PhD opening in my lab @jagiellonskiuni.bsky.social: using AI to predict how phage enzymes break down bacterial capsules — joint work with ML group GMUM and Zuzanna Drulis-Kawa's phage lab (Wrocław), spanning genomics, AI & evolution. mostowylab.com/job-phd-ai-d... Deadline: 15 August 2026

Interested in a PhD on bacteriophages? Check out www.academictransfer.com/nl/jobs/3623... #phagesky if you are interested and also happen to be at #VOM2026, send me a dm

How do phages kill dormant bacteria

Are you excited about exploring the biology behind phages infecting dormant bacteria? Join forces to uncover fundamental biology with great potential for clinical impact. We offer a fully funded PhD p...

academictransfer.com

Revisiting the life cycle of temperate phages @natrevmicro.nature.com by @jakob-tr.bsky.social, Cora Chmielowska, @albertomarina.bsky.social, and @jrpenades.bsky.social www.nature.com/articles/s41... #PhageSky

Revisiting the life cycle of temperate phages - Nature Reviews Microbiology

The life cycle of temperate bacteriophages involves lytic or lysogenic cycles and has historically served as a model for studying genetic regulation. This Review provides an updated overview of these ...

nature.com

Are gut phages friends or foes? A nice "forum" in Cell Host&Microbe by @naamagz.bsky.social discussing it's all about context. Depending on host inflammation and ecology, phages can shift between stabilizing and destabilizing our microbiome. www.cell.com/cell-host-mi... #phagesky

The gut phageome: Friend or foe?

Gut bacteriophages defy simple classification as beneficial or harmful, instead shifting between roles that stabilize or destabilize microbial communities depending on phage lifestyle dynamics, host i...

cell.com

Excited to share this interview on our lab's research!We're diving deep into the gut virome using AI and computational tools to read (and write?) viral genomes for the future of personalized medicine. Check it out: dangoor-medicine.biu.ac.il/node/416 #phagesky #Microbiome #Genomics #Virome

If you're a senior PhD student or recent graduate interested in doing work at the intersection of AI and microbial genomics and/or microbiomes, please feel free to reach out to discuss the possibility of applying together for an MIT Novo Nordisk Fellowship engineering.mit.edu/novo-nordisk

Novo Nordisk Fellowship

Potential areas of focus for postdoctoral fellows participating in the MIT-Novo Nordisk Postdoc Program include, but are not limited to, the following: Your complete application should include: In the...

engineering.mit.edu

I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.

Long read Metagenomics, #phage and #prophage in the gut by Ami Bhatt's group. Beautiful data showing changes in phages over two years #phagesky www.nature.com/articles/s41...

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

nature.com

#microsky #phagesky #phage in the gut www.nature.com/articles/s41...

Long-read metagenomics reveals phage dynamics in the human gut microbiome - Nature

Complex prophage integration dynamics, including low-level induction, cross-family host range and transposase-mediated mobilization, challenge existing paradigms and deepen our understanding of phage–...

nature.com

🚨New preprint out! We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8) www.biorxiv.org/content/10.1...

🐝🦠 New paper: rdcu.be/eOf7A Phages may drive microbial diversity, yet we often don’t even know how phages & bacteria correlate in nature. Our new study tackles this in the honeybee gut, thanks to the great work of PhD student @malickndiaye.bsky.social at @dmf-unil.bsky.social @fbm-unil.bsky.social

Phage diversity mirrors bacterial strain diversity in the honey bee gut microbiota - Nature Communications

Authors analyse paired viral and bacterial shotgun metagenomics data from individual honeybee guts, revealing modular, nested phage–bacteria networks, with viral diversity mirroring bacterial strain c...

nature.com

The average nucleotide identity (ANI) underpins how we map microbial diversity, compare species, and connect genomes to ecology. I wrote a short piece reflecting on the discovery and significance of this metric (and really enjoyed digging into the context and story behind it!) #microsky 🧬

Fantastic piece of research that discovered the atypical lifestyle of the prototypic crAssphage. This project showcased so much determination, brilliance, and open-mindedness, proving that great discoveries are made by following the evidence wherever it leads.

Cell Host & Microbe@cp-cellhostmicrobe.bsky.social · last yr.

The prototypic crAssphage is a linear phage-plasmid New work demonstrates that C. communis, a ubiquitous human gut phage that evades conventional plaque-based isolation, predominately replicates as a low-copy linear phage-plasmid w/ broad host range www.cell.com/cell-host-mi...

Phage people - does anyone have a lambda phage with a deletion/mutation in the integrase gene (unable to lysogenize)? If so, can you please share it with us to help us test a cool hypothesis? Thanks! Please RT. 🦠🙏

a cartoon character from south park says " i m gonna need your help "

ALT: a cartoon character from south park says " i m gonna need your help "

media.tenor.com

Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium https://www.biorxiv.org/content/10.1101/2025.03.16.643550v1

Talking about read-based methods to profile phages in metagenomes, check out Marker-MAGu by @miketisza.bsky.social —a marker gene-based method for identifying phages. bsky.app/profile/natu...

Yishay Pinto@yishay.bsky.social · 2y ago

Check out my "tools of the trade" piece on Phanta! I cover the need it addresses (phage inclusion in microbiome studies), the features we prioritized (sensitivity & ease of use), our vision (phage profiling as the norm), and the future we envision. Check it out and try Phanta! tinyurl.com/ToTPhanta

Check out my "tools of the trade" piece on Phanta! I cover the need it addresses (phage inclusion in microbiome studies), the features we prioritized (sensitivity & ease of use), our vision (phage profiling as the norm), and the future we envision. Check it out and try Phanta! tinyurl.com/ToTPhanta

This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after

bioRxiv Microbiology@biorxiv-microbiol.bsky.social · 2y ago

Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics https://www.biorxiv.org/content/10.1101/2025.01.16.633422v1

Starter pack for metagenomics and microbial genomics lovers. go.bsky.app/MFipoLH

I'm putting together a Microbial Bioinformatics starter pack to help get everyone connected in our community. Let me know if there are any bluesky users to be added and share so that twitter refugees can tune back in to the fantastic world microbes go.bsky.app/3ezLo7e

In the spirit of summaries, simple rules that, if everyone followed, would make academic publishing less painful in 2025. As a reviewer: *Separate major and minor comments *Write your explicit recommendation in the "for authors" section *If co-reviewing with trainees, read the paper yourself 1/2

Igor Ulitsky@igorulitsky.bsky.social · 2y ago

Time for the annual peer-review summary! I did 46 peer reviews in 2024. A busier year than 2022-23, but still sub-2021 levels. This year I attempted to review revisions same-day, which worked ~75% of the time (the other 25% took way longer...).

Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment [new] Empathi: Classifies phage proteins using embeddings, IDs multi-func.

What a great way to end the year! ✨ Today in @cellpress.bsky.social we report the structure and function of the Shedu anti-phage defense system. tinyurl.com/4crj6dnx A long 🧵...

Finally out! Phage therapy for diabetic foot ulcers www.sciencedirect.com/science/arti...

Randomized double-blind study on safety and tolerability of TP-102 phage cocktail in patients with infected and non-infected diabetic foot ulcers

Phage therapy offers a promising alternative for treating serious infections, including diabetic foot ulcers (DFUs), through the lytic action of phage…

sciencedirect.com

We wrote a new review paper in @cp-trendsmicrobiol.bsky.social on recently developed bioinformatic tools that facilitate elucidating protein functions in the era of big genomics data. www.sciencedirect.com/science/arti... This is the 1st paper of 2 talented students Shani Cheskis and Avital Akerman.

Deciphering bacterial protein functions with innovative computational methods

Bacteria colonize every niche on Earth and play key roles in many environmental and host-associated processes. The sequencing revolution revealed the …

sciencedirect.com

Nice study from @annechevallereau.bsky.social's lab! www.biorxiv.org/content/10.1...

Systematic functional assessment of antiphage systems in their native host

Bacterial resistance to bacteriophages (phages) relies on two primary strategies: preventing phage attachment and blocking post-attachment steps. These latter mechanisms are mediated by defence system...

biorxiv.org

New paper from the Faber lab in @plosbiology.org characterizing the C. difficle ncRNA ModT, with effects on sporulation and the transition into stationary phase, evidence for RBP association -- and similar abundance to some ribosomal RNAs! 🧫🦠 journals.plos.org/plosbiology/...

The conserved noncoding RNA ModT coordinates growth and virulence in Clostridioides difficile

Bacterial non-coding RNAs influence various cellular functions and often have complex tertiary structures. This study characterizes ModT, a conserved ncRNA found in 2,500 bacterial species, found to r...

journals.plos.org

nAtUrE iS bEaUtiFuL 🐞 #MedSky

Feel like this paper slipped under the radar on ‘the other platform’ so giving it another airing here. Phage can significantly remodel the bacteriome in faecal samples - yet another confounder 🙄 www.sciencedirect.com/science/arti...

Dynamic nature of viral and bacterial communities in human faeces

Bacteriophages are a major component of the gut microbiome and are believed to play a role in establishment and stabilization of microbial communities…

sciencedirect.com

Prophage induction contributes to alterations in the gut phageome during intestinal inflammation https://www.biorxiv.org/content/10.1101/2024.12.03.626644v1

Prophage induction contributes to alterations in the gut phageome during intestinal inflammation https://www.biorxiv.org/content/10.1101/2024.12.03.626644v1

Bacteriophages (phages) are abundant members of the gut microbiota and regulators of bacterial commu

biorxiv.org