Happy to have hosted a workshop on host-microbiome interactions @irhs-angers.bsky.social co-organized with IGEPP with more than 50 people 🌱🦠
Cool to see all the innovative approaches on our technical platforms, from single cell omics to metabolomics & sequencing
Thanks for the support of SFR QuaSav

Deciphering microbial interactions using a label-free microbead sorting approach Abstract. Microorganisms form communities, and their interactions shape the function and stability of these communities. Understanding these interactions c

Deciphering microbial interactions using a label-free microbead sorting approach academic.oup.com/ismecommun/a... #jcampubs

Microbial communities can harbor many species that do not coexist in pairs, yet can coexist in the full community. Here we provide the mathematical foundations of emergent coexistence, and explain why it can't be predicted from pairwise tests journals.plos.org/ploscompbiol...

Our work on 'hidden diversity' in unbinned contigs is now published in @natmicrobiol.nature.com :

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

See the linked threads for more details!

A roadmap for plant–microbiome breeding to enhance plant stress tolerance Plants constantly form associations with microorganisms, and some are vital for plant performance, especially under stress conditions. Although some microorganisms have been developed into commercial ...

A roadmap for plant–microbiome breeding to enhance plant stress tolerance
www.cell.com/trends/micro...

Efficient and accurate search in petabase-scale sequence repositories - Nature MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.

MetaGraph by Karasikov and coauthors makes the world’s DNA searchable. By turning 67 petabases of raw sequences into a compressed graph structure, it enables fast, low-cost search across global genomic data—bringing biology closer to having its own “search engine”. www.nature.com/articles/s41...

Nitrogen fixation, crop production and bacterial communities of common bean cultivars: a 77-year breeding perspective | Plant and Soil | Springer Nature Link

I’m very happy to see my fist article now officially published 🥳 great work by my partner in crime @wolki95.bsky.social and the rest of @teamthomma.bsky.social! Find it here: doi.org/10.1111/nph.... or have a look at the 🧵⬇️

Announcing StrainVis! 🦠🧫🧪

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

This nifty web-based tool allows you to visualize your strain level analyses. You can combine ANI and synteny based analyses and it will make all kinds of cool publication ready plots for you - examples follow. By Hagay Enav and Inbal Paz:

See the thread below for the newest story from the PATHOCOM consortium!

I initiated a plant pathology/plant microbe starter pack, feel free to self-nominate 🥀

go.bsky.app/LbYaW8k

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