Kicking off PHAVES, our virtual event series!

Issue 80 | June 19, 2020
13 min read
Capsid and Tail

We launched PHAVES (Phage Directory Virtual Event Series) this week! If you missed it, here’s your recap! Poster created by Stephanie Lynch, La Trobe University.

We kicked off PHAVES this Tuesday! We discussed Phage Directory’s origin story and future directions, answered questions from the community, and hosted a series of small-group breakout sessions. Here’s how it all went!

Urgent June 19, 2020

Urgent need for Citrobacter freundii phages for a patient

Phage Therapy

We are urgently seeking Citrobacter freundii phages (and phage manufacturing capacity) for a patient in the USA.

Ways to help at this stage:

  • By preparing clinical-grade phage preparations for this patient (one phage already identified, need manufacturing partner)
  • By sending your phages for testing on the patient’s strain
  • By receiving the strain and testing your phages
  • 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

Urgent June 19, 2020

Urgent need for Burkholderia cepacia phages for a patient

Phage Therapy

We are urgently seeking Burkholderia cepacia phages for a patient in the USA.

Ways to help at this stage:

  • By sending your phages for testing on the patient’s strain
  • By receiving the strain and testing your phages
  • 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

Armata Pharmaceuticals just received a $15 million award from the US Department of Defense to take its Staphylococcus aureus phage cocktail to phase 1b/2 clinical trials.

Biotech newsClinical TrialGrant funding newsPhage Therapy

How should we optimally design phage cocktail timing and dosage to deal with evolutionary escape of pathogens? Guanlin Li and Chung Yin Leung (Georgia Institute of Technology) and colleagues published a new paper on using mathematical modeling to optimize phage cocktail design. They show that optimized single-strain phage therapy may cure infections in immunocompetent patients, but may fail in immunodeficient hosts, though including a counter-resistant phage could restore therapeutic efficacy. Paper | Earlier preprint.

Mathematical biologyPhage TherapyResearch paper

Thilini Jayasinghe (University of Auckland, New Zealand) and colleagues published a new paper in Frontiers in Cellular and Infection Microbiology showing differences in compositions of gut bacterial populations and phages in 5–11 year-olds born preterm compared to full term. Paper | Tweet thread.

Gut phageomeResearch paper

Katarzyna Leskinen (University of Helsinki) and colleagues published a new paper in Viruses on how they determined the genome of a non-sequenceable Yersinia phage YerA41 via RNA-sequencing.

Phage genomicsResearch paper

Gang Wang (Jiangnan University) and colleagues published a new paper in Frontiers in Microbiology showing the diversity of the CRISPR-Cas system and prophages present in the genome reveals co-evolution of Bifidobacterium pseudocatenulatum and phages.

Research paper

What’s new in the world of molecular mechanisms of lysogeny? Margit Pedersen and colleagues (University of Copenhagen and Technical University of Denmark) have published a new paper in Scientific Reports investigating repressor binding interactions with the lysogenic promoter in the lactococcal bacteriophage TP901-1.

Molecular BiologyResearch paper

Intralytix is a phage company in Maryland, USA that began in 1998 developing phage products for food; recently they’ve moved toward human therapy. Read about their recent progress here, including their new NIAID-funded Shigella phage clinical trial, and the fact that they’ve seen a 1600% increase over the last 5 years in their phage (for food) product sales (4 FDA-approved phage products on the market), signaling growing acceptance of phage use in industry.

Biotech newsClinical TrialPhages for food

Latest Jobs

The Bikard Lab (Institut Pasteur, Paris) is hiring a postdoc to study the properties of Cas proteins in bacteria, their interaction with DNA repair pathways, and the mechanism and evolution of CRISPR-Cas systems as phage defense systems

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!

June 19, 2020

Special Issue of Pharmaceuticals journal

Paul Hyman, Ashland University

Are you modifying phages, genetically or chemically, to improve their ability to act as therapeutics? Attaching toxins so the phage capsid provides specificity to target bacteria? Creating phage based vaccines? If you are making modified phages for treatments, please consider contributing to a special issue of Pharmaceuticals titled “Bacteriophages as Therapeutic Delivery Vehicles” edited by Paul Hyman ([email protected]), Tina Schneider ([email protected]), and Bryan Gibb ([email protected]). Contact us for more information.

Engineered phagesSpecial Issue
June 19, 2020

Seeking collaborator

Emmanuel Nnadi, Plateau State University

We have in our collection, E. coli, P. aeruginosa and S. aureus phages. We would wish to characterize them molecularly and under the microscope. We do not have any such capacity in our lab. We see for collaboration to enable us to characterize these phages. If you are interested in these phages. Please reach me via [email protected]

Phage characterizationSeeking collaborator
June 19, 2020

Seeking collaborator

I’m looking for a collaborator on #phage #phagetherapy #Acinetobacter & antimicrobial resistance. The call is specifically for a collaboration with Japan. Please let me know if you know anyone - Thank you! DM or email: Leptihn(at)intl.zju.edu.cn - @LeptihnLab on Twitter

Antibiotic resistanceSeeking collaborator
June 19, 2020

Seeking advice

Hello, #phage tweeps! I have a question. Suppose you have a bunch of phage MAGs, each composed of more than 1 contig: how do you calculate their completeness? I have a couple of ideas, but I still need to evaluate their feasibility. - @MichaelTangher1 on Twitter; check thread for responses!

BioinformaticsPhage methods
June 19, 2020

Excited about your new paper? Consider writing a Behind-the-Paper blog post!

Phage Directory

Do you have a new or upcoming paper that you’re excited about sharing with the phage community? We’d like to publish more Behind the Paper articles (like last week’s by Prof. Yves Briers) in future Capsid & Tail issues. To take part, email [email protected], and we’ll get you set up as a guest writer.

Capsid & TailGuest writingPhage Directory

Kicking off PHAVES, our virtual event series!

Profile Image
Phage microbiologist and co-founder of Phage Directory
Co-founder
Phage Directory, Atlanta, GA, United States

Jessica Sacher is a co-founder of Phage Directory and has a Ph.D in Microbiology and Biotechnology from the University of Alberta.

For Phage Directory, she takes care of the science, writing, communications, and business aspects.

Here’s the link to the recording

The first session of Phage Directory’s Virtual Event Series (PHAVES) took place this Tuesday, June 16, 2020. Thanks so much to everyone who joined us!!

At this first event, Jan and I discussed Phage Directory’s origin story and current and future directions, and answered questions from the phage community. Then, we did a series of breakout sessions, where the community had a chance to meet each other in small groups. Here’s how it all went.

Lots of engagement!

We were excited to have a lot more engagement than we expected. This came in the form of questions in the chat, and nearly all participants introduced their research and their backgrounds through small-group breakout rooms and through a larger-group meetup at the end.

What we discussed

Introductions: Jan, Jessica, Stephanie and the idea behind PHAVES

We started the session introducing ourselves (me, Jan, and Stephanie Lynch, our volunteer #PHAVES coordinator). Stephanie was up from 1:00 AM - 3:00 AM for this event, so if that doesn’t illustrate dedication, I don’t know what does! We also introduced PHAVES, including why we started the series (because the community kept asking, and we thought it would be a great chance to help people connect). We talked about what future sessions would look like, with the first session intended to be more of a casual meet-and-greet, but future sessions aiming to experiment with different structures, such as seminars, Ask-Me-Anythings, Interviews, Journal Clubs, Flash Talks.

Want to present? Signups are open and slots will fill on a rolling basis.

A Q&A on Phage Directory’s past, present and future

Jan and I talked about Phage Directory, starting with a brief origin story and moving into some of the work we’re excited about for 2020 and 2021.

Coordinating compassionate phage therapy

We started out introducing how we started Phage Directory in 2017, and talked about the initial response from researchers. We answered several questions about our phage therapy coordination work, including how it got started and how it works now. For instance, we talked about how we go about helping researchers from various countries ship phages and the general approach we take when we encounter new roadblocks (learn as we go, take great care in documenting what we do and what we learn).

Connecting phage characteristics with outcomes

We explained that something we’re working toward is helping researchers and clinicians track the phages that are used in patients according to key characteristics. So far that’s been a major hurdle, and most compassionate phage therapy cases happen so fast, and involve ad hoc collaboration among disparate groups, that this data isn’t always collected, nor is it aggregated. Ideally we’d like to compare how a phage behaves in patients across multiple cases where they’re used, and to associate phage characteristics with outcomes in these cases.

Creating a PhageDex (Gotta catch 'em all!)

Jan made the analogy that collecting and tracking phages is similar to collecting Pokemon, where you want to “catch them all”, and you need to understand each one and keep track of the strengths and weaknesses of each (a “PokeDex” is essential!). He talked about why we need a system of tracking this information for phages (a “PhageDex”), and what it could look like. (Read more about our plans, and how you can get involved, here).

Phages for more than therapy

We also had questions about whether the phages we help source and track are ever sourced for industrial applications beyond phage therapy. This was a great opportunity to emphasize that although we are often associated with phage therapy, we are building community tools to accelerate understanding and use of all phages, for all types of applications, not just phage therapy.

Sharing phage protocols and genome reports

We were also asked about opportunities for the community to share phage protocols, which is something we are working to incorporate into the Phage Directory platform. We talked about our soft launch of a phage genome announcement publication platform last year. Many in the audience expressed interest in this, especially given the high current cost of genome announcements and how much work goes into characterizing phages and annotating genomes (much of which is done by undergraduates and underfunded institutions who can’t justify spending hundreds per genome announcements). It was great for us to hear that there is interest here, and we’re excited to move this project along in conjunction with the phage catalogue/data collection platform we’re building.

Breakout sessions

After our Q&A, we began part two of the event: breakout sessions! The breakout sessions involved randomizing attendees into groups of 3-4 (we did through Zoom, which accommodates this well). Groups were given 5 minutes together, and were asked to simply give each member a chance to introduce themselves and their phage interests. We did two sessions, coming together to the “lobby” for a few minutes after each to regroup. Between sessions, we answered more questions that had come in during our main Q&A at the beginning.

Bonus hour!

Originally we planned only to run this event for an hour, so at the end of that hour, we formally closed the session. However, we decided to stick around longer if people were still keen on meeting more people, and a group of about 15 decided to stick around! We decided to keep it to one large group instead of breaking it down further. Each person explained a bit about their research and their background, with opportunities to ask questions after each. This was impromptu, and yet seemed to work out well, as this group ended up staying and talking for the whole second hour!

Summary

All in all, we came away with a great feeling about how the event went. We always want to maintain the spirit of inclusivity, hence why we’ve prioritized giving the floor to as many attendees as possible, and giving researchers chances to meet scientists from around the world, no matter the stage of their career, their research, or where they’re from. We also want to keep the spirit of experimentation, which was why we were happy to explore where the impromptu “bonus hour” would take us. Now that we’ve gotten the first event under our belts, we’re excited to experiment on a few other dimensions throughout the summer and likely beyond, starting with experimenting with different presentation formats.

Next steps

We’re planning the next few PHAVES events now, and they will be announced soon (they’ll end up on our main PHAVES site). Keep an eye on Capsid & Tail, or on our Twitter/LinkedIn, and you shouldn’t miss the announcements.

Suggestions?

Please feel free to send us your feedback, whether you attended PHAVES 1 or not; we’d love to hear what you think worked, did not work, or might work!

Also, feel free to send us suggestions for speakers, topics, and formats! Get in touch via email ([email protected]), Slack, or Twitter anytime.

Event recording

Video recording, 35 min (breakout rooms excluded).

Other resources


Rohit Kongari helped us produce this week’s article by helping us source and write the What’s New section. Thanks Rohit!!

Interested in becoming a Phage Directory volunteer?
Email [email protected].

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