Issue 134
Raise your impact with Instill Science
Are your manuscripts meeting their potential? We're launching a new community initiative called Instill Science to help you raise your impact (and get credit for helping your fellow phage community members do the same).
Community digest5updates5jobs2posts
Updates
Felix Biotechnology announced a new collaboration with high-tech skincare company Biocogent. The project is focused on developing novel, chemical-free and safe phage-based solutions to target problematic bacteria in the skin microbiome.
Whitney Greene (Mote Marine Laboratory and Aquarium, Florida) and colleagues published a paper in the Journal of Aquatic Animal Health describing the successful treatment of Shelley* the sea turtle with phages!
*Some of you may remember us asking the community for help sourcing phages for Shelley's infection back on New Year's Eve of 2018. We though no one would reply, because hey, it was NYE! But it ended up being one of our most popular tweets, and it led to finding multiple phage labs willing to help search their collections for Citrobacter freundii phages to help treat this turtle's years-long shell infection. Another amazing success for the phage community!
Nichith Ratheesh (Arizona State University) published a preprint on how a member of the oral microbiota can actively transport phages by swarming, leading to disruption of E. coli biofilms. They found that Capnocytophaga gingivalis forms tunnels within the 'prey' (E. coli) biofilm, and when phages are actively delivered, curli fiber-containing E. coli biofilms are no longer protected against phage infection. Their results suggest that active delivery of phages by a self-propelled swarm might improve phage therapy pharmacokinetics.
Ankita Kothari (Lawrence Berkeley National Laboratory, USA) and colleagues published a paper in mSystems on how ecogenomics of groundwater phages suggests niche differentiation is linked to specific environmental tolerance. They analyzed groundwater plasmidomes and identified viral sequences, identified potential hosts, and linked sequences to a range of bacterial phyla. They also identified putative auxiliary metabolite genes for metal and antibiotic resistance, providing selective advantage to infected hosts.
Nicholas Swanson (Thomas Jefferson University, USA) and colleagues published a paper in Molecular Cell on the cryo-EM structure of the periplasmic tunnel of the T7 DNA-ejectosome. They reconstituted the phage T7 DNA-ejectosome components and solved the periplasmic tunnel structure. They found that the complex lacks channel-forming activity, suggesting that the pore for DNA passage forms only transiently during genome ejection.
Jobs
Scientist: Phage Biologist
A&P Inphatec, LLC is seeking an experienced bacteriophage biologist applicant to join our research and development team as a full-time Scientist. This individual will be responsible for characterizing the bacteriophages in A&P’s library, as well as developing new bacteriophage discovery and characterization techniques.
The Marquis lab (UNSW, Australia) is looking for a part-time Research Officer for a key role in supporting research projects in the area of phage purification.
The Penadés lab (Imperial College London) is looking for a postdoc to study the impact of phages on the emergence of antibiotic-resistant bacteria.
Felix Biotechnology is looking for a Scientist to help develop phage therapies targeting multidrug resistant bacterial infections. Responsibilities include engineering phages, isolating and characterizing phage-host interactions and more.
Intralytix is currently seeking an experienced Senior Research Scientist to lead various research projects focused on the development of phage-based products, with a focus on human health applications.
Community board
Note: date/time change!
For PHAVES #20 next week, Dr. Gina Suh, MD (Mayo Clinic, Rochester, MN) and John Haverty will present a doctor-patient experience with phage therapy on July 22 at 2:30 PM Eastern! Gina treated John's leg with phages, which led him to avoid amputation. Hear about their experience and ask them all your questions!
Sabrina Green (Baylor College of Medicine, Australia) has created a Facebook group Phage Phridays at Clubhouse. Join the group to get updates on exciting phage-related talks from phage researchers every Friday, and to catch recordings of past Clubhouse chats! Start with last week's chat with Dr. Joe Bondy-Denomy about anti-CRISPRs!
Could I have published in a higher impact journal?
When I (Jessica) was a grad student, I was getting ready to submit my first first-author paper. I’d been part of papers before as a middle author, but this was the first I really felt ownership of. I was excited, hopeful, and overwhelmed. In the final stages of getting it ready for submission, we added a new collaborator to the author list, since we ended up using data they'd helped us analyze. When I sent the manuscript to that collaborator for feedback, and told him the name of the journal we were planning to submit to, I remember him saying ‘wow, this could go in a higher journal’.
Initially it felt great to hear that, and I beamed with pride when I saw that email. I'd never thought that about my paper, and had assumed I'd be lucky to get it into the journal we'd been planning to submit to. However, it felt too late at that point to rework it for a different journal, and I was tired and graduating soon and needed that paper out. There was no time to make that kind of change. We submitted, it was accepted, and I was happy it was out. But that experience planted a seed in my brain, and I’ve always wondered if that paper met its potential. How might things have changed if I’d gotten that feedback sooner, and had time to make changes and aim higher?
It's hard to get a second opinion
Unfortunately there’s no structured way to get recommendations and suggestions from our scientific peers before submission to journals. It’s all based on knowing the right people and asking friends for favours. Of course, with years or decades of a career in science, these friendships accumulate and grow. But for everyone else, whether it be those just starting out, or those unable to attend the conferences where these connections are made and cultivated, there’s not much chance to get this kind of feedback when you need it. And even for those who do have the good fortune of a wide and solid network, asking for favours never feels great. Our colleagues are just as overworked as we are, and asking them to spend their precious time on our work instead of theirs, for little in return, feels wrong. So we make our best guesses and submit our manuscripts to the journal that seems like the best fit, and we wait for peer review.
What if our help went noticed?
It’s not like we don’t want to help our peers. It feels great to make a difference, and if our advice helps someone improve the impact of their work, that’s a win for both of us. It’s why many of us are here in academia in the first place. But with so many aspects of our jobs pulling at us from all directions, we have to prioritize doing work we can get credit for. It’s hard enough mentoring one’s own students, and getting one’s own research done and published, let alone helping those in other labs do the same.
A focus on contributing ideas
During the last Evergreen Phage Meeting, we presented the idea of launching Instill as a more affordable publication. We later decided that the world didn't need yet another journal. So we stepped back to focus on a smaller part of the publishing experience. We looked into ways we could help the Phage Directory community, which spans over 80 countries. We looked at ways we could improve equity and access to scientific publishing. And it dawned on us that what researchers need is a way to get help before they even submit to a journal; ideas from their peers that help catapult them into a higher journal altogether.
So the idea of the Instill Community was born. In this community, members can invite and contribute ideas that help manuscripts get into the highest-impact journals possible. Members ask the community for ideas about a specific topic — e.g. phage TEM — and experts with phage and TEM experience can chime in and contribute ideas unique to their backgrounds and expertise. Maybe new collaborations could even spawn from this opportunity!
Many thanks to Atif Khan for finding and summarizing this week's phage news, jobs and community posts!
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!
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.