Wiep Klaas Smits

CRISPR system reprograms bacteria to disarm deadly toxin Gene-editing technique disables Shiga toxin genes in <i>E. coli</i>

Antibiotics usually save lives—but against some bacteria, they can make things worse. Now scientists have developed a new gene-editing approach that circumvents this problem. cen.acs.org/biological-c... #chemsky 🧪

YouTube video by Ange M The Funeral (Nkosi Sikelel' Iafrika) (September 25, 1987)

South African anthems are powerful. Up to this day, "Nkosi Sikelel' Iafrika" gives me goosebumps because of the impact the movie Cry Freedom (and story of Steve Biko) had on me as a child www.youtube.com/watch?v=oUem...

Systematic benchmarking of basecalling models for RNA modification detection with highly-multiplexed nanopore sequencing Nanopore direct RNA sequencing (DRS) holds promise for advancing our understanding of the epitranscriptome by detecting RNA modifications in native RNA molecules. Recently, Oxford Nanopore Technologie...

Fresh preprint from the
@novoalab.bsky.social !😀📌 Do you want to barcode up to 96 #RNA samples in your #nanopore flowcells? How well do RNA #modification-aware models perform? What if there is #noBasecallingModel for your modification-of-interest? Find it out here!😊 www.biorxiv.org/content/10.1...

Yes, second half of this week, apparently :) (just back from Austria, no better there!)

DNA replication initiation timing is important for maintaining genome integrity | Journal of Bacteriology The regulation of DNA replication is fundamental to cell growth and cell cycle control. In eukaryotes, under-initiation or over-initiation leads to genome instability. In bacteria, it is unclear how c...

DNA replication initiation timing is important for maintaining genome integrity | Journal of Bacteriology journals.asm.org/doi/10.1128/...

Excited that our group was awarded a KIEM grant in collaboration with the @smitslab.bsky.social. Using this grant, we will establish establish new interdisciplinary connections and explore the development of #covalent #antibiotics against C. difficile.

www.staff.universite...

Non-antibiotics disrupt colonization resistance against enteropathogens Nature - Non-antibiotic drugs from a wide range of therapeutic classes can alter the ability of gut commensals to resist invasion by enteropathogens, a previously underappreciated side effect of...

Finally online!
Our latest research is out @nature.com: We show that non-antibiotic drugs can disrupt colonization resistance, raising the risk of enteric infections.
rdcu.be/ewwrG

Chromosomal capture of beneficial genes drives plasmids toward ecological redundancy Abstract. Plasmids are a ubiquitous feature of bacterial genomes, but the forces driving genes and phenotypes to become associated with plasmids are poorly

New paper with @rwheatley8.bsky.social and Cedric Lood

Actual title: Chromosomal capture of beneficial genes drives plasmids towards ecological redundancy.

Sensationalist title: Plasmids carry useless genes

academic.oup.com/ismej/articl...

“People don’t want to interact with a paper. They want to interact with the author” @valdavinson.bsky.social on lack of onsite commenting on papers at #FutureSciPub 1/2

We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5′→3′ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
1/

Now published, congrats Bevika, Kinki, Vincent, Florian and Paddy! #MicroSky
www.nature.com/articles/s41...

Awesome stuff @veeninglab.com and team!

Found: a human gut microbe that makes cancer therapy more effective in mice Cancer therapies called checkpoint inhibitor drugs, which ratchet up the immune system, work better when this bacterium is around.

A potent bacterium in the human gut can supercharge the effects of some cancer drugs

go.nature.com/4lqaBBI

AMR explained Antimicrobial resistance (AMR) is when microbes (including bacteria, viruses, fungi and parasites) evolve so that they are no longer affected by the medicines that have been developed to target them.…

Understanding the fundamentals is key to comprehending the threat that AMR poses.

Discover our Knocking Out AMR webpage! Packed with a bank of educational resources to help you increase your awareness of Antimicrobial Resistance 🦠📚

Vancomycin-resistant enterococci utilise antibiotic-enriched nutrients for intestinal colonisation - Nature Communications Here, the authors show that vancomycin-resistant enterococci grow in the antibiotic-treated gut microbiome by utilising enriched nutrients in the presence of reduced concentrations of inhibitory micro...

So excited to share a new paper from my lab just published in Nature Communications! We showed that vancomycin-resistant enterococci (VRE) occupied distinct intestinal niches in the antibiotic-treated intestine. doi.org/10.1038/s414... Amazing work by first author Olivia King and colleagues!

A Secreted Factor Coordinates Environmental Quality with Bacillus Development Entry into sporulation is governed by the master regulator Spo0A. Spo0A accumulates in its active form, Spo0A-P, as cells enter stationary phase. Prior reports have shown that the acute induction of c...

journals.plos.org/plosone/arti...

Never figured out what this factor was, but the active fraction had only two peptide hits by mass-spec analysis, corresponding to CwlO and YocH fragments. So b/f observing ProtK inactivated the activity, our best hypothesis was it was a peptidoglycan fragment

An endoribonuclease of the YicC-like family delays sporulation via sRNA degradation in Clostridioides difficile Abstract. Clostridioides difficile CD25890 is a YicC-like endoribonuclease involved in regulating sporulation initiation, a process critical for the host–h

endoribonuclease of the YicC-like family delays sporulation via sRNA degradation in Clostridioides difficile url: academic.oup.com/nar/article/...

looking at protein-DNA interactions at the single molecule level 👀
#MicroSky
thx ákos for pointing this out 🙏

In vivo CAR T cell generation to treat cancer and autoimmune disease Chimeric antigen receptor (CAR) T cell therapies have transformed treatment of B cell malignancies. However, their broader application is limited by complex manufacturing processes and the necessity f...

I have no other way to say it. This paper blows my f@&!ing mind:

www.science.org/doi/10.1126/...

Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice | mBio Clostridioides difficile is a significant healthcare-associated pathogen, with recurrent infections presenting a major treatment challenge due to further disruption of the microbiota after antibiotic ...

Host origin of microbiota drives functional recovery and Clostridioides difficile clearance in mice | mBio journals.asm.org/doi/10.1128/...

Third Annual Combatting CDI Conference is announced for Oct 14-15, 2025; organised by the C.DIFF TRUST. Check out the website for the program.

amethyst-cme.com/cdiconference/

Now online - the Review "Histone-mediated chromatin organization in prokaryotes and viruses" from @samuelschwab.bsky.social‬ @vikramalva.bsky.social @damelab.bsky.social‬ and co.

#histones #DNAorganization #chromatin #eukaryogenesis

Read it here 👉 authors.elsevier.com/sd/article/S...

The iron chelator pulcherriminic acid mediates the light response in Bacillus subtilis biofilms - Nature Communications Non-photosynthetic bacteria often respond to changes in light through the action of photoreceptor proteins. Here, Kobayashi et al. show that Bacillus subtilis biofilms display light responses that dep...

The iron chelator pulcherriminic acid mediates the light response in Bacillus subtilis biofilms

@natcomms.nature.com by Kazuo Kobayashi and colleagues

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

#MicroSky

Human gut bacteria bioaccumulate PFAS

Excited to share some key details on our latest research in @natmicrobiol.nature.com reporting intra-cellular accumulation of #PFAS (aka forever chemicals) by certain human gut bacteria. #microsky #mevosky #microbiomesky
www.nature.com/articles/s41...

Whole-genome ancestry of an Old Kingdom Egyptian - Nature Whole-genome sequencing of an ancient male Egyptian revealed a mixture of North African Neolithic and eastern Fertile Crescent ancestry, suggesting human migration between Egypt and Mesopotamia by the...

Forty years after Svante Pääbo kicked off this extraordinary field of science, today sees report of the first whole-genome sequence of an ancient Egyptian (from 2855–2570BCE). Exciting work from @pontus-skoglund.bsky.social, @flinklinus.bsky.social, & co at @ljmuofficial.bsky.social, @crick.ac.uk.🧬🧪

Expanding the diversity of bacterial DNA partitioning: A CTP-independent ParABS system for plasmid partitioning in Streptomyces | PNAS The ATP- and CTP-dependent ParA-ParB-parS segrosome is a macromolecular complex that segregates chromosomes/plasmids in most bacterial species. CTP...

Finally published! Many thanks to the reviewers and editor whose comments & suggestions improved this work significantly more than the first preprint version!!!

www.pnas.org/doi/10.1073/...

Bat-specific adaptations in interferon signaling and GBP1 contribute to enhanced antiviral capacity - Nature Communications Bats harbor diverse viruses but it’s less clear how they tolerate infection. Here, by characterizing innate immune responses in bat cells the authors show that IFN-beta signaling resists antagonistic ...

🚨Our new study out today in Nature Communications. Bats can asymptomatically host multiple viruses while remaining apparently healthy. Here we identify how interferon-mediated responses protect bats and identify molecular adaptations in GBP1. #LZCI
Link: www.nature.com/articles/s41...

Environmental microbiomes drive chemotactile sensation in octopus Microbial communities coat nearly every surface in the environment and have co-existed with animals throughout evolution. Whether animals exploit omni…

Environmental microbiomes drive chemotactile sensation in octopus www.sciencedirect.com/science/arti...

😮
#microsky #microbiomesky