C&T Round Up for October 2022!

Issue 199 | October 28, 2022

7 min read

This week, we highlight our October feature articles: Dive down the rabbit hole with us on designing phage data systems, building sustainable phage therapy, and get excited for this year’s World Phage Week!

Urgent October 18, 2022

Urgent need for Helicobacter pylori phages for a patient in the USA

Phage Therapy

We are urgently seeking Helicobacter pylori phages for a patient in the USA

Ways to help at this stage:

By sending your phages for testing on the patient’s strains
By receiving one or more of the patient’s strains and testing your phages
By receiving the strain(s) and using it/them to search for new phages
By offering to prepare phages supplied by others to clinical grade
By helping spread the word about this request
By providing us with names/email addresses of labs you think we should contact

Please email [email protected] if you can help in any way, or if you would like further details/clarification.

Let’s make a difference,
Phage Directory

What’s New

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Micreos, a Dutch/Swiss biotech company, has secured its next funding round of €25 million in growth capital for clinical development of its endolysin technology platform, set to replace antibiotics in many areas.

Adi Millman et al. published a new paper in Cell Host & Microbe entitled An expanded arsenal of immune systems that protect bacteria from phages. They report the discovery of 21 defense systems that protect bacteria from phages, based on computational genomic analyses and phage-infection experiments. Also check out this Twitter thread by the Sorek lab.

In a new paper in mBio, Eugen Pfeifer and colleagues report that phage-plasmids commonly encode different and multiple types of resistance genes of high clinical importance, often in integrons.

In a new paper in Microbiology Spectrum, Aude Ferran (Université de Toulouse) and colleagues report that the combination of phages and antibiotics can prevent the selection of resistant bacteria.

Brendan J. O’Hara (Tufts University School of Medicine) and colleagues published a paper in PLOS Genetics entitled The Vibrio cholerae Seventh Pandemic Islands act in tandem to defend against a circulating phage.

Latest Jobs

All Jobs Post a job

Postdoc position: Phage biology in FDA study at University of Pittsburgh, AAD Lab in Pittsburgh, PA, USA. .

The AAD Lab at the University of Pittsburgh is recruiting a 2-4 year post-doc position. The position is funded by the NIH. The objective of this proposal is to determine how changes in S. aureus WTA glycosylation vary under different conditions and impact phage activity. This work supports and directly relates to an ongoing FDA study. Please email a CV to Ken Urish MD PhD for more info: [email protected].

The SWBio DTP is advertising a PhD project on how biofilms protect themselves against bacteriophage infection and how they fail.

Edze Westra (University of Exeter) is looking for a PhD student to work on the evolution of viral communication systems.

The Dragos lab at the University of Ljubljana, Biotechnical Faculty is looking for a postdoc in microbiology with experience in microscopic analysis of bacterial cells, Bacillus sp gene regulation, genetic engineering of microbes and phage-host interactions to work on the ERC project entitled ‘The evolution of host manipulation by bacteriophage’.

This PhD project at the University of Exeter aims to understand mechanisms of synergy between bacterial anti‐phage defences.

This PhD project, co-supervised by Tiffany Taylor (University of Bath), Edze Westra (University of Exeter), and Andrew Preston (University of Bath), with collaborators Ben Ashby (Simon Fraser University) will study the interplay between a novel defence system and the CRISPR-Cas adaptive immune system of Pseudomonas aeruginosa. The project is based in the Taylor lab at the Milner Centre for Evolution at the University of Bath.

Community Board

All posts Post a message

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

Dear ISVM Members,
We are pleased to announce the results of our 2022 ISVM Executive Board election. Thank you to 292 of you who participated in the election of the new Board members. The New ISVM Board members for 2023-2024 are listed below:

ISVM Executive board members
President: Zuzanna Drulis-Kawa (Poland)
President-elect: Lone Brøndsted (Denmark)
Vice-President: Hany Anany (Canada)
Treasurer: Tracey Peters (USA)
Secretary/Information Officer: Aleksandra Petrovic-Fabijan (Australia)
Membership Secretary: Cedric Lood (Belgium)
Web Developer: Cristina Moraru (Germany)

ISVM Staff functions
Industry outreach: Sandra Morales (Australia)
Assistant Secretary: Milan Gerovac (Germany)

This new Board will convene in January 2023 and will represent ISVM members through 2023-2024.

— The ISVM Executive Board

Stephanie Lesage, Richard James and Francesca Hodges have spearheaded Phage-UK, which has >45 clinicians interested in phage therapy, who work in 15 different UK Hospital Trusts; with a Phage-UK Clinical Steering Group of 18 members. Their new website is now available: https://www.phageuk.com/

Viruses Journal is now accepting nominations for their 2022 Early Career Investigator Award. The prize will be awarded to two early-career investigators demonstrating excellence in virology, and will include an invitation to speak at the Viruses International Virology Conference in 2024.

Craig MacLean on Twitter: “Quick question: does anybody know of fluorescent dyes that can be used to stain phage? Want to measure ability of phage to adsorb to bacterial cells they cannot infect.”

C&T Round Up for October 2022!

Product designer and co-founder of Phage Directory

Co-founderProduct Designer

Phage Directory

Email [email protected]

Twitter @yawnxyz

Website https://janzheng.com

Skills

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 design and build tools, and help write and organize Capsid & Tail.

I’ve previously worked at the Westmead Institute, for the Iredell lab at Phage Australia. There, I helped connect bioinformatics outputs and databases like REDCap, Google Drive, and S3-compatible storage systems.

Currently, I’m building and designing AI-centric tools for biology, including experimenting with protein models, biobank databases, AI-supported schema and data parsing, and bioinformatics workflows. Hit me up at [email protected] if you’re curious to collaborate!

Here’s what we published this month!

Send us your thoughts, comments or questions (or write for us!) by email or Slack!

How to design a phage data system

by Jan Zheng

In this article, I argued for a phage data system that is auditable, replicable, and accessible in order to scale up phage treatment. The data system should be able to track and connect phage and bacterial data with outputs from the rest of the therapy pipeline. I also discussed the need for the data system to be able to generate safety and viability reports. Lastly, I concluded that the data system needs to make its code freely available so others can contribute to the growth of the system.

World Phage Week 2022

by Oluwasegun Isaac Daramola and Williams Timilehin Owoeye

World Phage Week is an annual event organized by the Ibadan Bacteriophage Research Team (IBRT) and the SEA-PHAGES program. The event features webinars with prominent speakers on the status of phage therapy development and related topics. This year’s event will feature discussions on: Implementation of Phage Therapy for Critical Infections, The Role of Early-Career Research, Engagement in Phage Research, and Phage Biobanks and how they facilitate phage therapy commercialization.

Building a sustainable ecosystem for phage therapy

by Ruby CY Lin

In Part One of Ruby’s series on phage sustainability, she defines commercialization pathways and discusses Phage Australia’s background. Phage Australia has established a clinical network and a nationally approved protocol to regulate phage therapy under the clinical trial framework, endorsed by expert groups and clinicians. The team has also mapped out the patient journeys for phage therapy in comparison to patients being treated with antibiotics only at a public hospital. Ruby discusses ways to make phage therapy cost effective, with substantial savings over traditional antibiotic treatment.

Throwback: NCTC re-launches its phage collection

by Juandem Agendia, Julie Russell, Jake Turnbull, Mohammed Fazal
August 1, 2019

A few years ago, NCTC re-launched its phage collection. How did they do that, and how did it come about? As we’re building up our internal phage collection at Phage Australia, this is a great issue to revisit.

Product designer and co-founder of Phage Directory

Co-founderProduct Designer

Phage Directory

Email [email protected]

Twitter @yawnxyz

Website https://janzheng.com

Skills

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 design and build tools, and help write and organize Capsid & Tail.

How to Cite

To cite this, please use:

Zheng, J. (2022). C&T Round Up for October 2022! Capsid & Tail, 199. https://phage.directory/capsid/round-up-oct-2022

BibTeX citation:

@article{Zheng-round-up-oct-2022,

author = {Zheng, Jan},
journal = {Capsid & Tail},
number = {199},
year = {2022},
publisher = {Phage Directory},
title = {C&T Round Up for October 2022!},

}

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All diagrams and text in this issue of Capsid & Tail is licensed under Creative Commons Attribution CC-BY 4.0, unless otherwise noted.

For every issue of Capsid & Tail, we are committed to getting our facts straight, but we’re not experts in the information we’re bringing to you. If you feel that we’ve missed an important viewpoint, or if you have something to add, please reach out to us by emailing [email protected]. We’d love to hear from you, and we’d be happy to revisit topics we’ve covered (ideally with added information and viewpoints from community members like you!).

Lastly, please reach out if you’re interested in writing for us, or have suggestions for future issues!

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