Reflecting back on 2021

Issue 157 | December 17, 2021
17 min read
Capsid and Tail

Peyto Lake, Banff, Canada | Image Credit: @jacdeng, Unsplash

It’s our last issue of the year! We reflect on what we’re especially proud of from this year, and highlight some stats on where we’re at as a community!
Also: a giant thanks to each of our amazing volunteers!

Urgent December 13, 2021

Urgent need for Mycobacterium kansasii phages for a patient in Germany

Phage Therapy

We are urgently seeking Mycobacterium kansasii phages for a patient in Germany (chronic but serious case).

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 receiving the strain and using it to search for new phages against the organism
  • 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

Paper: The genetic basis of phage susceptibility, cross-resistance and host-range in Salmonella.

Host rangePhage geneticsPhage resistanceResearch paper

Paper: Genomic analysis of prophages from Klebsiella pneumoniae clinical isolates.

ProphageResearch paper

Paper: Spontaneous phage resistance in avian pathogenic Escherichia coli.

Phage in agriculturePhage resistanceResearch paper

Review: Phages of phytopathogenic bacteria - high potential but challenging application

Phage in agricultureReview

Review: Phage therapy for antibiotic-resistant bacterial infections.

AMRPhage TherapyReview

Latest Jobs

Horizontal gene transferPhD project
PhD position to study horizontal gene transfer (HGT) and viral vectors at the University of York, England
Phage bioinformaticsPost Doc
Postdoctoral Fellowship to research phage therapy bioinformatics at CSIRO, Australia
Environmental microbiologyPost DocViromics
Postdoctoral position to develop and apply tools to study viruses and phage in the environment at the University of Wisconsin-Madison, Wisconsin
Food safetyPhage biologyProfessor
Professor to study phage biology and biocontrol for food safety at the University of Copenhagen, Denmark
Antibiotic resistancePhD project
PhD position to stuudy phage involvement in spread of resistance in Acinetobacter baumannii at Norwich Medical School, Norwich

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!

New Instill Request: Hi! I would like to get help on defining what is a phage-derived gene. I am often confused with defining the origin of a gene since it could be found in a phage genome but actually derived from a bacteria. If you want to help, we can set up a Zoom meeting to talk about it! Thank you very much, Carmen Gu Liu

Instill ScienceSeeking collaborator

Looking for a new phage podcast? Check out Phage Therapy Today, a podcast aimed to deliver insights into current advancements and challenges in phage therapy from academia, financial, regulatory, manufacturing and entrepreneurial perspectives!

Phage TherapyPodcast

Reflecting back on 2021

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.

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Product designer and co-founder of Phage Directory
Co-founder
Phage Directory, Atlanta, GA, United States
Skills

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

Jan Zheng is a co-founder of Phage Directory and has a Master of Human-Computer Interaction degree from Carnegie Mellon University, and a computer science and psychology background from UMBC.

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

Hi phage friends,

Another year under our belt! We hope everyone is safe and warm, getting ready to celebrate the holidays with friends and family, and taking some time to rest up before we all hit the ground running in 2022!

For our last issue of the year, to continue the tradition from last year, we’re reflecting back on the year’s progress, things we’re proud of, and of course highlighting some of the amazing collaborators and volunteers who have made it possible.

The phage community continues to rise to the challenge of providing phages for patients

This year we helped source phages for 7 more urgent patient cases (bringing our total to 33 since we started 4 years ago). Excitingly, three cases have led to successful treatment, and two of these were published in journals this year:

  1. Phages prevented amputation in a 7-year-old girl in Australia (treatment done by the Khatami and Iredell groups at the Children’s Hospital at Westmead and the Westmead Institute for Medical Research); read the paper here. (And watch Dr. Khatami’s and Dr. Iredell’s PHAVES webinars to hear more about this case)

  2. Phage saved a sea turtle from a years-long shell infection (treatment done by Dr. Whitney Greene, a veterinarian, and phages provided by researchers like Dr. Julianne Grose); read the paper here and hear Whitney and Julianne discuss this case in their PHAVES webinar here

Many thanks to all the labs who respond to our alerts — for most alerts we send, we get multiple replies within hours, and we are constantly amazed at the generous effort researchers put in for these cases.

Does your lab have phages you’d be interested in testing against a patient isolate in the future? Subscribe to get Phage Alerts.

The community is helping each other solve phage-related lab & writing issues

Our new peer feedback platform, Instill Science, is live!

We’re super excited about our new structured peer feedback and collaboration platform initiative, Instill Science, which we launched in the middle of this year! (Full update on Instill coming soon!)

For now, here’s some fast stats:

  • 5 collaborator requests
  • 2 ‘peer preview’ requests (advice on making manuscripts better)
  • 9 responses to requests
  • 4 advisors brought on board: Dr. Martha Clokie, Dr. Urmi Bajpai, Dr. Betty Kutter, Dr. Thomas Sicheritz-Pontén
  • 2 platform partners: Crowdfight, PHAGE Journal
  • 2 phage community volunteers working on bringing this project to life: Katharine Muscat and Atif Khan
  • Thanks so much to the following for funding Instill: Grant for the Web, Coil, Mozilla, Creative Commons

Read more about why and how we started Instill here!

Phage community Slack channel

We also almost doubled our Phage Directory Slack community members this year! We have 516 members now (up from 229 this time last year—wow!). (Join here!). Feel free to jump in and ask your questions or help your fellow phage community members, and browse through channels like #phage-protocols, #phage-ai-ml and #phage-manufacturing.

Capsid & Tail is going strong!

Capsid & Tail, our flagship community resource, has been going strong this year! We published 51 issues this year (getting us to 157 issues total!), and we passed 1200 subscribers! We’re proud of the rate that people open and read the newsletters; on average around 35-45% of our subscribers have a look at each new issue, and these numbers rise over time the longer an issue is out there.

Some of our favourites from this year:

We’re excited to report that our guest author program we started in 2019 has continued to be a success; this year we had 34/51 issues written by guest authors (Stephanie Lynch takes the cake this year for the most submissions this year — she wrote 12 of our feature articles this year!)

Each day new people list themselves on phage.directory

Not yet on the list? Create your profile here

Lots of engagement and great research shared this year at PHAVES: Phage Directory Virtual Event Series

We successfully hosted 15 PHAVES events this year (bringing our total to 25!). It was so much fun to hear about the research around the phage world and to chat with so many of you in breakout rooms after these events.

These are all on YouTube, and have been watched a collective 54,000 total minutes this year! (6,904 total views)

Most-viewed video

We also did a new experiment, Phage Phun, after the success of this ‘breakout room only’ format we piloted at Evergreen. We hosted four of these monthly events; it was a fun experiment!

The State of Phage Survey showed us a glimpse of how many phage collectors there are!

(And how many different ways there are of characterizing phage)

We’re proud of how the State of Phage survey came together, which started at the end of last year. We’ve been compiling results this year and releasing them in batches:

  1. State of Phage #1: A wide diversity of backgrounds & phage experience
  2. State of Phage #2: A wide diversity of strains
  3. State of Phage #3: Exploring phage collections
  4. Bringing it all together: inPhocus: “State of Phage” Survey Highlights Widespread Diverse Phage Isolation and Research in 40+ Countries (Published yesterday in PHAGE Journal!)

Overall it was amazing to see that 130+ labs report having collected a combined total of 3,500 to 10,000 phages against 126 species/genera. There are small, medium, large and extra large phage collections out there, across more than 40 countries (and this is of course a limited sample based on who filled out the survey and Phage Directory’s reach). It’s been so cool to see all this phage collecting! Even more interesting are the methods people use to characterize their phages and how frequently each is used. We’re collectively doing lots of different things to better understand our phages.

Hopefully in the coming year, in part through our Instill initiative, we’ll help foster sharing of complementary expertise to cross-pollinate and accelerate phage characterization across the board!

No shortage of new community-driven initiatives this year!

iVoM and Viruses of Microbes 2020 (now 2022)

iVoM Season 1 was a wildly popular series of virtual seminars by top microbiologists studying viruses of microbes from around the world. Season 2 started this month and will continue monthly for the next six months (sign up here)! This is all leading up to the in-person/hybrid VoM conference in Portugal, set to be held in July 2022. Registration opening soon!

Evergreen International Phage Meeting 2021

Evergreen was a huge success — we brought in over 500 participants from around the world for this hybrid conference, and created a platform for viewing all the recordings and posters online for registrants. Read about our take on Evergreen here and check out the favourite talks, as described by a group of student attendees, here!

Other community initiatives we’ve helped launch/run this year:

Tackling phage data collection to scale up phage therapy

A lot of the above focuses on our community initiatives, but much of our day-to-day effort at Phage Directory is devoted to working with organizations who are scaling up phage therapy. We help them build robust systems to collect and track their phages/phage data so they can streamline and optimize their compassionate use and clinical trial programs and tap into bigger pools of funding.

In 2020 we collaborated with two phage therapy consortia to submit national funding applications together, and we are thrilled that one was successful! This was in collaboration with the Iredell team at the Westmead Institute for Medical Research, which has led to the spearheading of Phage Australia, a new federally funded national initiative for phage therapy.

More to come on this initiative soon, but keep an eye on @PhageAustralia on Twitter to stay up to date!

If you want to learn more about the specifics of the vision, check out the perspective we co-wrote with this team, “Phage Biobank: Present Challenges and Future Perspectives” published this year in Current Opinion in Biotechnology.

If you’re building a phage library/biobank or seeking funding to scale up translational phage therapy work at your organization, don’t hesitate to get in touch about how we might work together!

More on where we’re going with Phage Directory

We had the opportunity to speak about some of our efforts and vision at Phage Directory at a few events and podcasts this year:

  • Jan: “Data and Collaboration to Defeat Antimicrobial Resistance” at CorrelAid Netherlands (watch here)
  • Jessica: “Science Communication to Defeat Antimicrobial Resistance” at World Phage Week (watch here)
  • Jessica: “Using viruses to battle superbugs (phage therapy)” for the Joyful Microbe podcast (listen here)
  • Jessica: “The enemy of my enemy: The return of phage therapy” for the EMBO Podcast (listen here)

A giant thank-you to our amazing volunteer squad!

(Phage community, if you’re hiring (now or in the future), you cannot go wrong with these stellar individuals! Email [email protected] anytime and I’ll gladly tell you why!)

  • Dr. Stephanie Lynch: a recent PhD grad from La Trobe University who studied phages to treat infections in dogs (watch her PHAVES talk here). Steph has been our PHAVES coordinator and this year moved into helping with Capsid & Tail blog, news, jobs, and community board. She helps coordinate the other volunteers and is key to our community operations.
  • Atif Khan, phage scientist at the Bhabha Atomic Research Centre who has been crucial to our C&T paper coverage, finding and summarizing new papers each week. Atif has recently joined our internal Instill team to help get that off the ground. He was also key in us getting funding for Instill, as he wrote a letter we included with our grant application!
  • Lizzie Richardson: Research scientist and phage enthusiast in Australia, and our amazing volunteer C&T editor — she makes sure our guest author submissions are in tip-top shape!
  • Dr. Rohit Kongari: Postdoc at FDA; Rohit helps us with C&T blogs and coverage of new research!
  • Sheetal Patpatia, PhD student at University of Helsinki; she helped us cover the Phage Futures conference twice this year!
  • Madhav Madurantakam Royam: PhD student at Warwick University. He’s compiled a giant list of phage protocol questions and answers we’ve seen come through on Slack and other places, so the rest of the community can benefit from them in the future! He also does interviews for C&T!
  • Curtis Hoffmann: BYU undergrad student, Curtis has been behind many of our tweets and LinkedIn posts, making sure we highlight phage researchers & industry milestones whenever possible!
  • Tolulope Oduselu, University of Ibadan undergrad student and Ibadan Bacteriophage Research Team leader, who helps us with C&T What’s New, Jobs and Community sections! He was also key in us getting funding for Instill, as he wrote a letter we included with our grant application!

Welcome, new volunteers!

  • Kyle Jackson, PhD student at McMaster University, he covers biotech for C&T!
  • Sayde Perry, undergrad student at Pomona College, currently working on writing C&T blog posts to cover PHAVES events!
  • Jessica Neubauer, MSc student at University of Vienna, currently working on amplifying phage research and news on the @PhageDirectory twitter account!
  • Katharine Muscat, PhD student at University of Sydney, currently working on helping us get our Instill platform off the ground!
  • Aël Hardy, MD-PhD student at the Forschungszentrum Jülich (Germany), he helped us cover the Phage Futures conference this year!

Thank you, sponsors!!

Last but not least, a giant thank you to our sponsors, JAFRALCellexusKisaco Research: Phage Futures, and PHAGE Journal. It’s been a pleasure to work with each of your teams, and we’re happy to help more of the phage community get to know what you’re doing. JAFRAL and Cellexus are addressing a major bottleneck for the phage field — phage manufacturing. Kisaco continues to organize valuable conferences for the phage biotech community (recap of their latest conference coming soon!). And PHAGE Journal is providing a much-needed place for phage research to be published. Looking forward to continuing to work together in the new year!

See you next year!

We’re so proud of the phage community and excited about what’s to come in 2022! Best wishes to all for a safe and restorative holiday season — see you in the new year!

— Jess and Jan <>{

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

Capsid & Tail

Follow Capsid & Tail, the periodical that reports the latest news from the phage therapy and research community.

We send Phage Alerts to the community when doctors require phages to treat their patient’s infections. If you need phages, please email us.

In collaboration with

Mary Ann Liebert PHAGE

Supported by

Leona M. and Harry B. Helmsley Charitable Trust

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