Bérénice Batut
@bebatut.bsky.social
She/her. Bioinformatics. Microbiome 🦠. Open Science. Training. Mentoring. Galaxy. OLS. ELIXIR Microbiome Community. Mother
What makes human guts and coral reefs similar? Here is a blog post with some thoughts on ecosystem stability, stress, and microbiome, following a fresh pre-print by Marko Terzin et al: merenlab.org/blog/coral-r...
From coral reefs to human guts: stress is stress
Reefs and colons share no taxa, no host, no timescale, but they report stress the same way, which tells us where NOT to look for solutions.
merenlab.org
June is busy month, with the #ELIXIR26 All Hands Meeting in Lyon 🇫🇷 🙌🏻 Had the opportunity to present my work with @bioconductor.bsky.social and the @elixir-europe.org Tools Platform Always a pleasure to meet with the community! @ifb-elixir-fr.bsky.social @bebatut.bsky.social @abretaud.bsky.social
Explore the results interactively: arg-pipelines.big-data-biology.org Project led by Juan Inda-Diaz with a great team across the whole SEARCHER Consortium!
This section highlights the difference in number of Antimicrobial Resistance Genes (ARGs) reported by each pipeline.
arg-pipelines.big-data-biology.org
How well do ARG detection pipelines agree when applied to the same data? Spoiler: not very well. In our new preprint, we ran 10 pipelines on 270M microbial unigenes from GMGCv1. The same data can support conflicting biological conclusions! 🧵 www.biorxiv.org/content/10.6...
The elusive resistome: a global comparison reveals large discrepancies among detection pipelines
Identifying antibiotic resistance genes (ARGs) from metagenomic data is critical for studying antimicrobial resistance across microbial communities and pathogens. However, there is no standardized methodology for ARG annotation. Here, we compare ten commonly used ARG detection pipelines by analysing over 270 million prokaryotic genes from the Global Microbial Gene Catalogue across 13 distinct habitats. We observed up to a 45-fold difference in the number of reported ARGs, with a mean Jaccard index of only 16% between pipelines. Pipeline selection profoundly impacted downstream biological interpretations, with drastic changes to estimates of ARG relative abundance and richness, to the characterization of pan- and core-resistomes, and to the class-level composition of the inferred resistome. ARG detection pipelines make different, defensible trade-offs, and no single approach should be treated as authoritative. Therefore, users should justify and communicate choices carefully, as our analyses show that, taken uncritically, the same data can support conflicting biological and ecological interpretations. ### Competing Interest Statement The authors have declared no competing interest. National Health and Medical Research Council of Australia (NHMRC), 2031902 Australian Research Council (ARC), FT230100724 International Development Research Centre (IDRC), 109304-001 Deutsche Forschungsgemeinschaft (DFG), FO1279/6-1 Bundesministerium für Bildung und Forschung (BMBF), F01KI1909A, 01KI2404B Swedish Research Council (VR), 2024-06123, 2019-00299, 2023-01721 Knut and Alice Wallenberg Foundation, KAW 2020.0239 Swedish Foundation for Strategic Research, FFL21-0174
biorxiv.org
I'm thrilled to co-organize and teach at the first-ever training event focused on advanced Galaxy features: workflows, API, and more! Registration is now open until June 5, so don’t miss your chance to dive deep into these powerful tools.
Galaxy Beyond Basics: Mastering Workflows, Automation, and Scalability
Join us for an **intensive, week-long, in-person training** designed to elevate your Galaxy expertise to new heights. This workshop is tailored for **data scientists, advanced Galaxy users, and team l...
training.galaxyproject.org
IFB/ELIXIR-Fr@ifb-elixir-fr.bsky.social · 3mo ago📢 Galaxy Advanced Training: Mastering Workflows, Automation, and Scalability: pre-registration open until June 5 2026!
📢 Galaxy Advanced Training: Mastering Workflows, Automation, and Scalability: pre-registration open until June 5 2026!
A short piece about what "the pangenome" is and is not. open.substack.com/pub/profmcin...
The Pangenome Is Not a Parts List
The pangenome is the total genetic repertoire of a group of organisms. It is a property of populations, maintained by evolutionary processes.
open.substack.com
How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...
Unfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism Study
The myth of open data, reproducibility, responsibility, and accountability in science, and your role in it
merenlab.org
✨ Know a woman making an impact in microbiology? Nominate her for recognition on the FEMS website and socials this International Women’s Day. 🗓️ Submit by 4 March: buff.ly/AKyMbQD Let’s elevate the female voices driving microbiology forward. #IWD2026
We are thrilled to announce that "Ten Common Misconceptions About Galaxy (And Why They Are Wrong!)" has just been published! This is the result of passionate discussions, collaborative debates, and a shared commitment to clarifying what Galaxy @galaxyproject.bsky.social truly is and what it can do.
BF Francis Ouellette@bffo.bsky.social · 6mo agoFrom @bebatut.bsky.social @abretaud.bsky.social @hrhotz.bsky.social et al. in @plos.org #Computational #Biology | Ten common misconceptions about Galaxy (and why they are wrong!) | #Bioinformatics #Education #UseGalaxy 🧬 🖥️ 🧪 🔓 CC/ @galaxyproject.bsky.social ⬇️ journals.plos.org/ploscompbiol...
From @bebatut.bsky.social @abretaud.bsky.social @hrhotz.bsky.social et al. in @plos.org #Computational #Biology | Ten common misconceptions about Galaxy (and why they are wrong!) | #Bioinformatics #Education #UseGalaxy 🧬 🖥️ 🧪 🔓 CC/ @galaxyproject.bsky.social ⬇️ journals.plos.org/ploscompbiol...
Ten common misconceptions about Galaxy (and why they are wrong!)
Author summary Galaxy is a free, community-built web interface that helps scientists analyse data in a way that’s easy to use, transparent and reproducible. While it is widely used in biology and othe...
journals.plos.org
The Galaxy Community Conference is coming to my hometown this year! 🎉 Mark your calendars & register by the end of February for early bird rates. It’s a fantastic opportunity to connect with the global Galaxy Community. Looking forward to seeing you there! @ifb-elixir-fr.bsky.social
Galaxy Project@galaxyproject.bsky.social · 6mo ago⏳ Reminder: Early bird registration for GCC2026 closes February 28, 2026! Join us in Clermont-Ferrand, France, June 22–24, followed by CoFest June 25–26. Learn more and register now: galaxyproject.org/events/gcc20...
🔬 C'est la Journée des femmes et filles de science ! #FemmesEnSciences #11février Envie de découvrir (ou faire découvrir) des femmes scientifiques ? J'ai rassemblé plein de ressources ici ⬇️ www.linkedin.com/pulse/envie-... Et mon starter pack de chercheuses sur bluesky go.bsky.app/TBEzKC
#Communities of experts collaborating on #scientific or technical projects are drivers of innovation across the life #sciences f1000research.com/articles/14-... @elixir-europe.org @sib.swiss @ergabiodiv.bsky.social #biodiversity #genomics
F1000Research Article: Fostering and sustaining collaborative innovation: Insights from ELIXIR Europe's life science Communities.
Read the latest article version by Clare Garrard, Katharina F Heil, Maria Cristina Aspromonte, Bérénice Batut, Magda Chegkazi, John M Hancock, Elaine Harrison, Naveed Ishaque, Giselle Ke...
f1000research.com
Connexion directe de Galaxy à Recherche Data Gouv
Galaxy Project@galaxyproject.bsky.social · 7mo agoGalaxy + Dataverse = better data sharing Galaxy now integrates with Dataverse, making it easier to publish, access, and reuse research data directly within your workflows, supporting FAIR and reproducible science. Learn more: galaxyproject.org/news/2026-01...
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
Get ready for GCC2026! Join the Galaxy community June 22–24, 2026, in Clermont-Ferrand, France, to learn new tools, share your work, and connect with researchers and developers from around the world. Followed by CoFest on June 25–26. galaxyproject.org/events/gcc20...
2026 Galaxy Community Conference (GCC2026)
The annual gathering of the Galaxy Community with opportunities to hear latest developments, get training, and meet everyone involved.
galaxyproject.org
Data visualization is a critical step in data analysis. 8 links to bookmark for better data visualization:🧵
As 2025 wraps up, we’re looking back at some of the most intriguing microbes that made their scientific debut this year. This blog highlights standout bacterial species that caught our eye. Read the full #FEMSmicroBlog: buff.ly/2wz7k16 #NewMicrobes
How effective are AI assistants like Claude and ChatGPT for literature reviews? Anton Nekrutenko ran a systematic experiment using multiple AI-assisted approaches to survey RNA-seq studies on Candida auris, a multidrug-resistant fungal pathogen. Summary here: galaxyproject.org/news/2025-12...
Huge preprint if you are interested in bacterial strain taxonomy! The why and how of cgMLST LIN codes: An extensively revised and expanded version doi.org/10.1101/2024... I will summarize it for you in this thread 👇
Life Identification Numbers: A bacterial strain nomenclature approach
Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...
doi.org
Proud to have contributed to this important work! STREAMS guidelines: standards for technical reporting in environmental and host-associated #microbiome studies. www.nature.com/articles/s41... @natmicrobiol.nature.com
STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies - Nature Microbiology
This Consensus Statement presents the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines.
nature.com
LorMe: a streamlined and interoperable R framework for end-to-end microbiome analysis www.biorxiv.org/content/10.1... #Rstats 🧬🖥️🧪 github.com/wangnq111/Lo...
📢🚀💻Le nouveau site internet de l’IFB/ELIXIR-FR est en ligne !!! Lancé début 2025, le projet de refonte/création du nouveau site internet de l’IFB/ELIXIR-FR atteint aujourd’hui l’une de ses étapes cruciales : sa publication ! www.ifb-elixir.fr
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social doi.org/10.1093/bioa... The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives. More information on globdb.org 1/5 🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
🧬 🔎 Ce 17 novembre a eu lieu la journée du consortium ABRomics à l’Institut Pasteur. L’occasion de présenter aux différents représentants de nos parties prenantes l’avancement du projet et les développements en cours !
De mon côté on m'a confié le micro pour la chronique sciences. Cette fois j'ai décidé de parler du fonctionnement scandaleux de l'édition scientifique, peu connu en dehors des labos : www.youtube.com/watch?v=Yg2C... Mais 4 minutes c'est court, alors j'ajoute quelques ressources ci-dessous !
Le beurre, l’argent du beurre et le c*l des chercheurs- La chronique de Tania Louis dans La dernière
YouTube video by Radio Nova
youtube.com
Dimanche dernier @ladernierenova.bsky.social était de retour à Toulouse. L'invitée de l'émission était @docteur-drey.bsky.social donc je recommande chaudement d'écouter le podcast entier : podcasts.nova.fr/radio-nova-l... @laradionova.bsky.social ...
L'intégrale : "La dernière" du 9 novembre 2025 avec Audrey Dussutour
Sur Radio Nova ce dimanche : Audrey Dussutour (biologiste), Doully, Florence Mendez et Tania Louis. La dernière, le dimanche à 18h en direct sur Radio Nova et ...
podcasts.nova.fr
Know metagenomics and could spare 2 mins? I'm applying for funding to build a visual repository for metagenomic classification data (not sequence data). To support the application, I have a short 2 minute survey and it would be a big help if you could fill it in: docs.google.com/forms/d/e/1F...
Metagenomic classification survey
Background: We're seeking the views of researchers on the possibility of a repository for metagenomic classification data, which we're hoping to build. The rationale is that people are familiar with t...
docs.google.com
It was a really nice week working on building MiCoReCa, a catalogue of resources (tools, workflows, etc) for microbiome research, and more importantly networking with the large @elixir-europe.org community. Thank you all! See next year!
IFB/ELIXIR-Fr@ifb-elixir-fr.bsky.social · 9mo ago🚀👩💻🧑💻 End of this week of #BioHackEU25, organised by @elixir-europe.org , to advance all projects in synergy! Thank you to the IFB/ELIXIR-FR team (on-site and remotely), and to our colleagues at @genouest.bsky.social 👏
