Joana Séneca, Petra Pjevac and David Berry from the Joint Microbiome Facility (JMF) and DOME | CeMESS contributed to a new study, led by scientists at Uniklinik RWTH Aachen, benchmarking a key method used to characterize the microbial contents of our digestive tracts. www.nature.com/articles/s41...

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 accuracy of metagenomic analy...

nature.com

PhD advert for the new lab in Hong Kong! We are hiring a PhD student to merge large-scale metagenomics with 3D structural analysis and immunology. If you have experience in any of these areas and are motivated to learn the others, get in contact; lnkd.in/ggr3T4sQ

#Probiotics Administration of a live gut bacterium (*) to Crohn's disease patients appears to be safe and modulates immune gene expression in the ileum, supporting its potential use as a biotherapeutic (* Faecalibacterium prausnitzii)

Faecalibacterium prausnitzii EXL01 for the Maintenance of Steroid-induced Clinical Response or Remission in Patients with Crohn’s Disease: a first in human trial - Nature Communications

In this clinical trial the authors show that EXL01, a live bacterial therapy based on F. prausnitzii, can be safely administered to Crohn’s disease patients, showing immune gene modulation in the ileum and supporting its potential as a biotherapeutic.

dlvr.it

We are recruiting a lab manager for my group in Oxford. This is a lovely team doing great things, and you could be an important part of it! See here: www.path.ox.ac.uk/vacancy/lab-... Please spread the word!

Lab Manager - Molecular Immunology - Dunn School

Laboratory Manager/Senior Scientist position in the Molecular Mucosal Immunology group at Oxford

path.ox.ac.uk

Universal microbiome signature for CRC Large gut microbiome meta-analysis of colorectal cancer uncovers CRC microbiome signatures universal across ages & sequencing methods & modifiable by dietary interventions, ie fiber. www.cell.com/cell-host-mi...

Meta-analysis reveals microbiome signatures for colorectal cancer that are universal across age groups and sequencing methods

Pekel, Karcher, et al. present the largest gut microbiome meta-analysis of colorectal cancer to date, integrating 6,779 amplicon and shotgun sequencing profiles. They establish a robust microbiome sig...

cell.com

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

Gut epithelium responses to bile acids 👉 rdcu.be/fmcUe

Modulation of intestinal bile acids influences colonic mucosal responses

Scientific Reports - Modulation of intestinal bile acids influences colonic mucosal responses

rdcu.be

📝 Only a few days left to submit your abstract! Take the opportunity to present your research, workflows, tools, and #FAIR data management approaches at the Boosting Biodata Bootcamp 2026! 👉 Abstract submission: events.hifis.net/event/3702/a... 📅 Submission deadline: 1 June #biology #rdm #nfdi

So happy to see this out 🎉 it all started with a discussion group of ECR brought together by the NCCR Microbiomes and cumulated in this primer on microbial community ecology. This was such a fun group project, where I learned a lot about how cool both microbial and human communities are 🤩

Oliver Meacock@olimeacock.bsky.social · 2mo ago

Delighted to see this out in its final form! doi.org/10.1093/isme... We established a discussion group focussed on the history of community ecology and how it informs our understanding of microbiota. This review distils those discussions to provide a guide for microbiologists entering the field

Come and work with us in a beautiful corner of Germany: 5 years of funding for your microbiology research and lots of great colleagues 🦠🧫

Andreas Peschel @andreaspeschel.bsky.social · 3mo ago

You are an ambitious young scientist, on the verge to independence, in a research field related to our Cluster of Excellence @cmfi.bsky.social “Controlling Microbes to Fight Infections”? Join our vibrant, interactive scientific community in Tubingen. Repost and apply! www.nature.com/naturecareer...

Out Now! Benchmarking shotgun metagenomics #MicroSky

Benchmarking shotgun metagenomics

Nature Microbiology, Published online: 24 April 2026; doi:10.1038/s41564-026-02344-0Shotgun metagenomic sequencing is a comprehensive untargeted next-generation sequencing method that enables culture-independent analysis of complex microbial communities. Comparing the results of several metagenome-based analyses at various sequencing depths for known input illustrates which methods and amounts of data are most suitable for determining microbial composition, accuracy of metagenome-assembled genomes and functional coverage.

go.nature.com

Check out our work on E. coli capsules! Including a 3x extended catalog of capsule loci from >37K genomes, a scalable tool to type them in silico (kTYPr) and new associations with ecology and disease! A joint effort from @microbiomeresearch.bsky.social @mucosalimmunology.bsky.social at @ethz.ch.

Nature Microbiology@natmicrobiol.nature.com · 3mo ago

Out Now! In silico typing maps the natural diversity of Escherichia coli transporter-dependent capsules #MicroSky

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

In my latest column, I explain some of my reasons for being deeply skeptical about AI models that claim to understand DNA, genes, and genomes: stevensalzberg.substack.com/p/ai-is-star...

AI is starting to look like pseudoscience

Not all of it, but some scientists are too eager to believe their own hype

stevensalzberg.substack.com

📢 Are you at #VAAM2026? 👉 Stop by the NFDI4Microbiota booth to learn how we can support you with training, data analysis, and making your microbiome research easier to share, reuse, and scale. And don’t miss today’s panel discussion at 1:30 in Lecture Hall B! We’d love to meet you 👋!

Are you at #DGE26? 👋 So are we! Stop by the NFDI4Microbiota booth to explore how we can help make your microbiome research FAIR and easier to share, reuse, and amplify. Let’s connect, exchange ideas, and talk data. We’d love to meet you! #microbiome #NFDI #FAIR #rdm

Registration for the 18th Annual Seeon Conference on Microbiota, Probiotics and Host is now open! 🎉 We’re looking forward to welcoming you in Seeon! When: June 24-26 Where: Seeon Monastery, Germany (near Munich) Program: www.dghm.org/seeon/ Registration: app1.edoobox.com/SPP1656/Seeo...

Seeon - Deutsche Gesellschaft für Hygiene und Mikrobiologie

Microbiota, Probiotics and Host    Seeon- Save the date 2026 Registration Abstract Template 2026   We are looking forward to meeting you there! Don’t forget your swimwear, sunscreen and running gear ...

dghm.org

☕ Join our next NFDI4Microbiota Tandem Coffee Talk! 📅 Mon, 23 Feb 2026 | 14:00–15:00 CET 🎙️ Prof. Dr. Bas E. Dutilh & Dr. Noriko Cassman 💬 “Learning phage-host interactions from curated big data” & “VirJenDB: a FAIR (meta)data and analysis platform for viruses” 👉 More info here: tinyurl.com/5y7h6wfh

Prof. Carolin Schneider von der Uniklinik RWTH Aachen forscht mit KI-Fachleuten zur Krebsprävention. Ziel ist die personalisierte Strategie: "Wir glauben, dass wir gute Modelle entwickeln können, die die Einzel-Faktoren berücksichtigen, die jemand mitbringt." ➡️ www1.wdr.de/mediathek/au...

Krebsforscherin: "Prävention ins Zentrum stellen"

Ärztin Carolin Schneider forscht mit KI-Experten an der RWTH Aachen zur Krebsprävention. Ziel ist die personalisierte Strategie: "Wir glauben, dass wir gute Modelle entwickeln können, die die Einzel-F...

www1.wdr.de

We’re hiring 2 Postdocs (f/m/d) in Drug–Microbiome–Host Interactions 🦠💊 Focus: how non-antibiotic drugs shape the gut microbiome, drug efficacy & side effects. #PostdocJobs #Microbiome #AcademicJobs Full job ad: lisamaierlab.com/wp-content/u...

Now published 🔥 Feeding your gut microbes with complex carbohydrates can help preventing colorectal cancer by reducing the production of secondary bile acids. Perhaps NiMe diet @jenswalter15.bsky.social? THX team & Sören Ocvirk ⭐ Thx www.sfb.tum.de/1371/microbi.... Article 👉 doi.org/10.1136/gutj...

Secondary bile acid production by gut bacteria promotes Western diet-associated colorectal cancer

Background Western diet and associated production of secondary bile acids (BAs) have been linked to the development of sporadic colorectal cancer (CRC). Despite observational studies showing that seco...

doi.org

Save the Date! 📅 The NFDI4Microbiota Annual Conference 2026 will take place 15–17 September 2026 and will be a joint event with other biodata-related NFDI consortia. Stay tuned for more details! #onenfdi #NFDI4Microbiota #rdm #microbiota

📍Our paper is out!📍 Here, we show the development of a GC-MS/MS method for the quantification of 120 compounds produced by gut bacteria, including short-chain fatty acids, indols, nucleotides, organic acids, and amino acid derivatives. Check it out! link.springer.com/article/10.1...

Development of a GC-MS/MS method to quantify 120 gut microbiota-derived metabolites - Analytical and Bioanalytical Chemistry

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....

link.springer.com

Franziska Faber and I are recruiting shared postdocs, PhD students to work on Fusobacterium & new BGCs. www.helmholtz-hiri.de/fileadmin/HI...

New paper from the lab! Led by Patrick Müller: we show that non-antibiotic compounds — but not macrolide antibiotics — can induce an efflux pump that protects Bacteroidaceae from macrolides. A neat twist on drug–microbe interactions... www.tandfonline.com/doi/full/10....

📣 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

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 ⭐⭐

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

A place to be 👇 Highly recommended ⭐⭐⭐⭐⭐

Emma Slack@mucosalimmunology.bsky.social · 9mo ago

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...