Nicole Treichel
@treichelnicole.bsky.social
Post doctoral researcher in the Clavel Lab at the RWTH University Hospital
I am happy to announce that the updated version of our manuscript "Benchmarking of shotgun sequencing depth highlights limitations of strain-level analysis and shallow metagenomics" is available on bioRxiv now. 🎉
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org
January 14, 2026 at 9:22 AM
I am happy to announce that the updated version of our manuscript "Benchmarking of shotgun sequencing depth highlights limitations of strain-level analysis and shallow metagenomics" is available on bioRxiv now. 🎉
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Nicole Treichel
Fecal filtrate is less effective than donor stool (FMT) for the treatment of C. difficile recurrence. Now shown in a multicentre trial, out today in @lancetgastrohep.bsky.social .
Congratulations to Dina Kao @ualberta.bsky.social & team!
Gift link:
authors.elsevier.com/c/1lphg8nByr...
Congratulations to Dina Kao @ualberta.bsky.social & team!
Gift link:
authors.elsevier.com/c/1lphg8nByr...
authors.elsevier.com
September 23, 2025 at 9:38 AM
Fecal filtrate is less effective than donor stool (FMT) for the treatment of C. difficile recurrence. Now shown in a multicentre trial, out today in @lancetgastrohep.bsky.social .
Congratulations to Dina Kao @ualberta.bsky.social & team!
Gift link:
authors.elsevier.com/c/1lphg8nByr...
Congratulations to Dina Kao @ualberta.bsky.social & team!
Gift link:
authors.elsevier.com/c/1lphg8nByr...
Reposted by Nicole Treichel
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 Nicole Treichel
There is still time to apply for #PhD studentships with us!
Thanks for spreading the word.
#phdchat #phdlife #academiclife
Thanks for spreading the word.
#phdchat #phdlife #academiclife
OPEN CALL for PhD positions in our lab through the semm_it program:
1️⃣ Microbiome signatures of early on-set colorectal cancer
2️⃣ High-resolution computational metagenomics for the study of human microbiome transmission
More info: www.semm.it/education/op...
Apply by June 9!
1️⃣ Microbiome signatures of early on-set colorectal cancer
2️⃣ High-resolution computational metagenomics for the study of human microbiome transmission
More info: www.semm.it/education/op...
Apply by June 9!
Open Positions | SEMM European School of Molecular Medicine
www.semm.it
May 19, 2025 at 7:59 PM
There is still time to apply for #PhD studentships with us!
Thanks for spreading the word.
#phdchat #phdlife #academiclife
Thanks for spreading the word.
#phdchat #phdlife #academiclife
Reposted by Nicole Treichel
🥁 NEW:
Commentary in @cellcellpress.bsky.social!
by @msabrysarhan.bsky.social Giacomo Antonello @whansi.bsky.social @cengoni.bsky.social @dmascalzoni.bsky.social @leviwaldron1.bsky.social Nicola Segata, Christian Fuchsberger
www.cell.com/cell/fulltex...
1/4
Commentary in @cellcellpress.bsky.social!
by @msabrysarhan.bsky.social Giacomo Antonello @whansi.bsky.social @cengoni.bsky.social @dmascalzoni.bsky.social @leviwaldron1.bsky.social Nicola Segata, Christian Fuchsberger
www.cell.com/cell/fulltex...
1/4
Human mitochondrial DNA in public metagenomes: Opportunity or privacy threat?
Human DNA is unavoidably present in metagenomic analyses of human microbiomes. While
current protocols remove human DNA before submission to public repositories, mitochondrial
DNA (mtDNA) has been ove...
www.cell.com
May 16, 2025 at 10:55 AM
🥁 NEW:
Commentary in @cellcellpress.bsky.social!
by @msabrysarhan.bsky.social Giacomo Antonello @whansi.bsky.social @cengoni.bsky.social @dmascalzoni.bsky.social @leviwaldron1.bsky.social Nicola Segata, Christian Fuchsberger
www.cell.com/cell/fulltex...
1/4
Commentary in @cellcellpress.bsky.social!
by @msabrysarhan.bsky.social Giacomo Antonello @whansi.bsky.social @cengoni.bsky.social @dmascalzoni.bsky.social @leviwaldron1.bsky.social Nicola Segata, Christian Fuchsberger
www.cell.com/cell/fulltex...
1/4
Reposted by Nicole Treichel
Next at the DECISION Networking Session at #EASL2025, Theresa Wirtz (UKA) presents scRNA-seq data showing a monocyte subset linked to ACLF risk.
Fascinating translational science in action!
@brunslab.bsky.social ky.social @easlnews.bsky.social ky.social
#scRNAseq #ACLF
Fascinating translational science in action!
@brunslab.bsky.social ky.social @easlnews.bsky.social ky.social
#scRNAseq #ACLF
May 9, 2025 at 8:09 AM
Next at the DECISION Networking Session at #EASL2025, Theresa Wirtz (UKA) presents scRNA-seq data showing a monocyte subset linked to ACLF risk.
Fascinating translational science in action!
@brunslab.bsky.social ky.social @easlnews.bsky.social ky.social
#scRNAseq #ACLF
Fascinating translational science in action!
@brunslab.bsky.social ky.social @easlnews.bsky.social ky.social
#scRNAseq #ACLF
Reposted by Nicole Treichel
Very happy that HiBC is out: rdcu.be/ekSCO 🔥 @natcomms.nature.com Excellent team spirit, and, as always, great driving factor by @tcahitch.bsky.social ⭐⭐⭐⭐ We hope that these bacterial isolates from the human gut will facilitate many studies by others... 😀
HiBC: a publicly available collection of bacterial strains isolated from the human gut
Nature Communications - Here, the authors present and characterise a collection of human gut bacteria including novel taxa associated with health conditions and a large diversity of plasmids. All...
rdcu.be
May 6, 2025 at 1:14 PM
Very happy that HiBC is out: rdcu.be/ekSCO 🔥 @natcomms.nature.com Excellent team spirit, and, as always, great driving factor by @tcahitch.bsky.social ⭐⭐⭐⭐ We hope that these bacterial isolates from the human gut will facilitate many studies by others... 😀
Reposted by Nicole Treichel
📣 Explore cutting-edge breakthroughs in #microbiome research, from methodological innovations to integrative approaches and personalised therapeutics. Join #EESMicrobiome 🦠🔍
📅 16 – 19 Sep 2025
📍 EMBL Heidelberg and Virtual
📥 Submit your abstract by 24 June
➡️ https://s.embl.org/ees25-08-bl
📅 16 – 19 Sep 2025
📍 EMBL Heidelberg and Virtual
📥 Submit your abstract by 24 June
➡️ https://s.embl.org/ees25-08-bl
May 6, 2025 at 10:37 AM
📣 Explore cutting-edge breakthroughs in #microbiome research, from methodological innovations to integrative approaches and personalised therapeutics. Join #EESMicrobiome 🦠🔍
📅 16 – 19 Sep 2025
📍 EMBL Heidelberg and Virtual
📥 Submit your abstract by 24 June
➡️ https://s.embl.org/ees25-08-bl
📅 16 – 19 Sep 2025
📍 EMBL Heidelberg and Virtual
📥 Submit your abstract by 24 June
➡️ https://s.embl.org/ees25-08-bl
Reposted by Nicole Treichel
Here we share thoughts on next-gen cultivation: rdcu.be/ejPSb. Hope it helps 😄 Was fun to write with great colleagues @lisamaierlab.bsky.social @jselkrig.bsky.social @baerboletta.bsky.social @typaslab.bsky.social @mmmicrobiomelab.bsky.social @leibniz-dsmz.bsky.social @westermannlab.bsky.social
Enabling next-generation anaerobic cultivation through biotechnology to advance functional microbiome research
Nature Biotechnology - Overcoming key hurdles for the development of next-generation anaerobic cultivation methods could have major impacts on microbial community research and applications.
rdcu.be
April 29, 2025 at 11:58 AM
Here we share thoughts on next-gen cultivation: rdcu.be/ejPSb. Hope it helps 😄 Was fun to write with great colleagues @lisamaierlab.bsky.social @jselkrig.bsky.social @baerboletta.bsky.social @typaslab.bsky.social @mmmicrobiomelab.bsky.social @leibniz-dsmz.bsky.social @westermannlab.bsky.social
Reposted by Nicole Treichel
Ever wondered if we are correctly predicting proteins from metagenomes? If so, we are happy to present our new work improving the prediction of proteins from the human gut microbiome: www.nature.com/articles/s41...! We corrected how each taxon's proteins are predicted and found WAY more proteins!
Lineage-specific microbial protein prediction enables large-scale exploration of protein ecology within the human gut - Nature Communications
Microbes within the gut vary in how they encode genes, both in terms of the genetic codes and gene structures, which are often unexplored in metagenomic analysis. Here, the authors develop a lineage-s...
www.nature.com
April 4, 2025 at 12:03 PM
Ever wondered if we are correctly predicting proteins from metagenomes? If so, we are happy to present our new work improving the prediction of proteins from the human gut microbiome: www.nature.com/articles/s41...! We corrected how each taxon's proteins are predicted and found WAY more proteins!
Reposted by Nicole Treichel
📣 Conference Announcement! Till Strowig, @lisamaierlab.bsky.social and I have organized a stellar lineup of speakers from different corners of the Microbiome field for the 17th SeeOn Conference in picturesque Bavaria. Open to all! Abstracts due April 6th. Spread the news! www.dghm.org/seeon/
Seeon - Deutsche Gesellschaft für Hygiene und Mikrobiologie
Microbiota, Probiotics and Host → Flyer 17th Seeon Conference Registration (click here for registration) The steering committee of the “Microbiota, Probiotics and Host”- group warmly invites you t...
www.dghm.org
March 12, 2025 at 7:59 AM
📣 Conference Announcement! Till Strowig, @lisamaierlab.bsky.social and I have organized a stellar lineup of speakers from different corners of the Microbiome field for the 17th SeeOn Conference in picturesque Bavaria. Open to all! Abstracts due April 6th. Spread the news! www.dghm.org/seeon/
Reposted by Nicole Treichel
If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!
Benchmarking of shotgun sequencing depth highlights strain-level limitations of metagenomic analysis https://www.biorxiv.org/content/10.1101/2025.03.27.645659v1
March 28, 2025 at 9:17 AM
If you generate, or use MAGs, you should really read the work we have done benchmarking their limitations. Using complex mock communities (70 species), we assessed how deeply you need to sequence to accurately conduct common metaG analyses. Webwere shocked to see even HQ MAGs are often chimeric!