Excellent work by our one and only #CharliePauvert. We use it in all our high-throughput anaerobic cultivation projects. More to come... 💫

Bioinformatics Advances@bioinfoadv.bsky.social · last mo.

🔬 New paper in Bioinformatics Advances: "maldipickr dereplicates microbial MALDI-TOF spectra to facilitate multiplexed isolation"  Find it here: https://doi.org/10.1093/bioadv/vbag171 Authors include: @tclavel.bsky.social

Das #Mikrobiom im #Darm hat großen Einfluss auf die #Gesundheit – doch wie zuverlässig lässt es sich bestimmen? Ein Team um @tclavel.bsky.social und @treichelnicole.bsky.social von der @rwth.bsky.social zeigt in einer neuen Studie, dass #Metagenomsequenzierung nicht immer das ganze Bild zeigt.

Studie: Mikrobiom-Analysen zeigen nicht immer das ganze Bild

Forscherinnen und Forscher der RWTH Aachen haben eine wichtige Methode zur Charakterisierung des Darmmikrobioms systematisch auf Potenzial und Grenzen geprüft. Ihre Ergebnisse ermöglichen Forschenden ...

healthcare-in-europe.com

Strain diversity influences microbiome functions, and can be assessed with metagenome-assembled genomes (MAGs). But many MAGs are inaccurate! Benchmarking of shotgun sequencing by ⭐ @treichelnicole.bsky.social ⭐ with @nfdi4microbiota.bsky.social , in @natmicrobiol.nature.com 👉 rdcu.be/feAWc

Benchmarking of shotgun sequencing depth reveals the potential and limitations of shallow metagenomics and strain-level analysis

Nature Microbiology - A comparison of sequencing of complex mock communities performed at multiple depths and analysed using different methods establishes minimum standards that can ensure the...

rdcu.be

🥁 NEW Our study on infant gut microbiome and #straintransmission is now published in @nature.com: doi.org/10.1038/s415... 1/10

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature

A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

doi.org

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...

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...

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...

There is still time to apply for #PhD studentships with us! Thanks for spreading the word. #phdchat #phdlife #academiclife

Segata Lab@cibiocm.bsky.social · last yr.

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!

🥁 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

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...

cell.com

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

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

📣 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

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

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...

nature.com

📣 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...

dghm.org

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!

bioRxivpreprint@biorxivpreprint.bsky.social · last yr.

Benchmarking of shotgun sequencing depth highlights strain-level limitations of metagenomic analysis https://www.biorxiv.org/content/10.1101/2025.03.27.645659v1