Issue 225
C&T Round Up for May 2023!
This month, we covered a new phage podcast, launched the Evergreen Phage Meeting sign up site, and talked about using databases for phage work!
Community digest5updates8jobs2posts
Updates
Phage utility against Burkholderia cepacia complex species has been restricted by the prevailing paradigm of only using rare, obligately lytic phages, due to the perception that lysogenic phages are therapeutically unsuitable. Philip Lauman and Jonathan Dennis here show that many lysogenization-capable phages exhibit powerful in vitro antibacterial activity both alone and through synergy with other phages.
Aleksandra Petrovic Fabijan and colleagues have written a perspective piece on translating phage therapy into the clinic. They delve into the history, turning points, recent studies and successes, and dig into the remaining biological, regulatory, and economic challenges to its implementation and acceptance.
Temperate phages drive bacterial genome evolution and impact human health. In a new paper, Justin Silpe and colleagues explore interprophage competition during polylysogeny, shedding light on induction mechanisms and strategies.
NL Haddock and colleagues published a preprint demonstrating that phage populations in infected bodily fluids mirror the abundance and diversity of bacterial pathogens, suggesting a close relationship between phages and bacteria at sites of infection.
Ana Georgina Cobián Güemes and colleagues published a preprint highlighting the potential of jumbo phages in combating Pseudomonas recently associated with the eyedrop outbreak that led to three deaths this year.
Jobs
If you are in Nigeria and looking for a lab to do your phage work, Nnadi Nnaemeka is offering their fully equipped lab for Phage research in Jos, Plateau State.
Li Deng's lab at Helmholtz Center Munich and the Technical University of Munich is looking for a Ph.D. candidate to develop targeted approaches for manipulating the human microbiome.
Professor Mathias Middelboe at University of Copenhagen is offering a postdoc position in phage-pathogen interactions and use of phages to control Flavobacterium pathogens in rainbow trout in aquaculture.
University of Gdańsk and the Medical University of Gdańsk is seeking a post-doc to study the role of prophages in environmental adaptation and virulence of pectinolytic bacteria.
Baylor College of Medicine is seeking a Research Technician II to join a group of Molecular Biologists and Microbiologists charged with understanding the molecular basis of mutation and cell evolution.
Colin Hill is recruiting a Research Assistant using job ID 067334) to join his Gut Phageomics Lab to investigate the role of phages in gut microbiome structure, function & assembly.
A Teaching Assistant position is available for SEA-PHAGES, instructed by Dr. Corinne Maurice, at McGill University. The TA will instruct and guide 26 undergrad students in lab-based phage research techniques.
Phage biologists, take note — join an incredible of community scientists who are turning transformative biomedical research into solutions for disease, including Phage Therapy. UCSF Dept of Microbiology and Immunology/Gladstone Institute of Virology is inviting applications for a faculty position (Assistant, Associate, or Senior Investigator).
Community board
Hi there, I am from a lab in National University of Singapore that is looking to see if anyone has any phage strains that are able to combat/infect MRSA? Thanks! Kind regards, Brian Chan (bielwbc@nus.edu.sg)
Sophie Elizabeth Smith via Twitter: Hey is there anyone else going solo to @vom2023 who might want to spend some time exploring Tbilisi with me the week before or after?
Time marches on, and another month has gone by! This month we launched the new Evergreen Phage Meeting site, and we’re currently planning the meeting’s events, talks and workshops. There’s a TON going on, and I can’t wait! There’s also a new hot phage podcast on the block I’ve been listening to on my runs. And we’ve been working a lot with data, and I’m excited to share a sliver of what I’ve been working on.
There’s so much excitement around handling phage, bacteria, and biobank data (both from collecting experiment data to clinical to workflow and process data), and we’ve been throwing the power and might of ChatGPT on it. This episode of the Data series is the last “fundamental” article I’ll be writing — this was a way for me to get my thoughts clear, but also a few articles I could point to in case I start throwing too much technical jargon around. The next Data episodes will go into some of the wilder experiments I’ve been working on for Phage Australia’s data management system, and both Jessica and I will share many tutorials on how to use ChatGPT programmatically to help you make sense of and sort your data. But for now, this is what we’ve published this month:
Launch of PhageCast: Bringing the Latest in Bacteriophage Research to Your Ears
by David Saéz, Maria Sequeira Lopes, and Alexandre Ferreira Lima
David Saéz, Maria Lopes, and Alexandre Lima from Dr. Azeredo's lab in Portugal introduced us to a new phage podcast: PhageCast. PhageCast offers interviews with phage researchers, unveils the latest discoveries, and shares valuable career advice. With this podcast, they aim to provide a combo of new phage papers and personal insights into the world of Academia.
Evergreen turns 50: celebrating Dr. Betty Kutter’s legacy
by Jan Zheng and Jessica Sacher
Evergreen Phage Meeting just turned 50! This (possibly last-ever) Evergreen celebrates the legacy of Dr. Betty Kutter, who has made significant contributions to the phage community. Jess and I share some memories of Evergreen, our favorite Phage conference (as it's more than just a "science conference" — it's Science Camp!). Some great memories include beach walks, dance nights, and salmon bakes. Since we wrote the post, we've had FOUR phage community members confirm workshops they'll be hosting at the conference this year. We've also secretly extended the Early Bird deadline with out telling Ria... so sign up before I'm forced to turn it off 😎
Working with Databases
by Jan Zheng
In this post, I discussed the benefits of working with databases compared to spreadsheets, emphasizing their ability to create relationships between data. I provided an example using Airtable to demonstrate the power of databases, and explained how tables of data can be connected through relationships. I also highlighted the advantages and limitations of databases, such as their ability to track and analyze data, but difficulty in handling certain types of information and tracking changes over time.
C&T Throwback!
I asked ChatGPT to give me a random number to use for C&T Throwback. Here it is… Episode 173. It’s a Roundup from last April… where we talked about How to organize your biobank data (how apt… I should probably re-read what I wrote from a year ago), and another article covering the state of phage therapy from Phage Futures 2021.
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.