Sophie Abby

The best stories are the personal ones. So before we get to the new preprint, stay awhile and listen

#MobileLabs #TREC

Giant multicellular magnetotactic prokaryotes in marine sediments academic.oup.com/ismej/advanc... #jcampubs

Check out our latest pre-print of our favourite pets - the breviates. This work was led by Zhezhen Yi in collaboration with @andrewjroger.bsky.social and many others! By studying diverse breviates we were able to see how different metabolic pathways can evolved in response to low-oxygen.

Archaea produce peptidoglycan hydrolases that kill bacteria Archaea regularly interact with bacteria but reports of archaea killing bacteria are very rare. This study shows that many archaea encode peptidoglycan hydrolases, which specifically target bacterial ...

Archaea are often surrounded by bacteria. But is there ever active conflict between the two? Can archaea kill bacteria? If so, how do they do it?

Work by @romainstrock.bsky.social shows that some archaea can kill bacteria by secreting peptidoglycan hydrolases. journals.plos.org/plosbiology/...

Evolution and diversity of oxidoreductases involved in redox balance and energy conservation - Nature Ecology & Evolution HORBEC are protein complexes involved in the regulation of redox balance and energy conservation. The authors develop a bioinformatic tool for HORBEC annotation in bacterial and archaeal genomes and r...

Passioned by #bioenergetics? Do not miss our new article on the evolutionary history of oxidoreductases with G. Borrel and @sgribaldo.bsky.social @archaeal.bsky.social @valdeanda.bsky.social @pasteur.fr @cnrs.fr @cnrsbiologie.bsky.social @natecoevo.nature.com (www.nature.com/articles/s41...).

Comparative Genomics of Unicellular Eukaryotes (San Feliu, Spain):
Abstract submission is open, with a short deadline! comparativegenomics2026.com

Join us as we explore the most diverse, surprising, and still largely uncharted branches of the eukaryotic tree.

A reminder to sign up for the 2026 EMBO archaeal meeting im Cambridge: meetings.embo.org/event/26-arc.... Registration is open. We are looking forward to hosting you!

My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵

🔁 🙏

#microSky #phagesky #UTIsky
@cnrs.fr

🚨 Postdoctoral Opportunity for Female Scientists🚨

The University of Vienna is awarding at least 20 fully funded 4 year postdoctoral positions to outstanding female scientists

Interested? Get in touch via direct message
careers.univie.ac.at/en/postdoc/e...

#MicroSky 🧪

#PostDoc @univie.ac.at

legend 2025 will be next Tuesday/Wednesday/Thursday.

The detailed program is on legend2025.sciencesconf.org?lang=en

If you are not attending the conference you can still follow the presentations online (Zoom links are on the website).

Dynamic protrusions mediate unique crawling motility in Asgard Archaea (Promethearchaeota) Crawling motility is a hallmark of eukaryotic cells and requires a dynamic actin cytoskeleton, regulated adhesion, and spatially organized signalling pathways1–3. Asgard archaea (phylum Promethearchae...

Asgard on the move ! Watch our videos!
Biorxiv.org/content/10.1101/2025.11.30.690169v1

Oxygen production as an electron overflow pathway in ammonia-oxidizing archaea www.biorxiv.org/content/10.6... #jcampubs

The CNRS is breaking free from the Web of Science From January 1st 2026, the CNRS will cut access to one of the largest commercial bibliometric databases, Clarivate Analytics'

From January 1st 2026, the CNRS will cut access to one of the largest commercial bibliometric databases, Clarivate Analytics' Web of Science, along with the Core Collection and Journal Citation Reports.

Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device Abstract. Because accessing the small intestine is technically challenging, studies of the small intestinal microbiome are predominantly conducted in patie

Exploring the human small intestinal luminal microbiome via a newly developed ingestible sampling device url: academic.oup.com/ismecommun/a....
I am proud to have contributed to this work with Alexandre Tronel, Thomas Soranzo (Pelican Health), @alegouellec.bsky.social + all other co-authors.

Une scientifique dit: "Attendez une minute... Les gens sur le spectre autistique sont sur-représentés dans la recherche scientifique. Mais... Mais ça veut dire que..." Un autre réalise soudain, et murmure: "Mon Dieu..." La légende dit: "L'autisme cause les vaccins."

Vaccines and Autism, par @zachweinersmith.bsky.social

🔥 At conferences, who asks the questions shapes who gets seen. Across 24 ID&CM meetings, women were 55% of delegates but asked 36% of questions.
💬 When women moderate or speak first, others follow.
Let’s change the pattern

bit.ly/47VL0eH
🙏 @maudsalmona.bsky.social & MicroID EmpowHERment consortium

So Nature-Springer, which absorbs several billion dollars in research funding each year, provides us with an API that attributes all citations to the first article in the volume.

Well done Springer Nature, at least I know where not to submit my next paper.

This paper has been a must! Great collaboration with @mkrupovic.bsky.social and @yifanzhou.bsky.social, a N&V by a legend of halophilic archaea tinyurl.com/yc3dcv72, and one picture of one of our expeditions to Dallol making the cover of the November issue of @natmicrobiol.nature.com

rdcu.be/eLtCH

JOB OFFER #PhageSky

We have a postdoc position opening in my group to investigate phage-MGE interactions !

We're based in the very nice city of Lyon, France @mmsb-lyon.bsky.social

Contact me for more info !

>> Apply on the CNRS webpage emploi.cnrs.fr/Offres/CDD/U...

The team at our research site in the alps

📣 New PhD student position opening in my lab!
Soils are full of microbes, but how many are active?
Surprisingly, we still lack reliable methods to answer this.
If you are interested in microbial dormancy and are fascinated by the Alps and glacier forefields, contact me.
🏔️ 🦠 💤 🧬 🎓

Open position to work on Type IX secretion (#T9SS) in our lab, in collaboration withe the group of Eric Reynolds at the Dental School of the University of Melbourne. Please spread the word, and forward to anyone potentially interested ! Apply here:
emploi.cnrs.fr/Offres/Docto...

Exploring the space of self-reproducing RNA using generative models, Martin Weigt Exploring the archaic introgression landscape of admixed populations through joint ancestry inference, Jazeps Medina Tretmanis [et al.] Predicting natural variation in the yeast phenotypic landscape with machine learning, Sakshi Khaiwal [et al.] Phylodynamic modeling with unsupervised Bayesian neural networks, Marino Gabriele [et al.] Likelihood-free inference of phylogenetic tree posterior distributions, Luc Blas- sel [et al.] Generative continuous time model reveals epistatic signatures in protein evolu- tion, Barrat-Charlaix Pierre Neural posterior estimation for high-dimensional genomic data from complex pop- ulation genetic models, Jiseon Min [et al.] A differentiable model for detecting diversifying selection directly from alignments in large-scale bacterial datasets, Leonie Lorenz [et al.] Detecting interspecific positive selection using transformers, Charlotte West [et al.] Predicting Multiple Sequence Alignment Uncertainty via Machine Learning, Lucia Martin-Fernandez [et al.] Graph Neural Networks for Likelihood-Free Inference in Diversification Mod- els, Amélie Leroy [et al.] Popformer: learning general signatures of genetic variation and natural selection with a self-supervised transformer, Leon Zong [et al.]

PRIVET: PRIVacy metric based on Extreme value Theory, Antoine Szatkownik [et al.] Generative models for inferring the evolutionary history of the malaria vector Anopheles gambiae, Amelia Eneli [et al.] Language Models Outperform Supervised-Only Approaches for Conserved Ele- ment Comprehension, Eyes Robson [et al.] Identification and Classification of Orphan Genes, Spurious Orphan Genes, and Conserved Genes from the human microbiome, Chen Chen Neural Simulation-based inference of demography and selection, Francisco De Borja Campuzano Jiménez [et al.] Species Identification and aDNA Read Mapping Using k-mer Embeddings, Filip Thor [et al.] Contrastive Learning for Population Structure and Trait Prediction, Filip Thor [et al.] Protein and genomic language models chart a vast landscape of antiphage de- fenses, Mordret Ernest The Phylogenomics and Sparse Learning of Trait Innovations, Gaurav Diwan [et al.]

The decisions for LEGEND are out: legend2025.sciencesconf.org/data/book_le...

I'm really looking forward to hearing these 21 exciting presentations (and additional 30 posters) next December.

If you want to attend too, registration is open until October 17th through legend2025.sciencesconf.org

Become my colleague @oxfordbiochemistry.bsky.social !
2 Associate Professorships in the areas of
- prokaryotic/eukaryotic microbiology
- metabolism

my.corehr.com/pls/uoxrecru...

Anaerobic breviate protist survival in microcosms depends on microbiome metabolic function Abstract. Anoxic and hypoxic environments serve as habitats for diverse microorganisms, including unicellular eukaryotes (protists) and prokaryotes. To thr

Now completely published :)
Really proud of this paper led with Karla at @cstairs.bsky.social lab.
doi.org/10.1093/isme...

We would like to thank the scientists across the world who characterize quinones in newly described species and publish their work e.g. in IJSEM from @microbiologysociety.org, Antonie van Leeuwenhoek, Archives of Microbiology and Systematic and Applied Microbiology. Quinones rock! 🤩 5/5

...and after the study brilliantly conducted by Dr. Chobert on the dynamics of the quinone repertoire in Pseudomonadota that accompanied their metabolic diversification, also published earlier this year in the ISME Journal from @isme-microbes.bsky.social. 4/5
doi.org/10.1093/isme...

A novel quinone biosynthetic pathway illuminates the evolution of aerobic metabolism | PNAS The dominant organisms in modern oxic ecosystems rely on respiratory quinones with high redox potential (HPQs) for electron transport in aerobic re...

This much-needed compendium of quinones in bacteria is the last chapter of S. Chobert's PhD thesis. This comes after the discovery of a high potential quinone, the methylplastoquinone, led by @lipidorama.bsky.social and colleagues published earlier in @pnas.org... 3/5
doi.org/10.1073/pnas...

Among other discoveries, we show that the two menaquinone pathways tend to replace one another frequently, and that a lineage outside of Pseudomonadota unexpectedly show the potential to produce ubiquinone, a high redox potential usually found in Pseudomonadota and Eukaryota. 2/5

Really glad to announce a new preprint from our lab: Global distribution of quinones in Bacteria! We here combine comparative genomics and text mining to leverage information on quinones distribution from thousands of articles describing new species and from dozens of thousands of genomes! 1/5

ATLASea #recrute:

Ingénieur développeur - DevOps (H/F) à RENNES
IT en contrat CDD de 13 mois
Date d'embauche prévue : 1 novembre 2025

Plus d'informations:
emploi.cnrs.fr/Offres/CDD/U...

#hiring #job