Guillaume GAUTREAU
@guigau.bsky.social
PhD in #CompBio. (Meta/Pan)genomics. Health Law. GDPR compliance. http://orcid.org/0000-0002-0970… INRAE scientist at MaIAGE.
Une nouvelle version de la plateforme #ABRomics est disponible ! Déployée ce 24 juillet, nous sommes heureux d'annoncer la sortie de la version 1.5.0 de la plateforme d'analyse ABRomics. De nombreuses nouvelles fonctionnalités sont à découvrir et explorer, telles que 👇
🧬 We're thrilled that PANORAMA has been published! An open-source method to predict & compare biological systems across bacterial pangenomes. Built on PPanGGOLiN, it runs at #pangenome scale in minutes vs. hours for genome-by-genome tools. 📄 doi.org/10.1371/jour... @jpjarnoux.bsky.social
📣 Meet Guillaume Gautreau at #JOBIM2026 poster session B! ℹ️ He’s presenting his #poster (41) on “Balancing Open Science and Data Privacy: The Challenge of Human Microbiome Research” #dataprivacy #openscience #metagenomics #FAIRprinciples #trainingmaterial @guigau.bsky.social
📣 Meet Benjamin Prehaud at #JOBIM2026 poster session B! ℹ️ He’s presenting his #poster (44) on “Could the methylome be a new lever for steering microbial communities?” #methylome #longreadsequencing #DNAmethylation #microbialecology #growthrateindex @guigau.bsky.social
2/ pan2met: because one genome rarely tells the whole metabolic story. This new tool predicts species-wide metabolic pathways from pangenomes — with plans to power a metabolic atlas for all of PanGBank 🌍🧬 #pangenomics Meet Samuel Ortion at poster 42 👋
1/ Kicking off with our MicroScope platform 🔬 a powerful tool for microbial genome analysis, annotation & comparative genomics. @ifb-elixir-fr.bsky.social @genopole.bsky.social Meet Noelle at poster 37 👋
Big year for LABGeM 🎉 Our lab members are presenting 7 posters this year at @jobim2026.bsky.social — proud to showcase the breadth of research happening in our group! @genoscopeumr.bsky.social @cea.fr
📣 Meet Meriem Youssef at #JOBIM2026 poster session A! ℹ️ She’s presenting her #poster (91) on “Few-shot learning strategy for Predicting Meropenem Resistance genes in Escherichia coli” 🫵 Do take a look at this very interesting work! #antibioticresistance #transformermodels #fewshotslearning
CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomic data [new] Identifies cross-sample contamination in metagenomic data without controls using a trained model, revealing its prevalence.
We also designed a webapp to explore CroCoDeEL results: scatterplots, networks, plates, verdicts, and clean reports. Try it out! 💻📊 metagenopolis.github.io/CroCoDeEL_in...
Alexander Rakitko@alexrakitko.bsky.social · 3mo ago🧬CroCoDeEL is a new tool for detecting cross-sample contamination in metagenomic data.🐊🦠 The idea behind CroCoDeEL is simple and elegant. Imagine different cocktails poured into a row of glasses...🧵 www.nature.com/articles/s41... #Microbiome #Metagenomics #Contamination
Last year CroCoDeEL was released, and now it is out in @natcomms.nature.com 🐊🎉 We also designed a webapp to explore CroCoDeEL results: scatterplots, networks, plates, verdicts, and clean reports. Try it out! 💻📊 Paper: www.nature.com/articles/s41... 🖥️: metagenopolis.github.io/CroCoDeEL_in...
Guillaume GAUTREAU@guigau.bsky.social · 2y ago1/9 🚨 New preprint alert! Frustrated by strange results with your metagenomic data? Meet CroCoDeEL, an accurate, easy-to-use tool to detect and quantify cross-sample contamination—no need for negative controls or sample positions! 🔗 doi.org/10.1101/2025...
New paper showing that bacteria with more genes for cooperation can live in a broader range of habitats and that genes for cooperation are more more likely to be in the accessory genome www.pnas.org/doi/10.1073/... @lauriebelch.bsky.social
Nearly ten years after starting my PhD, excited to share our study on the metabolic diversity of extraintestinal pathogenic E. coli. An exciting journey with @vallenet.bsky.social sky.social (@genolabgem.bsky.social) and Erick Denamur (@iame-umr1137.bsky.social). journals.asm.org/doi/10.1128/... 1/3
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This looks absolutely great. For those of us interested in pangenomes, I am sure this will be a super place to get data and the interface is very clean (plotly). Congrats to the authors (I don't know if they are on bsky): pangbank.genoscope.cns.fr
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pangbank.genoscope.cns.fr
The Microbe Atlas database paper is *finally* published! Out in @cellpress.bsky.social today: www.sciencedirect.com/science/arti...
The MicrobeAtlas database: Global trends and insights into Earth’s microbial ecosystems
Environmental DNA sequencing has revolutionized our understanding of microbial diversity and ecology. Microbiomes have now been sequenced across the e…
sciencedirect.com
We’re excited to announce the launch of the beta version of PanGBank website! 🧬🌐 pangbank.genoscope.cns.fr PanGBank is a web-based platform for exploring, analyzing, and downloading pangenomes created with #PPanGGOLiN. 🔗 Dive in, test it out, and let us know what you think! #pangenome
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scPRINT-2: Towards the next-generation of cell foundation models and benchmarks https://www.biorxiv.org/content/10.64898/2025.12.11.693702v1
scPRINT-2: Towards the next-generation of cell foundation models and benchmarks [new] Foundation model: ...evaluates features to enhance scRNA-seq analysis via pre-training on a vast, multi-organism dataset for diverse cell tasks.
Comparative metagenomics using pan-metagenomics graphs https://www.biorxiv.org/content/10.1101/2025.11.24.690211v1
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
science.org
The level of this conference was outstanding for a student-led event. It truly matched the quality of established research conferences. Congratulations to the students who organized it and to the excellent speakers!
@sdvupsaclay.bsky.social · 10mo agoJC2B 2025 - Junior Conference of Computational Biology - 13 novembre 2025
We are happy to share a new paper from our lab: The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals www.nature.com/articles/s42... which investigates environmental effects on microbiome interactions, using our previously published tool MANOCCA.
The influence of environment on bacterial co-abundance in the gut microbiomes of healthy human individuals - Communications Biology
Co-abundance analysis of 938 healthy individuals uncovers how host factors shape gut microbiome interactions, highlighting a core set of 200 impacted genera and additional factor-specific interactions...
nature.com
New publication🧬 𝐌𝐞𝐭𝐞𝐨𝐫𝟐 𝐢𝐬 𝐚𝐧 𝐨𝐩𝐞𝐧-𝐬𝐨𝐮𝐫𝐜𝐞 𝐭𝐨𝐨𝐥 𝐟𝐨𝐫 𝐭𝐚𝐱𝐨𝐧𝐨𝐦𝐢𝐜, 𝐟𝐮𝐧𝐜𝐭𝐢𝐨𝐧𝐚𝐥, 𝐚𝐧𝐝 𝐬𝐭𝐫𝐚𝐢𝐧-𝐥𝐞𝐯𝐞𝐥 𝐩𝐫𝐨𝐟𝐢𝐥𝐢𝐧𝐠 𝐨𝐟 𝐦𝐞𝐭𝐚𝐠𝐞𝐧𝐨𝐦𝐢𝐜 𝐬𝐚𝐦𝐩𝐥𝐞𝐬. 𝐟𝐨𝐫 𝐦𝐢𝐜𝐫𝐨𝐛𝐢𝐨𝐦𝐞 𝐫𝐞𝐬𝐞𝐚𝐫𝐜𝐡 microbiomejournal.biomedcentral.com/articles/10.... #metagenomic #science #data #lefrenchgut @inrae-france.bsky.social @institutpasteur.bsky.social
Accurate profiling of microbial communities for shotgun metagenomic sequencing with Meteor2 - Microbiome
Background The characterization of complex microbial communities is a critical challenge in microbiome research, as it is essential for understanding the intricate relationships between microorganisms...
microbiomejournal.biomedcentral.com
Seqwin: Ultrafast Identification of Signature Sequences in Microbial Genomes https://www.biorxiv.org/content/10.1101/2025.11.07.687294v1
I also talk about de-extinction in this paper & the need to have some name to call the organisms. Like many people, I know that the Colossal "Dire Wolves" are not the descendants of the extinct wolves they are named after. But they are *something*, so we need to have a name for them.
James McInerney@jomcinerney.bsky.social · 9mo agoI've often wondered about what we should call organisms whose similarity might be due to acquired genetic material. It got a little complicated, but I made a stab at it here Classifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes academic.oup.com/mbe/article/...
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years. academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
Predicting functions of uncharacterized gene products from microbial communities - @hutlab.bsky.social @hsph.harvard.edu @broadinstitute.org go.nature.com/435C4lp
Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology
FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.
go.nature.com
