Mathilde Boumasmoud
@mboum.bsky.social
Postdoc at @ETH_en 👩🏽🔬👩🏽💻 🧐
Microbial evolution | Human microbiome ecology | Infectious disease epidemiology
Microbial evolution | Human microbiome ecology | Infectious disease epidemiology
Reposted by Mathilde Boumasmoud
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...
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…
www.sciencedirect.com
February 10, 2026 at 2:10 PM
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...
www.sciencedirect.com/science/arti...
Reposted by Mathilde Boumasmoud
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
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
January 21, 2026 at 6:24 PM
🥁 NEW
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Our study on infant gut microbiome and #straintransmission is now published in @nature.com:
doi.org/10.1038/s415...
1/10
Reposted by Mathilde Boumasmoud
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, ...
www.tandfonline.com
January 12, 2026 at 4:11 PM
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....
Reposted by Mathilde Boumasmoud
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...
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 ...
www.nature.com
December 17, 2025 at 6:53 PM
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...
www.nature.com/articles/s41...
Reposted by Mathilde Boumasmoud
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...
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...
www.biorxiv.org
January 8, 2026 at 2:00 PM
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...
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...
Reposted by Mathilde Boumasmoud
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…
www.sciencedirect.com
December 13, 2025 at 7:41 AM
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...
Reposted by Mathilde Boumasmoud
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'
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
www.findaphd.com
December 13, 2025 at 4:59 PM
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'
www.findaphd.com/phds/project...
Deadline for applications 9 Jan 2026, UK students only.
Reposted by Mathilde Boumasmoud
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
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
December 12, 2025 at 4:44 PM
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
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
Reposted by Mathilde Boumasmoud
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!
December 2, 2025 at 1:12 PM
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!
Reposted by Mathilde Boumasmoud
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...
#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–...
www.nature.com
November 26, 2025 at 9:55 PM
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...
#phagesky
www.nature.com/articles/s41...
Reposted by Mathilde Boumasmoud
🚨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
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
November 20, 2025 at 8:40 PM
🚨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
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
Reposted by Mathilde Boumasmoud
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...
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
www.findaphd.com
November 12, 2025 at 1:20 PM
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...
We're looking for someone keen on bioinformatics and microbiome evolution.
Important info below on eligibility & URSA competition funding👇
www.findaphd.com/phds/project...
Reposted by Mathilde Boumasmoud
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...
www.biorxiv.org/content/10.1...
www.biorxiv.org
November 11, 2025 at 5:15 PM
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...
www.biorxiv.org/content/10.1...
Reposted by Mathilde Boumasmoud
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...
🧵 (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 ...
www.doi.org
July 17, 2025 at 12:13 PM
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...
🧵 (1/14)
www.doi.org/10.1038/s414...
Reposted by Mathilde Boumasmoud
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.
www.nature.com
November 7, 2025 at 10:34 PM
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.👇
🚨 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
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
Multi-layered ecological interactions determine growth of clinical antibiotic-resistant strains within human microbiomes
Nature Communications - The role of ecological factors in modulating the spread of antibiotic-resistance bacteria in the gut remains unclear. Here, the authors use anaerobic microcosms to study the...
rdcu.be
November 9, 2025 at 9:34 PM
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.👇
Reposted by Mathilde Boumasmoud
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...
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...
www.nature.com
November 5, 2025 at 7:32 AM
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...
www.nature.com/articles/s41...
Reposted by Mathilde Boumasmoud
🐝🦠 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
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...
www.nature.com
November 4, 2025 at 8:36 PM
🐝🦠 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
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
Reposted by Mathilde Boumasmoud
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
October 31, 2025 at 3:05 PM
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/...
Reposted by Mathilde Boumasmoud
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
July 14, 2025 at 9:11 AM
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!
Reposted by Mathilde Boumasmoud
OUT NOW - Long-read metagenomics method for strain tracking after FMT #microsky www.nature.com/articles/s41...
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...
www.nature.com
October 23, 2025 at 12:59 PM
OUT NOW - Long-read metagenomics method for strain tracking after FMT #microsky www.nature.com/articles/s41...
Reposted by Mathilde Boumasmoud
Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...
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
academic.oup.com
September 10, 2025 at 7:45 PM
Deciphering microbial spatial organization: insights from synthetic and engineered communities url: academic.oup.com/ismecommun/a...
Reposted by Mathilde Boumasmoud
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.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
August 15, 2025 at 4:33 PM
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.
PHLAME works on tough sample types -- including those with coexisting strains of a species and low depth.
Reposted by Mathilde Boumasmoud
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
July 30, 2025 at 3:26 PM
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
Reposted by Mathilde Boumasmoud
#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...
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...
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 ...
www.nature.com
July 30, 2025 at 3:40 PM
#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...
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...