Issue 124
C&T Round Up for April 2021
This week, we're highlighting the four feature articles we published in April: virtual event recaps by volunteers Rohit Kongari and Stephanie Lynch, a guide on responding to phage therapy requests, and an opinion piece by Mert Selimoglu on phage cocktail-based COVID-19 vaccines.
Community digest5updates5jobs7posts
Updates
Courtney Davies (Massey University, New Zealand) and colleagues published a new paper in Frontiers in Microbiology showing that Mycobacteriophage endolysins can kill Mycobacteria when fused to 'PLAN-M' biodegradable nanobeads, which can be rapidly tested and deployed to mitigate cell growth in liquid and on surfaces. And check out Heather Hendrickson's tweet thread for more about how the paper came about.
Not one but THREE new papers published today in Science on phage DNA modications; they collectively describe a new pathway for purine biosynthesis and substitution of adenine by diaminopurine, found to be widespread in phages! Check out this news article in The Scientist tying the three papers together.
Most tests for Lyme Disease detect antibodies, which are often not present until weeks after infection by the causative pathogen, Borrelia burgdorferi. Jinyu Shan (University of Leicester) published a new paper in Frontiers in Microbiology on their development of a new method for Lyme Disease detection that detects a gene encoded by prophages only found in Lyme Disease-causing bacteria.
Jutta Kasurinen (University of Helsinki) and colleagues published a paper in Viruses on a new method for screening for phage-encoded toxic proteins using a Next Generation Sequencing-based assay.
Pappu Mandal (University of Technology Sydney) and colleagues published a new paper in Microbiology showing that phage infection of E. coli leads to the formation of membrane vesicles via both explosive cell lysis and membrane blebbing.
Jobs
Adaptive Phage Therapeutics (APT) is hiring a Curator/Bioinformatician! APT is a group of seasoned veterans coupled with crazy smart biologists and engineers working to solve the problem of antibiotic resistant infections. Each day is different and at the end of the day, you’ve made a difference in someone’s life. It’s incredibly powerful when you meet somebody whose life you impacted by going to work. The work will challenge you and reward you professionally and personally. Apply here!
Nathan Ahlgren (Clark University) is seeking a Postdoc: Marine microbiology & ecology, who will conduct research on host range, community dynamics, and comparative genomics of marine cyanobacteria (Synechococcus) and their phages (cyanophage) in Narragansett Bay, Rhode Island in collaboration with Dr. Marcie Marston (Roger Williams University). More info about the project here.
Alice Rothnie (Aston University) is hiring Ph.D. students to work on bacterial nano-syringes, which are evolutionarily related to bacteriophages, and function in a very similar way. The application deadline is May 6, 2021.
Malcolm White (University of St Andrews) has received an Advanced Grant from ERC Research to investigate the mechanisms of cyclic nucleotide signalling in bacteria/phage conflict. Postdoc positions will be available from 1st August - please do get in touch if you are interested.
PhagePro is looking for a Principal Scientist to lead their preclinical research on PVC as we prepare for clinical trials. The position is located at PhagePro’s lab space at the Tufts Launchpad in Boston, MA and will include domestic/international travel 5-10% of the time.
Community board
The World Microbe Forum 2021 (June 20-24, online; an ASM and FEMS collaboration) this year will include a session on viruses of microbes convened by Madalena Pimental and Rob Lavigne, on behalf of the Viruses of Microbes 2020 team and ISVM, the International Society for Viruses of Microorganisms (become a member for free here: http://isvm.org).
The session will be on June 23, and is entitled 'What’s New in the World of Viruses of Microbes?' This symposium focuses on recent advances in the fundamental biology and utility of the viruses of microorganisms, archaeal viruses, bacteriophages (or phages, the viruses of bacteria) and the viruses of microbial eukaryotes. This session provides the opportunity for young researchers to present their work.
Register/submit an abstract now—early registration ends May 11; abstracts due by May 7.
We cordially invite you to participate in the 2nd German Phage Symposium, which will take place Sept 13-14, 2021 at the University of Hohenheim, and will include keynote speakers Prof. Anat Herskovits, Prof. Ian J. Molineux and Prof. Dr. John Chen.
For early career scientists, a "Young Scientists Poster Prize" will be awarded, and the winners have the chance to present their research on September 14.
Register here by June 15. Please note, the number of participants is limited to 100, because the Symposium is planned as a face-to-face event. If this option will not be possible due to the pandemic, we will switch to an online format.
As promised, the 24th biennial Evergreen International Phage Meeting will take place the first week of August 2021!
Assuming it is safe to do so, the conference will be hosted in person on the Evergreen campus, in the dorms, as done in the past. In-person attendance will be limited (max 100). Registration fees will be kept low similar to past meetings, just enough to pay for room and board (around $450 for students and postdocs, $550 for senior people). Talks will be recorded and made available online, likely for a small fee. Depending on speaker preference and experience, talks will range from 10 min to 25 min long.
For those interested in presenting, either online or in person, please reach out to Betty Kutter at kutterb@evergreen.edu. More details on registration and themes will soon follow.
Next week on Clubhouse Phage Phridays (audio-only, casual drop-in discussions), our guest will be Dominic Sauvageau from the University of Alberta, who will chat with us about the 'phage virulence index' his lab has developed to quantify phage infectivity (check out their paper here). When: May 7 at 1PM Central time. Welcome one and all!
Follow Phage Club within the Clubhouse app to find the event!
PHAVES #16 will be May 12 at 2PM Mountain time. Dr. Greg Canfield and Dr. Laura Damioli from the University of Colorado will give a joint talk entitled: Freedom from antibiotic purgatory?: Salvage phage therapy for cure of spinal hardware infection.
Sign up for this event and future ones at https://seminars.phage.directory/!
PHAVES #17 will be May 18, 5pm CEST (Paris time). Quentin Lamy-Besnier, a PhD student in the Debarbieux lab at the Institut Pasteur in Paris will present their team's newly launched Viral Host Range Database, an online tool for recording, analyzing and disseminating virus-host interactions.
Come learn from Quentin how to use this much-needed new tool for the phage community! Small group networking to follow.
Register for this talk and others in the PHAVES series at https://seminars.phage.directory!
Update from the PhageAI crew:
We're proud to announce to you the release of PhageAI 0.8.0: extended repository and two new features: closest phages and Expert form!
What's new:
- uploading your sample and discovering top-10 closest phages in a global repository (alignment-free sequence comparison);
- possibility of use an Expert form to share details about in silico analysis of phage life cycle if you are Expert user;
- more than 22 000 publicly available bacteriophage genomes with their updated characteristics (lifecycle, taxonomy, hosts, similarities);
- bug fixes and performance improvements based on your feedback.
Check it out at https://phage.ai
In this month’s Capsid & Tail Monthly Round Up issue, we’re highlighting the feature articles we published in April. 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!
- PHANOTATE: Gene finding in phages, a recap by Rohit Kongari of Katelyn McNair's seminar on the phage genome annotation software she developed
- How to respond when someone asks you for phage therapy, a guide by Jessica Sacher based on a frequently-asked question Phage Directory receives
- Phage cocktail-based COVID-19 vaccine may have potential for much longer-term efficacy, an opinion piece by Mert Selimoglu
- Clinical phage therapy, phages for plant pathogens & phage bioinformatics: A triple webinar recap issue!, a recap written by Stephanie Lynch of some of the virtual events Phage Directory hosted/co-hosted in April.
C&T Throwback!
There’s lots of great phage stuff in the C&T archive! This week, take a look back on this guest post by Panos Kalatzis on the use of phage in aquaculture!
Thanks to Atif Khan for finding and summarizing this week's phage jobs!
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!