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Pepe Flores

@ppflrs

Postdoc @ Plant-Microbe Interactions @MPIPZ.bsky.social Evolution and Ecology of microbial communities.

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09.09.2023
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Latest posts by Pepe Flores @ppflrs

Our group enjoyed this workshop last year, Highly recommend!

13.03.2026 22:55 πŸ‘ 2 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0
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Unifying Ecology Across Scales - Gordon Research Conference.

With @jennsunday.bsky.social as Chair

www.grc.org/unifying-eco...

07.03.2026 00:31 πŸ‘ 38 πŸ” 15 πŸ’¬ 1 πŸ“Œ 4

You could argue that the true core of a university is the intellectual relationship between teacher and student, and the shared pursuit of new knowledge through research... Everything else is infrastructure.
When we forget that, we mistake administration for mission and metrics for meaning.

28.02.2026 14:50 πŸ‘ 7 πŸ” 2 πŸ’¬ 0 πŸ“Œ 0

Beautiful image!

28.02.2026 22:40 πŸ‘ 1 πŸ” 0 πŸ’¬ 0 πŸ“Œ 0

I am honored that my microscopy image has been selected as the cover of a @newphyt.bsky.social issue for the third time. Thanks to the production team for selecting my image.

19.02.2026 19:17 πŸ‘ 8 πŸ” 3 πŸ’¬ 1 πŸ“Œ 0
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So when do authors preprint? Many do long before they submit to a journal (to get feedback to improve the work?); many submit around the same time (just want the work out?). Only a minority are submitting once the paper is under review [evidence against claims by some detractors]. 3/n

26.02.2026 16:08 πŸ‘ 27 πŸ” 15 πŸ’¬ 3 πŸ“Œ 2

Motion to stop referring to it as Next Generation Sequencing. That's like saying The Matrix is a recent movie

25.02.2026 20:48 πŸ‘ 220 πŸ” 32 πŸ’¬ 27 πŸ“Œ 4

Well, years are years, right? So still a mere 38 years. But the #LTEE is now past 82,000 generations. πŸŽ‰

26.02.2026 17:13 πŸ‘ 13 πŸ” 1 πŸ’¬ 1 πŸ“Œ 0

I have to say, I am quite impressed with Claude-Opus-4.6. I had very interesting conversation with it trying to explain a puzzling phenomenon that we observed in our experiments. The internal monologue is fascinating and reveals solid reasoning characteristic of a very good 1st year PhD student.

26.02.2026 17:32 πŸ‘ 9 πŸ” 1 πŸ’¬ 2 πŸ“Œ 0
On this day on February 26, 1948, the Max Planck Society was formally founded in GΓΆttingen as the successor organization to the Kaiser Wilhelm Society,  in the cafeteria of the KWS's aerodynamic testing facility in GΓΆttingen.

On this day on February 26, 1948, the Max Planck Society was formally founded in GΓΆttingen as the successor organization to the Kaiser Wilhelm Society, in the cafeteria of the KWS's aerodynamic testing facility in GΓΆttingen.

Happy birthday to....well, to us, actually! πŸ˜‰πŸŽ‚πŸ₯³ On this day on February 26, 1948, the Max Planck Society was formally founded in GΓΆttingen as the successor organization to the Kaiser Wilhelm Society, in the cafeteria of the KWS's aerodynamic testing facility in GΓΆttingen.

26.02.2026 15:41 πŸ‘ 50 πŸ” 9 πŸ’¬ 4 πŸ“Œ 0
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Best practices for moving from correlation to causation in ecological research - Nature Communications Different scientific traditions offer seemingly disparate approaches to inferring causal relationships in ecological systems. This Perspective unifies the causal assumptions and methods from...

Excited to share our new paper in @natcomms.nature.com We synthesize causal discovery & inference approaches across traditions (regression adjustment, quasi-expts, SEMs, Granger causality, convergent cross-mapping, and more) into a unified workflow for ecologists. www.nature.com/articles/s41...

24.02.2026 17:25 πŸ‘ 164 πŸ” 63 πŸ’¬ 3 πŸ“Œ 6

Happy Birthday!

I first read about the LTEE in high school in a science magazine my Bio teacher had in the classroom. I don't think I thought "I want to be a microbiologist," but the article planted the seed.

Amazing that it's nearly at "mid life" (by human standards)., excited for what's next!

24.02.2026 16:06 πŸ‘ 12 πŸ” 4 πŸ’¬ 0 πŸ“Œ 0

Happy 38th birthday to the #LTEE!
#BOTD in 1988.
Keep on evolving!

#science #evolution #microbiology

24.02.2026 15:20 πŸ‘ 186 πŸ” 47 πŸ’¬ 4 πŸ“Œ 6
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The editor:
We need a catchy title

Daniel Defoe:
The Life and Strange Surprizing Adventures of Robinson Crusoe, of York, Mariner: Who lived Eight and Twenty Years, all alone in an un-inhabited Island on the Coast of America, near the Mouth of the Great River of Oroonoque; Having been cast on ...

24.02.2026 19:16 πŸ‘ 3 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0
Career – Schneeberger Lab

🌾 We have an open postdoc position in Plant Genomics in our group at HHU Düsseldorf!

If you enjoy computational biology, asking big questions, and the satisfaction of code working on the first try, check out schneebergerlab.org/career/

Apply by Mar. 31 | 3-year postdoc | German skills required

23.02.2026 09:38 πŸ‘ 25 πŸ” 34 πŸ’¬ 1 πŸ“Œ 1

Existence of Causation without Correlation in Transcriptional Networks https://www.biorxiv.org/content/10.64898/2026.02.09.704821v1

10.02.2026 17:03 πŸ‘ 2 πŸ” 3 πŸ’¬ 0 πŸ“Œ 0
The incredible vulnerability that reproduction poses for plant species in a warming world

Crop scientists have long recognized that reproduction is going to be the first point of failure for plants with rising global temperatures. However, this has often been overlooked by those studying natural populations. In this new review, we try to change that. ecoevorxiv.org/repository/v...

17.02.2026 15:18 πŸ‘ 69 πŸ” 26 πŸ’¬ 1 πŸ“Œ 0
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I'm super happy to share my new preprint reporting a study in collaboration with the Seebeck (Basel) and Sasso (Leipzig) labs: www.biorxiv.org/content/10.6...
We discovered that ovothiol A, a thiohistidine, is a major antioxidant in the green alga Chlamydomonas. (1/4)

15.02.2026 22:08 πŸ‘ 16 πŸ” 7 πŸ’¬ 1 πŸ“Œ 0

She is an amazing skier but also a beautiful and brilliant woman! Just watch how she responded to the journalist who told her, "Two silver medals also mean two lost gold medals…”

19.02.2026 02:50 πŸ‘ 2 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0
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Good luck!

www.biorxiv.org/content/10.6...

15.02.2026 14:11 πŸ‘ 35 πŸ” 3 πŸ’¬ 1 πŸ“Œ 0

Koonin's lab in NIH is looking for postdocs. If you know someone who is interested, please spread the word. The details about the position are below: www.training.nih.gov/jobs/pdf-ecb...

17.02.2026 19:36 πŸ‘ 18 πŸ” 21 πŸ’¬ 0 πŸ“Œ 0
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Scientists have seen Asgard archaea crawling for the first time. When it comes to the origin of eukaryotes, this is like seeing a feathered dinosaur in the wild. (Video courtesy of Philipp Ralder)

18.02.2026 20:09 πŸ‘ 470 πŸ” 136 πŸ’¬ 10 πŸ“Œ 19

Beautiful structures, poetic name and great paper !

19.02.2026 05:23 πŸ‘ 11 πŸ” 1 πŸ’¬ 0 πŸ“Œ 0
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Congratulations to Sonomi Yamaguchi for her paper at @nature.com. Sonomi discovered Clover defense and explained how nucleotide signals control each step of viral sensing, immune regulation, and viral restriction – named for her beautiful "four-leaf" structures πŸ€

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

18.02.2026 17:11 πŸ‘ 59 πŸ” 31 πŸ’¬ 0 πŸ“Œ 4
graph showing number of each community profiling type (amplicon, shotgun-nanopore and shotgun-illumina). Amplicon and shotgun-illumina are in the millions of runs, while shotgun-nanopore is in the tens of thousands of runs.

graph showing number of each community profiling type (amplicon, shotgun-nanopore and shotgun-illumina). Amplicon and shotgun-illumina are in the millions of runs, while shotgun-nanopore is in the tens of thousands of runs.

There was a 34% increase in shotgun metagenomes in 2025 vs 2024 (64% increase for nanopore, now ~15,000), but amplicons are still king.

19.02.2026 09:54 πŸ‘ 10 πŸ” 2 πŸ’¬ 1 πŸ“Œ 1
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What happens to microbial genomic evolution in highly stable, closed ecosystems? In this preprint, authors look at 111 MAGs from a Romanian cave isolated from external influences for 5.5My(!) and see more pseudogenisation of core genes & limited HGT. Unsurprising?
πŸ”— www.biorxiv.org/content/10.1...

11.04.2025 05:50 πŸ‘ 30 πŸ” 10 πŸ’¬ 1 πŸ“Œ 0
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How do evolutionary forces shape bacterial adaptation to the plant environment? 🌱🦠

Curious? Read our new review in @femsjournals.bsky.social Microbiology Reviews.

#PlantMicrobiome #MicrobialEvolution #HostMicrobeInteractions #Rhizosphere #Microbiome

πŸ”— doi.org/10.1093/fems...

17.02.2026 06:34 πŸ‘ 12 πŸ” 7 πŸ’¬ 0 πŸ“Œ 1
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CEPLAS, the cluster of excellence on plants sciences, is looking for PhD candidates for a number of exciting projects. See below for more info on the topics and on the recruiting process, and here: www.ceplas.eu/en/training-...

18.02.2026 09:36 πŸ‘ 16 πŸ” 11 πŸ’¬ 0 πŸ“Œ 0
"Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea"
https://www.nature.com/articles/s41467-025-67002-1

"Seasonal enhancement of the viral shunt catalyzes a subsurface oxygen maximum in the Sargasso Sea" https://www.nature.com/articles/s41467-025-67002-1

Viruses transform microbes, populations, & ecosystems.

In new work jointly led w/@tn-marine-micro.bsky.social + more, we find a link between enhanced viral infection and productivity 50 meters below the surface in the otherwise nutrient limited Sargasso Sea.

a 🧡

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

12.01.2026 19:57 πŸ‘ 47 πŸ” 20 πŸ’¬ 3 πŸ“Œ 2
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Evolutionary mechanisms underlying bacterial adaptation to the plant environment Abstract. Plants and bacteria have coevolved over hundreds of millions of years, forming complex associations ranging from mutualism to pathogenicity that

Evolutionary mechanisms underlying bacterial adaptation to the plant environment

in @femsjournals.bsky.social Microbiology Reviews by @zakisaati.bsky.social et al

academic.oup.com/femsre/advan...

16.02.2026 10:22 πŸ‘ 13 πŸ” 9 πŸ’¬ 0 πŸ“Œ 0