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.

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/...

1/6 Excited to share our review 🚀
🧬 CRISPR–Cas therapies targeting bacteria!
#MicroSky

Global genetic structure of human gut microbiome species is related to geographic location and host health The human gut harbors thousands of microbial species, each exhibiting significant inter-individual genetic variability. Although many studies have ass…

Thrilled to share that our manuscript on strain-level gut microbiome variation across diverse populations and human phenotypes is out today in @cellpress.bsky.social
Curious about how strain diversity relates to human traits? Follow this thread! 🌍 (1/n)
www.sciencedirect.com/science/arti...

Very interesting! Congratulations:)

Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium - Nature Microbiology Genomic and functional analyses of healthcare-associated vancomycin-resistant Enterococcus faecium reveal that bacteriocin T8 is enriched in emergent lineages and provides a competitive advantage in v...

Excited to share our latest, out today in @naturemicrobiol.bsky.social Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium www.nature.com/articles/s41... @idpittstop.bsky.social

Community stability is usually assessed by invading single species from rare and measuring relative fitness. However does this hold up when multiple species invade from rare? We test this using our super stable microbial community 👇🏻

Are reads required? High-precision variant calling from bacterial genome assemblies Accurate nucleotide variant calling is essential in microbial genomics, particularly for outbreak tracking and phylogenetics. This study evaluates variant calls derived from genome assemblies compared...

New preprint is out!
We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling.

Read it here: www.biorxiv.org/content/10.1...
Data & code: github.com/rrwick/Are-r...
(1/8)

Residence Time Structures Microbial Communities Through Niche Partitioning Much of life on earth is at the mercy of currents and flow. Residence time (τ) estimates how long organisms and resources remain in a system based on the ratio of volume (V) to flow rate (Q). We test...

Congratulations to @emmiamueller.bsky.social on:

"Residence time structures microbial communities through niche partitioning"

Now out in Ecology Letters:

onlinelibrary.wiley.com/doi/10.1111/...

Roche's SBX sequencing by expansion - preprint out!
www.biorxiv.org/content/10.1...

The Oxford U. Foster and Slack labs are hiring! A chance to work in bleeding edge microbiome science with some really great mentors @mucosalimmunology.bsky.social

www.fosterlab.uk/vacancies

Disentangling the feedback loops driving spatial patterning in microbial communities - npj Biofilms and Microbiomes npj Biofilms and Microbiomes - Disentangling the feedback loops driving spatial patterning in microbial communities

Two (!) perspective pieces published today involving people from our lab! @adelpanta.bsky.social on spatial patterning in microbial communities www.nature.com/articles/s41... and @salazarafra.bsky.social on microbial communities as evolutionary individuals www.sciencedirect.com/science/arti...

Lysis of Escherichia coli by colicin Ib contributes to bacterial cross-feeding by releasing active β-galactosidase Abstract. The diffusible toxin ColIb produced by Salmonella enterica serovar Typhimurium SL1344 is a potent inhibitor of Escherichia coli growth. To identi

Really exciting work:
The Salmonella Colicin Col1b cannot only KILL a competing E. coli population, but also AMPLIFY metabolic contributions of susceptible bacteria by liberating β-gal…

From @nic-ler.bsky.social. @kroegerlab.bsky.social, Andrew Cameron and others ‼️

academic.oup.com/ismej/advanc...

Our special feature/passion project at AmNat, "Demystifying fundamental theories in ecology", co-organized with @sebastianschreiber.bsky.social is out now 🤩 www.journals.uchicago.edu/toc/an/2025/...

📣📣Genomic data sharing: you don’t know what you’ve got (till it’s gone) www.nature.com/articles/s41...

A comment @natrevgenet.bsky.social from @katholt.bsky.social and me

Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut Among coagulase-negative staphylococci, Staphylococcus haemolyticus is a primary cause of bloodstream infections in preterm infants, with gut colonisation being recognised as a risk factor for subsequent infection. Through a re-analysis of a 16S rRNA gene sequencing dataset (n=497 preterm infants), we found that S. haemolyticus was abundant and prevalent in the gut in the first month of life. To better understand the diversity of S. haemolyticus among preterm infants, we generated genome sequences of S. haemolyticus strains (n=140), which were isolated from 44 stool samples of 22 preterm infants from four different hospitals in the United Kingdom. Core genome phylogenetic analyses, incorporating 126 publicly available S. haemolyticus genome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 79/85 (92.9%) strains being assigned to Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were highly prevalent in the genome sequences. Using logistic regression, we found a strong association between the presence of the gene mecA and phenotypic resistance to oxacillin (odds ratio [OR]: 158.00, p<0.0001), and the aacA-aphD gene and phenotypic resistance to gentamicin aacA-aphD (OR: 162.00, p<0.001). None of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosome mec (SCCmec) element. The aacA-aphD gene was associated with the transposon Tn4001. Using hybrid genome assemblies, we found it to be present on the chromosome (54.5% of strains) or on diverse plasmids (27.3%). Four strains (18.2%) had Tn4001 copies on both plasmid and chromosome. Our data suggest the existence of a distinct sub-population of S. haemolyticus that has adapted to colonise the gut of preterm infants. Prevalent resistance to antibiotics is of clinical concern and the diversity of genetic contexts of mecA and Tn4001 suggests widespread horizontal gene transfer and recombination in this species. ### Competing Interest Statement The authors have declared no competing interest.

New preprint from the group just landed

‘Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut’

www.biorxiv.org/content/10.1...

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The mutational landscape of Staphylococcus aureus during colonisation Nature Communications - The authors applied a genomic and evolutionary approach to study Staphylococcus aureus in host adaptation during colonisation revealing signals of adaption in metabolic...

Happy to share the findings of our latest work on mutational adaptation of Staphylococcus aureus during colonisation now published on @NatureComms
rdcu.be/d55l3

A phylogenetic approach to comparative genomics Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2

We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets.

These methods must be considered an essential part of the comparative genomics toolkit.

@lauriebelch.bsky.social @stuwest.bsky.social

@microbiologysociety.org Microbial Genomics is looking for new Senior Editors and Editors, particularly those with expertise across the breadth of eukaryotic microbiology, viral genomics, and ecological microbiology. Candidates can send their CVs and cover letters by Friday 17 January 2025!

Home A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

New year, new assemblies!
I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes!
It's the successor to Trycycler, designed to be faster and less reliant on user intervention.
Check it out: github.com/rrwick/Autoc...
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Antimicrobial activity of iron-depriving pyoverdines against human opportunistic pathogens Iron-chelating pyoverdines from environmental Pseudomonas spp. show promising antibacterial activity against key human pathogens through the induction of iron starvation, while associated toxicity for...

Are #pyoverdines effective antibacterials?🦠💊
Yes! We found strong competitive and antibacterial effects against #ESKAPE pathogens via iron depletion.
Out now in @elife.bsky.social: doi.org/10.7554/eLif... (1/4)
With @rkmicrobes.bsky.social and amazing collaborators from #UZH & @ethzurich.bsky.social

Congrats🎆

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics - Nature Microbiology Resistance to one antibiotic can make bacteria resistant or sensitive to another antibiotic, opening paths for combinatorial treatments. This study presents an approach to systematically discover and ...

Excited to share our study led by @SakenovaNazgul! We used chemical genetics to identify and understand cross-resistance & collateral-sensitivity (CS) between antibiotics and reduced AMR development with CS drug pairs @embl.org with @camille_goemans @EPFL_en www.nature.com/articles/s41...

Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria Abstract. Microbial communities that maintain symbiotic relationships with animals evolve by adapting to the specific environmental niche provided by their

Co-evolution and Gene Transfers Drive Speciation Patterns in Host-Associated Bacteria 🤓

academic.oup.com/mbe/advance-...

Strain phylogroup and environmental constraints shape Escherichia coli dynamics and diversity over a twenty-year human gut time series Abstract. Escherichia coli is an increasingly antibiotic-resistant opportunistic pathogen. Few data are available on its ecological and evolutionary dynami

I remember the preprint last Feb about this 20y follow-up of stool E. coli in 1 individual with zero antibiotic intake (& code-named "ED" from a famous French E. coli lab?🤔😅)
➡️B2 resided longer than transient clones
➡️pangenomic singularity exists within individuals
academic.oup.com/ismej/advanc...

Diverse phage communities are maintained stably on a clonal bacterial host Bacteriophages are the most abundant and phylogenetically diverse biological entities on Earth, yet the ecological mechanisms that sustain this extraordinary diversity remain unclear. In this study, w...

Nora finished her paper with a sentence I like a lot "Our results show that even under extremely restrictive, competitive conditions, the simplest biological entities on Earth can still find paths to coexistence." There is a curious dichotomy in her experiments... 1/3
www.science.org/doi/10.1126/...