Professor Lesley Hoyles

MRC curiosity-driven research reopens with new approach The Medical Research Council (MRC) unpauses curiosity driven research funding and improves the funding process.

MRC have announced their new approach to curiosity-driven research: www.ukri.org/news/mrc-cur...
Boards gone (?) replaced with flexible panels and interviews. DPFS and Gap fund renamed.

Antibiotic use and gut microbiome composition links from individual-level prescription data of 14,979 individuals - Nature Medicine Using individual-level data from the Swedish Prescribed Drug Register and fecal metagenomes of 14,979 individuals in Sweden, the authors examined the association between oral antibiotic use over 8 yea...

🚨 New paper! Very excited to have been part of this collaborative work looking at the effect of antibiotics on the gut microbiota even years after prescription. Amazing effort led by Gabriel @tovefall.bsky.social and many others published today in Nature Medicine!
🔗 www.nature.com/articles/s41...

2 year fellowship available in AMR research www.medicalresearchfoundation.org.uk/grants/antim...

When Referee 3 is too lazy to review the paper and their AI-generated response cites hallucinated papers to “prove” non-originality! This is mind-boggling. #AcademicSky

The textbooks say #archaea are non-pathogenic. True.
But maybe we’re not as irrelevant as you thought.

New preprint on the limits of detecting higher-order interactions in microbial communities.
www.biorxiv.org/content/10.6...
We find that the dominance of additive and pairwise interactions on community function may not reflect biological simplicity, but fundamental limits of statistical detection.

BBC Audio | The Interview | Samantha Power, former US Ambassador to UN: Closing USAID was soft power suicide Caitriona Perry speaks to the former US ambassador Samantha Power who led USAID

“The destruction of USAID is not only one of the cruellest acts that I've seen in my career, but of course also one of the dumbest.”

bbc.com/audio/play/w...

Tryptophanase disruption promotes insect–bacterium mutualism - Nature Microbiology Disruption of a single gene encoding tryptophanase makes Escherichia coli mutualistic in a stinkbug model owing to the accumulation of tryptophan and a reduction in toxic indole. This gene is typicall...

www.nature.com/articles/s41...

#microsky #symbiosky

New post-doctoral research position in my phage-host interactions (Phi) laboratory in @otagomicroimmuno.bsky.social at @universityofotago.bsky.social New Zealand. The project is focused on defences against jumbo phages. Please share and if interested apply using the link in the comments.

New personal view article

The role of microbial genomics in delivering the UK’s national action plan for confronting antimicrobial resistance 2024–29

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #AMR #OpenAccess #OA

Deacon can now run in the browser using WebAssembly. Sequence data never leaves your machine. It currently supports FASTA/Q filtering using indexes up to 1GB in size.

Demo: bede.im/deacon

AI Keeps Failing at Microbiome Prediction Why simple models keep winning, where deep learning still shines, and where the field is headed

AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction.

My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed

blekhman.substack.com/p/ai-keeps-f...

Worth signing up to twickets for resales. Quite a few London tickets have become available in the last few days.

Basher Science: Microbiology This latest book from the Basher Science series investigates the unseen world of microbes. Basher's distinctive style presents key microbes as characters with their own voice and personality. Micr...

We used this one to explain things to an afterschool club.

Any recommendations for books / vids for little ones interested to learn about microbiology?

My 5yo has picked up on work chatter and keeps asking “Tell me about Klebsiella?” and I am running out of ideas! 😂

#MicroSky

Go to settings, then moderation. You can mute single words, phrases and tags.

So I pleased to announce the conceptual spawn of FigTree: PearTree (acronym still to be finalised). If you want to dive right in it is hosted as a web app here: artic-network.github.io/peartree (click the “Example...” button for immediate candy and then click every button you can find).

Amazing peppered moth story from Saccheri lab - same locus, but different structural variants, underly parallel evolution of industrial melanism in the UK and across continental Europe.

Surveyed misconceptions around #AntibioticResistance are fascinating:

• 66% believe they aren't at risk of resistance when taking antibiotics
• ~70% assume ‘antibiotic resistance’ refers to the body gaining resistance
• ~25% expect antibiotics for viral infections

#AMR #SciComm

Sources below:

Can you trust the results from gut microbiome tests? Maybe not Seven firms reported inconsistent results on the same sample, some over multiple tests. These gut microbe discrepancies could have health consequences.

"Can you trust the results from gut microbiome tests? Maybe not." www.sciencenews.org/article/resu...

I understand why the authors didn't disclose the different company IDs...but I'm very curious to know which is which

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...

18 authors... Aargh!

a close up of a man 's face with his eyes closed ALT: a close up of a man 's face with his eyes closed

TFW you spend an hour filling in an online manuscript submission only to accidentally delete the record instead of approving it for submission.

Very happy to see Wasm gaining traction as a low barrier to entry alternative for programming thanks to the massive efforts by @quantstack.bsky.social 🎉 We're collecting Wasm resources for bioinformatics and beyond at wasmodic.github.io

@wytamma.bsky.social 's WASM tools have transformed my experience of teaching Python to first year undergraduate biologists this year. Since last year, I've been teaching ~400 undergrads how to code (functions, lists, dictionaries, loops) over (one hour intro lecture +) two 2-hour practicals. 1/n

Protease-Controlled Prophage Activation in Staphylococcus aureus: New Mechanisms Driving Antimicrobial Resistance and Virulence at University of St Andrews on FindAPhD.com PhD Project - Protease-Controlled Prophage Activation in Staphylococcus aureus: New Mechanisms Driving Antimicrobial Resistance and Virulence at University of St Andrews, listed on FindAPhD.com

📢 Funded PhD in molecular microbiology & phage biology

How do bacterial stress responses control prophage activation and horizontal gene transfer?

Join us at St Andrews to dissect Clp protease–mediated regulation in Staphylococcus aureus.

Apply:
www.findaphd.com/phds/project...

Host Pathogen Interactions during Catheter-Associated Urinary Tract Infections As a leading cause of healthcare-associated infections, catheter-associated urinary tract infections (CAUTIs) present a unique challenge due to the high prevalence of multidrug-resistant and polymicrobial pathogens. Distinct from uncomplicated UTIs, the insertion of a urinary catheter provokes tissue damage that triggers inflammation, plasma extravasation, and the deposition of host fibrinogen. This inflammatory response drives the robust recruitment of immune cells and plasma extravasation, leading to the accumulation of fibrinogen─a key coagulation protein─on the device and bladder epithelium. This fibrinogen-rich environment creates a unique niche for intricate host–pathogen interactions. Crucially, uropathogens exploit these deposits to establish persistent biofilms, while the protein scaffold simultaneously modulates host immunity. Understanding these mechanisms, particularly the role of fibrinogen-binding adhesins, is vital for developing targeted, antimicrobial-sparing therapeutics. In this perspective, we examine the strategies uropathogens employ to persist in the catheterized bladder, the corresponding host immune response, and emerging strategies to prevent CAUTI.

Ever wonder what really goes down in the microscopic battleground of a catheter-associated UTI? 🦠⚔️ Our new review unpacks the Host-Pathogen Interactions during CAUTIs. Thank you, Kurt Kohler and Alyssa La Bella @alabella14.bsky.social for putting this together!!! pubs.acs.org/doi/full/10....

Nutrient competition predicts gut microbiome restructuring under drug perturbations Systematic profiling of 707 drugs on their impact on stool-derived microbial communities shows that nutrient competition explains and predicts species shifts under drug treatment and that post-drug re...

Fascinating discovery by team @stanfordbiosci.bsky.social

www.cell.com/cell/abstrac...

What’s holding back clinical use of phage therapy in the UK?

Our workshop last year brought together international experts, biotech and regulators to find out

Meeting Report out now in Nature Microbiology with our take on the challenges and opportunities facing the UK phage therapy sector

In case you missed it: our review titled "Spatial structure: shaping the ecology and evolution of microbial communities" is out! 🚨

Let me hit you with some highlights on why spatial structure matters. (and why you should care!)

Sharing is appreciated 🙏 🧵👇

doi.org/10.1093/fems...