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Reposted by Thomas Clavel

Michael Zimmermann Lab @zimmermannlab.bsky.social · 14d

📍Paper alert 📍

Our new preprint is available on: chemrxiv.org/engage/chemr...

Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including SCFA, indols, organic acids, and amino acid derivatives.

Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites

The gut microbiota produces metabolites that are important for host physiology and have critical roles in the development of diseases, such as metabolic disorders, cardiovascular diseases, and cancer....

chemrxiv.org

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Reposted by Thomas Clavel

Tom Hitch @tcahitch.bsky.social · 14d

The main work from my time in Aachen is now out 🎉 if you have wanted to make a SynCom that captures the functional-landscape of microbiota, MiMiC2 makes that possible based on metagenomic data! 1/7 doi.org/10.1093/isme...

Function-Based Selection of Synthetic Communities Enables Mechanistic Microbiome Studies

Abstract. Understanding the complex interactions between microbes and their environment requires robust model systems such as synthetic communities (SynCom

doi.org

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Thomas Clavel @tclavel.bsky.social · 20d

Interested in the design of defined microbial communities for fundamental research and applications? Hope this work & tool will help you 👇 As always @tcahitch.bsky.social has been a driving factor ⭐⭐⭐! github.com/ClavelLab/Mi...; academic.oup.com/ismej/advanc...

Validate User

academic.oup.com

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Reposted by Thomas Clavel

Emma Slack @mucosalimmunology.bsky.social · 28d

Come and be my colleague at the Dunn School! It‘s a brilliant place to work and exciting to be building up our immunology team. Do apply. Do pass on the news 💉🧬🦠🔬🧫

The Dunn School, Oxford @dunnschool.bsky.social · 28d

We're hiring (again)!

We are looking for an associate professor in cell and molecular biology, with a particular focus on immunology (defined broadly)

If you have a great record and exciting plans, consider joining our thriving and welcoming department

www.path.ox.ac.uk/vacancy/asso...

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Reposted by Thomas Clavel

NFDI4Microbiota @nfdi4microbiota.bsky.social · 27d

We’re heading to Jena for two exciting events!
📍 DGHM 2025 – 24 Sept
Workshop: Data madness: Navigating Host Microbiomes
Featuring VirJenDB – virus sequence discovery & analysis
Details 👉 programme.conventus....

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Reposted by Thomas Clavel

Steven Salzberg @stevensalzberg.bsky.social · Sep 3

We're still not finding any good evidence for a microbiome in any cancer type: see our new paper in @ScienceTM led by PhD student Yuchen (Peter) Ge www.science.org/doi/10.1126/... and the accompanying news piece, www.science.org/content/arti...

Comprehensive analysis of microbial content in whole-genome sequencing samples from The Cancer Genome Atlas project

An analysis of TCGA whole-genome sequencing samples yields a comprehensive resource for investigating the role of microbes in cancer.

www.science.org

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Reposted by Thomas Clavel

Carolin Wendling @ccwendling.bsky.social · Sep 4

Interested in exploring prophages in your (meta)genomes, but don't know how and where to start? We've put together a beginners guide to exploring viral diversity in prokaryotes @marievasse.bsky.social
@sebwielgoss.bsky.social
@oxunipress.bsky.social

Séb Wielgoss @sebwielgoss.bsky.social · Sep 4

Our new review is out in
Briefings in Bioinformatics

Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world

@ccwendling.bsky.social
@marievasse.bsky.social
@sebwielgoss.bsky.social
@oxunipress.bsky.social

doi.org/10.1093/bib/...

Phage quest: a beginner’s guide to explore viral diversity in the prokaryotic world

Abstract. The increasing interest in finding new viruses within (meta)genomic datasets has fueled the development of computational tools for virus detectio

doi.org

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Reposted by Thomas Clavel

NFDI4Microbiota @nfdi4microbiota.bsky.social · Aug 19

Planning, sequencing… and now analysis. 📊
☕ Coffee Talk: Getting Your Microbiome Research on the Road – Managing Your Data using Qiita
🗓️ Aug 25, 2025 | 14:30 CEST
👉 More info: tinyurl.com/2m9jpf2p
👉 Workshop (Oct 22–24, Gießen): tinyurl.com/4w8mczh7

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Reposted by Thomas Clavel

Geraldine Zimmer-Bensch @zimmer-bensch.bsky.social · Aug 18

🌍 Open Call! RWTH Aachen University invites postdocs from outside the EU to apply for the “Port to Europe” Fellowship (24 months funding, all disciplines). Start your research journey at one of Europe’s top universities! 🚀 Deadline: Oct 5, 2025. 👉https://rwth-aachen.de/go/id/botjje/lidx/1

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Reposted by Thomas Clavel

Michael Zimmermann Lab @zimmermannlab.bsky.social · Aug 1

Do you have experience in metabolomics/lipidomics/exposomics?

Check out the EMBL ARISE2 Fellowship Programme!
🔗 www.embl.org/training/ari...

📩 Contact: Juan Antonio Vizcaíno — Team Leader, EMBL-EBI
🔗 www.ebi.ac.uk/people/perso...

📌 Applications close soon!
📆 30/09/2025
More info below👇

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Reposted by Thomas Clavel

Typas Lab @typaslab.bsky.social · Jul 30

Ready to lead pioneering research that bridges systems-level investigations of biological systems to molecular mechanism? The EMBL Molecular Systems Biology Unit in Heidelberg is hiring a Group Leader!

Group Leader – Molecular Systems Biology Unit

Are you ready to lead groundbreaking research in Molecular Systems Biology? Join us at EMBL! We are seeking a motivated scientist to lead an independent research group, addressing original biological ...

embl.wd103.myworkdayjobs.com

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Reposted by Thomas Clavel

Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · Jul 16

Finally online!
Our latest research is out @nature.com: We show that non-antibiotic drugs can disrupt colonization resistance, raising the risk of enteric infections.
rdcu.be/ewwrG

Non-antibiotics disrupt colonization resistance against enteropathogens

Nature - Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of...

rdcu.be

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Reposted by Thomas Clavel

François Leulier @francoisleulier.bsky.social · Jul 12

A pure « délice » to have followed this story unfolding under our eyes.
Congrats @ameliejoly.bsky.social brilliantly followed-up by @lucasrebiffe.bsky.social.
@filipedevadder.bsky.social and I were/are so lucky to work with gifted Ph’D candidates like you!

Filipe De Vadder @filipedevadder.bsky.social · Jul 12

📢 New preprint:
“Liver FGF21 mediates sex-specific adaptation to juvenile protein malnutrition”
Led by @ameliejoly.bsky.social, co-supervised with @francoisleulier.bsky.social.
We’re proud to share this story.
👉 www.biorxiv.org/content/10.1...

Liver FGF21 mediates sex-specific adaptation to juvenile protein malnutrition

Dietary protein sufficiency during childhood is essential for healthy growth and tissue development. Chronic protein deficiency leads to stunting, height-for-age more than two standard deviations belo...

www.biorxiv.org

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Reposted by Thomas Clavel

NFDI4Microbiota @nfdi4microbiota.bsky.social · Jul 8

Try cloud-based microbiome workflows with CloWM—no installation needed!
📍 4th NFDI4Microbiota Annual Conference |Cologne
📆 Oct 2 | Registration is free
🔗 events.hifis.net/eve...

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Thomas Clavel @tclavel.bsky.social · Jul 2

Congrats @baerboletta.bsky.social 👏 Highly deserved & best possible ambassador for the field www.embo.org/press-releas...

Outstanding life scientists elected to the EMBO Membership – Press releases – EMBO

Sixty-nine new members join the community of leading life scientists in Europe and beyond

www.embo.org

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Reposted by Thomas Clavel

Nature Microbiology @natmicrobiol.nature.com · Jul 1

#NewResearch

🚨Out now!

Human gut bacteria bioaccumulate forever chemicals, in intracellular aggregates and colonization of gnotobiotic mice with these bioaccumulating bacteria increases faecal PFAS excretion. @kiranrpatil.bsky.social

#MicroSky #MicrobiomeSky 🦠

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

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances - Nature Microbiology

Human gut bacteria bioaccumulate per- and polyfluoroalkyl substances (PFAS), commonly known as forever chemicals, in intracellular aggregates. Colonization of gnotobiotic mice with bioaccumulating bac...

www.nature.com

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Reposted by Thomas Clavel

NFDI4Microbiota @nfdi4microbiota.bsky.social · Jun 19

Join our NFDI4Microbiota Coffee Talk: Ivan Belyaev @microverse.bsky.social presents BEXIS2, a flexible platform for microbiology metadata. June 30 at 14:30 CEST.
More info here: tinyurl.com/mudhdnra

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Reposted by Thomas Clavel

NFDI4Microbiota @nfdi4microbiota.bsky.social · Jun 30

🧫 Registration is open!
Join the 4th NFDI4Microbiota Conference in Cologne
📅 Sept 30–Oct 2 | Theme: From Lab to Publication
Hands-on workshops, keynotes, posters | Registration is free
📝 Register by Aug 31: events.hifis.net/eve...
#FAIRdata #Microbiome

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Reposted by Thomas Clavel

Noah Fierer @noahfierer.bsky.social · Jun 21

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

Guidelines for preventing and reporting contamination in low-biomass microbiome studies

Nature Microbiology - In this Consensus Statement, the authors outline strategies for processing, analysing and interpreting low-biomass microbiome samples, and provide recommendations to minimize...

rdcu.be

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Reposted by Thomas Clavel

NFDI4Microbiota @nfdi4microbiota.bsky.social · Jun 16

The #NFDI4Microbiota Flex Funds Call 2026 opens June 16!
Support for infrastructure, workflows, training & more in microbiology.
Deadline: Aug 11. Details: nfdi4microbiota.de/n...
#OpenScience #FAIRdata

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Reposted by Thomas Clavel

Lisa Maier Lab | Tübingen @lisamaierlab.bsky.social · Jun 17

Ever wondered why proton pump inhibitors raise the risk of C. diff infections? Is it due to pH shifts or direct antibacterial effects on the gut microbiome? We think it’s the pH. 🧪💡 Dive into Julia & Patrick’s new paper for the full story! 📖👇 #Microbiome #PPI
doi.org/10.1080/1949...

Proton-pump inhibitors increase C. difficile infection risk by altering pH rather than by affecting the gut microbiome based on a bioreactor model

Clostridioides difficile infections often occur after antibiotic use, but they have also been linked to proton-pump inhibitor (PPI) therapy. The underlying mechanism – whether infection risk is due...

doi.org

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Reposted by Thomas Clavel

Westermann Lab @westermannlab.bsky.social · Jun 17

Our latest: www.cell.com/cell-reports/fulltext/S2211-1247(25)00615-1. Links Bacteroides cell size w/ gene expression. Protocol works even for single cells. 🦠
Shoutout to @elisebor.bsky.social, @emmanuel-saliba.bsky.social, @lbarquist.bsky.social, @jorg-vogel-lab.bsky.social, Till Strowig & KC Huang.

Low-input RNA-seq suggests metabolic specialization underlying morphological heterogeneity in a gut commensal bacterium

Bornet et al. investigate the morphological heterogeneity of Bacteroides thetaiotaomicron cells observed both in laboratory culture and inside the mammalian GI tract. The authors show that cell size i...

www.cell.com

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Reposted by Thomas Clavel

Karina Xavier Lab @karinaxavierlab.bsky.social · Jun 17

Call for our new PhD program is open. Come join one of our labs at Gulbenkian Institute for Molecular Medicine - Lisbon-Oeiras, Portugal. Help us spread the word

Gulbenkian Institute for Molecular Medicine @gimmfoundation.bsky.social · Jun 6

Exciting opportunities are now available!
GIMM offers a distinctive PhD Program designed to attract & cultivate highly skilled researchers in biology & biomedicine.

Deadline: July 9
👉 Apply now! gimm.pt/education-and-training/phd-program/

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Reposted by Thomas Clavel

NFDI4Microbiota @nfdi4microbiota.bsky.social · May 20

Join NFDI4Microbiota as a participant for 2026–2031! Gain early access to tools, bilateral exchange via an early-career ambassador, and targeted support for ELNs, DMPs, SOPs & FAIR data. Apply by June 10, 2025: www.nfdi4microbiota....

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Reposted by Thomas Clavel

Karina Xavier Lab @karinaxavierlab.bsky.social · Jun 1

Call for Group Leaders - Join us at GIMM, 7 days till the deadline!

Gulbenkian Institute for Molecular Medicine @gimmfoundation.bsky.social · Apr 15

We’re hiring: GIMM is launching its first call for Group Leaders.

Looking for scientists ready to push boundaries, ask bold questions & build the future of biomedical discovery.

🔗 gimm.pt/jobs/open-ca...
📅 Apply by June 8

#ScienceJobs #GroupLeader #BiomedicalResearch

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