We’re back! Hello 2024!

Issue 253 | February 24, 2024
19 min read
Capsid and Tail

ChatGPT depicting our new city, San Francisco!

We’re excited to embark on another new chapter this year, this time in the San Francisco Bay Area! Here’s some reflections on the transition now that we’re stateside, what we’re thinking about these days, and a sneak peek into what’s in store for this year.


Bacteriophage Summit banner

Returning to Boston next week (February 27-29), the Bacteriophage Therapy Summit is the only global platform for industry-dominated phage drug developers.

Check the agenda & get your ticket ASAP!

Join 18+ expert speakers from Merck, Pfizer, SNIPR Biome, Locus Biosciences, AMR Action Fund and more to evaluate the future of phage, navigate the challenges of clinical translatability and understand the application of bioinformatics to improve sequencing and data processing for phage therapy.

What’s New

Cytophage, a Canadian phage biotech, recently made its debut on the Toronto Stock Exchange (TSX), and just announced that they’ve completed R&D on their OvaPhage product, to be sprayed over chicken eggs to reduce Salmonella, Escherichia, and Shigella. They are preparing to conduct field trials in Canada as a final step before commercialization.

Biotech newsPublic listing

BiomX got orphan drug designation from the FDA for its BX004 phage cocktail for CF P. aeruginosa. This helps lower the cost and risk of drug development through extended exclusivity, lower filing fees and access to grants.

Orphan DrugFDABiotech news

Madison Stellfox and colleagues at the University of Pittsburgh published a new paper on phage-antibiotic combination therapy for recurrent E. faecium. Phages were administered to a patient with increasingly severe E. faecium bloodstream infections over 7 years. Her health initially improved after phage treatment, but after a relapse she unfortunately passed away.

STAT News also wrote a piece covering this patient’s story and phage therapy’s current challenges more broadly.

Phage TherapyCase report

Silvia Würstle and colleagues at the Center for Phage Biology & Therapy at Yale University published a paper on their optimized pipeline for emergency phage therapy against P. aeruginosa. Their pipeline includes evaluation of useful evolved trade-offs in phage-resistant bacteria and excludes ‘deleterious trade-ups’ caused by phage selection pressure.

Phage productionPhage therapyMethods

Julie Fletcher and colleagues at the University of Exeter published a paper showcasing their Citizen Phage Library’s end-to-end approach for rapidly isolating phages and purifying them for patient use. They’ve responded to four Phage Directory alerts, and detail their timelines and protocols here.

Phage TherapyCitizen ScienceMethod

Latest Jobs

PostdocProphage biology
The Chevallereau group at CNRS, Université de Lyon, France is hiring a postdoc to decipher whether and how prophages mediate resistance against, and coevolve with, virulent phages in P. aeruginosa. For further information: [email protected].
River EcosystemsStream Biofilms
Little is known about the interactions between phages and bacteria in densely packed and spatially structured biofilm communities. The River Ecosystems Laboratory at EPFL, Switzerland is hiring a postdoc to study interactions between phages and bacteria in alpine stream biofilms.
BioinformaticsPhD projectPhage defense
The Atkinson lab at Lund University, Sweden are seeking a bioinformatics PhD student to be involved in the Novo Nordisk funded project: ‘Development of phage biocontrol to overcome the antiphage defense system arsenal of phytopathogenic Ralstonia solanacearum bacterium’.
Phage biologyPhD project
The Anany lab at the University of Guelph, Ontario (@GuelPHage_lab on Twitter) has a couple of open positions (both PhD and postdoc) to study Salmonella and S. suis phage biology, host interaction, and applications.
Phage defenseMachine learningPostdoc
The Fossati lab at the Karolinska Institutet, Sweden is hiring a postdoc in the field of bacterial antiphage systems. The lab investigates bacterial immune system composition and mechanisms by employing bulk NGS and high-throughput proteomics, and develops computational solutions using machine learning and deep learning.
Phage BiocontrolPlant pathogensPhage defense
The Friman lab at the University of Helsinki, Finland is hiring a postdoc to develop phage biocontrol to overcome the antiphage defense system arsenal of phytopathogenic Ralstonia solanacearum bacterium.

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!

PhageCast recently interviewed Lorenzo Corsini about why Staph phages don’t work well in plasma or synovial fluid, and talked to Jean-Paul Pirnay (2-part series) about the Queen Astrid Military Hospital’s first 100 documented cases of phage therapy in Belgium. Tune in on Spotify to catch up!

Phage TherapySynovial FluidIn vivo studiesPodcast

In an article featured in BioSpectrum India, Atif Khan, a scientist at the Biofouling and Biofilm Processes Section of the Bhabha Atomic Research Centre, India discusses the likely establishment of phage infrastructure in India within the next five years. He describes how CIBA in Chennai has developed phages for controlling Vibrio in prawn farming, how the University of Madras is working on phages for agricultural applications, and how the polish biotech Proteon Pharmaceuticals is settling up its plant in India.

Phage industryIndiaInterview

Michael Shamash, a gut phageome PhD student at McGill University, explores the influence of gut phages on the human microbiome and their potential impact on health in a podcast interview with Justine Dees at the Joyful Microbe.

Gut viromeMicrobiomePodcast

Hugo Oliveira (University of Minho) will share insights from in vitro and in vivo studies on a phage-derived protein on February 29th at 11 AM GMT as part of the Africa Phage Forum series. Register here.

WebinarAfrica Phage Forum

Only 5 months remain until the Viruses of Microbes 2024 Meeting! Phage researchers are encouraged to confirm their participation early to plan for the trip down under.

ConferenceViruses of Microbes

From David Bikard via Twitter: A question to the phage aficionado. Do you have clear examples of anti-phage defense systems that block the production or assembly of phage particles without targeting the phage DNA and without resulting in cell death or dormancy?

Phage defenseQuestion

Dear phage researchers, for receptor-binding experiments, we are looking for phage T2. If anyone is still actively working with T2, we’d appreciate a small sample. With best wishes, Mark van Raaij, [email protected]

Seeking phage for research

Dear researchers and Professors: This is a small bio-technology company in China. We urgently need to buy or share some Streptococcus mutant phage M102, M102AD, e10, f1, SMHBZ8, APCM01, phiKSM96, to continue our research, If you got some or have some information, please email us,many thanks. David ([email protected])

Seeking phages

Hi, everyone in phage community, my name is Dr. Prince, I belong to India, and I completed my doctorate in phage characterization and its application. I am looking for a postdoc position in phage biology. Please help me for the postdoc position, my email is [email protected].

Seeking postdocPhage biology

Greg German (Unity Health Toronto) has been awarded a Professorship at the University of Toronto for Bacteriophage Research and Innovation with a five year term. Congrats Greg!

ProfessorshipPhage research

We’re back! Hello 2024!

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.

Hello phage friends, we’ve missed you. Thank you for the break; we needed it! We’ve spent it packing up our apartment in Sydney, visiting New Zealand, getting our cat ready to cross the ocean, visiting my grandma in Hawaii, and most recently, setting up camp in San Francisco!

Mivi the cat, hoping we take her with us (and ideally never get rid of our cardboard boxes).

Mivi the cat, hoping we take her with us (and ideally never get rid of our cardboard boxes).

We’ve been able to land on our feet here thanks to the hospitality of some amazing (phage) friends like Tobi Nagel of Phages for Global Health, Paul Bollyky, and Jan’s awesome cousin Tim. Soon we’ll find our own spot, but for now it’s been great exploring various areas of the city, from downtown SF to Oakland to Palo Alto.

That moment when I realized everything I own has something in common.

That moment when I realized everything I own has something in common.

It’s so cool to be here, and so surreal to see giant buildings with names we’ve only ever seen on the internet, like FitBit and SurveyMonkey and Away Bags… I also just learned that different neighborhoods in SF actually have very different weather, due to it being right between a bay and the ocean, and having lots of hills… so people aren’t joking when they list their houses as ‘in the sunny area’ or ‘in the foggy area’. So wild!

Leaving Sydney

We’re so sad to leave Sydney, but we’re simultaneously excited for the next chapter.

For those wondering why, it’s about 50% wanting to be on the same continent as our families at this stage of our lives, and about 50% wanting to be part of the AI(+bio) wave that’s happening in the San Francisco Bay Area right now.

While Jan’s been building clinical trial database infrastructure for the Phage Australia team, he’s also been spending his nights and weekends working to learn how to wield generative AI tools. All so he can ultimately integrate this new tech into our systems for collecting/learning from lab and clinical data. For this next phase, he wants to immerse himself in the epicenter of AI + bio knowhow, so he can keep building tools for (phage) scientists and physicians long-term.

Plus, our Australian adventure was always planned to be 2 years, so we’re ending right on the mark (though 2 years was definitely not enough!).

P.S. Sydney is a beautiful, special city and you should definitely go there — visit, do a postdoc, whatever it takes! It’s so relaxing, safe, clean, full of fantastic food and kind people who actually deeply believe in work-life balance — so liveable. (Plus we only saw about 4 spiders in our house in 2 years, and they were all very respectful).

Jan exemplifying Aussie work-life balance.

Jan exemplifying Aussie work-life balance.

Reflecting on Phage Australia

The Phage Australia project was so much fun and so rewarding! It was actually life-changing to get to be a part of it, and I’ll never forget the kindness of everyone we met and the open-mindedness of the researchers, physicians, patients and families, and even the government representatives we met. It felt like everyone was ready to move things forward, ready to take steps (and sometimes leaps) and move the red tape aside for the benefit of the patients.

I think the fact that the STAMP clinical trial is well on its way now, and the fact that Australia is actively and publicly doing phage therapy and working toward a regulatory framework, has really made other similar countries (like my home in Canada!) take notice and start making real moves too. We’ve seen initiatives pop up and even adopt the same naming structure, which is pretty cool and powerful, like Phage Canada, Phage UK, Phage Nepal, and Phage Singapore, and some are working to adopt a version of the STAMP trial (or at least use it as a model/precedent that they can point their governments toward).

For more thoughts on this, I recently wrote a larger reflection on the last few years from Phage Directory to Phage Australia for The Microbiologist magazine. It may be paywalled for you, so let me know if you encounter issues and want to read it. Or stay tuned as we’ll be re-publishing it here in C&T soon.

Phage Australia by the numbers

I’m super proud that we were able to help create a system for producing purified personalized phages for patients in under two years. We treated the first patient with in-house produced phages in October 2022, and in the year that followed we treated a dozen more.

Here are some stats to date (detailed in this tweet thread):

  • Fourteen patients’ phage preparations produced at Westmead Institute.
  • Clinical responses were cure (2/14), partial response (8/14), or no response (4/14).
  • Phage neutralization activity in serum was detected in 3/10 patients tested.
  • No related serious adverse events occurred.

And of course these stats are changing fast — last I heard the team was prepping 9 phage treatments at once this month!

For this next phase, the team will be scaling up thanks to funds from the New South Wales government and some kind philanthropists. As we were leaving, an array of new team members had just begun joining the team (hopefully you’ll meet them soon — perhaps at VoM Downunder 2024?!). They’ll be awesome, and will no doubt help take the Phage Australia system to the next level in 2024 and beyond.

Our documentary is out!

Some of you may have heard that a documentary crew (led by Emma Watts at Genepool Productions) followed us and Jeremy Barr’s team in Melbourne around for the last two years. Excitingly, it just came out (on Aussie TV) last week!

Tweet: https://twitter.com/WestmeadInst/status/1757947839374922231

Tweet: https://twitter.com/WestmeadInst/status/1757947839374922231

The director wanted to follow patients receiving phage therapy from end to end, highlighting the patient, the physicians, and also the scientists screening and preparing the phages. They followed two patients who received phage therapy, one we treated at Westmead, one that Jeremy Barr’s team treated in Melbourne, and a third who sadly couldn’t get treatment. It does a great job highlighting the complexity of phage therapy, the needs of patients, how it can work, and its limits. (And you can see my unfortunate short haircut that I had at the beginning of our Aussie adventure).

(The film is currently only available for streaming in Australia — maybe you can watch it while you’re there for VoM 2024 this July!).

Here’s the trailer, which anyone can watch!

Until we meet again, Australia

So goodbye Australia, but also, it’s not forever! We made some lifelong friends and we’re excited to keep the collaborations going from here on out. We’re still figuring out what that will look like, but we’re all keen to keep working together.

Jan will likely still be working on data systems for the Westmead team, and I will likely continue helping with the team’s communications/liaisons with international phage groups, and helping the team source and exchange phages internationally (like Ben Temperton’s Citizen Phage Library, who shipped our team hundreds of phages recently!).

We’re keen to help Phage Australia continue to expand and share its insights with the phage community, and explore new partnerships along the way.

The end of an unforgettable era… we will miss you Sydney, and most of all we’ll miss our legendary Aussie friends and colleagues. We’ll be back to visit for years to come!

The end of an unforgettable era… we will miss you Sydney, and most of all we’ll miss our legendary Aussie friends and colleagues. We’ll be back to visit for years to come!

Now for the next chapter

We still don’t have the details locked down, but stay tuned for more official announcements very soon! For now, we’re in a bit of an exploratory/transition phase, doing things like:

  • Organizing getting our cat, Mivi, sent over from Sydney (hopefully in a few weeks!)
  • Figuring out where we should live in this ginormous place (Sydney absolutely SPOILED us with its public transit, we’re realizing… last week we actually took 3 Ubers in one day 😱)
  • Jan is doing a bunch of projects with phage, AI, and data analysis! He’s currently helping Ramy Aziz, ICTV, BV-BRC to understand how protein language models (PLMs) could help annotate and characterize phage genomes.
  • Capsid & Tail will resume! (Starting today!). We may experiment with some tweaks, though… so if you have feedback on what aspects you love or don’t, we’d be super grateful. Things like:
    • What sections do you like best? (papers / jobs / community posts / events / feature blogs written by us / guest blogs)
    • What format/style do you find most helpful/interesting? (roundups / blogs about lab progress / blogs about wrangling phage data / conference recaps / behind-the-papers / interviews)
    • When/where/how often do you read C&T? Skim on the train or between incubation steps, or read with a coffee on the weekend?
    • What other newsletters/blogs do you love? Have you seen other formats/creative ideas that we should try?
  • One thing I want to explore more this year is going deeper into phage papers I read (almost like a journal club — let me know if you’d like to join me)
  • In the spirit of group accountability, I also think I may try… gasp… recording a few podcast episodes (Jan wants to call it Podovirus, which I love…). I’ve got some conversations with phage folks that I really want to have, and I want to force myself to go much deeper into papers and topics, so I would use this as my own personal tool (but then share it with all of you). I’d love to also write up reflections/summaries of these conversations as blog posts here in C&T. Stay tuned!

Want to get involved in the phage community?

  • If you want to volunteer with us at Phage Directory, we are always looking for writers, scouts (find us people who should write, find papers we should feature), social media assistants to attend conferences and help promote them, etc, let us know!
  • Please don’t hesitate to send us announcements or papers you’re proud of, or nominate a colleague’s work for us to feature! Bookmark https://phage.directory/msg and plunk links/suggestions in the box whenever you think of it. Rough notes/scraps/links with no context are totally fine; we’ll format it for you before posting.
  • If your company/org wants to sponsor phage directory or Capsid & Tail, we would love to help you highlight the work you’re doing to the phage research community, and we would thoroughly appreciate the support! It really helps to keep the engine turning on this phage machine. If you want to keep it extra simple, you can sponsor us via a banner on our website, or a brief blurb at the top of the newsletter, like Jafral, PHAGE Journal, Phage Futures, Bacteriophage Summit, and Cellexus have done over the years. Our sponsor page is here: https://phage.directory/sponsor

That’s it for now!

For now, we’ll keep this post light, just mainly as a way to say hello, we miss you, we’re excited to be back, and we’re sorry for all who we haven’t emailed back yet! Spending months living out of a suitcase is super fun, but I can’t wait to have a closet and consistent cell phone data again…

Here’s to an extra awesome 2024 full of new phagey surprises! Hope to see many of you much more from here on out, as we’re finally back within reasonable flying distance from so many of you!

Capsid & Tail

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