Kröger Lab kroegerlab - Bluesky Statics

Methylome and transcriptome mapping reveal miniscule DNA methyltransferase regulons in Salmonella enterica serovar Typhimurium DNA methylation is a regulator of bacterial gene expression and adaptation, influencing traits such as virulence and antimicrobial resistance. The dynamic nature of DNA methylation enables rapid responses to changing environments and is a source of heterogeneity in bacterial populations. However, condition-dependent DNA methylation and consequences for transcriptional output remain poorly understood. We applied Oxford Nanopore sequencing to profile DNA methylation during exponential growth and late stationary phase of Salmonella enterica serovar Typhimurium and integrated these data with transcriptomic analyses. We found that each DNA methyltransferase (MTases) exhibits a distinct activity pattern across growth stages, which could not be explained by transcriptional levels of the corresponding enzymes. As predicted, DNA methylation patterns determined by regulatory MTases were dynamic across growth conditions whereas methylation patterns of MTases belonging to R-M systems were comparatively stable. We identified growth stage–specific methylation patterns for all studied MTases and correlations between methylation states and gene expression patterns. Together, these findings chart DNA methylation networks in the epigenetic regulation of bacterial physiology. Author summary DNA methylation in bacteria is best known for its role protecting DNA from endonucleases, such as restriction–modification, and coordinating chromosome replication and mutation repair, yet DNA methylation also regulates gene expression and cell physiology. Previous studies primarily examined bacterial DNA methylation at single time points or in limited genomic regions, providing only a partial view of its biological significance. In this study, we used Oxford Nanopore sequencing to compare DNA methylation patterns in Salmonella enterica during exponential growth and late stationary phase then integrated these data with corresponding gene expression profiles. We identified numerous methylation target motifs, all of which demonstrated constitutively methylated or unmethylated regions. This systems-level analysis clarifies the role of DNA methylation in bacterial adaptation across growth stages and demonstrates the utility of Oxford Nanopore sequencing for genome-wide methylation profiling. ### Competing Interest Statement The authors have declared no competing interest. European Union, https://ror.org/019w4f821, Marie Skłodowska-Curie grant agreement No. 896441 University of Regina Fir cluster of the Digital Research Alliance of Canada

Always good to start the year with a new preprint. We charted DNA methylation in Salmonella enterica: www.biorxiv.org/content/10.64898/2026.01.27.702048v1.

30.01.2026 11:53 — 👍 5 🔁 3 💬 0 📌 0

Job offer for a PhD student position at the Chair of Microbiology

🔊 Interested in doing a PhD on RNA-binding proteins in an abundant microbiota species and becoming a member of the German Priority Programme “Illuminating Gene Functions in the Human Gut Microbiome”? Apply here: www.uni-wuerzburg.de/karriere/sin...

01.12.2025 09:20 — 👍 7 🔁 15 💬 0 📌 1

This work is now out in Microbiology! www.microbiologyresearch.org/content/jour.... Congrats to first author Aalap Mogre!

Publish with the Microbiology Society! A membership charity and not-for-profit publisher: @microbiologysociety.org !

26.11.2025 14:03 — 👍 2 🔁 0 💬 0 📌 1

Junior Group Leader - Phage Biology & Biotechnology As a leading research institution for microbial biotechnology the Institute of Bio- and Geosciences - Biotechnology (IBG-1, https://www.fz-juelich.de/de/ibg/ibg-1 ) at the Forschungszentrum Jülich foc...

Please RT:
We have an opening for a junior group leader position in „Phage Biology & Biotechnology“.
www.fz-juelich.de/de/karriere/...

Interested candidates are encouraged to contact me via email for further details.

@spp2330.bsky.social; @mibinet.bsky.social

08.10.2025 06:50 — 👍 35 🔁 57 💬 0 📌 1

Happy International Microorganism Day! 🎉

Today, we are celebrating the tiny powerhouses that have a massive impact on our world. From the bacteria in our gut to the fungi that give us antibiotics, these incredible organisms are essential to life.

Let's make some noise for the microscopic!

17.09.2025 07:01 — 👍 41 🔁 20 💬 2 📌 4

Poster quoting from a reviewer saying "I have been supported by the Microbiology Society so much, so I will always support them."

Publish with us and invest in the research community. Supported by income from our journals, the Microbiology Society awards hundreds of grants every year, providing opportunities and experience for microbiologists at all career levels.

29.08.2025 15:05 — 👍 5 🔁 3 💬 2 📌 0

Cool stuff! Many congrats Lauren and Team!

11.08.2025 11:55 — 👍 2 🔁 0 💬 1 📌 0

New preprint! We characterise the small, regulatory RNA Arp which controls DNA uptake and twitching motilty in A. baumannii. Led by our Dr Fergal Hamrock @hamrockfergal.bsky.social and in collaboration with @westermannlab.bsky.social and Mike Gebhardt's lab!

21.07.2025 14:56 — 👍 3 🔁 6 💬 0 📌 1

New preprint! We characterise the small, regulatory RNA Arp which controls DNA uptake and twitching motilty in A. baumannii. Led by our Dr Fergal Hamrock @hamrockfergal.bsky.social and in collaboration with @westermannlab.bsky.social and Mike Gebhardt's lab!

21.07.2025 14:56 — 👍 3 🔁 6 💬 0 📌 1

Woohoo! Many, many congratulations Charline! Well deserved!🥳

21.07.2025 14:50 — 👍 0 🔁 0 💬 0 📌 0

Human endothelial cell infected with Acinetobacter baumannii strain ABC141. Bacteria are visible with Dapi in white along with the nucleus of the cell. Bacteria are mostly organized in a large cluster with a few scattered ones. Mitochondria are visible in red.

Charline studied how some clinical strains of Acinetobacter baumannii create a transient intracellular niche before infecting neighboring cells.
Great collaboration with @kroegerlab.bsky.social

If you are interested, check out her preprint!

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

21.07.2025 12:05 — 👍 3 🔁 2 💬 0 📌 0

Great to see that our pgtE story continues! Congrats to the cool work!

18.07.2025 16:00 — 👍 1 🔁 0 💬 0 📌 0

Latest preprint from our lab describing a new 2-plasmid system to investigate sRNAs-target molecule interactions in A. baumannii.

14.07.2025 07:26 — 👍 8 🔁 3 💬 0 📌 1

Transposon-directed insertion-site sequencing (TraDIS) analysis of Enterococcus faecium using nanopore sequencing and a WebAssembly analysis platform https://www.biorxiv.org/content/10.1101/2025.03.03.641140v1

05.03.2025 03:20 — 👍 5 🔁 1 💬 0 📌 0

CsrA-mediated regulation of a virulence switch in Acinetobacter baumannii | mBio The World Health Organization has ranked Acinetobacter baumannii atop its “priority pathogens” list highlighting the urgent need for new therapeutics against this pathogen. Many A. baumannii strains i...

Our lab contributed to this including @hamrockfergal.bsky.social : CsrA-mediated regulation of a virulence switch in Acinetobacter baumannii. Great work led by Phil Rather's group.

journals.asm.org/doi/10.1128/...

26.02.2025 08:17 — 👍 6 🔁 3 💬 0 📌 0

A work that started 10y ago with a simple experiment with a curious result. Great to see it finally published. Massive effort by @nic-ler.bsky.social and Andrew Cameron! Happy to have contributed to this!

24.02.2025 11:21 — 👍 7 🔁 3 💬 0 📌 0

The taxonomy & lifestyle of Salmonella Typhimurium

www.microbiologyresearch.org/content/jour...

23.01.2025 22:56 — 👍 22 🔁 9 💬 0 📌 0

Hi Matt. Could you add me please? Thank you :-)

17.01.2025 11:24 — 👍 1 🔁 0 💬 1 📌 0

Global analysis of the RNA–RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO Abstract. Acinetobacter baumannii is an opportunistic Gram-negative pathogen that infects critically ill patients. The emergence of antimicrobial resistant

Delighted to share our work led by IRC GoI PG Scholar Fergal Hamrock:
Global analysis of the RNA–RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO.
academic.oup.com/nar/advance-...

19.08.2024 08:37 — 👍 9 🔁 3 💬 0 📌 0

Posts by Kröger Lab (@kroegerlab.bsky.social)