Pepe Flores

Hello BSVoM Blueskyers,

Are you in need of some #phage, #phage therapy and other viruses of microbes conferences?!! 👁️👇🏽

🦠 BSVoM Symposium (Sept 12): Keynotes
from @jeanpaulpirnay.bsky.social and @antoniasagona.bsky.social and more!!

🗓️ Abstracts: Aug 8 | Reg: Sept 1

www.bsvom.be/en/abstract-...

How many plasmids can bacteria carry? A synthetic biology perspective | Open Biology Plasmids are pinnacle tools in synthetic biology and other biotechnological applications. They serve as the simplest approach to introduce recombinant DNA, which is then transcribed into RNA that func...

How many #plasmids can #bacteria carry? royalsocietypublishing.org/doi/10.1098/...

Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes Abstract. High-throughput sequencing has provided unprecedented insights into microbial biodiversity in marine and other ecosystems. However, most sequenci

Quantitative metagenomics for marine prokaryotes and photosynthetic eukaryotes #USC_MEB #jcampubs 🌊 academic.oup.com/ismecommun/a...

A Phylogenetic Host‐Range Index Reveals Ecological Constraints in Phage Specialisation and Virulence Phages are typically known for having a limited host range, targeting particular strains within a bacterial species, but accurately measuring their specificity remains challenging. Factors like the g...

After many years in the making, here is our host range #phage paper with #ecology, #evolution and #biocontrol perspectives published in Molecular Ecology! @phimresearch.bsky.social‬ @inrae-pv.bsky.social‬ #PVBMT #JulianGarneau onlinelibrary.wiley.com/doi/10.1111/...
These are our key findings:

In silico encounters: Harnessing metabolic modelling to understand plant-microbe interactions Abstract. Understanding plant-microbe interactions is vital for developing sustainable agricultural practices and mitigating the consequences of climate ch

In silico encounters: Harnessing metabolic modelling to understand plant-microbe interactions

#FEMS Microbiol Rev by Martina Feierabend and Nadine Töpfer @ceplas.bsky.social

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

Design of a rhodopsin-based light-driven proton pump to improve acid tolerance of yeast www.sciencedirect.com/science/arti...

v3 loaded. Oceanic cyanobacterial photosynthesis is negatively affected by viral NblA proteins www.biorxiv.org/content/10.1...

Cyanophage Infections in a Sponge Intracellular Cyanobacterial Symbiont Intracellular cyanobacterial symbionts of sponges are shown to be susceptible to cyanophages, challenging assumptions about their isolation from viral exposure. The study reveals novel phage–host int...

Our paper on cyanophages of marine sponge symbionts is finally out. It is the outcome of a great collaboration with Laura Steindler's lab and was led by Tzipora Perez.

Hey #StatsSky, what are you favorite papers to cite when you need to justify something that is obvious (I once had a reviewer ask we justify the use of logistic regression on a binary outcome)
or when you need to push-back on silly reviewer requests (e.g., asking for p-values in table 1)?

📌

Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity - Nature Microbiology The authors examine several defense systems and find that increased expression enhances their protection range, albeit at a cost of autoimmunity.

Expression level of anti-phage defence systems controls a trade-off between protection range and autoimmunity | Nature Microbiology https://www.nature.com/articles/s41564-025-02063-y

🦠🧍‍♀️From bacterial to human immunity.

We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity.
Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social

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

Taxonomic and environmental distribution of bacterial amino acid auxotrophies - Nature Communications Many microorganisms are auxotrophic, that is, unable to synthesize the compounds they require for growth. Here, Ramoneda et al. predict amino acid biosynthetic capabilities of over 26,000 bacterial ge...

First paper we've found that validates auxotrophy predictions from genomes. in non-host associated communities (e.g. soils) auxotrophy is rare. I believe the assumption of prevalent auxotrophies emerging out of pervasive cross-feeding needs to be reconsidered.. www.nature.com/articles/s41...

This work was supported by @nitmb.bsky.social, National Science Foundation, NIH, @cziscience.bsky.social , Simons Foundation, UChicago. bsky.app/profile/sepp...

Retraction The Research Article “A bacterium that can grow by using arsenic instead of phosphorus” by F. Wolfe-Simon et al. (1) has been the subject of discussion and critique since its online publication in 201...

The reply from the authors is a bit odd. A paper can be retracted not only for misconduct/fraud; if the conclusions are not supported, one can retract, & this can come from honest errors, wrong analyses, etc. Retractions are a way to signal to readers that the conclusions of a study are not reliable

Retraction The Research Article “A bacterium that can grow by using arsenic instead of phosphorus” by F. Wolfe-Simon et al. (1) has been the subject of discussion and critique since its online publication in 201...

15 years later, finally, Science did the right thing at retracted the As life disaster paper! www.science.org/doi/10.1126/...

Fifteen years later, Science retracts ‘arsenic life’ paper despite study authors’ protests Belated decision on widely disputed 2010 study pleases some critics but puzzles and dismays others

Fifteen years later, Science retracts ‘arsenic life’ paper despite study authors’ protests | Science | AAAS www.science.org/content/arti...

A group of curious locals along the way

Oberer Schwarzhornsee

Unterer Schwarzhornsee (2543 m elevation) with Großelend glacier in the background

Gentiana, but which species?

We are now in the High Tauern National Park in Austria. Fantastic landscapes, warm-hearted people, but the lakes are not that easy to reach! With Oberer Schwarzhornsee at 2650 m elevation, we sampled the highest lake on the tour.
#CAPSOLUTION
@mpimarinemicrobio.bsky.social @erc.europa.eu

Oberer Plenderlessee in the Stubai Alps

Catching a break from the rain at Mittlerer Plenderlessee

Testing if the pumps are waterproof

Dinoflagellates and other protists

The next two lakes on the sampling tour were Upper and Middle Plenderlessee in Austria. We got lots of water from the lakes, and also from the skies... Dinoflagellates live here!
#CAPSOLUTION
@mpimarinemicrobio.bsky.social @erc.europa.eu

The Genetic Basis of Bacterial Adaptation to Hosts Microbes colonize and interact with diverse multicellular hosts using specialized genes, many of which remain unidentified. Better understanding of host-associated gene functions is a key aspect of mi...

📢 New preprint alert!
We used comparative genomics on 72,000+ bacterial genomes to uncover the genetic basis of microbial adaptation to multicellular hosts—plants and animals alike.
www.biorxiv.org/content/10.1...

Characterizing organisms from three domains of life with universal primers from throughout the global ocean www.nature.com/articles/s41...

What makes a temperate phage an effective bacterial weapon? | mSystems journals.asm.org/doi/10.1128/...

“how phage impact the structure and dynamics of an artificial four-species bacterial community that includes either Pseudomonas aeruginosa wild-type or an isogenic mutant unable to evolve phage resistance through CRISPR-Cas” 😳👇🏼

The impact of phage and phage resistance on microbial community dynamics Phages shape the microbial world. This study uses an evolution experiment to explore how phage impact the structure and dynamics of a four-species bacterial community, finding that phage enables compe...

Our paper on "The impact of phage and phage resistance on microbial community dynamics" is finally out in PLOS Biology! What a journey it's been to get here, and I couldn't have done it without my fab co-authors journals.plos.org/plosbiology/...

🌍🌱📈 Taxonomic revisions affect plant biodiversity quantification and conservation strategies. Great thread!

A lesson we should closely follow in 🦠🧫 #MicrobialEcology, where OTUs, ASVs, MAGs and Bins are interchangeably used.

#Microbiology #MicroSky

Coming back from 5 days of great science at #2025ISMPMI, I wanted to share some of my highlights, and particularly to mention my favourite presentations by early career researchers.

A thread 🧵 ⬇️

Read out all of the text on your slides I have a simple rule for better public speaking: If you’re using slides that contain text, you must read it out, word-for-word.

A simple rule for better public speaking: If you’re using slides that contain text, you must read it out, word-for-word.

clauswilke.substack.com/p/read-out-a...

Beyond homology: This mind blowing work demonstrates the power of genomics driven analogy for discovery in the era of structure predictions.

The diversity of defense systems emerged thx to "guilt by association approaches". New analogies to uncover molecular novelties 👇.
👏 Nitzan, Rotem & al.

🤞

v2 in bioRxiv!! Oceanic cyanobacterial photosynthesis is negatively affected by viral NblA proteins www.biorxiv.org/content/10.1...