Year in Review 2023

Issue 252 | December 22, 2023
11 min read
Capsid and Tail

Celebrating our last New Years’ in Sydney, and our two years working on the STAMP trial at Phage Australia! Co-created with GPT-4.

This week we wrap up 2023 and reflect on our biggest surprises and proudest moments! Things are also changing in 2024…

Urgent December 21, 2023

Urgent need for Campylobacter phages for a patient in the USA

Phage Therapy

We are urgently seeking Campylobacter 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 the patient’s 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

Cristina Leal Rodríguez (Copenhagen University Hospital) and colleagues published a new paper on how the infant gut virome is associated with preschool asthma risk independently of bacteria.

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Infant gut phageomeAsthmaResearch paper

Yue Clare Lou and colleagues from the University of California, Berkeley, published a new study on the persistence of infant gut DNA phage strains during the first 3 years of life.

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Infant gut phageomePersistenceResearch paper

Alan Schmalstig (University of North Carolina at Chapel Hill) and colleagues published a new paper on phage infection and killing of intracellular Mycobacterium abscessus.

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IntracellularPhage-host interactionsResearch paper

Asher Leeks (Yale University) and colleagues explore open questions in the social lives of viruses in a recent invited review, including cooperation, conflict, and their impact on the population dynamics, evolutionary trajectory, and clinical progression of viral infections.

ReviewVirus-virus interactionsViral ecology

Kishen Patel and Kimberley Seed (University of California, Berkeley) published a new preprint on how a sporadic phage defense in epidemic Vibrio cholerae (mediated by the toxin-antitoxin system DarTG) is countered by a phage-encoded antitoxin mimic.

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Phage DefenseToxin-Antitoxin SystemPreprint

Latest Jobs

FacultyPhage biology
University of Tartu (Tartu, Estonia) is hiring a faculty member in phage biology & therapy to develop research and teaching activities in close collaboration with an antibiotic resistance containment program. Please contact [email protected].
ProphagesEnvironmental Adaptation
University of Gdansk and the Medical University of Gdansk, Poland is seeking a PhD student to study the role of prophages in the environmental adaptation and virulence of pectinolytic bacteria.
PhagesInfectionsClinical Therapy
Thilo Köhler and Christian van Delden at University of Geneva and Hôpitaux Universitaires de Genève offer a PhD position funded by NCCR AntiResist on clinical phage therapy of Pseudomonas aeruginosa and its microbiological basis.
Phage DefencePostdoc
Durham University, UK is hiring a postdoc to study the biochemistry of phage defence with a focus on Bacteriophage Exclusion (BREX) defence mechanisms.
BioprocessingManufacturing
Intralytix (a phage biotech company in Columbia, Maryland) is hiring a Bioprocess Engineer and a Manufacturing Technician.
Laboratory TechnicianPhage Researcher
California Institute of Technology is hiring a lab technician to assist with ongoing projects investigating mechanisms and functions of prokaryotic Argonaute proteins.
PostdocCryo-EMCryo-ET
Novo Nordisk Foundation Center for Protein Research, Copenhagen, Denmark is hiring 3 postdocs to unravel novel mechanisms in phage defense and biology using cryo-EM, cryo-ET, and protein bioinformatics/design.
Research AssociatePhage foundry
Lawrence Berkeley National Lab, Berkeley, USA is hiring a Biologist/Project Scientist and a Research Associate to work in the Phage Foundry, which aims to establish a high-throughput platform for rapid design and development of countermeasures to combat drug-resistant pathogens.
Educational ContentAMR
University of Salford, UK is hiring a Microbiology Educational Content Developer to develop educational materials about phage and bacteria for a knowledge exchange project on tackling antimicrobial resistance.
Antibiotic ResistancePhage Therapy
University of Pittsburgh, USA is hiring a Research Specialist to perform experiments aimed at understanding phages and their infection of Mycobacterium hosts.

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!

Phage Phriday on Clubhouse returns for a holiday special on Dec 22, featuring Amanda Burkardt, CEO of new therapeutic phage company Phiogen, and Iddo Weiner, VP of research at BiomX, who recently generated some exciting new phage clinical trial results. Register/check your time zone here!

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Phage PhridayClubhouseHoliday

The International Bacteriophage Research Consortium (IBRC) & Open Source Pharma Foundation (OSPF) in association with the Indian Society for Bacteriophage Research and Therapy (SBRT) have started a series of talks by clinicians with experience in delivering Phage Therapy.

Dr. Mzia Kutateladze from the G. Eliava Institute of Bacteriophages, Microbiology, and Virology will be giving the last talk of the series on December 22, 2023, at 7.00 PM IST. Join to learn about latest developments and successful case studies of phage therapy.

Register here.

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Phage therapyWebinar

Did you know that VoM is heading down under? The Viruses of Microbes (VoM) Conference will take place in Cairns, Queensland, Australia, July 15-19th, 2024.

Registration is open now!

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Viruses of MicrobesISVMConference

Year in Review 2023

Profile Image
Product designer and co-founder of Phage Directory
Co-founderProduct Designer
Iredell Lab, Phage Directory, The Westmead Institute for Medical Research, Sydney, Australia, Phage Australia
Twitter @yawnxyz
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 take care of the product design, full-stack engineering, and business / operations aspects.

As of Feb 2022, I’ve recently joined Jon Iredell’s group in Sydney, Australia to build informatics systems for Phage Australia. I’m helping get Phage Australia’s 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.

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
Skills

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.

Hey everyone,

Welcome to the last issue of 2023!

What a whirlwind of a year it’s been – I feel like it was only yesterday when we were all trapped on that mountain at Evergreen 😒. Compared to the Covid years, these couple of years in Australia completely flew by.

Proudest Moments

For us, 2023 has been filled with deep phage work and coding and AI deep dives.

Jessica’s spent much of her time working on phage production and purification — and learned to use the AKTA Flux and AKTA Pure to purify phages. She’s then developed dozens of SOPs and logs for data collection, and has written about her lab techniques and learnings throughout Capsid. Between her and Steph (who handles everything upstream of production) they’ve been able to identify, produce, and purify phages for one patient per month (and in one month, three patients!!). Oh, and she’s also found time to host many lab visits, present her work at 5 (or 6?) conferences, help co-organize Evergreen, and learn how to code on Replit’s 100 days of Code.

As for me, I’ve spent a lot of the year working in the background, cooking together data streams like our REDCap electronic data capture system for our clinical data, setting up tools like Cloudflare R2 for data backups and versioning, experimented with building data-crunching and UI-generating “agents” with GPT-4, and other prototypes like Instill.xyz, a simplified commenting / forum system) and blogalog.net, a system for hosting simple blog pages on top of Notion. I’m SUPER proud of how Evergreen turned out, from the signup, registration, and payment process itself to the actual event (massive shoutout to Ria!). I’m also proud of Capsid & Tail’s articles this year, as I took over much of the article writing, editorial, and begging for guest posts 😉 work. I’m also happy I was able to convince to turn Capsid’s tone to lean more conversational!

Biggest Surprises

The biggest surprise of the year is that phage work is getting more funding! And that phage therapy collectives like Phage-UK, UK Phage Therapy, Phage Canada are getting together to pave the regulatory pathway like at the UK Parliament. There’s also an uptick in new phage startups, and whispers of more funding for fundamental phage research towards better understanding the mechanisms of phage therapy.

On a personal note, Jess is surprised that people love to nerd out about her technical lab articles, and happily email her about her writing! (💡 tip: want others to nerd out YOUR lab work? Write for Capsid & Tail to find collaborators!)

For me, the (obvious) surprise of the year is the rise of AI and large language models (LLMs). They bring capabilities (like text extraction, recommendation, and ranking) that were previously only available to organizations with deep pockets and armies of ML researchers. For me, this meant having to rethink how to build a lab inventory and data processing system for an AI-centric future. I’ve been writing a lot about phage and lab data, and using AI to process it. The advent of LLMs means biology will get even more computational… for better or worse!

Favorite Capsid Articles

Here’s a selection of our favorite articles from this year. Every article is my favorite because I planned, scheduled them (and wrote many of them!) this year. But if we had to choose…

S. aureus phage therapy: we need further research

Jessica: I like the S. aureus article we published last week, by David Sáez and Lorenzo Corsini, because we need more articles digging into what doesn’t work with phages, and this one did a great job highlighting that.

Discovering coding (& building an AI tool) as a biologist, thanks to ChatGPT and Learning to Code as a Lab Rat

I’m cheating and picked two articles — one by Thomas Hunt on learning to code and building lab automations in the lab, and one by Jessica about using AI to discover coding. Learning to code used to be very hard, because sometimes you’d get stuck on a hard problem for days (or weeks!), and you had to pour through textbooks and manuals. Nowadays, it’s a couple queries away from GPT-4. (Heck, I used cursor.sh to write much of the code for me)

What we look forward to

We’re moving back to the US!

And we have our sights set on moving to the heart of AI and biotech (the Bay Area), and work with the amazing phage labs, biotechs, and AI startups there.

I’m keen to use all my experience I gained from working with Phage Directory and Phage Australia to work on AI-centric tools that make lab work and lab informatics easier — and this might mean joining a phage lab, a biotech or “tech-bio” startup, or even an AI company. I’ll still be working on the biobank lab inventory and data system (codenamed Atlas), which will continue as labspace.ai.

Jessica is excited about completing handover of phage work to the new, rapidly expanding team here, and being on call for support as they scale up — while being on the same continent as her family again, and reuniting with her horse!

We’re spending the next few weeks to think about where we can go next and be most of value. For me, that’s exploring more AI projects, and for Jessica, that could be to phage companies, phage research labs, phage therapy centers, or even beyond phage…

The next chapter of Phage Directory

Just because we’re moving back to the US doesn’t mean Phage Directory will go anywhere!

We’re planning to simplify it and take it back to its roots: Capsid & Tail, helping the community, improving the Directory, and Phage Alerts.

I have lots of plans to rebuild and redesign Phage Directory, integrate some of the new AI and data tools. We also have more plans to experiment with Capsid & Tail (we’d love if you wrote for us! 😉), and I really hope to expand the phage and phage host directories with expanded details like synergy/antagonism, citations, receptors, etc. — with the help of AI. I’m also excited to rebuild the Lab and Member directories with editable profiles, but also…

We will also launch Phage Directory Profiles, which gives everyone a CV site like janzheng.com, jess.bio, Atif Khan’s site, and for labs and organizations like ivom.phage.directory, Phages for Global Health: Online, PhageBiotics, womeninphage.phage.directory.
Because we’re moving, we’re taking a break with Capsid & Tail in January, and publishing fewer articles February.

In 2024, we’re looking forward to bring both Phage Directory (and ourselves) back to our roots!

Happy Holidays!
~ Jan & Jessica <>-{

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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