Our study analysing ~5,000 single-cell transcriptomes of Vibrio cholerae is now out in Frontiers in Microbiology! doi.org/10.3389/fmic...

#microsky #phagesky #phage defence www.science.org/doi/10.1126/...

Registration is open for September’s Vibrio2026 conference in Berlin! event.fourwaves.com/vibrio2026/p...

Protist–bacteria partnerships are more common in wastewater treatment plants than we thought. In this ISME communications paper, we uncovered widespread denitrifying endosymbionts inside ciliates, their global distribution, and their temporal dynamics across WWTPs.🦠 academic.oup.com/ismecommun/a...

📢 New preprint is out on bioRxiv 📢: How much does virome prep influence our view of the human gut virome? Short answer: a lot. Long answer: doi.org/10.1101/2025... Different methods lead to distinct community structures, richness, and major virus-host abundance patterns. 🧵 1/5

By analysing microbial signatures from urine and catheters, we built a machine-learning tool that can distinguish harmful UTI-causing bacteria from harmless ones. This could help clinicians make better decisions about treatment and catheter changes, and importantly, avoid unnecessary antibiotics.

Thrilled to share our most challenging project yet! Our 3 years of longitudinal research, study on AI-based prediction of urinary tract infections (UTIs) in people with spinal cord injury is now published in Microbiome journal. Here’s the link to the paper 👇 link.springer.com/article/10.1...

All artifact? 😬 www.pnas.org/doi/10.1073/...

Occurrence and temporal dynamics of denitrifying protist endosymbionts in the wastewater microbiome url: academic.oup.com/ismecommun/a...

🚨 Top microbiology jobs. The FEMS opportunities board has new PhD, Postdocs , & Junior Research Group roles in Methane Flux, AI in Health, Marine Symbiosis, & Evolution. Apply here buff.ly/9r6E3Er or sign up for the monthly newsletter FEMS buff.ly/EQc3WTm .

Claude scientific skills 🧬🖥️🧪 github.com/K-Dense-AI/c... 🧬 Bioinformatics & Genomics 🧪 Cheminformatics & Drug Discovery 🔬 Proteomics & Mass Spectrometry 🤖 Machine Learning & AI 🔮 Materials Science & Chemistry 📊 Data Analysis & Visualization

Great to see this finally published! Metalog: curated and harmonised contextual data for global metagenomics samples now out in @narjournal.bsky.social academic.oup.com/nar/advance-...

www.nature.com/articles/d41... "Researchers welcome the initiative…" - no I fucking don't! This idea is dumber than a sack of hammers. Basing any judgement on author position is crass - it captures very little of use and has no universal meaning.

A comprehensive review on microbial degradation of polyethylene plastics: ecotoxicity, deterioration process, recurrent intermediates and key enzymes involved link.springer.com/article/10.1... #jcampubs

Check out our work on biofilm degrading enzyme. 👉Crude preparation of a phage-encoded biofilm-dispersing factor expressed in E. coli and its potential application in bacteriological analysis of environmental water samples | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...

Check out my PhD student Fiona Facey’s first first-author paper on finding microbes that can degrade multiple types of plastics in the Galleria mellonella gut microbiome 👇 enviromicro-journals.onlinelibrary.wiley.com/doi/10.1111/...

Glad to share a collaboration with Yicen Lin's group at Kunming University of Science and Technology published in ISME Journal Synergistic biodegradation of polyethylene by experimentally evolved bacterial biofilms academic.oup.com/ismej/advanc... #MicrobiomeEcology at #LeidenBiology

Manually curated and harmonized metadata for over 110k metagenomic samples! (58k samples from the human gut alone!)🦠 Proud to have contributed to Metalog, the latest @borklab.bsky.social resource: www.biorxiv.org/content/10.1... #microsky #microbiome

Cool PNAS paper by @jordivangestel.bsky.social and colleagues Contributed by Carol Gross [reviewed by @polzlab.bsky.social and @wcratcliff.bsky.social] Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation www.pnas.org/doi/10.1073/...

Delighted to announce that The International Meeting on the Biology of Vibrios will be back next year! Vibrio2026 will be held in Berlin in September 13-16. See you there Vibriologists! event.fourwaves.com/vibrio2026/p...

Our second paper with @tcostalab.bsky.social and GoogleDeepMind reports our experience with Google’s co-scientist: remarkably, the AI independently recapitulated our experimental discovery on cf-PICIs, showcasing AI’s potential to accelerate biology. www.cell.com/cell/fulltex...

Lots of heterogeneity in capsule production in Klebsiella and Acinetobacter. Given the pleiotropic impact of capsules, this provides opportunities for multiple types of phenotypical heterogeneity. Check @julielebris.bsky.social thread on our recent publication.

It’s was a great experience being part of the awesome organising team. 🥳

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years? Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen: www.microbiologyresearch.org/content/jour...

Vibrio cholerae motility is associated with inter-animal transmission www.nature.com/articles/s41... 🦠

My google skills are failing... Back in 2011, NCBI (started to?) close the SRA. The SRA is still with us. Anyone know of any articles from around then about how they saw the light? For those that this is news to... genomebiology.biomedcentral.com/articles/10....

Awesome to see the transparent, systematic, and evidence-based approach behind the WHO Bacterial Priority Pathogens List 2024 out in the Lancet Infectious Diseases www.thelancet.com/journals/lan...

My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology: www.ebi.ac.uk/training/onl... Including both molecular and epidemiological examples

The countdown is on! Only three weeks to #MicroSeq2025 🎊 Abstract submission CLOSES this Friday, August 15th at 11:59pm. Successful applicants will be notified by Tuesday, August 19th. Registration remains open until September 2nd 👇 trybooking.com/events/landing/1424679

Excited to share new #program, STEPS, which can simulate #dynamics of the E. coli Long-Term Evolution Experiment (#LTEE) or other microbes in serial transfer regime. telliamedrevisited.wordpress.com/2025/08/12/s... STEPS developed by @devinmlake.bsky.social, Zachary Matson, Minako Izutsu, and me.

🏆 #MicroSeq2025 has plenty of awards on offer! 💰 Cash prizes for best talks are sponsored by @aussocmic.bsky.social, @ausvirologysoc.bsky.social, and #MGen. Plus, loads of merch on offer for the best question of each session! 🖊️📔 Register to submit an abstract👇 trybooking.com/events/landing/1424679

⏱️ Closing THIS FRIDAY! ⏱️ Register for #MicroSeq2025 below to send through your abstract: trybooking.com/events/landing/1424679

🚨Heads up! 🚨 Abstract submission closes in ONE WEEK! Don’t miss out on this chance to share your research, register and submit your abstract for #MicroSeq2025 now 👇 trybooking.com/events/landing/1424679

The Virtual Lab is open source and can be applied to many problems! github.com/zou-group/vi... 👏Great job @kylewswanson.bsky.social John Pak, Wes Wu, Nash Bulaong @czbiohub.bsky.social

Have you registered for #MicroSeq2025? Are you keen to get even MORE involved? 🤔 Great news! We're seeking chairpeople for each session! To submit an EOI, hit up our DMs or send us an email at [email protected]. Register for MicroSeq2025 here👇 trybooking.com/events/landing/1424679

Congratulations @anshika22.bsky.social and Anna Zemke on this useful paper demonstrating superiority of full length 16S sequencing for profiling respiratory samples from tracheostomy patients. h/t @seqcoast.bsky.social journals.asm.org/doi/10.1128/...

#MicroSeq2025 has many opportunities for medium and lightning talks. Submit your abstract by August 8 and take advantage of this valuable opportunity to present your work to a welcoming community of fellow ECRs and PhD students! 👇 www.microseqconference.com/registration...

🚨Abstract submission & registration for #MicroSeq2025 is OPEN! 🚨Get in quick! The first 50 registrations are FREE for PhD students and ECRs who are current ASM members, thanks to @aussocmic.bsky.social. Head to our website to register now 👇 www.microseqconference.com/registration...

Interesting review on the contribution of resident bacteria in sewage infrastructure and how they can potentially skew wastewater monitoring efforts on AMR www.sciencedirect.com/science/arti...

Today's reading: Nature should be the model for microbial sciences journals.asm.org/doi/10.1128/... by @brettbakker.bsky.social @emilyraehyde.bsky.social and @pedroleao.bsky.social Looks ideal for a talk I am working on on model organisms ...

journals.plos.org/plosgenetics... #MicroSky

En route to the GRC for Microbial Population Biology, my conference home for 30🤯 years. In this spirit, gladly sharing this new paper led by Henriette Roder who visited us a few years back, featuring an innovative new biofilm passage + microscopy system www.nature.com/articles/s41...

🦋Hello BlueSky!🦋 Let's get right into it. MicroSeq is back September 3-4, 2025! Stay tuned for more details on registration and abstract submission coming soon here and at www.microseqconference.com. 🌟Save the date!🌟 #MicroSeq2025

One of my favourite serendipitous results from the lab came about because we were long-read sequencing bacterial: Vibrio cholerae, which is "supposed to" have TWO circular chromosomes (3 + 1 million base pairs) often has just ONE fused chromosome (4 Mbp). www.nature.com/articles/s41... (1/n)

My newsletter is about looking for jobs in the current academic job market....please feel free to add any advice you have.... open.substack.com/pub/matthias...

🧵🦠🖥️🧬🧪 Please RePost 🙏 We just released reference genomes for another 250 strains to the ATCC Genome Portal (genomes.ATCC.org)! We now have assemblies for _5,750 microbial genomes_ AND all assemblies w/ @nanoporetech.com data will include DNA methylation profiles too (details👇) #genomics 1/

Whole-Genome Phenotype Prediction with Machine Learning: Open Problems in Bacterial Genomics academic.oup.com/bioinformati... 🧬🖥️🧪 gitlab.com/leoisl/dbgwas

www.nature.com/articles/s41... #MicroSky Bacteria to the rescue…

Global Metagenomics Reveals Hidden Protist Diversity. #ProtistsonSky www.biorxiv.org/content/10.1...