Our Phage Picks for March 2024!

Issue 254 | March 1, 2024
8 min read
Capsid and Tail

A 100% accurate depiction of San Francisco

We’re starting off the year by trying a new format: Phage Picks — where we share the papers we keep bookmarked… and keep coming back to.

What’s New

Pherecydes has a new phage therapy patent. It covers new S. aureus phages and their manufacture and combination for use in phage therapy and as a companion diagnostic.

PatentPhage therapy

NIAID seeks applications from single institutions or consortia ready to generate, validate, and advance medical countermeasures against drug-resistant bacteria or fungi.

Funding opportunity

Nicholas Smith (University at Buffalo) and colleagues published a new paper exploring the pharmacodynamics of three unique Pseudomonas phages by simulating different dosing strategies (cocktails vs. single phage, bolus vs. prolonged dosing) using a hollow fibre infection model and mathematical modeling.

Research paperModelingPK/PD

Ana Rita Costa (Delft University of Technology) and colleagues published a new paper showing that clinical P. aeruginosa strains accumulate phage defense systems (some have at least 19!), that many individual defense systems target specific phage genera, and that defense systems with complementary specificities co-occur in P. aeruginosa genomes.

Phage defenseResearch paper

Ritu Arora (University of Delhi) and colleagues isolated 100+ mycobacteriophages over the last two years, and here announce five genomes from different clusters, infecting M. tuberculosis and M. fortuitum.

MycobacteriophageGenome announcementPhage isolation

Latest Jobs

Postdoctoral position: Bacteriophage biology at CNRS in Lyon, France.

The project aims at deciphering if and how prophages mediate resistance against, and coevolve with, virulent phages in the opportunistic pathogen Pseudomonas aeruginosa. The candidate will join a newly created group at the Molecular Microbiology and Structural Biology (MMSB) unit (CNRS, Université de Lyon, France)

Apply here

For further information: [email protected]

Research associateJumbo phage
UC San Diego is hiring a Staff Research Associate to design and construct jumbo phage genomes for new phage production, involving computational design, synthetic biology, and yeast genetics.
Phage therapyPost Bac
FDA (Silver Spring, Maryland) is offering a postbac fellowship to develop and characterize phage therapy for decolonizing Vancomycin-resistant Enterococci, focusing on overcoming bacterial resistance.
Phage-host interactionsBiofilmsPostdoc
EPFL (Lausanne, Switzerland) is hiring a postdoc to explore phage-bacteria interactions within stream biofilms using microfluidic techniques.
PhD projectPhage therapySynthetic Biology
University of Nottingham, UK, is offering a PhD Studentship to develop phage therapy strategies against C. difficile, involving synthetic biology, CRISPR/Cas genome editing, and microbiology.
Research technicianPhage-host interaction
Washington University (St. Louis, USA) is hiring a Research Technician II to support phage and bacterial host interaction studies, involving molecular biology, cell biology, and genomics.
Research specialistMolecular Interactions
The University of Pennsylvania is hiring a Research Specialist to lead a project on molecular interactions between bacteria and phage.
PostdocType IV secretion
FAPESP, São Paulo, Brazil is hiring a postdoc to explore the applications of bactericidal type IV secretion systems, focusing on interspecies bacterial warfare and the development of new tools for targeting pathogens.

Community Board

Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

This week on PhageCast, the team talked to Paul Turner about how his lab is predicting the trade-offs of bacterial resistance to phage, to achieve killing by reversing the antibiotic resistance. They also covered how these findings are translated from in vitro to in vivo, and he also gave really inspiring advice for the people in the field.

PodcastPhagecastPhage therapyPhage-host interactions

The International Society of Microbiota will host their 11th Annual Meeting, Targeting Microbiota, on October 17-18 at the Corinthia Palace Malta, to explore the role of microbiota in health and disease, advancements in microbiome medicine, and the clinical applications of phage therapy, among other topics.

International Society of MicrobiotaAnnual MeetingConference

Our Phage Picks for March 2024!

Profile Image
Product designer and co-founder of Phage Directory
Co-founderProduct Designer
Iredell Lab, Phage Directory, The Westmead Institute for Medical Research, Sydney, Australia, Phage Australia
Twitter @yawnxyz

Bioinformatics, Data Science, UX Design, Full-stack Engineering

I am a co-founder of Phage Directory, and have a Master of Human-Computer Interaction degree from Carnegie Mellon University and a computer science and psychology background from UMBC.

For Phage Directory, I take care of the product design, full-stack engineering, and business / operations aspects.

As of Feb 2022, I’ve recently joined Jon Iredell’s group in Sydney, Australia to build informatics systems for Phage Australia. I’m helping get Phage Australia’s phage therapy system up and running here, working to streamline workflows for phage sourcing, biobanking and collection of phage/bacteria/patient matching and monitoring data, and integrating it all with Phage Directory’s phage exchange, phage alerts and phage atlas systems.

Profile Image
Phage microbiologist and co-founder of Phage Directory
Co-founderPostdoctoral Researcher
Iredell Lab, Phage Directory, The Westmead Institute for Medical Research, Sydney, Australia, Phage Australia

Phage characterization, Phage-host interactions, Phage Therapy, Molecular Biology

I’m a co-founder of Phage Directory and have a Ph.D in Microbiology and Biotechnology from the University of Alberta (I studied Campylobacter phage biology). For Phage Directory, I oversee community building, phage sourcing, communications, science, and our awesome team of volunteers.

As of Feb 2022, I’ve recently joined Jon Iredell’s group in Sydney, Australia as a postdoctoral research scientist for the Phage Australia project. I’m diving back into the lab to help get Phage Australia’s country-wide phage therapy system up and running here, working to streamline workflows for phage sourcing, biobanking and collection of phage/bacteria/patient matching and monitoring data, and integrating it all with Phage Directory’s phage exchange, phage alerts and phage atlas systems. I’m also delving into phage manufacturing and quality control.

Hi everyone!

We thought we’d kick off the year with a new format.

We’ve been reading phage papers for years — and have amassed a trove of our favorites. These are papers we come back to: over and over and over. They make us think. Reflect. And get us excited to get back in the lab (or computer) again!

We call these Phage Picks, and we urge you to take a look. These are casual recommendations of papers — from colleague to colleague.

We hope these papers excite you as much as they excite us!

Rapid assessment of changes in phage bioactivity using dynamic light scattering

What is it about?

Tejas Dharmaraj (Stanford University) and colleagues show us how to use Dynamic Light Scattering (DLS) as a simple, fast way to measure phage stability. DLS is commonly used in physics to quickly measure particle size, and many university departments likely have one of these machines already (try asking around!). Instead of always needing to do plaque assays, we can use DLS to get a quick readout on whether a phage has degraded or aggregated in solution, or if it’s still stable (and thus active — crucially, this paper shows how DLS correlates nicely with plaque assay-derived titres, although one thing it can’t detect is UV-induced damage).

Why we’re excited about it:

Anything that cuts down on time spent doing endless titres is golden in my books. DLS is a reliable, cheap, fast, and non-destructive alternative to check for phage activity. By having this assay running in our phage labs, we can keep regular tabs on our phage preps and rapidly get a much better sense of phage stability across different conditions. Also, this paper gets into other super handy tools like a nice area-under-the-curve assay for quantifying how much a phage has degraded/aggregated in solution, as well as software to readily analyze the DLS data (called PhageELF). Overall this is an awesome tools paper that everyone in the phage field needs to read!

~ Jessica

Tejas Dharmaraj, Michael J Kratochvil, Julie D Pourtois, Qingquan Chen, Maryam Hajfathalian, Aviv Hargil, Yung-Hao Lin, Zoe Evans, Agnès Oromí-Bosch, Joel D Berry, Robert McBride, Naomi L Haddock, Derek R Holman, Jonas D van Belleghem, Tony H Chang, Jeremy J Barr, Rob Lavigne, Sarah C Heilshorn, Francis G Blankenberg, Paul L Bollyky, Rapid assessment of changes in phage bioactivity using dynamic light scattering, PNAS Nexus, Volume 2, Issue 12, December 2023, pgad406, https://doi.org/10.1093/pnasnexus/pgad406

Large language models improve annotation of prokaryotic viral proteins

What is it about?

In this paper, the authors documented how they used protein language models (PLMs) to annotate proteins, as opposed to traditional methods. The team trained existing PLMs with well-annotated databases like PHROGS — and found 29% more protein annotations — including finding new integrases and a capsid protein.

Why we’re excited about it:

Using a rough analogy, traditional annotation tools are like “spell checkers” while PLMs are like ChatGPT. While spell checkers are decent at identifying and correcting words and sentences, they’re fairly rigid. While they can infer “Mivi is a cat” is about a cat, they fall apart on sentences like “Mivi loves tuna and purrs when it rains.” Meanwhile, large language models like ChatGPT can infer these because they’ve “seen” relationships between “tuna” and “purr” with cats in their training data.

This is super exciting because these tools can find “synonymous annotations” that we previously missed. This could help us detect more integrases before taking a phage to therapy, help us clean up annotation databases, and potentially even lead to discovering new patterns that could open up new research areas. Excitingly all the code and data is also contained in the paper (as a Github repo), so anyone can go in and reproduce it (I haven’t done this myself yet.)
~ Jan

Flamholz, Z.N., Biller, S.J. & Kelly, L. Large language models improve annotation of prokaryotic viral proteins. Nat Microbiol 9, 537–549 (2024). https://doi.org/10.1038/s41564-023-01584-8

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!

Oh and if you have suggestions for new papers, or how we can improve the format, let us know ([email protected]). Any feedback (nice or mean) will help us make Capsid more useful for you!

~ Jan & Jess

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In collaboration with

Mary Ann Liebert PHAGE

Supported by

Leona M. and Harry B. Helmsley Charitable Trust

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