Finally, PHORAGER is freely available as open-source software (github.com/aponsero/PHO...) and the ESKAPE prophage collection generated in this study is available online as a reusable resource for further investigations (zenodo.org/records/1832...) Happy PHORAGING! 🦠🧬🧺

We also investigated anti-phage defence systems and found that 23.6% of prophages encoded at least 1 system 🛡️ Additionally, we observed that bacterial defence carriage is negatively correlated with prophage carriage among the ESKAPE pathogens 📉

We screened the recovered prophages for AMR genes (ARGs) and virulence factors, and found that putative ARGs were detected at very low frequencies, with only 0.48% of prophages encoding an ARG 💊 Putative virulence factor genes were found to be more common, particularly in S. aureus prophages⚡

In total 23,132 putative prophages were identified, 99.9% belonging to the class Caudoviricetes, and exhibiting a high degree of host-specificity 🦠 Further taxonomic analysis classified the prophages into 115 viral families and 2,250 viral genera, the majority representing putatively novel taxa!

To validate PHORAGER, we tested it on a dataset of 30,824 publicly available ESKAPE pathogen genomes. PHORAGER recovered more high-quality prophages than individual mining tools alone, and through extensive quality assessments removed a substantial number of false-positive predictions ✅

PHORAGER incorporates robust bacterial genome pre-processing steps 🦠, methods to de-replicate predictions generated by multiple prophage mining tools 🧬, and advanced quality assessments to reduce the number of false positives identified ✅

I am excited to share that our manuscript titled 'Defining the ESKAPE pathogen prophage repertoire with PHORAGER' is now available online as a preprint in BioRxiv! 🤩 (doi.org/10.64898/202...) Here we present PHORAGER, a Nextflow pipeline for the identification and quality assessment of prophages 🧬

I’m embarrassed that this is the first I’ve heard of the amazing courage of Linda Guamán. Amazing read on what it means to be a scientist in the face of political pressure.

Nature@nature.com · 3w ago

Linda Guamán wanted to serve her country, but became mired in a political controversy that led to her being arrested and facing years in prison go.nature.com/4poutIA

I've been using Sanger's Artemis to view #genomics since ... who knows (it was first published in 2000). It's still super useful, but getting harder to install. I vibe-coded a lightweight browser-only version that views #GenBank files: linsalrob.github.io/genbank_view... 🧬💻 #phagesky

📢 We're hiring a postdoc! If you're passionate about microbial biosynthetic pathway elucidation and enzyme discovery we'd love to hear from you! www.kuleuven.be/personeel/jo...

Postdoc Microbial Biochemistry: Biosynthetic Enzyme Discovery in Cable Bacteria

Elucidating the biosynthesis of a unique nickel-containing conductive structure for long-range electron transport in cable bacteria

kuleuven.be

This is a first: got reviews back for a manuscript and there are 9 reviewers 😱 Upside: I feel the paper is well-assessed Downside: my postdoc's wellbeing leading the rebuttal

What microbes shared between parents and children? And what microbes are shared between grandparents, parents and children? 👪 Take part in our PEARL-AGE study to help us find out ➡️ buff.ly/48VykCL @earlhaminst.bsky.social

Starting with the DNA sequence of a #phage genome, #PholdAPhage will create a 3D reconstruction of the complete phage, almost like you did cryoEM on it! Check out Renee's awesome software github.com/reneegreen81... to assemble unknown phage particles one protein at a time

#Vom2026: Had a fantastic opportunity to share my work on Maternal influence in shaping up the infants' virome at this year's VoM in front of 900 researchers. Thank you all for the wonderful feedback so far, and I will be happy to talk more about it. @evelienadri.bsky.social @ryancook94.bsky.social

In our final poster at #VoM2026, @rapher97.bsky.social explores the gut virome in healthy ageing. Visit his poster to find out what to expect when you get older…

If you work with Klebsiella phages, you would probably like to know what genes are involved in resistance. Check out @deuskamya.bsky.social’s poster at #VoM2026 featuring lots of mutants.

Today @ryancook94.bsky.social is presenting his posters on the trials and tribulations of working with phages and organoid models. #VoM2025

Have you ever wondered about prophages in an important gut bacterium? Check out @xenadyball.bsky.social’s poster at #VoM2026

Banning a #Pride display may feel minor, but remember: rights & #visibility are often eroded 1 small step at a time. Today's display. Tomorrow something else E.g. Italy, 2023: After political change, authorities banned recording both parents in same-sex couples & retrospectively amended birth certs

Ben Goldsborough MP@bengoldsborough.bsky.social · last mo.

Reform says banning Pride displays from Norfolk libraries is about "neutrality". It isn't. Erasing LGBT+ visibility doesn't make people equal, it makes people invisible. I've written to Cllr David Bick calling on him to reverse this divisive decision. Love is love. 🏳️‍🌈

Who infects whom? A big question in virome research. If you want to learn more, check out the work from @apedramfar.bsky.social from her PhD. #VoM2026

A little sad to be missing #VOM2026 this year, but excited that our lab will still be well represented! 🎉 look out for @lucasmoriniere.bsky.social talk on 1000+ phage receptor predictions @fmaucourt.bsky.social poster on 70+ M smeg 😳phage screens using CRISPRi!! Cheering 🙌 them on from afar.

Earlier today at #VoM2026 @revathykri.bsky.social presented her work on the virus population sharing between mothers and infants. She did a amazing job! Find her during breaks to talk methods, findings and everything virome!

Day 2 of #vom2026 starts with virus host interactions

If you’re at the Viruses of Microbes conference, interested in Pseudomonas or phage therapy, check out @hannahvpye.bsky.social ‘s poster no84. #VoM2026

🆕 Blog! Dr Hannah Morelli reflects on her journey from studying animal health to launching Quadlytics, a new spinout company developing bacteriophage therapies to tackle Salmonella in livestock 🧪 buff.ly/0wCCXJW

From phages to pigs: turning research into a spinout company - Quadram Institute

“I’m currently a postdoctoral researcher here at the Quadram Institute. My day-to-day research is looking at bacteriophages, which are viruses that can infect and kill bacteria, and how they can be…

quadram.ac.uk

It's that time of year when the JIFs are out. Over-reliance on it fuels integrity risks like papermills & fraud. Everything is connected! Join us in shifting the focus from venue prestige to merit. Explore RRA resources & course: sfdora.org/reports/ & bit.ly/DORA-Intro-Course

How does a phage cocktail affect the healthy human microbiota? We tested the Intestiphage cocktail from the Eliava Institute in a human colon model system and observed an E. coli phage bloom and minimal disruption of the microbiota. www.microbiologyresearch.org/content/jour... Led by Teagan Brown

The effects of bacteriophage cocktail treatment on healthy gut microbiota: an in vitro human colon model study

The human gut microbiome is a complex community that plays an important role in health, where perturbations can result in dysbiosis and disease. Bacteriophages (phages) can provide treatment for bacte...

microbiologyresearch.org

With Eugene Koonin, we wrote a rather comprehensive review on the origin, evolution and organization of the #virosphere. We describe all 10 viral realms and the logic behind them, and so much more. Check it out! comptes-rendus.academie-sciences.fr/biologies/ar...

In raw numbers, the number of complete phage genomes from cultured isolates has doubled but the amount of unique genomes has slightly decreased- we're starting to sequence the same phages again. People are also getting better at giving their phages unique names! (Please no more phages named P1)

During my PhD, @milja001.bsky.social and I started counting phage genomes, and tried to make them available in useful formats with useful metadata. We also described the extent of sequenced phage genomes at the time. Five years on, we've had a look at what's changed www.biorxiv.org/content/10.6...