Thomas Clavel
@tclavel.bsky.social
Passoniate microbiome research; www.clavel.ukaachen.de
Reposted by Thomas Clavel
📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️
You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪 #career #taxonomy
You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪 #career #taxonomy
November 22, 2025 at 3:36 PM
📣 Open position: We are looking for a new #ScientificLead for the #SILVA database 🧬🖥️
You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪 #career #taxonomy
You will be responsible for guiding the development of this important resource and for curating the SILVA taxonomy🌳and more!
👉 www.dsmz.de/dsmz/career/...
Read and share ‼️
#sciencejobs 🦠🧪 #career #taxonomy
Reposted by Thomas Clavel
Want to delineate genera? We have been optimising POCP, and propose POCPu, which stops the 'double counting' of proteins in POCP by only allowing unique matches. We also speed up, and benchmarked, the analysis using DIAMOND; peerj.com/articles/202... (now implemented in Protologger)
Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies...
peerj.com
November 14, 2025 at 9:31 AM
Want to delineate genera? We have been optimising POCP, and propose POCPu, which stops the 'double counting' of proteins in POCP by only allowing unique matches. We also speed up, and benchmarked, the analysis using DIAMOND; peerj.com/articles/202... (now implemented in Protologger)
Great work from our FAIR science master Charlie (www.linkedin.com/in/charliepa...) to delineate bacterial genera: peerj.com/articles/202.... We hope this will help many. The POCPu calculation is now implemented in protologger.bi.denbi.de by @tcahitch.bsky.social. Thanks for the hard work you 2 ⭐⭐
Fast and robust estimate of bacterial genus novelty using the percentage of conserved proteins with unique matches (POCPu)
Accurate taxonomic assignment of bacterial genomes is essential for identifying novel taxa and for stable classification to enable robust comparison between studies. Bacterial genus delineation relies...
peerj.com
November 14, 2025 at 2:08 PM
Great work from our FAIR science master Charlie (www.linkedin.com/in/charliepa...) to delineate bacterial genera: peerj.com/articles/202.... We hope this will help many. The POCPu calculation is now implemented in protologger.bi.denbi.de by @tcahitch.bsky.social. Thanks for the hard work you 2 ⭐⭐
Reposted by Thomas Clavel
Need a hand with your #Nextflow or #nfcore pipeline?
Join our weekly drop-in session — every Friday 10–11 CET with Daniel Straub (Uni Tübingen).
Ask questions, get tips, and connect with the community!
📍 Zoom: tinyurl.com/mwz84xvb
#Bioinformatics #OpenScience #NFDI4Microbiota
Join our weekly drop-in session — every Friday 10–11 CET with Daniel Straub (Uni Tübingen).
Ask questions, get tips, and connect with the community!
📍 Zoom: tinyurl.com/mwz84xvb
#Bioinformatics #OpenScience #NFDI4Microbiota
November 5, 2025 at 8:18 AM
Need a hand with your #Nextflow or #nfcore pipeline?
Join our weekly drop-in session — every Friday 10–11 CET with Daniel Straub (Uni Tübingen).
Ask questions, get tips, and connect with the community!
📍 Zoom: tinyurl.com/mwz84xvb
#Bioinformatics #OpenScience #NFDI4Microbiota
Join our weekly drop-in session — every Friday 10–11 CET with Daniel Straub (Uni Tübingen).
Ask questions, get tips, and connect with the community!
📍 Zoom: tinyurl.com/mwz84xvb
#Bioinformatics #OpenScience #NFDI4Microbiota
A place to be 👇 Highly recommended ⭐⭐⭐⭐⭐
We have an opening for a postdoctoral researcher in my group at the Botnar Institute for Immune Engineering in Basel, Switzerland. The project is aimed at developing novel mucosal adjuvants for application in oral vaccines. Deadline to apply 16.11.25! Please re-post 🔬🧬
join.com/companies/im...
join.com/companies/im...
Botnar Institute of Immune Engineering - BIIE (Zürich): Postdoctoral Researcher (100%): Mechanisms of action of mucosal adjuvants
Botnar Institute of Immune Engineering - BIIE has a job opening for Postdoctoral Researcher (100%): Mechanisms of action of mucosal adjuvants in Zürich (published: 30.10.2025). Apply now or check the ...
join.com
October 30, 2025 at 4:37 PM
A place to be 👇 Highly recommended ⭐⭐⭐⭐⭐
Reposted by Thomas Clavel
We have an opening for a postdoctoral researcher in my group at the Botnar Institute for Immune Engineering in Basel, Switzerland. The project is aimed at developing novel mucosal adjuvants for application in oral vaccines. Deadline to apply 16.11.25! Please re-post 🔬🧬
join.com/companies/im...
join.com/companies/im...
Botnar Institute of Immune Engineering - BIIE (Zürich): Postdoctoral Researcher (100%): Mechanisms of action of mucosal adjuvants
Botnar Institute of Immune Engineering - BIIE has a job opening for Postdoctoral Researcher (100%): Mechanisms of action of mucosal adjuvants in Zürich (published: 30.10.2025). Apply now or check the ...
join.com
October 30, 2025 at 1:03 PM
We have an opening for a postdoctoral researcher in my group at the Botnar Institute for Immune Engineering in Basel, Switzerland. The project is aimed at developing novel mucosal adjuvants for application in oral vaccines. Deadline to apply 16.11.25! Please re-post 🔬🧬
join.com/companies/im...
join.com/companies/im...
Reposted by Thomas Clavel
☕ Grab your coffee and join our next NFDI4Microbiota Coffee Talk! 📅 Mon, 27 Oct 2025 | 14:30–15:30 CET
🎙️ Daniel Straub (QBiC Tübingen)
💬 “Meta-omics Analysis at a Bioinformatics Core Facility – As FAIR as Possible”. More info here: nfdi4microbiota.de/c...
🎙️ Daniel Straub (QBiC Tübingen)
💬 “Meta-omics Analysis at a Bioinformatics Core Facility – As FAIR as Possible”. More info here: nfdi4microbiota.de/c...
October 24, 2025 at 4:08 PM
☕ Grab your coffee and join our next NFDI4Microbiota Coffee Talk! 📅 Mon, 27 Oct 2025 | 14:30–15:30 CET
🎙️ Daniel Straub (QBiC Tübingen)
💬 “Meta-omics Analysis at a Bioinformatics Core Facility – As FAIR as Possible”. More info here: nfdi4microbiota.de/c...
🎙️ Daniel Straub (QBiC Tübingen)
💬 “Meta-omics Analysis at a Bioinformatics Core Facility – As FAIR as Possible”. More info here: nfdi4microbiota.de/c...
Reposted by Thomas Clavel
A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales https://www.biorxiv.org/content/10.1101/2025.10.10.681549v1
October 11, 2025 at 3:16 AM
A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales https://www.biorxiv.org/content/10.1101/2025.10.10.681549v1
Reposted by Thomas Clavel
📍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.
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
September 24, 2025 at 12:21 PM
📍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.
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.
Reposted by Thomas Clavel
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
September 24, 2025 at 1:22 PM
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...
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
September 18, 2025 at 12:11 PM
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...
Reposted by Thomas Clavel
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 💉🧬🦠🔬🧫
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...
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...
September 10, 2025 at 8:11 PM
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 💉🧬🦠🔬🧫
Reposted by Thomas Clavel
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....
📍 DGHM 2025 – 24 Sept
Workshop: Data madness: Navigating Host Microbiomes
Featuring VirJenDB – virus sequence discovery & analysis
Details 👉 programme.conventus....
September 11, 2025 at 7:55 AM
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....
📍 DGHM 2025 – 24 Sept
Workshop: Data madness: Navigating Host Microbiomes
Featuring VirJenDB – virus sequence discovery & analysis
Details 👉 programme.conventus....
Reposted by Thomas Clavel
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
September 3, 2025 at 8:45 PM
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...
Reposted by Thomas Clavel
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
@sebwielgoss.bsky.social
@oxunipress.bsky.social
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/...
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
September 4, 2025 at 3:15 PM
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
@sebwielgoss.bsky.social
@oxunipress.bsky.social
Reposted by Thomas Clavel
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
☕ 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
August 19, 2025 at 9:56 AM
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
☕ 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
Reposted by Thomas Clavel
🌍 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
August 18, 2025 at 6:18 PM
🌍 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
Reposted by Thomas Clavel
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👇
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👇
August 1, 2025 at 2:04 PM
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👇
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👇
Reposted by Thomas Clavel
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
July 30, 2025 at 3:15 PM
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!
Reposted by Thomas Clavel
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
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
July 16, 2025 at 9:20 PM
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
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
Reposted by Thomas Clavel
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!
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!
📢 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”
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
July 12, 2025 at 3:37 PM
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!
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!
Reposted by Thomas Clavel
Try cloud-based microbiome workflows with CloWM—no installation needed!
📍 4th NFDI4Microbiota Annual Conference |Cologne
📆 Oct 2 | Registration is free
🔗 events.hifis.net/eve...
📍 4th NFDI4Microbiota Annual Conference |Cologne
📆 Oct 2 | Registration is free
🔗 events.hifis.net/eve...
July 8, 2025 at 1:24 PM
Try cloud-based microbiome workflows with CloWM—no installation needed!
📍 4th NFDI4Microbiota Annual Conference |Cologne
📆 Oct 2 | Registration is free
🔗 events.hifis.net/eve...
📍 4th NFDI4Microbiota Annual Conference |Cologne
📆 Oct 2 | Registration is free
🔗 events.hifis.net/eve...
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
July 2, 2025 at 9:55 AM
Congrats @baerboletta.bsky.social 👏 Highly deserved & best possible ambassador for the field www.embo.org/press-releas...
Reposted by Thomas Clavel
#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...
🚨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
July 1, 2025 at 3:18 PM
#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...
🚨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...
Reposted by Thomas Clavel
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
More info here: tinyurl.com/mudhdnra
June 19, 2025 at 9:57 AM
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
More info here: tinyurl.com/mudhdnra