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...

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…

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…

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...

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...

🥁 NEW

Our study on infant gut microbiome and #straintransmission is now published in @nature.com:

doi.org/10.1038/s415...

1/10

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, ...

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....

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 ...

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...

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...

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...

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…

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...

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

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.

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...

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

Diagram illustrating "feed the enemy's enemy": ampicillin inhibits Pseudomonas aeruginosa. Citrobacter freundii acidifies the environment, further inhibiting P. aeruginosa.

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 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–...

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...

🚨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

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

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...

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...

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 ...

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...

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.

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...

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.👇

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...

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...

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...

🐝🦠 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

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...

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/...

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...

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!

Long-read metagenomics for strain tracking after faecal microbiota transplant - Nature Microbiology A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains and revealing genomic ch...

OUT NOW - Long-read metagenomics method for strain tracking after FMT #microsky www.nature.com/articles/s41...

Deciphering microbial spatial organization: insights from synthetic and engineered communities Abstract. Microbial communities are frequently organized into complex spatial structures, shaped by intrinsic cellular traits, interactions between communi

Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...

Our high-precision metagenomic strain caller, PHLAME, is now published in Cell Reports!! www.cell.com/cell-reports...

PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.

Mechanisms of microbiome assembly and approaches to uncover the ecological forces driving it.

Deriving ecological models solely from observational data limits our ability to understand mechanisms driving microbiome assembly. This #mSystems articles explores how experimental approaches can address these challenges. asm.social/2wj

Within-host bacterial evolution and the emergence of pathogenicity - Nature Microbiology In this Review, Tonkin-Hill et al. discuss the processes driving bacterial evolution and emergence of pathogenesis within hosts, the importance of understanding within-host genetic diversity, and the ...

#Review

A discussion on the processes driving bacterial evolution and emergence of pathogenesis within hosts, the importance of understanding within-host genetic diversity, and the implications for transmission analysis and infectious disease control.

#MicroSky 🦠

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

Our paper demonstrating that within-species warfare interactions are ecologically important on human skin is now published in Nature Micro! www.nature.com/articles/s41...

This is such a cool read on the fascinating topic of nutrient competition in microbiomes😍 I couldn t agree more with «A key challenge in understanding microbiomes is that the species composition often differs among individuals, which can thwart generalization. »

The microbiome of the human facial skin is unique compared to that of other hominids | mSystems Understanding how and why human skin bacteria differ from our closest animal relatives provides crucial insights into human evolution and health. While we have known that human facial skin hosts disti...

Our work on the facial skin microbiome of non-human primates is out in mSystems!

We show there is no close relative of Cutibacterium on the faces of gorillas and chimps at the Lincoln Park Zoo, furthering the mysterious origin of the dominant human skin colonizer.

journals.asm.org/doi/10.1128/...