Nicolas Tromas

Felicidades Santi!!

Three UK research councils suspend funding opportunities Temporary block on grant applications by MRC, BBSRC and EPSRC heightens concerns over funding cuts

Scientists are concerned that curiosity-driven research is set to be further cut back after three research councils confirmed they have paused funding opportunities. @jgro-the.bsky.social reports #academicsky #researchfunding
https://ow.ly/lpvO50Y67ku

Curious, what's the best-practice tool at this point for taxonomically classifying long reads from metagenomes from less well-characterised environments?

My impression is that Kraken will give lots of false positives and mis-classify taxa not in its database.

Please share around for visibility.

The most important public health story in America right now is that the Trump administration is kidnapping 2-year olds

🚨4-year fully funded PhD in the lab of @magicmicrobe.bsky.social (& collaborating with me!): How does iron availability shape the ability of pathogens to invade the gut microbiome?
Apply by Jan 26th
Advert: research.reading.ac.uk/foodbiosyste...
How to apply: research.reading.ac.uk/foodbiosyste...

Stephen Colbert on the ICE murder of Renee Nicole Good: “The message from this administration is clear. Only they determine the truth. And when their forces come to your city: obey or die. And if you die, you clearly didn’t obey. This should be an alarm bell for the entire country.”

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...

Comparison of short-read and long-read metagenome assemblies in a natural soil community highlights systematic bias in recovery of high-diversity populations Abstract. Comparisons of long-read and short-read (meta)genome assemblies typically show that short-read sequence assemblies are less error-prone, but stru

100%, both ONT and PacBio (although most of what we do is not marine / streamlined genome). We just published a specific study of soil metag short- vs long-read, and we see that, among other things, long-reads assemble regions too complex for short reads academic.oup.com/nargab/artic...

GC content is ~40-45% and we have the microscopy counts :) so we know they are present and dominating the phytoplankton.

Thanks for the input! I'm working on freshwater cyano :) Long-reads is definitely on the todo list! Still thinking on how many sample for the multiplexing.

Thanks a lot everyone! Will try this asap and keep you informed :)

Exactly! I know it is super abundant but probably higly diverse...

Thanks Robin! Does that mean that you did a subsampling?

Releases · tseemann/abricate :mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate

💾 ABRicate 1.2.0 has been released!

This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics

github.com/tseemann/abr...

For metagenomics folks: what would be alternative approach to recover MAGs from highly diverse taxa where "classical" approaches have failed (megahit + mulitple binners like metabat2,vamb,...). I am trying metaSpades now...

Some days are tougher than others... 2 rejected grants in the same day

Une importante étude concluant à la sûreté du glyphosate vient d'être désavouée par la revue scientifique qui l'a publiée, il y a 25 ans. Cette étude avait été utilisée par Santé Canada pour sa réévaluation de l'herbicide. Les réels auteurs de l'étude ne seraient pas les chercheurs, mais Monsanto.

Graphic representation of the recombination events in the Sugarlandvirus I and J variants. Top left: Representation of the variants isolates in the different strains in the three lines. Genome fragments of each parent are represented in a different color. Regions with the most abundant recombination events are marked and associated with a schematic representation of the functional annotation and intergenomic similarity between the two parental phages. Bottom left: 3D folding of the RBPγ. The consensus recombinant region, which is associated with the infection of the K-type 47, is represented in light orange. Variable positions detected in the protein sequence alignment of the variants are represented as hot pink spheres. The table indicates the percentage of identity of the parental protein sequences in three protein regions limited by the amino acids indicated. Right: Transmission electron microscopy (TEM) image of Klebsiella myoviruses artificially coloured, showing their characteristic contractile tails and icosahedral capsids. Image acquired by the Environmental and Biomedical Virology group (Institute for Integrative Systems Biology, Universitat de València-CSIC).

Capsule diversity limits #phage host range by affecting receptor-binding protein (RBP) interactions in capsulated #bacteria. @pilardomingoc.bsky.social &co show that generalist phages evolve host range via RBP mutation & recombination, but specialists remain stable @plosbiology.org 🧪 plos.io/48nvOqY

Congrats Hervé!!!

A great story to read!!

I dropped out of high school. Now, I’m living my dream as a fish scientist This Ph.D. student from a working class background writes that no one should be made to feel inferior because of their roots

Le parcours (singulier) de mon (dernier) thésard mis en avant dans une revue internationale : www.science.org/content/arti...

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf

Still time to apply to work on #symbioses #mosses #cyanobacteria! Join us in #Copenhagen! @voltcenter.bsky.social

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...

Evolution induced state shifts in a long-term microbial community experiment Biological communities are complex, dynamic systems that underpin ecosystem functionality, yet their long-term dynamics and predictability remain poorly understood. Understanding how Darwinian evoluti...

Evolution induced state shifts in a long-term microbial community experiment www.biorxiv.org/content/10.1...

Dr. Jane Goodall filmed an interview with Netflix in March 2025 that she understood would only be released after her death.

We're hiring for several positions (a post-bac researcher in #transcriptomics, a #phage #postdoc, a senior researcher (broad topics) and a graduate student to work on #ciliates) - find info here: www.marine.usf.edu/genomics/app...

Jane Goodall, la primatologue qui a révolutionné le regard porté sur les chimpanzés, est morte Pionnière de l’éthologie moderne, devenue ambassadrice de la protection de la faune sauvage, la chercheuse britannique est morte à 91 ans.

www.lemonde.fr/disparitions...

Elle était de celles dont on ne peut que s'inspirer. Son travail est juste énorme et j'espère que ses paroles et ses conseils continueront d'être partagés.

Headline in the Guardian. Trump warns pregnant women not to take paracetamol making contentious autism claim.

Come on @theguardian.com!

Wrong, incorrect, irresponsible. Not contentious.

schematic pictures and microscopic photos showing various aspects of movement in single-celled algae

#Arctic #algae aren't immobile or entombed. They're not just surviving either—they're gliding into record books phys.org/news/2025-09...

Ice gliding #diatoms establish record-low temperature limits for motility in a eukaryotic cell www.pnas.org/doi/10.1073/...

#protists #microbes #extremophiles