Wiep Klaas Smits

🚨Publication alert! Stoked to report the structural basis for activity of a novel class of antimicrobials targeting Gram positive priority pathogens in @NatureComms. There is something for everyone on this paper; highlights 👇 1/9 doi.org/10.1038/s41467…

Pangenome-GWAS analysis of Clostridioides difficile resistant traits from healthcare- and non-healthcare-associated settings cdnsciencepub.com/doi/10.1139/cj…

CSPG4 Mediates Inflammatory, Cell Death, and Senescence Responses in Enteric Glia Exposed to Clostridioides difficile Toxins - Marques - 2026 - The FASEB Journal - Wiley Online Library faseb.onlinelibrary.wiley.com/doi/10.1096/fj…

Vancomycin-resistant gut commensal Clostridium innocuum emerges as a pathobiont through synergy with toxigenic Clostridioides difficile sciencedirect.com/science/articl…

New bookchapter published! The book Clostridioides difficile has a chapter on Nanoluciferase use by Jeroen Corver, Ana Paiva and myself: #toc" target="_blank" rel="nofollow noopener">link.springer.com/book/10.1007/9… Also check out the contributions of all the other experts in this volume!

S. copri keeps pace with modern lifestyles Subset of Segatella copri strains have acquired an additional oxygen regulator via horizontal gene transfer, which confers increased oxygen tolerance. These strains are more prevalent in industrialized countries cell.com/cell-host-micr…

Streptomyces produce a diphtheria toxin-like exotoxin that targets insects dlvr.it/TSJB0r #MicroSky

BisCEET: A Visual Browser for Biosynthetic Gene Clusters Aiding in the Identification of Natural Product Variants and Distinct Tailoring Enzymes "a tool for the comparison of related BGCs and visualization of core and novel tailoring enzymes" pubs.acs.org/doi/10.1021/ac…

I knew this was coming. We are so f*cked - fake and real now look the same. We desperately need tools to show journals and researchers that data is real, not AI-generated.

Researchers uncover the role of nucleotide metabolism in #antibiotic #tolerance and targeting nucleotide synthesis synergises antibiotic killing of Vibrio cholera nature.com/articles/s4425…

Most bacteria remain uncultured and don’t grow in the lab.. to address this am excited to share EDEN - an enhanced domestication method to grow uncultured bacteria & new diversity. Using EDEN we isolate a new species active against MDR pathogens.. doi.org/10.1093/ismeco…

Bacteria are full of diverse molecular tricks. This Science article reports an interesting one that is being misrepresented by news coverage, including the coverage in Science. The study describes an enzyme complex that synthesizes alternating dinucleotide repeat DNA as part of an immune response. Protein templating DNA is a cool observation, even if the sequence is only a repeating dinucleotide. The headline-grabbing takeaway is the mechanism of the Drt3b subunit. While its partner, Drt3a, uses a canonical RNA template (reverse transcription), Drt3b synthesizes the complementary strand in the absence of a nucleic acid template. Instead, it uses specific amino acid residues (a glutamate and an arginine) to stabilize and "select" the incoming dNTPs. It is tempting to view this as a radical shift in our understanding of information transfer, a "protein-templated" genetic sequence. However, we should be cautious with the "paradigm shift" narrative. Why this isn't "rewriting" the Genetic Code: Despite claims in the news coverage, this finding does not represent a new form of hereditary information transfer. This is not a protein "reading" itself to create a complex message; rather, it is a highly specialized structural constraint. The protein is essentially a "stuttering" machine, physically keyed to produce a simple, repetitive sequence. The "information" is hard-coded into the protein's fold to perform a single, specific defensive task, rather than acting as a general-purpose template for diverse genetic messages. The Parallel to tmRNA: This observation is not entirely unprecedented when we look at how bacteria handle biochemical "dead ends." It reminds me of transfer-messenger RNA (tmRNA). In trans-translation, when a ribosome stalls on a broken mRNA, the tmRNA molecule steps in to provide both the tRNA component and a short mRNA "tag" to rescue the ribosome: - The "Non-Standard" Template: Much like tmRNA provides an external sequence to fix a stalled process, the DRT3 ncRNA and the Drt3b protein provide "internal" instructions to create DNA where no genomic template exists. - Specialized Rescue: Both mechanisms are niche "emergency" responses, one for proteostasis (tmRNA) and one for viral defense (DRT3). In the end, this discovery doesn't replace our understanding of the genetic code; it expands the "toolbox" of how cells can synthesize polynucleotides when the standard rules don't apply. It is a beautiful reminder that in the microbial world, if a chemical shortcut is possible, evolution has likely found it.

If you ever want to know if your favorite molecule or molecular family has been seen in public data and what metadata is associated with it - this is now possible. It searches four major repositories using a name or structure as in put to search the molecule or substructure.

Genomic Analysis of Community-Associated C. difficile Infection Demonstrates Integration With National and International Strain Clusters and Limited Direct Transmission academic.oup.com/jid/article-ab…

Wonderful review: An update on Clostridioides difficile population structure and genomics | Clinical Microbiology Reviews journals.asm.org/doi/10.1128/cm… @thejoesorg

EM crowd: for a project we are looking for Quantifoil R0.6/1 copper grids that are currently unavailable from the manufacturer. If anybody has any stock to spare, please let me know! #cryoEM

The impact of artificial sweeteners on bacterial physiology and the microbiome dlvr.it/TS1SjC

CenIR, an essential BlaIR-family regulatory system in C. difficile biorxiv.org/content/10.648…

DNA uptake in Cholera does more than spread genes—it may actually enhance the bacteria's defense mechanisms! 🦠🧬 New research sheds light on how these pathogens protect themselves and evolve. #Cholera #InfectiousDiseases #Microbiology #CDBioSciences science.org/doi/10.1126/sc…