Professor Lesley Hoyles

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.

Lookback meme. Woman in red dress with caption: "Antibiotics". Man in blue shirt checking out woman in red dress captioned: "The public". Partner of man in blue shirt glaring at man who is checking out woman in red dress, captioned: "Cold/flu symptoms"

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...

Human hippocampal neurogenesis in adulthood, ageing and Alzheimer’s disease - Nature Mapping of neurogenesis in human hippocampi across ages and different cognitive abilities using multiomic single-cell sequencing reveals distinct signatures between cognitive preservation and decline.

New @nature.com
The brains of Super Agers produce more neurons than people some 50 years younger, a neurogenesis resilient signature linked to exceptional cognitive health and memory skills
nature.com/articles/s41...

Oral–systemic links: periodontal microbes and the blood-brain barrier at Queen Mary University of London on FindAPhD.com PhD Project - Oral–systemic links: periodontal microbes and the blood-brain barrier at Queen Mary University of London, listed on FindAPhD.com

Fully Funded PhD Studentship Opportunity (4 years) at Queen Mary, University of London

Why is gum disease a risk factor for dementia? Come and help us find out!

🗓 Application deadline: 15th May 2026
Apply here: tinyurl.com/4xvdzpjs

Please share! #Microbiome #Dementia #neuroskyence 🧪
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VWR ULT freezer panel

Does anyone have this -80 freezer and/or have the manual and/or know how to turn it on and set the temperature?

Does it go through an automatic burn in period before setting temp?

(Never mind the cracking panel…that was from me breaking it open)

Tilivalline (produced by some K. oxytoca complex strains) has been proposed as an alternative to the chemotherapy drug paclitaxel (aneugen, so indirect genotoxin that causes cell cycle arrest). Would be interesting to see how TV acts in combination with antibiotics.

This is kinda how I've felt too. The students are saying they didn't get what they paid for which is 100% true without in any way being a critique of staff efforts or a suggestion we shld have ignored law + importantly, it's DRIVEN BY A PREDATORY LAW FIRM who are the actual villans, not the students

Yeah, my partner had to learn to teach online from scratch with zero guidance because nobody had moved entire courses online, loads of reworking of lectures, practicals etc. massive increases in pastoral care needed (which was fair enough) with no solid info about timescales. They tried their best.

Yes, some things could have been done better. I'm still angry about many things that happened, but hindsight really can't be applied to 20/21.

My 2 issues with this case: the lack of collective empathy; how royally this is going to further fuck HE provision in the UK if cases are successful. /end

I have never experienced such relentless work stress as that caused by my working environment during the pandemic.

It left me with burnout, which took 18 months to recover from.

University lecturers genuinely did the best they could at the shittiest time in all our lives. /6

Having to provide online pastoral care, with no training, to students who had lost relatives was brutal.

The day I dealt with 3 such students back-to-back online, having to find bereavement counselling for one, my wife found me in floods of tears. /5

I ended up having to design and generate data for 10s of data-driven online projects and train other staff in how to deliver and grade them.

This was while still having to try and keep an active research group going. /4