Our Phage Picks for October 2024!

Howdy phage phans!

For most of you, summer’s been over for well over a month now. In San Francisco, we just got a heat wave of more than a week of 30°C+ days. And we don’t have AC. Yikes.

In the past week, Jess was invited to speak at the Canada SynBio Conference up in Toronto, I’ve been re-building most of Phage Directory from ground up, and we both got a chance to present Phage Directory and our work at Phage Australia to the lovely team at the Lawrence Berkeley National Lab, headed up by Dr. Vivek Mutalik. If you don’t follow him on Twitter… you really should (but maybe not, since that’s actually where I get most of my Phage Picks haha).

For Phage Directory, we’ve had our Profiles for a long time — for people, labs, and organizations. In the beginning, when the Directory was tiny, this worked well. Not anymore. The site wasn’t really designed around “real” profiles like Twitter and Facebook, where you can sign up, sign in, edit your information, and so on. Well, we’re re-thinking and re-building all that!

We’ve long wanted a place for labs to share their latest work, their on-going thoughts and experiments, capabilities, and most importantly invitations to collaborate on large grants.

Sometimes a collaborator with a specific expertise (or a piece of equipment!) is what stands between your lab and that massive grant.

We’re starting with a small group of labs and individuals. Here’s Jessica’s site (jess.bio) and Atif Khan, our awesome volunteer’s site (atif.phage.directory).

Let me know if you want to be first to get a site setup for your lab and members by emailing (jan@phage.directory)! We’ll otherwise gradually upgrade labs to the new system.

Best,

~ Jan

Plazomicin (Achaogen) financial post-mortem: #PassPASTEUR

Well, I can’t exactly say I’m “excited” about Achaogen going bankrupt, but this is a fascinating read. According to the authors “there’s no viable path for new drugs however valuable they are to society.” Achaogen was the last biotech company that was brave enough to try to invent a new antibiotic — they raised $800M, but ended up selling for $16M. They went bankrupt despite coming up with a new mechanism and getting all the way through clinical trials. This blog post (and the full paper) breaks down all the pieces of what didn’t work. There’s some crazy information here — apparently it costs $350M just to maintain the antibiotic on the market, fort the first ten years AFTER approval.

Honestly? This makes me surprised that anyone works in drug development in the first place. This is definitely worth a read, and I’ll probably write a bigger post on this later in the year.

~ Jan

Blog Post: https://amr.solutions/2024/10/14/plazomicin-achaogen-financial-post-mortem-passpasteur

Outterson, J.R.& K. (2024) Plazomicin (Achaogen) financial post-mortem: #PassPASTEUR, AMR.Solutions. Available at: https://amr.solutions/2024/10/14/plazomicin-achaogen-financial-post-mortem-passpasteur/ (Accessed: 17 October 2024).

Full Paper: https://doi.org/10.1057/s41599-024-03452-0.

Nadya Wells, Vinh-Kim Nguyen, & Stephan Harbarth. Novel insights from financial analysis of the failure to commercialise plazomicin: Implications for the antibiotic investment ecosystem. Humanit Soc Sci Commun 11, 941 (2024).

Tapping the treasure trove of atypical phages

What is it about?

In this review paper, Vivek and Simon go in-depth into non-typical (aka non dsDNA phages), and go into ssRNA and ssDNA phages — like leviviruses and inoviruses (aka filamentous phages). Mostly they analyzed and discussed metagenomic analyses around these, and their diversity. Apparently most of our isolation methods bias our selection towards pilus-specific phages (I always wondered about that) and how there’s a huge diversity of phages (that we can see metagenomically).

Why I’m excited about it:

This is a cool collaboration between two heavy hitters (and my favorite people) in the phage world: Simon Roux and Vivek Mutalik. This paper also covers something I think more phage folks should get into — weird phages that don’t infect your typical E. coli! Of course, they come with a whole host of problems, like how the heck do you isolate them, etc. It probably will come down new techniques, methods, protocols, and tools for screening and isolating phages. We’re just at the very very beginning of phages — and keeping in mind so many cool findings in biology, like DNA and CRISPR, all came from phage more. There’s way more out there to uncover!

~ Jan

Paper: https://www.sciencedirect.com/science/article/pii/S1369527424001310

Roux, S., & Mutalik, V. K. (2024). Tapping the treasure trove of atypical phages. Current Opinion in Microbiology, 82, 102555. https://doi.org/10.1016/j.mib.2024.102555

Directional Immobilisation of SpyTag Bacteriophage on PDMS surfaces for Phage based Microfluidics

What is it about?

This preprint describes a new method for designing phage-based biosensors for bacteria detection. They use a technique for directionally immobilizing phages onto a surface using a pair of protein systems (SpyTag/SpyCatcher), on Polydimethylsiloxane (PDMS) surfaces, commonly used to make microfluidic diagnostic devices. They then built a proof of concept detector with an E. coli K1 phage.

Why I’m excited about it:

This preprint came our Phage Directory email, and caught my eye because I don’t get to see very many new chip / microfluidics phage projects. Plus, the technicality of the paper’s way too deep for me — but we’ve replied and hope to either get a Capsid article or a blog post from the team!

~ Jan

Preprint: https://www.biorxiv.org/content/10.1101/2024.10.11.617866v1

NotebookLM Audio Summary: https://media.phage.directory/capsid/phage-picks-oct-2024/spycatcher.mp3

bioRxiv 2024.10.11.617866; doi: https://doi.org/10.1101/2024.10.11.617866

Why a good lab website matters

What is it about?

This short editorial from Nature Metabolism lays out a few reasons behind why having lab website is important, as a good website helps attract students, staff, and collaborators, and makes the work look more legit. A good websites shows current staff, past staff (and where they’ve gone), paints the culture of the lab, and highlights key publications.

Why I’m excited about it:

Well, I couldn’t have said it better. Also, I didn’t make it up — Nature Metabolism wrote a short editorial piece about… why good lab sites matter?!

They miss a couple of key points — the purpose of a good lab site is to attract the best people for your lab. This means attracting those that shares the culture, work ethic, complements skill sets, and fills in the gap for the lab. Though painting the science behind the lab is important, it’s also necessary to show how the lab thinks, and where its science is going in the future.

Anyway, both Jess and I share that sentiment, but getting one built and published is often a mess. If you set it up yourself, e.g. with Wordpress, it’s always a hassle to update. If you pay for someone else to build it, then you have to keep paying them. There has to be a middle ground, and that’s what we’ve been exploring with the future of Phage Directory!

~ Jan

Editorial, Nature metabolism: https://www.nature.com/articles/s42255-023-00797-9

Why a good lab website matters. (2023). Nature Metabolism, 5(4), 533–533. https://doi.org/10.1038/s42255-023-00797-9