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...

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...

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 🤓

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

👩‍🔬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'en ai encore sous le coude! @corinnevacher.bsky.social @hpidon.bsky.social @hblaszki.bsky.social @mireiagoga.bsky.social @melaniegasser.bsky.social @joellefournier.bsky.social @gaelle-mrlc.bsky.social @audrey-goman.bsky.social @marccamb.bsky.social

@luciezinger.bsky.social @olayarendueles.bsky.social @sundymaurice.bsky.social

Merci ! @tiffany-grn.bsky.social @clara-inrae.bsky.social @chloe-feltin.bsky.social @amina-ilyas.bsky.social @amaugarny.bsky.social @mfdignac.bsky.social @ashley17061.bsky.social @paduba.bsky.social @prokaryote22.bsky.social @justinefoucher.bsky.social @gersendel.bsky.social @ifudal.bsky.social

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

Transient microbial architects: tracing the legacy effects of ephemeral taxa during plant microbiome assembly

Current Opinion in Microbiology by @logansuteau.bsky.social et al from @microbialmarie.bsky.social

www.sciencedirect.com/science/arti...

Uncertainty Modeling Outperforms Machine Learning for Microbiome Data Analysis Microbiome sequencing measures relative rather than absolute abundances, providing no direct information about total microbial load. Normalization methods attempt to compensate, but rely on strong, of...

New Paper!

Machine learning models that attempt to predict microbial load collapse outside of their training context with an R2<0!

In contrast, our Bayesian Partially Identified Models embrace uncertainty in unmeasured microbial load and consistently outpreform.

www.biorxiv.org/content/10.1...

Excited to summarize our most recent paper, "Explicit Scale Simulation for analysis of RNA-sequencing count data with ALDEx2" on controlling the false discovery rate (FDR) when analyzing high throughput sequencing (HTS) data. This has been an open problem since the dawn of HTS.

Pleased to share our new article in Cell Host & Microbe, a collaboration with the group of Zhong Wei at NJAU

Common mycorrhizal networks facilitate plant disease resistance by altering rhizosphere microbiome assembly

Free share link: authors.elsevier.com/c/1lnTD6t8JE...

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...

DAGs showing confounding, mediator and collider variables

Super awesome new paper in #MEE describing #causal #detection of shifts in #biodiversity! So many great insights here—a must read for those interested in #causalinference

And love Fig 3! Congrats team! @lsantinieco.bsky.social

doi.org/10.1111/2041...

Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change Abstract. The relationship between, and joint selection on, a host and its microbes—the holobiont—can impact evolutionary and ecological outcomes of the ho

Within-host microbial selection and multiple microbial generations buffer the loss of host fitness under environmental change

@femsjournals.bsky.social Microbiol Ecology by @williampearman.bsky.social et al

academic.oup.com/femsec/advan...

Top: Experimental design where five laboratories across three continents conducted the same experiment using shipped materials. These included a detailed protocol, SynComs and Mock solution stocks, light and temperature loggers, Brachypodium distachyon seeds, EcoFAB 2.0 device parts, and various lab supplies (growth medium, filters, sampling tubes). The authors inoculated B. distachyon plants with either a 16- or 17-member SynCom, with controls being axenic plants and medium-only technical control (Mock-inoculated), n = 7. They tested sterility and imaged roots at multiple time points, quantified plant biomass, analyzed exudate metabolite composition, and measured root and medium microbiomes. Bottom: An illustration showing a global centralized network of laboratories collaborating to study the rhizosphere microbiome and metabolome. Image credit: Kent Leech

Reproducibility in #plant #microbiome experiments. This collaborative effort involving 5 labs achieved consistent, inoculum-dependent results, providing detailed protocols, datasets & best practices to promote #reproducibility in #PlantMicrobiome studies @plosbiology.org 🧪https://plos.io/41IVzzk

Interested in exploring prophages in your (meta)genomes, but don't know how and where to start? We've put together a beginners guide to exploring viral diversity in prokaryotes @marievasse.bsky.social
@sebwielgoss.bsky.social
@oxunipress.bsky.social

Pig breeds reared on the same farm exhibit rippling waves of #phylosymbiosis with their bacterial communities, viruses, mobile genetic elements, and antibiotic resistance genes (ARGs). ARGs is a first. 👀
www.sciencedirect.com/science/arti...

Revisiting the cry-for-help hypothesis in plant–microbe interactions The ‘cry-for-help hypothesis’ (CHH) is broadly used to study how root exudate modulation under stress influences recruitment of beneficial microbes in the rhizosphere. Here, we explored common misconc...

Revisiting the cry-for-help hypothesis in plant–microbe interactions

@cp-trendsplantsci.bsky.social Forum from @fdiniandreote.bsky.social

www.cell.com/trends/plant...

Ep. 539 - Exploring the Seed Microbiome — In Defense of Plants In Defense of Plants' Matt Candeias talks with Dr. Gillian Bergmann about the microbiomes of seeds.

I did an interview with the In Defense of Plants podcast about my journey into researching seed microbiota, some of what we currently know and what remains to be explored! You can check it out here: www.indefenseofplants.com/podcast/2025...

Holobiont-based genetic analysis reveals new plant and microbial markers for resistance against a root rot pathogen complex in pea - BMC Plant Biology The pea root rot complex is caused by various soil-borne pathogens that likely reinforce each other, influencing the composition of the root microbiome and leading to significant yield reductions. Pre...

It’s simply the right way. A hologenome approach increases predictive accuracy: “Likewise, when using the OTU abundance to predict the pea resistant phenotype, significantly higher prediction abilities were observed than all SNP marker-based approaches” bmcplantbiol.biomedcentral.com/articles/10....

Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops Plant domestication is a coevolutionary process shaped by human selection, favoring traits supporting modern-day agriculture. This process has reduced…

Born to rewild: Reconnecting beneficial plant-microbiome alliances for resilient future crops

@cp-cellhostmicrobe.bsky.social review by Dario X. Ramirez-Villacis, Antonio Leon-Reyes, @cornepieterse.bsky.social and Jos Raaijmakers @niooknaw.bsky.social

www.sciencedirect.com/science/arti...

My team has updated our free database of POSTDOC fellowships.

This database contains 286 entries. For each entry, we provide a link, short description, deadline, amount, and eligibility criteria.

Download this updated and expanded database here: research.jhu.edu/rdt/funding-...

The microbiome of plant woody tissues is far more diverse than we thought 🤩

How thoughtful experimental design can empower biologists in the omics era - Nature Communications Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

Great publication from Maggie Wagner (KU) and Manuel Kleiner (NCS) on how to design microbiome (+ other Omic) projects with downstream statistics in mind!

A must read for trainees!
www.nature.com/articles/s41...

Applying ecological principles to microbiome engineering - Nature Microbiology This Perspective discusses the application of ecological principles of macro-ecosystems to microbiome engineering. The authors propose research priorities necessary to facilitate the application of th...

#Perspective

In this perspective, the authors propose research priorities necessary to facilitate the application of these ecological principles to improve microbiome functionality.

#MicroSky #MicrobiomeSky 🦠

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