Issue 252
Year in Review 2023
This week we wrap up 2023 and reflect on our biggest surprises and proudest moments! Things are also changing in 2024...
Community digest1alert5updates10jobs3posts
Phage alert
Urgent need for Campylobacter phages for a patient in the USA
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 staff@phage.directory if you can help in any way, or if you would like further details/clarification.
Let’s make a difference, Phage Directory
Updates
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.
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.
Alan Schmalstig (University of North Carolina at Chapel Hill) and colleagues published a new paper on phage infection and killing of intracellular Mycobacterium abscessus.
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.
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.
Jobs
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 tanel.tenson@ut.ee.
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.
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.
Durham University, UK is hiring a postdoc to study the biochemistry of phage defence with a focus on Bacteriophage Exclusion (BREX) defence mechanisms.
Intralytix (a phage biotech company in Columbia, Maryland) is hiring a Bioprocess Engineer and a Manufacturing Technician.
California Institute of Technology is hiring a lab technician to assist with ongoing projects investigating mechanisms and functions of prokaryotic Argonaute proteins.
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.
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.
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.
University of Pittsburgh, USA is hiring a Research Specialist to perform experiments aimed at understanding phages and their infection of Mycobacterium hosts.
Community board
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!
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.
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!
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 <>-{
Jan Zheng, MHCI
I'm Jan, the other half of Phage Directory, and co-write Capsid & Tail.
Previously, I did data work at Phage Australia / Westmead Institute, where I built the biobank databases, data systems, and bioinformatics workflows for the clinical trial
I have a background in computer science and human-computer interaction, and I'm currently full-time at building the agentic layer for science at Nvidia.
Jessica Sacher, PhD
I'm a co-founder of Phage Directory and have a PhD in Microbiology from the University of Alberta (I studied Campylobacter phage biology). For Phage Directory, I help physicians find phages for their patients, and I'm always trying to find new ways to help the phage field grow (especially through connecting people and highlighting awesome stuff I see happening in the field).
I spent 2022-2024 as a postdoc in Jon Iredell's group at Westmead Institute for Medical Research in Sydney, Australia, helping get Phage Australia off the ground. I helped set up workflows for phage sourcing, biobanking, diagnostics, production, purification and QC of therapeutic phage batches, and helped build data collection systems to track everything we did. We treated more than a dozen patients in our first year, and I'm so proud of that!
As of 2024, I joined the Bollyky lab at Stanford University as a Staff Scientist, where I'm focused on phage engineering and delivery (to both microbial and human cells) and hydrogel-embedded phage cocktail development for wounds!