Human milk oligosaccharide mediates mutualism between Escherichia coli and Bifidobacterium bifidum - Nature Communications Escherichia coli is widespread in healthy breastfed infants, yet its ecological role is unclear. Here, the authors provide insights into the mechanisms supporting its persistence and co-existence with...

New paper out in Nature Comms 🎉

Congrats to first author @sekid.bsky.social & thanks team & collaborators

We show that B. bifidum & E. coli can cooperate in the breastfed infant gut through nutrient cross-feeding, helping shape early-life microbiome development 🦠👶

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

Microplastics have been found to interact with the gut microbiome – here’s what health effects they might have If the gut microbiome is disturbed, it could jeopardise our gut health.

Microplastics are everywhere. They are difficult to measure in human samples but may be interacting with our gut microbiomes to increase inflammation!

Read about it in a piece I wrote for The Conversation @theconversation.com

theconversation.com/microplastic...

ICYMI: New online! Gut microbiota induce browning of white adipose tissue

This is figure 1, which shows factors shaping gut microbiome composition.

A Review in Nature Reviews Endocrinology examines the effect of the gut microbiome on ageing and frailty risk, including potential therapies to modify gut microbiome composition to promote healthy ageing. go.nature.com/3QbymTx 🔒

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery - Nature Communications Benchmarking metagenomic binning tools with simulated and real datasets reveals factors affecting genome recovery and provides practical guidelines for improving metagenome assembled genome reconstruc...

Comprehensive benchmarking of metagenomic binning tools reveals key factors for improved genome recovery www.nature.com/articles/s41... #jcampubs

Does an imbalanced gut microbiome worsen chronic kidney disease?

By elucidating the ecological causes for changes in the gut microbiota composition during chronic kidney disease and its consequences for disease progression we were able to answer this question.

Absolutely love your work - always linking up multiple systems governed by microbial metabolism. Very inspiring!

A few weeks ago we had the pleasure of being part of the first Kennedy Institute Choir! With a great song choice by Fiona (Running Up That Hill), we had a lot of fun - huge thanks to our wonderful conductor Lizzie!🎶👩‍🎤🎤

Watch here: youtu.be/IOXLjGvkChU?...

@kiroxford.bsky.social @ndorms.bsky.social

Clostridia from preterm infants metabolize human milk oligosaccharides to suppress pathobionts and modulate intestinal function in organoids - Nature Microbiology Clostridium perfringens lacking perfringolysin O toxin isolated from preterm infants metabolizes human milk oligosaccharide disialyllacto-N-tetraose to produce metabolites that promote the growth of c...

🚨 A new piece of the preterm gut microbiome puzzle just fell into place!

Bifidobacterium metabolise human milk oligosaccharides (HMOs) in early life — shaping immunity, supporting gut development, and protecting against diseases like necrotising enterocolitis (NEC).

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

When attacked by the same virus, individuals produce #antibodies that target different parts of that virus. For a given #virus, some antibodies increase with #age while others decrease, depending on the viral fragment targeted. bit.ly/40kYPzG bit.ly/4rlralr [open access]

The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health Nature Reviews Gastroenterology & Hepatology, Published online: 18 February 2026; doi:10.1038/s41575-026-01176-xThis Consensus Statement provides a definition of the term ‘gut health’, as well as a discussion of the relevant domains that contribute to gut health and a framework for appropriate use of the term in the context of therapeutic interventions.

New online! The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of gut health

Discovery of bioactive peptidoglycan fragments from Lactobacillaceae that confer intestinal protection in hosts Liang et al. quantified and profiled natural peptidoglycan fragments (PGNs) released by a panel of bacterial species. They found that prolonged exposure to Lactobacillaceae-derived PGNs induced tolerance in murine macrophages to subsequent TLR stimulation. They demonstrated that the intraperitoneal administration of the natural PGN GM-AQK protected mice against DSS-induced colitis.

Discovery of bioactive peptidoglycan fragments from Lactobacillaceae that confer intestinal protection in hosts

Congratulations again! From a very proud supervisor ❤️

We’re really pleased to share that our excellent DPhil student, Amit, successfully defended his PhD thesis last week! We had a great time celebrating with you and look forward to seeing what your next chapter holds!🎉🧑‍💻🥂

@kiroxford.bsky.social
@amit-halkhoree.bsky.social @nickilott.bsky.social

Genome-wide association analyses highlight the role of the intestinal molecular environment in human gut microbiota variation - Nature Genetics Population-based studies from Sweden with replication in Norway identify associations between host genetic variants and gut microbial composition and implicate short-chain fatty acid chemosensors as m...

Delighted to have contributed to this impressive work led by @tovefall.bsky.social & many others👏 (w/ @gazollavolpiano.bsky.social from our side). This novel microbiome GWAS (n=~16k+12k valid) expands knowledge on genetic factors associated w/ gut microbiota variation.
www.nature.com/articles/s41...

🖥️🧬🚀 I am excited to share that our #omnideconv study is finally published on Genome Biology: doi.org/10.1186/s130...

Congratulations to the wonderful Natasha for successfully defending her DPhil thesis! We’re excited to see what comes next for Natasha and her MAIT cell story whilst she continues her project as a postdoctoral researcher🥳👩‍🔬

@kiroxford.bsky.social

Gut E. coli (esp. pks+/colibactin+) have been thought to be a link between CRC & liver metastasis, possibly by translocating via the portal vein. This work explores in-depth causal mol. mechanisms of liver metastasis promotion by E. coli strains enriched in CRC cases
www.nature.com/articles/s41...

DEPower: approximate power analysis with DESeq2 www.biorxiv.org/content/10.6... 🧬💻🧪

Genetic dissection of stool frequency implicates vitamin B1 metabolism and other actionable pathways in the modulation of gut motility Background Genetic studies of stool frequency (SF), an indirect proxy for gastrointestinal transit, may reveal therapeutically tractable pathways relevant to IBS and other dysmotility disorders. Obje...

New GWAS on stool frequency (n=268K) highlights vitamin B1 (thiamine) metabolism as a new modulator of gut motility via SLC35F3/XPR1. In ~98K UKB participants, dietary thiamine intake correlates with stool frequency too w/ these loci + MR predicts causal effects with IBS.
gut.bmj.com/content/earl...

Host factors dictate gut microbiome alterations in chronic kidney disease more strongly than kidney function - Nature Microbiology A covariate-aware analysis reveals that microbiome changes in the gut of patients with chronic kidney disease are better explained by intestinal transit time than by kidney function.

Big congrats to our colleague @krukowskihubert.bsky.social
on the Nature Microbiology paper linking gut transit time and diet to CKD microbiome changes. Another step in microbiome research!🧫
www.nature.com/articles/s41...

Do you know someone who needs support returning to research? @macularsociety.org are funding a Daphne Jackson Fellowship to be held at any UK university or research institute.

Please share with your network to get one more #ResearchReturner back to their career. daphnejackson.org/fellowship/m...

In vivo detection of immune responses via cytokine activity labeling Cytokine receptor dimerization, induced by the binding of cytokines, can be converted into a genetically traceable fluorescent signal and engineered into reporter mouse lines to visualize processes in...

Tools
'To address this knowledge gap, we developed “cytokine cellular locating platforms” (CyCLoPs), a reporter system that translates cytokine receptor engagement into a genetically traceable signal.'
#Immunology
www.cell.com/cell/abstrac...

The Trust are grateful for the ongoing support from The University of Surrey, who continue to build on the legacy of Professor Daphne Jackson. The Trust spoke with two Daphne Jackson Fellows who were hosted at The University of Surrey about their experience returning to research here.

Glowing bacterial sensors detect gut illness in mice before symptoms emerge UBC researchers have engineered gut bacteria that dim their fluorescent glow in the presence of illness.

Excited to share our latest publication, led by Dr. Ellie McCallum and Juan Burckhardt!
bit.ly/4kfzQaf
You can access the article for free here: authors.elsevier.com/a/1mWb4L7PXu... And more information is available on the updated preprint: www.biorxiv.org/content/10.1...

Looking for a tool to estimate abundances of aerobes versus anaerobes directly from metagenomes? Here you go: www.biorxiv.org/content/10.6...

Huge thanks to @pscsupport.bsky.social for supporting our work and being a driving force for PSC research! Find out how they have helped us delve into research into a role for the small intestine in PSC pscsupport.org.uk/new-research...

New #PSCSupport research finds high ALP associated with decreased protective genes in the small intestine in #PSC. This suggests the small intestine could be a key target for future treatments, perhaps via the #gutmicrobiome.
Full details: buff.ly/TVpOLd2
#Mission2030

PhD studentships available through our BBSRC-funded doctoral programme.

🦠🧫💻 Contact me if you're interested in using bioinformatics/lab-based approaches with cultivated and uncultivated bacteria of the human microbiome, to identify and characterize novel enzymes with potential biotech applications.