant pairs over the first 6 months of life:

doi.org/10.1038/s414...

Ecological ubiquity and phylogeny drive nestedness in phages–bacteria networks and shape the bacterial defensome Author summary Viruses that infect bacteria, known as phages, are part of microbial communities and influence the abundance, diversity, and traits of their hosts. In an agriculture-related context, th...

#microsky #phagesky #phage
At last! Great to see this one out: journals.plos.org/plospathogen...

Here, we discovered a nested phage-bacteria network despite their high genetic and ecological diversity. Kudos to everyone involved, especially @chloe-feltin.bsky.social !
@phimresearch.bsky.social

The microbial keystone concept is a very cool topic in microbiome ecology. This review summarises mechanisms, prediction methods and implications, with "keystoneness" being highly context/time dependent + new methods approaches suggested. Very nice read!
www.nature.com/articles/s41...

Constructing a “periodic table” of bacteria to map diversity in trait space academic.oup.com/ismej/advanc... #jcampubs

Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial...

New paper up on bioRxiv! This is my third and hopefully final paper on rarefaction. It's still better than the other available methods.

www.biorxiv.org/content/10.6...

Il n'est plus tenable que notre gouvernement et, par là même, les médias qui relaient ses communications (ainsi que les verbatims de toutes les personnalités politiques), s'expriment via un outil de propagande fasciste étranger !

À vos signatures 👇
petitions.assemblee-nationale.fr/initiatives/...

Seed germination traits reveal naturalization potential: Global insights from temperate European herbaceous species This study provides global-scale evidence that the naturalization of European herbaceous species is related to specific germination traits acquired in the native range. The findings indicate that tra...

Seed germination traits reveal naturalization potential: Global insights from temperate European herbaceous species besjournals.onlinelibrary.wiley.com/doi/10.1111/... Enjoyable collaboration led by Margherita Gioria, now out #openaccess in @journalofecology.bsky.social #seedecology #invasivespecies

Scikit-bio: a fundamental Python library for biological omic data analysis - Nature Methods Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

Postdomestication selection of MKK3 shaped seed dormancy and end-use traits in barley "Anthropogenic selection of grain traits such as dormancy has shaped the developmental trajectories of crops. In cereals, shortening dormancy provides rapid and even postharvest germination, but increases the risk of weather-induced preharvest sprouting, with yearly harvest losses beyond 1 billion dollars. Our understanding of how, why, when, and where cereal dormancy diversification arose is fragmentary. Here, we show in the founder crop barley (Hordeum vulgare) that dormancy is primarily regulated through a mosaic of locus haplotypes comprising copy number variation and inherent kinase activity of Mitogen-activated protein kinase kinase 3 (MKK3). We provide evidence supporting the historical selection of specific MKK3 haplotypes that shaped dormancy levels according to changing climatic pressures and outline a genetic framework for breeders to balance grain dormancy and preharvest sprouting avoidance".

Postdomestication selection of MKK3 shaped seed dormancy and end-use traits in barley, https://pubmed.ncbi.nlm.nih.gov/41196947/

Troubleshooting common errors in assemblies of long-read metagenomes - Nature Biotechnology Long-read sequence assemblies from metagenomes contain frequent errors.

Troubleshooting common errors in assemblies of long-read metagenomes www.nature.com/articles/s41... #jcampubs

RAMBO: Resolving Amplicons in Mixed Samples for Accurate DNA Barcoding with Oxford Nanopore www.biorxiv.org/content/10.6... #jcampubs

A free, open-access library of high-quality organism illustrations for science communication We create vector graphics of model organisms and emerging biological research organisms to enhance our publications. We’re sharing these editable graphics under a CC0 license for other scientists to...

A free, open-access library of high-quality organism illustrations for science communication

Cooperation is a universal feature of complex systems, from the origins of life and microbiomes to societies. What universal patterns can be found in these systems? Here's our new @pnas.org paper. @jordipinero.bsky.social @artemyte.bsky.social @sfiscience.bsky.social www.pnas.org/doi/epdf/10....

Transformer-based Prediction of Microbial Growth Rates from
Genomic Data
doi.org/10.1145/3765...

Check our new perspective paper exploring how the seed holobiont goes to sleep 😴 and reactivate for germination.
A lot of exciting research to be done to understand dormancy mechanisms in microbes and plants ☘️
@emersys-irhs.bsky.social @irhs-angers.bsky.social

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...