Podovirus
Podovirus
Podcast Description
Phages (bacteriophages) are viruses that kill bacteria. In an age of antibiotic resistance, we need them! Luckily there are 1000s of researchers studying phages, using them, and making them available for humans (phage therapy), agriculture, and beyond!
But phages don't quite fit our modern regulatory systems, so there's lots to do.
Jessica will have conversations with guests across the phage field (and beyond - whatever it takes to get answers). From diving into current research and initiatives, to getting to the root of bottlenecks in our field, to making sense of new trends and findings.
Podcast Insights
Content Themes
The podcast covers a diverse range of topics related to phage therapy and its applications, including episodes discussing the business viability of phage therapy, personalized medicine, regulatory challenges, and microbiome editing, with specific examples such as the journey of companies like Intralytix and Phiogen Pharmaceuticals.
Phages (bacteriophages) are viruses that kill bacteria with sniper-like precision. They can be incredibly useful for treating life-threatening infections (‘phage therapy’), and can help us reduce our dependence on antibiotics. They’ve been known for 100 years… so WHY do we still not see them on the shelves?
Jessica Sacher, PhD (Staff Scientist at Stanford and cofounder of Phage Directory) and Joseph Campbell, PhD (former NIAID program officer) talk to phage therapy practitioners, researchers and entrepreneurs to understand one question: why don’t we have phage therapy yet?
Can AI design living organisms from scratch? Samuel King and Claudia Driscoll from the Arc Institute used genome language models to generate functional phages—and 16 of them actually worked in the lab. Not only that, they killed bacteria equally or better than the natural phage the team used as a template.
In this episode, we dig into how they did it, what it means for phage research, and why this could be a new way to explore evolution and design genomes.
What we covered:
• How genome language models work (ChatGPT, but for DNA)
• Training on millions of phage genomes with Evo-1 and Evo-2
• The creativity (from biologists!) required to figure out how best to filter generated sequences
• Going from 4000 selected sequences in silico, to 300+ synthesized candidates, to 16 working phages
• Fresh phage lab protocols for new ways to look at phage fitness
• Phage ”personalities” that emerged from the generated candidates
• Watching recombination occur among a cocktail of designed phages
• Cost realities: hundreds of dollars per 5kb genome candidate, but emerging ways to reduce it exist!
• Good news: All tools are open source and free to use!
The preprint:
Samuel H. King, Claudia L. Driscoll, David B. Li, Daniel Guo, Aditi T. Merchant, Garyk Brixi, Max E. Wilkinson, Brian L. Hie (2025-09-17). Generative design of novel bacteriophages with genome language models | bioRxiv. biorxiv.org. Retrieved November 8, 2025, from https://www.biorxiv.org/content/10.1101/2025.09.12.675911v1
More resources:
• Arc Institute Evo browser interface: https://arcinstitute.org/tools/evo
• GitHub (open source code): Evo2: https://github.com/ArcInstitute/evo2)
• Hugging Face (model downloads): https://huggingface.co/arcinstitute
Guests:
Samuel King: PhD candidate, Stanford/Arc Institute, Brian Hie's lab; follow @samuelhking on X
Claudia Driscoll: Postdoc, Arc Institute, Brian Hie's lab, follow @driscoll_cl on X
Also follow @BrianHie, @arcinstitute, @stanford on X for more from this team!
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