Issue 212
C&T Round Up for February 2023!
This month, we featured a new UK Phage Therapy initiative and wrote about lessons in scaling bio and how to think about data.
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The 6th World Congress on Targeting Phage Therapy 2023 will take place in Paris, France June 1-2, 2023.
The conference will highlight the recent innovations and clinical applications of phages, validation and limitations. Targeting Phage Therapy 2023 will also cover how phages will transform the medicine of tomorrow. A discussion will be held on how to overcome barriers between experts, academics, industrials, and regulators. Phages will be the hottest topic not only to combat infection and antibiotic resistance, but also to modulate microbiota.
Community digest5updates6jobs2posts
Updates
Erytech (a red blood cell-based therapeutics company) and Pherecydes (a phage therapy company) will merge to form a new company, whose name is yet to be disclosed, and redirect Erytech's financial resources, people and network toward Pherecydes' phage therapy programs.
The Japanese government is moving forward with a pull incentive for developing new antibiotics, called the Antimicrobial Securement Project. According to CARB-X's director, Kevin Outterson, this is a revenue guarantee pull incentive, akin to what Sweden is doing, but higher in funding amount, and is an exciting step in the right direction.
In a new Nature Microbiology paper, Jan Wohlfarth (ETH Zurich) and colleagues show that Listeria and Enterococcus can evade phage predation by transient conversion to a cell wall-deficient L-form state, which is triggered by endolysins disintegrating the cell wall 'from without'. Results suggest this represents a population-level persistence mechanism to evade eradication by phage. Read also this discussion of the paper by Thomas Denes (University of Tennessee, Knoxville).
A subset of jumbo phages have recently been shown to encode a 'phage nucleus' for sequestering the phage genome away from host nucleolytic attack. Eliza Nieweglowska (University of California, San Francisco) and colleagues published a new paper in Nature Communications on how the ϕPA3 phage nucleus is enclosed by a self-assembling 2D crystalline lattice.
In a new paper in Cell Reports, Beatriz Beamud (Universidad Complutense de Madrid) and colleagues report on their study of the genetic determinants of host tropism in Klebsiella phages. They isolated 46 phages to challenge 138 representative clinical Klebsiella pneumoniae isolates, and found that <2% of 6,319 phage-host combinations tested yielding detectable interactions. Capsule diversity was found to be the main factor restricting phage host range.
Jobs
Research Scientist at A&P Inphatec in Palo Alto, CA
A&P Inphatec, LLC has commercialized the first product to treat Pierce’s Disease in grapevines. Our unique solution utilizes bacteriophages to target and kill the bacteria at the source of the problem – giving wine growers an organic and sustainable solution to a rising threat in California. A&P Inphatec, LLC is seeking an experienced microbiologist applicant to join our research and development team as a full-time Research Scientist.
Fixed Phage is building platforms to enable phage immobilisation and stabilisation, to expedite commercialisation of phages to safeguard animal and human health. They are hiring a Laboratory Scientist (microbiologist) to join their team in Glasgow.
The NIH's National Library of Medicine is hiring a postdoctoral fellow in the area of bioinformatics and data science. Several projects are currently available including 1) identifying and characterizing microbial gene clusters of interest; 2) knowledge-based functional annotations of biosynthesis pathways; 3) building phage and bacterial interaction networks.
University of Exeter is recruiting a PhD student for a project that combines classical microbiology, microbial genetics and single cell microscopy to determine how bacterial defences evolve, and how they shape the spread of antimicrobial resistance (AMR).
The Centre for Integrative Biology of Toulouse (CBI) is seeking talented group leaders in microbiology, with a focus on projects involving integrative approaches, interactions between microbes and their hosts, mechanisms of resistance to antibiotics, or quantitative and computational biology of microbes.
The National Research Council of Canada is seeking a Postdoctoral Fellow to develop a cell-free expression system for rapid and cost-effective host-independent production of therapeutic and engineered phages for multidrug-resistant bacteria. The successful applicant will leverage NRC’s expertise in bacteriophage biology, genomics, proteomics, fermentation and downstream purification.
Community board
From the Phagebiotics Research Foundation:
Greetings Phage friends!
The 25th biennial International Evergreen Phage Meeting is set to kick off in person, in full Evergreen fashion, with Dr. Betty Kutter at the Evergreen State College. Mark your calendar for AUG 6-11th 2023! Phagebiotics Research Foundation is looking forward for you to participate and we are counting down these final few days until the launch of the 2023 website!
We ask you to hold tight, while we are hard at work finalizing the details and preparing for a great meeting. Stay tuned for further announcements and please follow us on social media to catch the latest announcements and updates.
P.S. We are going to Mt. Rainier on Betty's Birthday, Fri. AUG 11th 2023! Please plan on attending this special day to celebrate and hike with Betty.
Hosted by: Phagebiotics Research Foundation & Phage Directory Phage Meeting: Aug 6-11 2023 Multiple Workshops: Aug 6 and TBA Mt. Rainier: AUG 11 2023
In a talk entitled “Bacteriophage Therapy: From Soviet Clinical Experience to Current Activities at the Eliava Institute”, Dr. Mzia Kutateladze (Eliava Institute of Bacteriophage, Georgia) will present her latest research at the Targeting Phage Therapy Congress in Paris (June 1-2, 2023).
Another month is behind us! This time, we’re posting this Roundup in the mountains of New Zealand! We’re really proud of the pieces we’ve put out this month, as we’ve spent a long time thinking about these topics. We also think the UK Phage Therapy is a really cool effort.
Are you working on a phage project? Write about it on Capsid!
UK Establishing Phage Therapy Infrastructure
by Dr. Josh Jones
The UK is establishing a national clinical phage center, UK Phage Therapy, to provide sustainable phage therapy for NHS patients in collaboration with academic and commercial partners, including CPI, Fixed Phage, and the University of Leicester. The consortium aims to establish a sustainable source of phages for the UK, which will be critical to maintain and expand phage therapy provision for patients in need of an antimicrobial therapy that could save their lives.
Lessons in scaling bio, team science & priorities
by Jessica Sacher
In this post, Jessica describes lessons learned from setting up a phage therapy center to treat patients with antibiotic-resistant infections. Jessica highlights the importance of sample tracking and communication systems, designing protocols to keep in mind that lab members can get distracted, tired, or sick. She reminds us that scaling phage therapy is more about communication, documentation, and process design than the science itself.
How to think about data
by Jan Zheng
In this post, I write about different types of data (measurements, artifacts, presentational data, records and relational data, and metadata) and their uses. I also outline and share a few tips for data management, including using a single source of truth, providing easy access, building processes, using templates/forms, scheduling/reminders, assigning ownership, and balancing high expectations with burden.
C&T Throwback: OSU Viromics Workshop
Now that we’re exploring more data engineering, we’re crawling through our archives for past bioinformatics posts. This post on the OSU Viromics Workshop by Anushila Chatterjee is worth a read!
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.