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Emrah Simsek

@esimsek.bsky.social
19 followers 27 following 10 posts

Assistant Professor of (bio)Physics at University of Florida. Studying life and death of microbes. biophysics, qBio, systems biology.

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Reposted by Emrah Simsek
Ákos T Kovács @evolvedbiofilm.bsky.social · 09/12/2025
Our recent collaborative paper is now published in the latest issue of Cell Reports @cp-cellreports.bsky.social accompanied by a cover image highlighting how Bacillus gathers iron in the biofilm for promoting plant growth www.cell.com/issue/S2211-...
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Reposted by Emrah Simsek
Ákos T Kovács @evolvedbiofilm.bsky.social · 05/12/2025
Spatial proximity dictates bacterial competition and expansion in microbial communities @natcomms.nature.com by @esimsek.bsky.social et al from @lingchongyou.bsky.social www.nature.com/articles/s41...
nature.com
Spatial proximity dictates bacterial competition and expansion in microbial communities - Nature Communications
Here, the authors show that immotile bacteria degrade antibiotics to alter their environment and facilitate nearby motile competitors to expand. As expansion proceeds, the immotile degrader is outcomp...
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
8/8: @lingchongyou.bsky.social and I realized that, even though Klebsiella disappeared, it was indispensable for Pseudomonas to expand, serving as a hidden initiator. More in the paper for enthusiasts. Now, I continue this line of investigation in my own lab.
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
7/8: The study started when I tried altering Pseudomonas branching patterns by mixing it with Klebsiella. Expansion stopped well before the dish boundary, and I wanted to know why. My local CFU checks revealed Klebsiella was rare or absent in the final community.
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
6/8: Bacteria can kickstart spatial expansion under antibiotics and then vanish. Focusing only on dominant species captures the aftermath, potentially missing such hidden initiators.
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
5/8: Key biophysical insights: 1️⃣ An outsized role of minority bacteria 2️⃣ Context is key – effect cannot be captured in well-mixed cultures. 3️⃣ Proximity flips competition into facilitation – movement occurs only within helper-created safe zones.
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
4/8: First tested in a pairwise community (P. aeruginosa + Klebsiella) under cefotaxime. Then, using a sink-drain sample from a hospital room, we built SynkC, a synthetic community, showing the same phenomenon under carbenicillin.
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
3/8: We call these helper bacteria “hidden initiators.” They enable expansion by locally degrading antibiotics, creating safe zones where P. aeruginosa can move.
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
2/8: Unexpectedly, otherwise competing nonmotile bacteria can “rescue” P. aeruginosa if nearby. These helpers vanish quickly as P. aeruginosa outcompetes them.
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
1/8: In our new paper with @lingchongyou.bsky.social doi.org/10.1038/s414..., we show that antibiotics don’t just kill bacteria—they can paralyze Pseudomonas aeruginosa at sublethal doses, halting its spatial expansion.
doi.org
Spatial proximity dictates bacterial competition and expansion in microbial communities - Nature Communications
Here, the authors show that immotile bacteria degrade antibiotics to alter their environment and facilitate nearby motile competitors to expand. As expansion proceeds, the immotile degrader is outcomp...
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Emrah Simsek @esimsek.bsky.social · 06/12/2025
thanks for your kind words and for patiently reading it several times 😉
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Emrah Simsek @esimsek.bsky.social · 05/12/2025
thanks for posting this.
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