Issue 195
C&T Round Up for September 2022!
This week, we highlight the feature articles we published in September! Learn about main themes from Phage Futures Europe 2022, MetaPhage: a new pipeline for turning raw reads into phage insights, and how to set up a basic phage QC system in the lab.
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PHAGE: Therapy, Applications, and Research has published a special issue on Phage/Host Combat: Phage Strategies for Taking Over the Host and Host Strategies for Defense.
Read and share the special issue with free access through October 18, 2022.
Community digest5updates3jobs2posts
Updates
In a new paper in Molecular Ecology, Tue Kjærgaard Nielsen (University of Copenhagen) and colleagues review current approaches to detect nucleotide modifications, including hardware and software, and look onward to future applications, especially for studying unusual, rare, or complex genome modifications in bacteriophages.
Paweł Działak (AGH University of Science and Technology) and colleagues published a new paper in the journal Biogeosciences entitled Do bacterial viruses affect framboid-like mineral formation?
Bennett J. Davenport et al. published a new paper in npj Vaccines entitled Phage-like particle vaccines are highly immunogenic and protect against pathogenic coronavirus infection and disease.
In a new paper in International Journal of Food Microbiology, Amel Chaïb (University of Bordeaux) and colleagues review the current knowledge about bacteriophages of Oenococcus oeni and their possible impacts on the trajectory of the microbiota during winemaking.
In this Nature Microbiology paper, Christopher N. Vassallo and colleagues used an experimental selection scheme agnostic to genomic context to identify phage defence systems in 71 diverse E. coli strains. They found 21 conserved defence systems, none of which were previously detected as enriched in defence islands.
Jobs
PhD candidate: Utrecht University (NL) and Friedrich Schiller University Jena (DE) are looking for a Joint PhD candidate to study the complex evolution of bacteriophage genomes in a unique joint PhD project.
Postdoc: The Laboratoire de Chimie Bactérienne (LCB) at Aix-Marseille University in Marseille, France is hiring a postdoc to adapt biosensor technologies to build bacteriophage-based biosensors to detect Streptococcus agalactiae.
Postdoc: The University of Copenhagen is looking for a postdoc to work on developing novel antibacterials based on phage enzymes and components as a part of the project INNOLYSIN funded by The Open Lab Foundation.
Community board
The 1st hybrid event co-organised by Phage-UK will be held in Oxford, UK on Friday 7th October 2022 from 17:30 to 20:00.
Very generously hosted by the #saidbusinessschool in Oxford, UK, co-organised with Will Battersby, film director, and Diane Shader Smith, mother of the late patient featured in the film. The in-person evening will start at 17:30 with the screening of Salt in My Soul, a powerful and touching film featuring Mallory, a patient with cystic fibrosis, who sadly could not be treated early enough with bacteriophages to survive an antibiotic-resistant super-bug.
The screening will be followed by a panel discussion on bacteriophage therapy in the UK, shared live, online, from 19:15.
If you would like to attend the event in person in Oxford at 17:30, kindly send an email to stephaniellesage@gmail.com directly.
For those who are further away and would like to attend the event remotely, please register for the online event.
Genome Startup Day Fall 2022: Bacteria Breakthroughs is a virtual event on October 5th, 2:00-3:00 pm PST that will feature a fireside chat with John Eisen, PhD, UC Davis professor and renowned genomics and microbiology researcher, and Ivan Liachko, PhD, Founder and CEO for Phase Genomics, as well as a panel discussion with startup founders Jessica Sacher, PhD, of Phage Directory, Nathan Brown, PhD, of Parallel Health and Minmin (Mimi) Yen, PhD, of PhagePro.
In this month's Capsid & Tail Monthly Round Up issue, we're highlighting the three feature articles we published in September. Be sure to check them out if you missed them, and let us know if you have thoughts, comments or questions! Reach us anytime by email!
Looking back on Phage Futures Europe 2022 — Part 2
by Jessica Neubauer and Madhav Madurantakam Royam
Phage Futures Europe 2022 was a three-day conference that brought together scientists, clinicians, and industry experts to discuss the latest advances in phage research and therapy. Highlights from the conference include the importance of communicating the benefits of phage therapy to the public, the use of phages in food production, and CRISPR-armed phages.
MetaPhage: Towards user-friendly phage bioinformatics
by Jan Zheng
MetaPhage is a new pipeline for turning raw reads into phage insights. The goal of MetaPhage is to make phage bioinformatics easy for anyone to run a "quick and dirty analysis" of any sequenced phage. MetaPhage uses MultiQC to create an HTML report of the findings, which makes it easy for bioinformaticians to upload the data to the web - and for others to get access to the information. MetaPhage is exciting because it takes all the grunt-work of setting up and connecting tools out of the picture. However, easy-to-use tools are not a replacement for understanding the underlying biology, statistics, and data analysis.
How do we prove our phages are safe?
by Jessica Sacher
In this article, Jessica Sacher shares her recent foray into learning about phage quality control and working toward setting up a basic phage QC system in the lab. She discusses the challenges of phage quality control in Australia, where there is no official guidance on what 'safe' means. She outlines the steps she is taking to ensure the safety of her phage product, including testing for sterility and endotoxin levels. She also reflects on the importance of quality control in the production of other kinds of new biological entities and the transferability of quality control skills.
C&T Throwback!
There's lots of great phage stuff in the C&T archive! Check out this article on Flipping the turtle back on its flippers: Phage therapy to combat a shell infection in a sea turtle by Stephanie Lynch.
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!