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)
🚨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.
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Repair of DNA double-strand breaks leaves heritable impairment to genome function
Upon DNA breakage, a genomic locus undergoes alterations in three-dimensional chromatin architecture to facilitate signaling and repair. Although cells possess mechanisms to repair damaged DNA, it is ...
tinyurl.com
November 6, 2025 at 11:05 PM
𝗖𝗮𝗻 𝗰𝗲𝗹𝗹𝘀 𝗲𝘃𝗲𝗿 𝘁𝗿𝘂𝗹𝘆 𝗿𝗲𝗰𝗼𝘃𝗲𝗿 𝗳𝗿𝗼𝗺 𝗗𝗡𝗔 𝗱𝗮𝗺𝗮𝗴𝗲?Excited to share our new study “Repair of DNA double-strand breaks leaves heritable impairment to genome function”, revealing DNA repair’s hidden cost, out now @science.org tinyurl.com/5n6zw3ye. Led by @sbantele.bsky.social and Jiri Lukas.🧵👇1/n
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
November 7, 2025 at 10:44 AM
An Asgard archaeon with internal membrane compartments
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Brilliant study led by @fmacleod.bsky.social and Andriko von Kügelgen. Tight collaboration with @buzzbaum.bsky.social and lab. Congrats to all authors!
www.biorxiv.org/content/10.1...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Enabling options for review: from training and transparency to author-centered AI tools - openRxiv
Peer review is widely viewed as a critical aspect of biomedical communication. Ideally, it provides authors with feedback so they can improve manuscripts and gives readers, particularly nonspecialists...
openrxiv.org
November 6, 2025 at 2:32 PM
Excited to launch an openRxiv partnership with the scientist-run AI review service qed (@qedscience.bsky.social), the brainchild of @odedrechavi.bsky.social 1/n
openrxiv.org/enabling-rev...
openrxiv.org/enabling-rev...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
To all visionary microbe enthusiasts: @femsmicro.org is looking for an editor-in-chief for their flagship journal FEMS Microbiology Reviews! More details can be found here: fems-microbiology.org/opportunitie...
Editor-in-Chief for FEMS Microbiology Reviews - FEMS
The Federation of European Microbiological Societies (FEMS) is looking for an Editor-in-Chief to join its prestigious journal FEMS Microbiology Reviews for an initial period of three years, starting i...
fems-microbiology.org
November 5, 2025 at 5:38 PM
To all visionary microbe enthusiasts: @femsmicro.org is looking for an editor-in-chief for their flagship journal FEMS Microbiology Reviews! More details can be found here: fems-microbiology.org/opportunitie...
🚨 Publication alert! We are stoked to report the structural basis for activity of a novel class of antimicrobials targeting Gram positive priority pathogens in @natcomms.nature.com. There is something for everyone on this paper, and I will highlight a few things below 👇 1/9 doi.org/10.1038/s414...
A unique inhibitor conformation selectively targets the DNA polymerase PolC of Gram-positive priority pathogens - Nature Communications
In this work, Urem et al. characterize the mode of action as well as mechanism of reduced susceptibility related to a class of antimicrobials that is in development for the treatment of infections wit...
doi.org
November 6, 2025 at 10:29 AM
🚨 Publication alert! We are stoked to report the structural basis for activity of a novel class of antimicrobials targeting Gram positive priority pathogens in @natcomms.nature.com. There is something for everyone on this paper, and I will highlight a few things below 👇 1/9 doi.org/10.1038/s414...
Bacteria sense virus-induced genome degradation via methylated mononucleotides www.biorxiv.org/content/10.1...
www.biorxiv.org
November 6, 2025 at 9:24 AM
Bacteria sense virus-induced genome degradation via methylated mononucleotides www.biorxiv.org/content/10.1...
The rise of ‘nightmare bacteria’: antimicrobial resistance in five charts www.nature.com/articles/d41...
The rise of ‘nightmare bacteria’: antimicrobial resistance in five charts
Data reveal how the global challenge to reduce deaths and infections from drug-resistant bacteria is not going according to plan.
www.nature.com
November 6, 2025 at 8:29 AM
The rise of ‘nightmare bacteria’: antimicrobial resistance in five charts www.nature.com/articles/d41...
Reposted by Wiep Klaas Smits (ExpBac/CMAT)
Now online! journals.plos.org/plospathogen... #MicroSky
November 5, 2025 at 12:21 PM
Now online! journals.plos.org/plospathogen... #MicroSky
HT Ed Kuijper: a rise in "Letters to the Editor" generated with AI. A potentially big problem! www.nytimes.com/2025/11/04/s...
The Editor Got a Letter From ‘Dr. B.S.’ So Did a Lot of Other Editors.
www.nytimes.com
November 5, 2025 at 9:59 AM
HT Ed Kuijper: a rise in "Letters to the Editor" generated with AI. A potentially big problem! www.nytimes.com/2025/11/04/s...
Acquired Resistance during Short-Course Treatment for Rifampicin-Resistant Tuberculosis - Clinical Microbiology and Infection www.clinicalmicrobiologyandinfection.org/article/S119...
Acquired Resistance during Short-Course Treatment for Rifampicin-Resistant Tuberculosis
Shorter regimens represent a significant advancement for rifampicin-resistant tuberculosis
(RR-TB) treatment. However, data on acquired drug resistance (ADR) remain limited.
www.clinicalmicrobiologyandinfection.org
November 5, 2025 at 9:55 AM
Acquired Resistance during Short-Course Treatment for Rifampicin-Resistant Tuberculosis - Clinical Microbiology and Infection www.clinicalmicrobiologyandinfection.org/article/S119...