Wiep Klaas Smits (ExpBac/CMAT)
@smitslab.bsky.social
Assoc. prof. at LUMC/@unileiden. Cdiff, DNA replication, AMR, microbiome, anaerobes. Clostpath Steering committee. Education officer ESGCD. Previously: @unigroningen and @mitofficial. https://sites.google.com/view/expbac-lumc/homepage
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
An amazing article. Highly recommended!
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
The Penicillin Myth
Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.
press.asimov.com
November 26, 2025 at 1:07 PM
An amazing article. Highly recommended!
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
Our paper mapping the effects of hundreds of pesticides and industrial chemicals on gut bacteria is out in @natmicrobiol.nature.com today!
Turns out many such chemicals, although labelled as 'fungicides' or similar, can inadvertently inhibit friendly gut bacteria.
www.nature.com/articles/s41...
Turns out many such chemicals, although labelled as 'fungicides' or similar, can inadvertently inhibit friendly gut bacteria.
www.nature.com/articles/s41...
November 26, 2025 at 11:07 AM
Our paper mapping the effects of hundreds of pesticides and industrial chemicals on gut bacteria is out in @natmicrobiol.nature.com today!
Turns out many such chemicals, although labelled as 'fungicides' or similar, can inadvertently inhibit friendly gut bacteria.
www.nature.com/articles/s41...
Turns out many such chemicals, although labelled as 'fungicides' or similar, can inadvertently inhibit friendly gut bacteria.
www.nature.com/articles/s41...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
‼️Research update - the last-resort 💊antibiotic daptomycin attacks🧫bacteria through two independent mechanisms & IM30 protein LiaH helps remodel membranes under stress. Great work by @henrikstrahl.bsky.social & @jbuttresssci.bsky.social @newcastleuni.bsky.social team
#microsky #BBSRC #sLoLa ⬇️
#microsky #BBSRC #sLoLa ⬇️
Now properly published at @natcomms.nature.com with few additional experiments incl. demonstration of Daptomycin's ability to depolarise non-growing cells.
See the original preprint-thread for a summary of our findings.
www.nature.com/articles/s41...
#microsky
See the original preprint-thread for a summary of our findings.
www.nature.com/articles/s41...
#microsky
November 25, 2025 at 2:39 PM
‼️Research update - the last-resort 💊antibiotic daptomycin attacks🧫bacteria through two independent mechanisms & IM30 protein LiaH helps remodel membranes under stress. Great work by @henrikstrahl.bsky.social & @jbuttresssci.bsky.social @newcastleuni.bsky.social team
#microsky #BBSRC #sLoLa ⬇️
#microsky #BBSRC #sLoLa ⬇️
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
(bacterial) chromosome segregationists & SMC aficionadas/os take note 👇
(stephan, you can bypass the obstacle of tagging your post with #MicroSky yourself, easily. just do it, unhinged 🙂)
(stephan, you can bypass the obstacle of tagging your post with #MicroSky yourself, easily. just do it, unhinged 🙂)
The hinge bypass gate paper is finally out! doi.org/10.1038/s414...
We show how loop-extruding SMC complexes can maintain DNA entrapment while bypassing obstacles on DNA — including transcription machinery & potentially other SMCs.
A lucky convergence of 3 projects lead to the initial discovery!
We show how loop-extruding SMC complexes can maintain DNA entrapment while bypassing obstacles on DNA — including transcription machinery & potentially other SMCs.
A lucky convergence of 3 projects lead to the initial discovery!
The SMC Hinge is a Selective Gate for Obstacle Bypass - Nature Communications
SMC complexes are ring-shaped motors that fold DNA by extruding loops, but how they navigate large DNA obstacles is unclear. Here, Liu et al., show that SMC complexes bypass obstacles by threading obs...
doi.org
November 25, 2025 at 7:16 PM
(bacterial) chromosome segregationists & SMC aficionadas/os take note 👇
(stephan, you can bypass the obstacle of tagging your post with #MicroSky yourself, easily. just do it, unhinged 🙂)
(stephan, you can bypass the obstacle of tagging your post with #MicroSky yourself, easily. just do it, unhinged 🙂)
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins www.biorxiv.org/content/10.1...
November 25, 2025 at 5:59 AM
Arbitrium systems control lysis/lysogeny through the regulation of small antirepressor proteins www.biorxiv.org/content/10.1...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases | Science www.science.org/doi/10.1126/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
www.science.org
November 26, 2025 at 11:17 AM
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases | Science www.science.org/doi/10.1126/...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...
Multi-omics profiling reveals atypical sugar utilization and a key membrane composition regulator in Streptococcus pneumoniae - Nature Communications
The pathogen Streptococcus pneumoniae can adapt to diverse microenvironments in the human body. Here, De Bakker et al. study these adaptation responses, showing unusual sugar utilization and identifyi...
www.nature.com
November 25, 2025 at 1:44 PM
Really cool paper from @vincentdebakker.bsky.social @jonbakerlab.bsky.social now published @natcomms.nature.com #MicroSky www.nature.com/articles/s41...
Naturally occurring CodY variants alter ligand binding, DNA target affinity, and virulence in Clostridioides difficile www.biorxiv.org/content/10.1...
Naturally occurring CodY variants alter ligand binding, DNA target affinity, and virulence in Clostridioides difficile
Clostridioides difficile is an important nosocomial pathogen that has been classified as an “urgent threat” by the CDC. Antibiotic use is the primary risk factor for the development of C. difficile -a...
www.biorxiv.org
November 25, 2025 at 4:04 PM
Naturally occurring CodY variants alter ligand binding, DNA target affinity, and virulence in Clostridioides difficile www.biorxiv.org/content/10.1...
ENGINEERING AND PRECLINICAL EVALUATION OF DRIED FOOD-FORMULATED YEAST-SECRETED ANTIBODIES AS PERI-EXPOSURE PROPHYLAXIS AGAINST CLOSTRIDIOIDES DIFFICILE DISEASE www.biorxiv.org/content/10.1...
ENGINEERING AND PRECLINICAL EVALUATION OF DRIED FOOD-FORMULATED YEAST-SECRETED ANTIBODIES AS PERI-EXPOSURE PROPHYLAXIS AGAINST CLOSTRIDIOIDES DIFFICILE DISEASE
Clostridioides difficile gastrointestinal infection (CDI) causes significant disease burden, often following gut dysbiosis induced by antibiotic treatment in at-risk individuals. A non-invasive, easy ...
www.biorxiv.org
November 25, 2025 at 4:01 PM
ENGINEERING AND PRECLINICAL EVALUATION OF DRIED FOOD-FORMULATED YEAST-SECRETED ANTIBODIES AS PERI-EXPOSURE PROPHYLAXIS AGAINST CLOSTRIDIOIDES DIFFICILE DISEASE www.biorxiv.org/content/10.1...
November is #CdiffAwarenessMonth. Amazing work by @lizahaart.bsky.social turned my idea into a cartoon to help explain why antibiotics are a risk factor for #CDI. More to come! The English version is supported by the #ESGCD (@escmid.bsky.social). Let me know if you think these cartoons are useful!
November 24, 2025 at 1:46 PM
November is #CdiffAwarenessMonth. Amazing work by @lizahaart.bsky.social turned my idea into a cartoon to help explain why antibiotics are a risk factor for #CDI. More to come! The English version is supported by the #ESGCD (@escmid.bsky.social). Let me know if you think these cartoons are useful!
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
🚨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 Wiep Klaas Smits (ExpBac/CMAT)
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
www.science.org
November 20, 2025 at 9:42 PM
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
A ubiquitin-like protein controls assembly of a bacterial type VIIb secretion system
Cryo-EM structure reveals how a ubiquitin-like protein orchestrates assembly of a bacterial weapon system.
www.science.org
November 21, 2025 at 7:05 PM
Our latest T7SS study is now out in Science Advances!
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
We solved the cryoEM structure of the T7SSb core unit (T7bCU) composed of YukB, YukC, and YukD from Bacillus subtilis, revealing how these components assemble within the secretion machinery.
www.science.org/doi/10.1126/...
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin - @theriotmicrobe.bsky.social et al. www.nature.com/articles/s41...
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin - Nature Microbiology
A bile acid-bound structure of toxin TcdB revealed the mechanism of inhibition and guided the design of a synthetic bile acid that alleviated Clostridioides difficile infection in mice.
www.nature.com
November 19, 2025 at 11:43 AM
Structure-guided design of a synthetic bile acid that inhibits Clostridioides difficile TcdB toxin - @theriotmicrobe.bsky.social et al. www.nature.com/articles/s41...
Effects of Sexual Dimorphism and the Estrous Cycle on Clostridioides difficile Infection Prophylaxis in Two Rodent Models | ACS Infectious Diseases pubs.acs.org/doi/10.1021/...
Effects of Sexual Dimorphism and the Estrous Cycle on Clostridioides difficile Infection Prophylaxis in Two Rodent Models
Clostridioides difficile infection (CDI) is responsible for the majority of identifiable antibiotic-associated diarrhea. Epidemiological studies have consistently shown that women are more at risk for...
pubs.acs.org
November 14, 2025 at 2:30 PM
Effects of Sexual Dimorphism and the Estrous Cycle on Clostridioides difficile Infection Prophylaxis in Two Rodent Models | ACS Infectious Diseases pubs.acs.org/doi/10.1021/...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
New paper with @statsepi.bsky.social and @deevybee.bsky.social in which we show there's really no evidence for a link between the gut microbiome and autism www.cell.com/neuron/fullt...
Conceptual and methodological flaws undermine claims of a link between the gut microbiome and autism
Claims that the gut microbiome causally contributes to autism regularly appear in
the scientific literature and popular press. Mitchell et al. critically examine influential
studies underpinning these...
www.cell.com
November 13, 2025 at 4:10 PM
New paper with @statsepi.bsky.social and @deevybee.bsky.social in which we show there's really no evidence for a link between the gut microbiome and autism www.cell.com/neuron/fullt...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases
Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce ...
www.science.org
November 13, 2025 at 8:53 PM
Very excited to share our latest work in Science on metagenomic editing (MetaEdit) of the gut microbiome in vivo & directly modifying unculturable immune-modulatory SFB bug in the small intestine. 🦠🧬🛠️
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
Nice highlight by the LUMC about our recent @natcomms.nature.com publication: www.lumc.nl/en/news/2025...
Promising new antibiotic reveals its secrets | LUMC
Researchers at LUCID (LUMC) have used advanced techniques to demonstrate how a new antibiotic works. The molecule anchors itself with a hook in an important enzyme, thereby blocking the production of ...
www.lumc.nl
November 10, 2025 at 1:32 PM
Nice highlight by the LUMC about our recent @natcomms.nature.com publication: www.lumc.nl/en/news/2025...
Limitations of genomic surveillance: a C. difficile case study in the Netherlands www.sciencedirect.com/science/arti... - new manuscript by Joffrey van Prehn et al.
Limitations of genomic surveillance: a C. difficile case study in the Netherlands
www.sciencedirect.com
November 10, 2025 at 9:19 AM
Limitations of genomic surveillance: a C. difficile case study in the Netherlands www.sciencedirect.com/science/arti... - new manuscript by Joffrey van Prehn et al.
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
Delighted that our review on resistance to last-resort antibiotics in Enterococci has been published in FEMS Microbiology Reviews
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
Resistance to last-resort antibiotics in enterococci
Abstract. The genus Enterococcus comprises a diverse group of species, many of which are commensal members of the gut microbiota of humans and animals. The
academic.oup.com
November 8, 2025 at 5:41 PM
Delighted that our review on resistance to last-resort antibiotics in Enterococci has been published in FEMS Microbiology Reviews
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
academic.oup.com/femsre/advan... (accepted manuscript version)
TL;DR: the Enterococci are really good at evolving resistance to antibiotics in new and creative ways.
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
What Rosalind Franklin truly contributed to the discovery of DNA’s structure. A really informative article, perfect for a weekend coffee read. www.nature.com/articles/d41...
What Rosalind Franklin truly contributed to the discovery of DNA’s structure
Franklin was no victim in how the DNA double helix was solved. An overlooked letter and an unpublished news article, both written in 1953, reveal that she was an equal player.
www.nature.com
November 8, 2025 at 9:21 AM
What Rosalind Franklin truly contributed to the discovery of DNA’s structure. A really informative article, perfect for a weekend coffee read. www.nature.com/articles/d41...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
🧪Thrilled to share our new study "The monoclonal antibody AZD5148 confers broad protection against TcdB-diverse Clostridioides difficile strains in mice” in PLoS Pathogens! @bordenlacy.bsky.social
➡️We show that this mAb alone protects against infection with strains encoding TcdB variants. 1/20
➡️We show that this mAb alone protects against infection with strains encoding TcdB variants. 1/20
journals.plos.org
November 7, 2025 at 7:11 PM
🧪Thrilled to share our new study "The monoclonal antibody AZD5148 confers broad protection against TcdB-diverse Clostridioides difficile strains in mice” in PLoS Pathogens! @bordenlacy.bsky.social
➡️We show that this mAb alone protects against infection with strains encoding TcdB variants. 1/20
➡️We show that this mAb alone protects against infection with strains encoding TcdB variants. 1/20
Impact of Hanks Kinase-Dependent Phosphorylation of CodY on the Physiology and Virulence in Bacillus cereus - onlinelibrary.wiley.com/doi/10.1002/...
Impact of Hanks Kinase‐Dependent Phosphorylation of CodY on the Physiology and Virulence in Bacillus cereus
CodY is a global regulator whose phosphorylation at serine 215 by PrkC/YbdM alters its DNA binding, thereby modulating gene expression and impacting motility, biofilm formation, cytotoxicity, and pat...
onlinelibrary.wiley.com
November 7, 2025 at 2:30 PM
Impact of Hanks Kinase-Dependent Phosphorylation of CodY on the Physiology and Virulence in Bacillus cereus - onlinelibrary.wiley.com/doi/10.1002/...
Essential and dispensable domains of DivIVA for walled growth in filamentous Actinomycetota | Open Biology royalsocietypublishing.org/doi/10.1098/...
Conflicts between the DNA replication and repair machineries promote cell death in Gram-positive bacteria
Cellular proliferation relies on the successful coordination and completion of genome replication and segregation. To help achieve this, many bacteria utilize regulatory pathways that ensure DNA repli...
doi.org
November 7, 2025 at 2:28 PM
Essential and dispensable domains of DivIVA for walled growth in filamentous Actinomycetota | Open Biology royalsocietypublishing.org/doi/10.1098/...
Conflicts between the DNA replication and repair machineries promote cell death in Gram-positive bacteria doi.org/10.1099/mic.... b @winterhalterlab.bsky.social @heathmurraylab.bsky.social et al.
Conflicts between the DNA replication and repair machineries promote cell death in Gram-positive bacteria
Cellular proliferation relies on the successful coordination and completion of genome replication and segregation. To help achieve this, many bacteria utilize regulatory pathways that ensure DNA repli...
doi.org
November 7, 2025 at 2:25 PM
Conflicts between the DNA replication and repair machineries promote cell death in Gram-positive bacteria doi.org/10.1099/mic.... b @winterhalterlab.bsky.social @heathmurraylab.bsky.social et al.