Hey all,
Both Jess and I have been hard at work — heads down, thumbs up — in the last month.
Jess has been giving her lab’s phages a *Richard Simmons treatment,* getting them shaped up for compassionate use. She’s also been on a mean streak, recording podcast interviews with people doing cool phage projects. Find her on Spotify!
Meanwhile, I’ve been building out the next system that underpins Phage Directory, which adds a proper profile system, better search, and lets lab create their own lab websites, where they can share their own phage and other biobank data! There’s still a lot of work left to do though, but I’m about 80% there! The goal is to get it shipped before the end of the year.
Lots of exciting stuff (and changes) coming in the fall!
~ Jan & Jessica
by Ažbe Žnidaršič, Lucija Rebula
This article by Ažbe Žnidaršič and Lucija Rebula from Sartorius examines the use of CIMmultus monolithic chromatography for purifying phages. The authors explain how this technique addresses challenges in phage production, such as separating phages from bacterial cell debris and reducing endotoxin levels. CIMmultus columns, made from methacrylate-based materials, offer advantages like laminar flow to protect viral particles, high flow rates, low backpressure, and reusability. For human therapy applications, Znidarsic and Rebula recommend a two-step process: first using a hydroxy (OH) ligand column to remove host cell impurities, followed by a weak anion exchange column (PrimaS) for endotoxin removal. This method maintains high phage infectivity while reducing impurities. The authors note that despite initial investment challenges, CIMmultus monolithic chromatography provides long-term benefits in both research and industrial phage purification applications, offering efficiency, scalability, and versatility.
by Jan Zheng
In September’s Phage Picks, I really got to nerd out: I shared a a study on filamentous Pseudomonas bacteriophage Pf and how it messes with the mucociliary transport in airway cells; shared an article on how antibiotics damage the mucus barrier, and talked about the massive deluge of new AI tools coming down the pike — from a new foundation model for molecular structure prediction, to a slew of tools like NotebookLM and OpenAI’s new o1-series of models. We should really start running a series on how to use these tools (hint: don’t use them for writing; they’re terrible at it).
by Aaryan Harshith
In this post, Aaryan describes his project PhageBase, an online atlas of phage TEM images and data. He talks about how he got started, and how he’s been able to amass a dataset on over 1000 phages across 150+ bacterial hosts. Their eventual goal is to expand their dataset to over 10,000 phages, develop an API, and add more collaboration features — with the help and collaboration of the phage It emphasizes PhageBase’s role in centralizing phage data and fostering community growth. This is a really cool project in a similar vein as Phage Directory — and they’re looking for contributors!
C&T Throwback!
Behind the curtains, we’ve been thinking hard about biobanks, digitally tracking and sharing phage and bacteria data, and how to tie it together in a simple to use system. This work has been in the works for a loooong time, but things are finally gelling. We’ll have something great to share very soon — including a complete re-haul of the Phage Directory website, new Profile system, Capsid & Tail, and way better search. The building blocks are clicking into place!
In the meantime I’ve been looking over our past articles like how the NCTC re-launches its phage collection, and our old articles on Phage Directory itself, like — Phage Directory expands! What’s changing and what’s staying the same.
