Catching up on some personal #prophage work. Couple of tooling changes worth noting.

1> Genomad is noticeably faster at bulk processing compared to other comparable pipelines. If you haven't already you should really try it out

2> Latest Phold gpu performance feels a LOT faster and lighter

💻🧬🧫🦠

Symbiosis through lysis: prophage activation underlies Lactiplantibacillus plantarum probiotic function The release of bacterial bioactive molecules across the gut barrier is a crucial yet poorly understood step in microbe-host communication. Here we unravel a phage-driven mechanism that enables this pr...

Another great collaboration with Grangeasse Lab from @mmsb-lyon.bsky.social 🔗 Preprint: www.biorxiv.org/content/10.6...
#phagebiology #microbiome #drosophila #symbiosis #prophage #Lactobacillus

Investigate the molecular and physiological Interactions between the Prophages - The phage jobs Understand the molecular and physiological principles of prophage interactions and their role in horizontal gene transfer and antimicrobial-resistance dissemination in clinically derived S. aureus str...

PhD position in investigating the molecular and physiological principles of #prophage interactions and their role in horizontal #gene transfer and antimicrobial-resistance ( #AMR ) dissemination.

thephage.xyz/jobs/jobs/in...

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...

Last week, part of our team was busy at Bioisi (U. of Lisbon @cienciasulisboa.bsky.social ), talking all things #phage and #prophage with our collaborator Filipa Vale

PSOSP uncovers pervasive SOS‐independent prophages with distinct genomic and host traits in bacterial genomes Prophages are ubiquitously present in bacterial genomes, significantly influencing host physiological and ecological functions. We present Prophage SOS-dependency Predictor (PSOSP), a novel bioinform...

🚀 PSOSP predicts #prophage induction!
From 49,333 genomes, we uncovered 11,806 SiPs, showing unique genomic/host traits and hinting at SiP–SdP interconversion.
onlinelibrary.wiley.com/doi/10.1002/...
Available: vee-lab.sjtu.edu.cn/PSOSP/
#Bioinformatics #microbiome

GitHub - mujiezhang/PSOSP: PSOSP (Prophage SOS dependency Predictor) is a novel bioinformatics tool to predict prophage induction modes by analyzing the heterology index (HI) of LexA protein binding t... PSOSP (Prophage SOS dependency Predictor) is a novel bioinformatics tool to predict prophage induction modes by analyzing the heterology index (HI) of LexA protein binding to target DNA, classifyin...

🧪Struggling to induce #prophage?
🧬 Meet PSOSP, a tool to predict prophage induction mode!
🚀Distinguishes SOS-dependent vs independent prophages.
🖥️Available on web server: vee-lab.sjtu.edu.cn/PSOSP and Github: github.com/mujiezhang/P...
#Bioinformatics #phage #viruse #microbiome #GutHealth

@evolvedbiofilm.bsky.social finally made it to Bsky:) only 4 followers so far😭 #Prophage, #Bacillus, #SPbetavirus researchers, follow some news and views from #Ljubljana phage group. Recent group photo😊

Cytoplasmic incompatibility factor proteins from Wolbachia prophage are costly to sperm development in Drosophila melanogaster | Proceedings of the Royal Society B: Biological Sciences The symbiosis between arthropods and Wolbachia bacteria is globally widespread, largely due to selfish-drive systems that favour the fitness of symbiont-transmitting females. The most common drive, cy...

🚨 New pub alert! 🚨 Our study shows that #Wolbachia #prophage Cif proteins come at a cost to #Drosophila sperm development. @symbionticism.bsky.social
royalsocietypublishing.org/doi/10.1098/...

A prophage competition element protects #Salmonella from lysis.

RemAIN is an antiphage defense element encoded in a Salmonella #prophage, which blocks the lytic cycles of co-residing prophages.

www.cell.com/cell-host-mi... #MicroSky

Pf4 as a common good
#Pseudomonasaeruginosa #prophage

-in ISME Journal

academic.oup.com/ismej/advanc...