Intriguing case! Completeness measured with CheckM2? I'm curious about the total completeness once you merge the 4 chromosomes. Binning based on coverage + 4mers has a lot of limitations.

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

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

Thank you for sharing @jomcinerney.bsky.social 🙂 I've just received confirmation of acceptance for what we had discussed. I'll email you with more details 😉.

Thank you Patrick, for spotting this message. I began developing PanGbank during my PhD thesis, but recently @tlemane.bsky.social and Jean Mainguy did a fantastic job making it openly available with a nice interface.

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…

The Microbe Atlas database paper is *finally* published! Out in @cellpress.bsky.social today:

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

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

scPRINT-2: Towards the next-generation of cell foundation models and benchmarks www.biorxiv.org/content/10.64898/2025.12...

scPRINT-2: Towards the next-generation of cell foundation models and benchmarks

Table 1

Figure 2

Figure 3

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.

Transformer-based Prediction of Microbial Growth Rates from
Genomic Data
doi.org/10.1145/3765...

Comparative metagenomics using pan-metagenomics graphs www.biorxiv.org/content/10.1101/2025.11....

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...

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/...

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!

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...

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.

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...

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

Seqwin: Ultrafast Identification of Signature Sequences in Microbial Genomes www.biorxiv.org/content/10.1101/2025.11....

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.

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

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-...

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.

Predicting functions of uncharacterized gene products from microbial communities - @hutlab.bsky.social @hsph.harvard.edu @broadinstitute.org go.nature.com/435C4lp

Bravo !

Après six-ans (à mi-temps), bientôt plus #étudiant !

www.instagram.com/p/DP6FgQRitUJ/

Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets www.biorxiv.org/content/10.1101/2025.10....

Efficient and accurate search in petabase-scale sequence repositories www.nature.com/articles/s41... 🧬🖥️🧪
MetaGraph: metagraph.ethz.ch
Code: github.com/ratschlab/me...

Crayon à papier du Conseil Constitutionnel rouge - Liberté d'expression L'article 100 de la Constitution dispose que « la liberté d'expression, y compris le droit d'obtenir, de conserver et de distribuer des informations et de manifester ses opinions, est garantie à tous ...

Et que dire de la boutique officielle ?

www.boutiquesdemusees.fr/fr/product/c...

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe www.biorxiv.org/content/10.1101/2025.09....

Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.

Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...

kSanity: A k-mer based application forprecision bacterial strain detection andquantification www.biorxiv.org/content/10.1101/2025.09....

Clustering of plasmid genomes for genomic epidemiology by using rearrangement distances, with pling Integration of plasmids into genomic epidemiology is challenging, because there are no clearly defined evolving-units (equivalent to species), and because plasmids appear to evolve as much by structur...

For anyone who has used pling for comparing plasmids using rearrangement distances ("how many structural events apart are these plasmids"), here's how to tweak parameters, and integrate it with typing info, and the host phylogeny
www.biorxiv.org/content/10.1...
github.com/iqbal-lab-or...

Preprint out for myloasm, our new nanopore / HiFi metagenome assembler!

Nanopore's getting accurate, but

1. Can this lead to better metagenome assemblies?
2. How, algorithmically, to leverage them?

with co-author Max Marin @mgmarin.bsky.social, supervised by Heng Li @lh3lh3.bsky.social

1 / N