C&T Round Up for October 2021

Issue 151 | November 5, 2021

7 min read

This week, we highlight the feature articles we published in October! Learn about the phages being collected around the world, a doctor-patient experience with phage therapy, successful use of phage to treat bacterial prostatitis, and Cytophage and BiomX’s thoughts on overcoming barriers to phage commercialization.

What’s New

TechnoPhage announces first clinical safety results with their phage cocktail, TP-102, now advancing to phase 2. TP-102 is assessed for its safety and tolerability in individuals with diabetic foot ulcers, and showed no adverse effects in the phase I/IIa clinical trial.

Adaptive Phage Therapeutics announced a strategic agreement with the Antibacterial Resistance Leadership Group to support a phase 1b/2 cystic fibrosis (CF) study. The randomized, double-blind, placebo-controlled trial will assess the safety and microbiological activity of a single dose of phage therapy in cystic fibrosis subjects colonized with Pseudomonas aeruginosa.

Victoria Turzynski (University of Duisburg-Essen, Germany) and colleagues published a new paper in Viruses showing imaging techniques for detecting prokaryotic viruses in environmental samples.

Rubén González (University of Valencia, Spain) and colleagues published a new paper in mBio showing the interplay between the host microbiome and pathogenic viral infections.

WIsH predicts the hosts of phages from their genomic sequences. It achieves 63% mean accuracy when predicting the host genus among 20 genera for 3 kbp-long phage contigs. WisH is also fast and accurate on phage sequences of a few kbp, making it suited for metagenomics studies.

Latest Jobs

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The Department of Biosystems Science and Engineering at ETH Zurich (Zürich, Switzerland) is seeking a PhD student to determine the crystal structures of ssDNA binding proteins and use cryo-electron microscopy to determine structures of macromolecular assemblies to guide directed evolution experiments.

The Adriaenssens Lab at the Quadram Institute (Norwich, UK) are seeking a PhD student to investigate how phages contribute to adaptation of commensal bacteria to the human gut.

The Ahlgren Lab at Clark University (Massachusetts, US) is seeking a PhD student to study the phylogenetic and genomic determinants of host range in Synechococcus and cyanophages.

The Kenny Lab at University College Cork (Cork, Ireland) is hiring a research assistant to develop phage therapy solutions to target Streptococcus suis in pigs.

The Microbiology & Immunology unit for SEA-PHAGES at McGill University (Montreal, Canada) is hiring a teaching assistant.

The Van Tyne lab at the University of Pittsburgh (Pennsylvania, US) is hiring a laboratory technician to study phages and how they can be developed into new antimicrobial therapeutics.

Community Board

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

Thank you to everyone who participated in our very first #WorldPhageWeek #scicomm challenge! Overall we had just over 70 individual phage researchers participate, and it was great seeing all the phage posts on Twitter! Thank you again to Dr. Ellie Jameson who kindly agreed to create a custom phage art piece for the winner! We spun a wheel to decide the winner, and the winner is… Karen Adler!!! Congratulations Karen!

For PHAVES #24 next week, veterinarian Dr. Whitney Greene & phage researcher Prof. Julianne Grose will give a talk entitled ‘Phage Researcher & Veterinarian Perspective: Phage therapy to combat a shell infection in a sea turtle’ on November 10 at 3 PM EST! Register here! (If you’re already signed up for the PHAVES series, no need to register again; we’ll send you the link closer to the date).

Phage Directory’s new structured peer feedback platform, Instill Science, is now live, and the first few requests have been posted and replied to!

Can you help your fellow phage researchers by providing a second set of eyes on their work? If so, check out the active requests. Currently, Bharat Jhunjhunwala, Steve Abedon, Stephen Amankwah, Noutin Fernand Michodigni and Jan Zheng are looking for feedback or collaborators, ranging from feedback on a study on phage therapy and a phage book chapter, to help with experiments and tools, to those willing to have a conversation about phage databases.

Become an Instill member!

What does feedback look like? Spend 30 mins reading through and giving your first impressions and overarching thoughts on any given piece of work. Your contributions will be tracked and recognized, and you’ll be helping fellow researchers by sharing your expertise.

Thanks so much to those who have already responded to these requests and are working to provide feedback already: Betty Kutter, Urmi Bajpai, Tobi Nagel, Daniel Schwartz, Katharine Muscat, and Atif Khan! You are all amazing and we are so grateful for your support!

Submit your own request for help!

Conventional homology-based comparative genomic analyses can only do so much in extracting information from databases. We used phages to test our comparative genomics tool (CALANGO) that considers annotation terms besides sequence data. By focusing on E. coli genomes and prophages, we found that pathogenic E. coli have more prophages than non-pathogenic ones, and genes of viral origin are associated to prophages. Genes annotated as virulence factors are also associated to prophage density, but several are not coded by the prophages themselves. We also found genes negatively associated to prophage presence.

Read our preprint here and try the CALANGO package on your organisms of choice. We are looking forward for your findings, feedback and criticism! I (@Gabriel_MFA) am only a non-coding contributor, so please look for the masterminds behind the project for more info: @_fcampelo and @chicao_lobo.

Check out the phage community question on Twitter by Dr. Sabrina Green (@MotherOfPhage). “This is a long shot maybe but does anyone have any Pseudomonas #phages that use the type IV pilus as a receptor? This is not for me but a collaborator. Thanks phage community!”. If you can help, reply to Sabrina’s Twitter thread.

Head to YouTube and check out Bacteriophage in Arabic, a channel with a series of seminars and explanation videos about phage!

C&T Round Up for October 2021

Postdoctoral Researcher

Iredell Lab, The Westmead Institute for Medical Research, Sydney, Australia, Phage Australia

Email [email protected]

Twitter @stephh_lynch

Stephanie is a postdoctoral researcher for the Iredell Group at Westmead Institute for Medical Research, NSW. Her project focuses on phage therapy for compassionate human cases (as part of Phage Australia), with a particular interest in Staphylococcal phages. In 2021, Stephanie completed her thesis titled ‘Exploring phage therapy for Staphylococcus pseudintermedius infections in canines’. Steph is always willing to chat about phage research and would like to connect with phage biotech companies.

In this month’s Capsid & Tail Monthly Round Up issue, we’re highlighting the four feature articles we published in October. Be sure to check them out if you missed them, and let us know if you have thoughts, comments or questions! Reach us anytime by email or Slack!

State of Phage #3: Exploring phage collections, an article by Jan Zheng and Jessica Sacher summarising the third part of the results from the State of Phage survey!
Phage therapy: a doctor-patient experience, a recap of Dr. Gina Suh’s PHAVES seminar with patient John Haverty by Rohit Kongari.
Phage therapy successfully treats bacterial prostatitis after multiple failed antibiotic treatments – Behind the case report, a ‘behind the paper’ article by Apurva Virmani Johri and Pranav Johri.
Overcoming barriers to phage commercialization: a conversation with leaders at Cytophage and BiomX, an interview article by Kyle Jackson with Cytophage and BiomX executives.

C&T Throwback!

There’s lots of great phage stuff in the C&T archive! Check out this article on the state of the regulatory affair: regulation of phage therapy in Australia by Ruby Lin, Aleksandra Petrovic Fabijan, Lani Attwood and Jon Iredell, phage researchers and clinicians from the Westmead Institute for Medical Research and Westmead Hospital.

Many thanks to Atif Khan and Stephanie Lynch for finding and summarizing this week’s phage news, jobs and community posts!

Postdoctoral Researcher

Iredell Lab, The Westmead Institute for Medical Research, Sydney, Australia, Phage Australia

Email [email protected]

Twitter @stephh_lynch

How to Cite

To cite this, please use:

Lynch, S. (2021). C&T Round Up for October 2021. Capsid & Tail, (151). Retrieved from https://phage.directory/capsid/round-up-oct-2021

BibTeX citation:

@article{round-up-oct-20212021,

journal = {Capsid & Tail},
number = {151},
publisher = {Phage Directory},
title = {C&T Round Up for October 2021},
url = {https://phage.directory/capsid/round-up-oct-2021},
author = {Lynch, Stephanie},
date = {2021-11-05},
year = {2021},
month = {11},
day = {5},

}

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