Wiep Klaas Smits (ExpBac/CMAT)

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has...

New preprint!

Ever wondered why only a fraction of genomes encode CRISPR immunity? 🧬 🦠

Turns out CRISPR is rarely beneficial against virulent phages, being most beneficial against those for which resistance mutations are rare!

An epic effort by Rosanna Wright

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

Clostridioides difficile pathogenesis and control Nature Reviews Microbiology, Published online: 02 October 2025; doi:10.1038/s41579-025-01242-2Clostridioides difficile infection is challenging to diagnose and treat and is associated with considerable mortality, morbidity and economic costs worldwide. In this Review, Chilton et al. discuss changes in global epidemiology, breakthroughs in pathogenesis and antibiotic resistance, the role of microbiota dysbiosis and the potential for microbiota-based therapeutics for Clostridioides difficile infection.

New online! Clostridioides difficile pathogenesis and control

They’re coming y’all…the megaplasmids are coming

(I say this in a slightly frustrated manner as someone who has been thoroughly unsuccessful in getting funding to study megaplasmids for the better part of 15 years)

A miniature CRISPR–Cas10 enzyme confers immunity by inhibitory signalling - Nature Panoptes, an anti-phage defence system against virus-mediated immune suppression, is revealed.

Today in @nature.com , we highlight how a cousin of CRISPR-Cas10, mCpol, establishes an evolutionary trap in anti-phage immune systems.

Check out @erinedoherty.bsky.social and my work from @doudna-lab.bsky.social lab here:
www.nature.com/articles/s41...

Temporal and spatial coordination of DNA segregation and cell division in an archaeon. Cells must coordinate DNA segregation with cytokinesis to ensure that each daughter cell inherits a complete genome. Here, we explore how DNA segregation and division are mechanistically coupled in ar...

We are excited to share our preprint describing how Sulfolobus cells coordinate DNA segregation with cell division! In eukaryotes this type of regulation involves checkpoints and CDK-cyclins. But how does this work in archaea? This is the question we ask in our paper: www.biorxiv.org/content/10.1...

Wildlife advocate, primate expert Jane Goodall dies at 91 Scientist and global activist Jane Goodall, who turned her childhood love of primates into a lifelong quest for protecting the environment, died on Wednesday at the age of 91, the institute she founded said.

Wildlife advocate and primate expert Jane Goodall dies at 91 - www.reuters.com/business/env...

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics Antibiotic resistance is frequently observed shortly after the clinical introduction of an antibiotic. Whether and how frequently that resistance occurred before the introduction is harder to determin...

What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years?

Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen:
www.microbiologyresearch.org/content/jour...

Bacillus subtilis in defense mode: Switch-like adaptations to protistan predation | PNAS www.pnas.org/doi/10.1073/...

A roadmap for equitable reuse of public microbiome data - Nature Microbiology In this Consensus Statement, a consortium of microbiome scientists discuss current sequencing data sharing policies and propose the use of a Data Reuse Information (DRI) tag to promote equitable and collaborative data sharing.

Our own @alexjprobst.bsky.social @geomicrosoares.bsky.social and Cristina Moraru have recently authored a @natmicrobiol.nature.com Consensus Statement where they discuss new mechanisms for sequencing data reuse! 🧬💻

Check out their manuscript here:
www.nature.com/articles/s41...

The emerging view on the roles of butyrate in Clostridioides difficile pathogenesis | Infection and Immunity The Centers for Disease Control and Prevention classifies Clostridioides difficile as an urgent threat to the nation’s health, as it causes 450,000 infections, 15,000 deaths, and 1 billion dollars in ...

The emerging view on the roles of butyrate in Clostridioides difficile pathogenesis | Infection and Immunity journals.asm.org/doi/10.1128/...

De novo design of potent inhibitors of clostridial family toxins | PNAS Clostridioides difficile remains a leading cause of hospital-acquired infections, with its primary virulence factor, toxin B (TcdB), responsible fo...

De novo design of potent inhibitors of clostridial family toxins | PNAS www.pnas.org/doi/10.1073/...

The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin Accumulating evidence has connected the chemically unstable, DNA-damaging gut bacterial natural product colibactin to colorectal cancer, including the identification of mutational signatures that are ...

The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin www.biorxiv.org/content/10.1...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV Accurate detection of mutations within bacterial species is critical for fundamental studies of microbial evolution, reconstructing transmission events, and identifying antimicrobial resistance mutati...

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV www.biorxiv.org/content/10.1...

Wearing #red today in honour of #worldheartday - raising awareness for #CVD.

Happy to finally show our story of the connection between nucleoid conformation, transcription & predation in our favorite predator Bdellovibrio bacteriovorus. 🧵 1/n

Service announcement. If you don't want LinkedIn to use your posts for generative AI improvement, be sure to toggle this off: www.linkedin.com/mypreference... (#checkedbydefault)

#microsky

Fecal filtrate is less effective than donor stool (FMT) for the treatment of C. difficile recurrence. Now shown in a multicentre trial, out today in @lancetgastrohep.bsky.social .

Congratulations to Dina Kao @ualberta.bsky.social & team!

Gift link:

authors.elsevier.com/c/1lphg8nByr...

A targeted cell lysis mechanism facilitates toxin release in Clostridioides difficile Clostridioides difficile infection is associated with the production of two large toxins, TcdA and TcdB. The toxins are encoded in a pathogenicity locus along with a phage-like holin protein, TcdE, th...

A targeted cell lysis mechanism facilitates toxin release in Clostridioides difficile www.biorxiv.org/content/10.1...

CRISPR-Cas9 enables efficient genome engineering of the strictly lytic, broad-host-range staphylococcal bacteriophage K | Applied and Environmental Microbiology Phage engineering, the process of modifying bacteriophages to enhance or customize their properties, offers significant potential for advancing precision antimicrobial therapies and diagnostics. While...

CRISPR-Cas9 enables efficient genome engineering of the strictly lytic, broad-host-range staphylococcal bacteriophage K | Applied and Environmental Microbiology journals.asm.org/doi/10.1128/...

The oral microbiome of King Richard III of England Metagenomic investigation of archaeological dental calculus has provided insights into the changing oral health, disease, and diet of past human societies, but little is known about the oral microbiot...

The oral microbiome of King Richard III of England www.biorxiv.org/content/10.1...

Single-cell quantification of the microbiota by flow cytometry: MicFLY The intestinal microbiota regulates multiple host functions, including digestion and immune development. Our knowledge of the microbiota has been shaped by available technology that primarily measures...

Single-cell quantification of the microbiota by flow cytometry: MicFLY www.biorxiv.org/content/10.1...

Congratulations, @selinpekel.bsky.social @zellerlab.bsky.social !

Phages with a broad host range are common across ecosystems - Nature Microbiology Proximity-ligation-based sequencing from 111 samples and 5 environments reveals that a substantial proportion of phages infect multiple species.

You like phages ? In this publication, we use metaHiC and our new version of the MetaTOR pipeline to challenge the traditional view of phages with a narrow host range.
@rkoszul.bsky.social @natmicrobiol.nature.com @cnrs.fr @institutpasteur.bsky.social

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

What is 'exporesue'?

Glycans, gut bugs, and Cayman in Heidelberg!

Quinten Ducarmon presented his work at #EESMicrobiome2025, sharing insights into glycan metabolism of the human gut microbiome and introducing the Cayman tool.

#Microbiome #Glycobiology #Metabolism #EMBO #EMBL #HumanGut

Meta-analyses, CRC, and microbes in Heidelberg!

@selinpekel.bsky.social presented a poster at #EESMicrobiome
2025, showing how a universal microbiome signature for CRC emerges across cohorts, ages of onset , and sequencing methods.

#Microbiome #ColorectalCancer #EMBL #MetaAnalysis #LUMC

In vivo efficacy of fidaxomicin against rpoB mutant Clostridioides difficile infection Clostridioides difficile infection (CDI) is a well-known healthcare-associated diarrheal disease. Fidaxomicin, a key antibiotic used to treat CDI, tar…

In vivo efficacy of fidaxomicin against rpoB mutant Clostridioides difficile infection www.sciencedirect.com/science/arti...

High prevalence and clonality of Clostridioides difficile isolates from cryptic clades in household composters and small mammals We aimed to investigate the prevalence, genotypic diversity, and clonality of Clostridioides difficile strains from household composters and faeces of…

High prevalence and clonality of Clostridioides difficile isolates from cryptic clades in household composters and small mammals www.sciencedirect.com/science/arti...

Maternal Transmission of Symptomatic Clostridioides... : The Pediatric Infectious Disease Journal a complicated course in a 48-year-old mother who had prior hospitalization and antibiotic treatment. She gave birth to a triplet at a gestational age of 31 weeks and transmitted toxin-producing C. dif...

"...clinicians should be aware that CDI can occur in (premature) neonates by transfer of C. difficile at labor of a symptomatic mother" journals.lww.com/pidj/fulltex...