Muriel Derrien

See you TOMORROW at the Atlantic #MVIF!

There's still time to register 👉 cassyni.com/s/mvif-42

Strainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets https://www.biorxiv.org/content/10.1101/2025.10.10.681738v1

Excited to share our preprint led by Carlos Voogdt et al

We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...

A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales https://www.biorxiv.org/content/10.1101/2025.10.10.681549v1

Targeted protein evolution in the gut microbiome by diversity-generating retroelements Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, su...

www.science.org/doi/10.1126/...

#microsky #microbiome

DGRs FTW

Carbon source diversity shapes bacterial interspecies interactions academic.oup.com/ismej/advanc... #jcampubs

Metabolic interplay drives population cycles in a cross-feeding microbial community - Nature Communications Here the authors leverage a crossfeeding, engineered microbial community to demonstrate that strain abundance cycles are robust across environmental conditions. They pair this with a nonlinear dynamic model to elucidate population cycles.

Metabolic interplay drives population cycles in a cross-feeding microbial community www.nature.com/articles/s41... #jcampubs

Sergio Andreu Sanchez @seandreu.bsky.social (DSM-Firmenich): Understanding the role of the human gut microbiota in aging and health

#HumanMicrobiome

#NIME2025

Another great day at #UEGWeek 2025! 🎉Congratulations to our colleague Jorge Vazquez Castellanos for presenting his exciting work on microbial dysbiosis, inflammation, and the gut–brain axis in IBS at the United European Gastroenterology Week in Berlin🇩🇪 @myueg.bsky.social @vibmicrobes.bsky.social

MVIF Season 5 program

💫 #MVIF Season 5 💫

Feel free to join the keynotes by presenting your work–abstract submission is open:
www.microbiome-vif.org/en-US/how-to...

#MVIF is proudly supported by #illumina @corundumsb.bsky.social
and our non-commercial co-organizing partners Seerave Foundation @cunysph.bsky.social

Huge congratulations to our colleague @arnauvich.bsky.social for presenting his research on FODMAP restriction and gut microbiota in IBS patients at United European Gastroenterology Week 2025 in Berlin🇩🇪👏! #UEGWeek @myueg.bsky.social @vibmicrobes.bsky.social

How nutrient starvation impacts the gut microbiome - Nature Microbiology In this Perspective, Estrela and Huang discuss nutrient starvation in the context of the gut microbiome, outlining what is known and highlighting key questions for future research to address knowledge gaps.

#Perspective

Estrela and Huang discuss nutrient starvation in the context of the gut microbiome, outlining what is known and highlighting key questions for future research to address knowledge gaps.

#MicroSky #MicrobiomeSky 🦠

www.nature.com/articles/s41...

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

Jane Goodall’s legacy: three ways she changed science Nature - The primatologist challenged what it meant to be a scientist.

Jane Goodall, known for her pioneering work with chimpanzees, has passed away aged 91

go.nature.com/46QHIZk

Jane Goodall with monarch butterfly scarf

“It actually doesn’t take much to be considered a difficult woman. That’s why there are so many of us.”
― Jane Goodall

💙 RIP to a real one. My childhood hero

Jane Goodall reaches out and touches a small monkey.

Jane Goodall was my first childhood hero, as I loved animals as a kid and was inspired by her story. I still remember the National Geographic specials about her. RIP.

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

Precisely calling mutations across hundreds of bacterial isolates has been hard, requiring manual filtering and expertise.

Until now, using AccuSNV.

Herui Liao trained an ML model based on our previous meticulously called SNVs.
www.biorxiv.org/content/10.1...

Dual transposon sequencing profiles the genetic interaction landscape in bacteria Gene redundancy complicates systematic characterization of gene function as single-gene deletions may not produce discernible phenotypes. We report dual transposon sequencing (dual Tn-seq), a platform...

This week @science.org Dual #transposon sequencing profiles the #genetic interaction landscape in #bacteria | Science www.science.org/doi/10.1126/... 🦠🔬🧫🧬

microbetag: simplifying microbial network interpretation through annotation, enrichment tests, and metabolic complementarity analysis - Genome Biology Microbial co-occurrence network inference is often hindered by low accuracy and tool dependency. We introduce microbetag, a comprehensive software ecosystem designed to annotate microbial networks. No...

our software, microbetag, for the annotation of microbial co-occurrence networks with phenotypic traits & metabolic complementarities was just published

A Cytoscape app is also available to make your life easier (and prettier)

#microbiome #metabolic-modeling #networks

The gut remembers: the long-lasting effect of medication use on the gut microbiome | mSystems Over the past decades, medication use has steadily increased worldwide, with individuals frequently taking multiple medications (polypharmacy), often repeatedly over extended periods of time (1). Yet,...

My commentary article, featuring the work of Aasmets et al. on the long-lasting effects of medications on the gut microbiome, is now out in mSystems @asm.org
#microbiome #microsky

doi.org/10.1128/msys...

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin Despite Cutibacterium acnes being the most abundant and prevalent bacteria on human skin, only a single type of phage has been identified that infects this host. Here, we leverage this one-to-one syst...

How much of selection in human microbiomes is driven by phage?

Excited to share our latest, led by A. Delphine Tripp, showing a case where phage is just not that important:

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin

www.biorxiv.org/content/10.1...

🧵

Fusobacterium nucleatum: ecology, pathogenesis and clinical implications Nature Reviews Microbiology, Published online: 22 September 2025; doi:10.1038/s41579-025-01237-zFusobacterium nucleatum is a commensal microorganism and opportunistic pathogen, with a pathogenic role in periodontal disease, inflammatory bowel disease and various cancers, most notably colorectal cancer. This Review discusses F. nucleatum and its ecological niches and virulence factors, links with disease, oncogenic mechanisms, and emerging diagnostic approaches and therapeutic strategies.

New online! Fusobacterium nucleatum: ecology, pathogenesis and clinical implications

If you missed Dr Chudan Xu's talk on what happens when we don't eat enough fibre, the preprint is now live 👇

www.medrxiv.org/content/10.1...

#EESMicrobiome @events.embl.org

The human microbiome

Starting my journey from Australia to Heidelberg 🇩🇪 to the @embl.org Human Microbiome conference

It’s not every day we get the chance of 4 days of human microbiome research 🤩🤩🤩 I’m so excited

Still chance to attend it online 👇

www.embl.org/about/info/c...

We want to explore the metabolic interactions among gut bacteria, when the human host eats different foods - maybe this explain partly the Enterosignature structure?
Please do apply for our bioinformatic post to explore this question in metagenomes: jobs.quadram.ac.uk/Details.asp?...

Dissecting microbial communities with single-cell transcriptome analysis Revealing insights into the function of microbial communities requires moving beyond measuring bulk taxonomic composition to detecting interactions between subpopulations. Following the transformative...

Dissecting microbial communities with single-cell transcriptome analysis www.science.org/doi/abs/10.1... #jcampubs

Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial

Exams = stress. 📚 Our new study shows that a probiotic strain (L. rhamnosus CNCM I-3690) modulated the gut microbiome during academic stress, with ties to lower anxiety.

🔗 Vázquez-Castellanos et al. doi.org/10.1038/s415...

Started off as a reading group and led to a nice mini-review of microbiome evolution in natural communities. Complete credit to Abby for leading this fun collab! #mevosky

Investigating bacterial evolution in nature with metagenomics
doi.org/10.1016/j.mi...

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 ...

This first-author publication is my… first! Archaea kill bacteria by targeting their Achilles’ heel: peptidoglycan. Big shoutout to @ahocher.bsky.social‬, @valeriesoo.bsky.social‬, Pauline Misson, @tobiaswarnecke.bsky.social‬ and MRC LMS Proteomics. A thread 🔽
journals.plos.org/plosbiology/...

Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - Probiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial

Academia is stressful, maybe fermented milk could keep your gut microbiome in check!

#MicroSky #MicrobiomeSky

www.nature.com/articles/s41...