New Perspective out co-led with Lisa Pagani! We look at how microbiome ecology and evolution shape AMR across scales, from within-host communities to hospitals and environments, and how mathematical models can help us understand them. @natmicrobiol.nature.com www.nature.com/articles/s41...

Modelling the role of the microbiome in antimicrobial resistance across scales - Nature Microbiology

The microbiome plays a significant yet underexplored role in antimicrobial resistance by influencing ecological and evolutionary processes. This Perspective proposes a framework to integrate microbiom...

nature.com

Less than 1 week to apply for this postdoc! If you want to find out more about the project have a look at our recent preprint: www.biorxiv.org/content/10.6... #mevosky

Michael Brockhurst@brockhurstlab.bsky.social · 3mo ago

Why does antibiotic resistance evolution vary between patients? Come to @officialuom.bsky.social @mermanchester.bsky.social to help us find out! 2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...

A new method for inference and tracking the transmission of strains in metagenomes #MicroSky #MicroEco www.nature.com/articles/s41...

Strain-level transmission inference across multi-kingdom metagenomic data using TRACS - Nature Microbiology

The TRACS algorithm tracks bacteria, viruses and parasites in metagenomic or population sequencing data, detecting microbial transmission even when multiple strains coexist within a host.

nature.com

Why does antibiotic resistance evolution vary between patients? Come to @officialuom.bsky.social @mermanchester.bsky.social to help us find out! 2.5 year @wellcometrust.bsky.social postdoc position in experimental evolution Closing 15 May. Apply here: www.jobs.manchester.ac.uk/Job/JobDetai...

Research Associate in Microbial Evolution:Oxford Road

jobs.manchester.ac.uk

Check our new preprint by Knopp M. et al.! Human gut microbiomes can impose strong +/- selection for resistant versions of resident opportunistic pathogens. In the case we follow up, selection is driven by altered carbohydrate utilisation that the resistant mutant evolves. doi.org/10.64898/202...

Really happy to see this out! Great work led by @mboum.bsky.social A nice example of how microbiome-specific ecological constraints can shape E. coli growth www.pnas.org/doi/10.1073/... @pnas.org

Mathilde Boumasmoud@mboum.bsky.social · 3mo ago

New paper out in @pnas.org 🎆! Across healthy humans, the same bacterium encounters markedly different gut microbiomes. How does this shape the ecological interactions it experiences? We explored this focusing on commensal E. coli.
 www.pnas.org/doi/10.1073/... Image: @illuzation.bsky.social

Missed this paper last week, very interesting by Ami Bhatt and her group. www.nature.com/articles/s41... 'Transposable elements are driving rapid adaptation of Enterococcus faecium'

Transposable elements are driving rapid adaptation of Enterococcus faecium - Nature

Over three decades, rapid expansion of the transposable element ISL3 has reshaped Enterococcus faecium, which helps to explain this pathogen’s growing clinical threat.

nature.com

New paper out in @pnas.org 🎆! Across healthy humans, the same bacterium encounters markedly different gut microbiomes. How does this shape the ecological interactions it experiences? We explored this focusing on commensal E. coli.
 www.pnas.org/doi/10.1073/... Image: @illuzation.bsky.social

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

Quantifying the real-world impact of antibiotic use and genetic determinants of resistance on gonococcal dynamics

Nature Microbiology - Phylodynamic modelling shows how the changing antibiotic landscape and genetic determinants of resistance shape real-world gonococcal dynamics. Experiments validated that...

nature.com

Yonatan Grad@yhgrad.bsky.social · last yr.

New preprint! How much does antibiotic use shape bacterial lineage dynamics, and how does that relate to the fitness costs/benefits of resistance determinants? All sorts of fun findings and a method that we hope will be broadly useful. See @dhelekal.bsky.social's thread and the preprint!

How does treatment induced antibiotic resistance happen in real-world infections? We analysed 25k Pseudomonas isolates from 180 patients in a clinical trial to find out! TLDR: The ecological and evolutionary paths are surprisingly diverse & complex even in patients receiving identical treatment…

Matthew J Shepherd@matthewjshepherd.bsky.social · 6mo ago

🚨 New pre-print! 🚨 In the largest study of its kind to-date, we investigate the ecological and evolutionary mechanisms driving within-patient evolution of antimicrobial resistance (AMR). Read here: www.biorxiv.org/content/10.6... , and follow along with this thread, discussing our findings (1/21)

Great work again from @alexmsalmeida.bsky.social et al highlights uncultured genus CAG-170 (Oscillospiraceae) to be central node in healthy co-abundance networks in >11k gut metagenomes, with predicted B12 biosynthesis/cross-feeding functions possibly involved. www.sciencedirect.com/science/arti...

Meta-analysis of the uncultured gut microbiome across 11,115 global metagenomes reveals a candidate signature of health

The human gut microbiome is important for host health, yet over 60% of gut species remain uncultured and inaccessible to experimental manipulation. He…

sciencedirect.com

🥁 NEW Our study on infant gut microbiome and #straintransmission is now published in @nature.com: doi.org/10.1038/s415... 1/10

Baby-to-baby strain transmission shapes the developing gut microbiome - Nature

A metagenomic survey of babies attending the first year of nursery detected extensive baby-to-baby microbial strain transmission, pointing to social interactions in infancy as crucial drivers of infan...

doi.org

Our team wrote a review for Gut Microbes on the role of the gut #microbiome in modulating enteric infections. Great team effort by Qi Yin, @samriddhigupta.bsky.social and Efrat Muller: www.tandfonline.com/doi/full/10....

The human gut microbiome in enteric infections: from association to translation

Enteric infections remain a leading global cause of morbidity, mortality and economic loss, increasingly compounded by the rise of antimicrobial resistance. The gut microbiome — spanning bacteria, ...

tandfonline.com

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible. www.nature.com/articles/s41...

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature

Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

nature.com

How do interactions with resident nasal microbiota shape colonisation resistance to MRSA? Excited to share this preprint in collaboration with @mboum.bsky.social @anaellefait.bsky.social Silvio Brugger and Alex Hall. www.biorxiv.org/content/10.6...

Individual bacterial taxa drive colonisation resistance to methicillin-resistant Staphylococcus aureus in human nasal microbiome samples

Identifying bacterial interactions that determine susceptibility of human microbiomes to colonisation by pathogenic bacteria has crucial implications for understanding health and disease and, conseque...

biorxiv.org

Now available online: the new 2.0 version of gutSMASH, with capabilities to detect 12 new types of catabolic gene clusters relevant to gut microbiome ecology, as well as predictions of their regulation through transcription factor binding site detection. www.sciencedirect.com/science/arti...

gutSMASH 2.0: Extended Identification of Primary Metabolic Gene Clusters From the Human Gut Microbiota

Microbiota-derived metabolites serve as key messengers mediating host–microbe and microbe–microbe interactions, often through specialized primary meta…

sciencedirect.com

New PhD project, supervision by @alanmcn1.bsky.social and me. 'Nationwide Clostridioides difficile population dynamics' www.findaphd.com/phds/project... Deadline for applications 9 Jan 2026, UK students only.

Nationwide Clostridioides difficile population dynamics. at University of Birmingham on FindAPhD.com

PhD Project - Nationwide Clostridioides difficile population dynamics. at University of Birmingham, listed on FindAPhD.com

findaphd.com

Thrilled to share that our new paper is out now in @natcomms.nature.com 🎉 Huge congrats to @vhrcabral.bsky.social and @karinaxavierlab.bsky.social on this major work. We found that our Klebsiella ARO112 can break the antibiotic/inflammation cycle in an IBD model

Klebsiella ARO112 promotes microbiota recovery, pathobiont clearance and prevents inflammation in IBD mice

Nature Communications - Here, the authors provide evidence of the biotherapeutic potential of Klebsiella ARO112 for gut inflammatory conditions by showing it accelerates pathobiont clearance and...

urldefense.com

New preprint from our lab www.biorxiv.org/content/10.1...! Andrea Dos Santos and Clément Vulin combine experiments and models showing how adding glucose can strengthen negative interactions between microbial species. This can be used in tandem with antibiotic treatment to inhibit pathogens!

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

nature.com

🚨Preprint alert - this is a big one! We transfer the revolutionary power of TnSeq to bacteriophages. Our HIDEN-SEQ links the "dark matter" genes of your favorite phage to any selectable phenotype, guiding the path from fun observations to molecular mechanisms. A thread 1/8

New PhD position in my lab at @uniofbath.bsky.social (with both @tweethinking.bsky.social & Dr Bethan Littleford-Colquhoun)! We're looking for someone keen on bioinformatics and microbiome evolution. Important info below on eligibility & URSA competition funding👇 www.findaphd.com/phds/project...

The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath on FindAPhD.com

PhD Project - The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath, listed on FindAPhD.com

findaphd.com

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n) www.biorxiv.org/content/10.1...

Our paper “Global dissemination of npmA mediated pan‑aminoglycoside resistance via a mobile element in Gram‑positive bacteria” is now in @natcomms.nature.com. Part of my freshly defended PhD, so doubly happy! 😄🎉 🧵 (1/14) www.doi.org/10.1038/s414...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria - Nature Communications

The authors investigate the distribution of the aminoglycoside resistance gene npmA in Gram-positive bacteria via a mobile genetic element, highlighting its global presence and cross-species transfer ...

doi.org

Can we leverage bacterial competition for targeted replacement of harmful strains? Maybe! Our recent piece in @natmicrobiol.nature.com provides a theoretical framework and a set of experiments to show what it might take: www.nature.com/articles/s41...

Strain displacement in microbiomes via ecological competition - Nature Microbiology

Mathematical modelling and experimental tests reveal principles that govern displacement of a resident strain by an invader in microbial communities.

nature.com

New paper out 🎆 When an antibiotic-resistant E. coli strain lands in our gut microbiome, whether it will get established or not depends on the ecological context. We studied how other microbes, nutrients, and antibiotic exposure shape its fate.👇

Ricardo León-Sampedro@rleonsampedro.bsky.social · 9mo ago

🚨 Excited to share our new paper is out! 🎉 We show how interactions within gut microbiomes allow certain antibiotic-resistant E. coli strains to persist even without antibiotics, helping explain how resistance is maintained in the human gut. Now published in @natcomms.nature.com rdcu.be/eOf63

So happy to share this! Bacteriocins were first discovered over 100 years ago, but what do they actually do? We look at >1000 bacteriocin plasmids and find links to virulence and antimicrobial resistance, and frequent bacteriocin sharing in Enterobacteriaceae. www.nature.com/articles/s41...

Bacterial warfare is associated with virulence and antimicrobial resistance - Nature Communications

Bacteria employ a range of competition systems that deliver toxins to inhibit competing strains. This study shows that these systems are particularly important for the ecology of virulent and antibiot...

nature.com

🐝🦠 New paper: rdcu.be/eOf7A Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social

Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications

Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...

nature.com

New(ish!) paper on how within-host competition and antibiotic resistance shape the fitness of Streptococcus pneumoniae serotypes, out in August in Plos Biology. journals.plos.org/plosbiology/...

Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae

Competition significantly influences bacterial population dynamics, particularly in how strains interact within and between hosts. This study shows that within-host competition in Streptococcus pneumo...

journals.plos.org

So excited to share a new paper from my lab just published in Nature Communications! We showed that vancomycin-resistant enterococci (VRE) occupied distinct intestinal niches in the antibiotic-treated intestine. doi.org/10.1038/s414... Amazing work by first author Olivia King and colleagues!

Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation - Nature Communications

Here, the authors show that vancomycin-resistant enterococci grow in the antibiotic-treated gut microbiome by utilising enriched nutrients in the presence of reduced concentrations of inhibitory micro...

doi.org