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...

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

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 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–...

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–...

#microsky #phagesky #phage in the gut

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

🚨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...

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...

🐝🦠 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

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 🧬

A very cool piece. Thank you Luis

Sure

Big congratulations to danica, Gavin, Ami, and the entire team on this publication!

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.

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 "

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. 🦠🙏

Replicative selfish genetic elements are driving rapid pathogenic adaptation of Enterococcus faecium www.biorxiv.org/content/10.1101/2025.03....

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...

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

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

Empathi: Embedding-based Phage Protein Annotation Tool by Hierarchical Assignment

Figure 1

Figure 2

Figure 3

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

Amazing. Congrats!

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 🧵...

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…

Finally out!
Phage therapy for diabetic foot ulcers

www.sciencedirect.com/science/arti...

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 …

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.

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...

Nice study from @annechevallereau.bsky.social's lab!

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

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...

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/...

🙋‍♂️🙏

nAtUrE iS bEaUtiFuL 🐞
#MedSky

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…

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...