Hi everyone!
It’s Phage Picks time! This is a new monthly format we’re testing out. These are casual recommendations of papers — from colleague to colleague.
We hope these papers excite you as much as they excite us!
Phage Genome Annotation: Where to Begin and End
What is it about?
In this paper, Anastasiya Shen and Andy Millard provide us a much-needed and thorough guide to phage genome assembly and annotation. The paper covers anything from raw sequencing reads to submission of phage genomes through ENA. They include really helpful examples and scripts, databases, and software for all stages of the bioinformatics pipeline, as well as a decision-tree for phage genome reordering.
Why we’re excited about it:
Honestly, I’ve always been very confused whenever “bioinformatics” and “pipelines” were mentioned in the same sentence. I’ve always been confused as to why you couldn’t just “run a script and be done with it,” why it couldn’t be automated, and why sometimes “doing bioinformatics” on a phage or host could be so fast, and other times so slow. This paper shows how complicated phage bioinformatics can be, and how many decisions have to be made by the bioinformatician along the way to paint a “correct picture” of the phage, using its genome sequence.
~ Jan
Access: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9041514/pdf/phage.2021.0015.pdf
Shen A, Millard A. Phage Genome Annotation: Where to Begin and End. Phage (New Rochelle). 2021 Dec 1;2(4):183-193.
In Vitro Evolution to Increase the Titers of Difficult Bacteriophages: RAMP-UP Protocol
What is it about?
Danielle Kok and a few others from Heather Hendrickson’s lab down in NZ shows us two methods for experimentally evolving phages to increase their titers. The first method uses a traditional agar-overlay method over 25 days, whereas the other was a 96-well liquid infection protocol called RAMP-UP (Rapid Adaptive Mutation of Phage - UP) over 4-30 days — where phages are serially passaged with a modified Appelmans protocol. They also defined a math model to describe the limits of the approach.
Why we’re excited about it:
I’m not too good in the lab, but it doesn’t take a lab genius to figure out this could really benefit phage therapy. This protocol could possibly also help good phages get even higher titer yields. I’m also curious what happens when you make this higher throughput with liquid handling robots. Maybe the method could even unlock novel phages? But also… I’m curious if this changes the fundamental characteristics of the phage. Would this make the phage worse at therapy? No idea.
~ Jan
Access: https://www.liebertpub.com/doi/pdf/10.1089/phage.2023.0005
Danielle N. Kok, Joanne Turnbull, Nobuto Takeuchi, Philippos K. Tsourkas, and Heather L. Hendrickson. In Vitro Evolution to Increase the Titers of Difficult Bacteriophages: RAMP-UP Protocol. PHAGE. Jun 2023. 68-81.
The contribution of neutrophils to bacteriophage clearance and pharmacokinetics in vivo
What is it about?
Arne Echterhof and others from the Bollyky lab at Stanford and Felix Biotech wanted to know if neutrophils are one of the reasons phages don’t last forever in the body. This fits into a field called pharmacokinetics, which tracks the ‘impact of the body on a drug’. All drugs have to go through this, and yet phages generally haven’t. First, the team injected mice with phages; then they used qPCR and plaque assays to count phages in the blood and the spleen over time. They used two groups of mice; healthy and ‘neutropenic’ (given a drug to reduce its neutrophils). In both, phages dropped in the blood, but accumulated happily in the spleen; neutrophils didn’t matter! They did see plaque assays lagging qPCR counts in blood though, suggesting there IS something inactivating phages… it’s just not neutrophils.
Why I’m excited about it:
This is a nice, straightforward example of phage pharmacokinetics! You put phages in the body, and you track where they go and how long it takes before they’re gone. This is a crucial part of drug development and one that the phage field hasn’t contended with too much (we just seem to skip animals and go straight to compassionate use in humans). (For years at phage therapy conferences I’ve heard grumpy pharma execs mumbling ”the PK/PD studies haven’t been done!”, and it was always on my to-do list to learn more.) With this study, we’re one step closer to understanding what phages have to deal with (or don’t) in the body! At least for the phage they tested (Pseudomonas phage LPS-5), neutrophils don’t matter, but there’s something in the blood that does.
~ Jess
Access: https://www.biorxiv.org/content/10.1101/2024.01.25.577154v1.full
Echterhof, A., Dharmaraj, T., McBride, R., Berry, J. D., Hopkins, M., Selvakumar, H., … & Bollyky, P. (2024). The contribution of neutrophils to bacteriophage clearance and pharmacokinetics in vivo. bioRxiv, 2024-01.
That’s it, those are our favorite drops for this week! We’ll experiment with bringing you a new bunch of fresh picks every month — of a mix of 80’s, 90’s and today!
How were our picks this time?
Suggest new papers, or tell us how to improve — just send them to me (Jan — [email protected])! Any feedback (nice or mean) will help us make Capsid more useful for you!
~ Jan & Jess
