Year One of Capsid & Tail

Issue 49 | October 24, 2019
12 min read
Capsid and Tail

Happy birthday, Capsid & Tail! Image by Jessica Sacher / Jan Zheng

We’ve been publishing Capsid & Tail for a year now, and while some of you have been here since the early days, we know many of you have found us relatively recently. So this week, we’ve gone through our archive to dig up some of our favourite issues (and some of our audience’s!) from some key categories we’ve covered over the past year.

Also in this issue: hosts hiding from phages in vivo, applying phages in the “right” order, history of viral communication, vaginome editing, new rules for food phages in Europe, a bunch of exciting phage jobs, & more!

What’s New

We collectively don’t know much about how phages work in cocktails, or how best to optimize phage therapy when multiple phages are combined. Rosanna Wright (University of York) and colleagues have shown, using P. aeruginosa and pairs of phages targeting shared or distinct receptors, that timing and order of phage exposure determines strength, cost, and mutational basis of phage resistance.

ResearchPhage TherapyPhage resistance

Marta Lourenço (Institut Pasteur) and colleagues have published a preprint on how inaccessible sites in the mouse gut mucosa serve as a spatial refuge for bacteria, limiting phage predation, and leading to phage-bacterial coexistence that is not dependent on an arms race or on phage ability to extend their host range.

ResearchPhage-host interactionsAnimal ModelIn vivo studies

There’s been lots of talk recently about communication between virus-infected bacterial cells, but it’s actually an old phenomenon. Stephen Abedon (Ohio State University) has published a new review on the history of lysis inhibition, “the Granddaddy" of virus-virus communication, as well as other, more recent, examples of viral communication.

ReviewPhage ecologyViral Communication

PhagoMed has announced it will develop a phage lysin for bacterial vaginosis (targeting Gardnerella vaginalis). This means the company is extending its portfolio, as prior to this it was only working on complete phages. Press Release | News article

BiotechMicrobiome editingLysin

The European Court of Justice has issued a Court Order that enables food companies to continue the use of phages to prevent Listeria on all ready to eat foods in the EU in the absence of a legal EU framework. Using Listeria phages on food has been legal in the US for a while (Listex was approved by the FDA as “Generally Recognized as Safe” in 2006), but regulations in Europe have been ambiguous until now.

Press releaseEuropean RegulationPhages in food

Save the date for Phage Futures Congress 2020, coming up Feb 5-6, 2020 (note that the date has changed!) in Washington, DC, USA.

ConferencePhage Therapy

Latest Jobs

Industry Scientific Director Antimicrobial DevelopmentResearch and developmentPharma

Microbiology Leader, Scientific Director at Janssen R&D

Spring House, Pennsylvania

Janssen R&D LLC. is currently seeking to recruit a Microbiology Leader, Scientific Director, for a research and development team within the Infectious Diseases and Vaccines Therapeutic Area to be located in Spring House, PA.

The Microbiology Leader, Scientific Director, will be responsible for overseeing the day-to-day operations of a small a multi-disciplinary team focused on the discovery and development of novel antibacterial agents, such as bacteriophage, targeting key bacterial pathogens for infectious diseases associated with high unmet medical needs.

Industry Post Doc Phage EngineeringSynthetic Biology

Postdoctoral position: reverse genetic tools for viruses using synthetic genomics

J. Craig Venter Institute, Rockville, Maryland

This position will focus on developing improved reverse genetic tools for viruses using synthetic genomics and CRISPR-based tools to manipulate virus genomes and recover viable virus leading towards a more complete understanding of viruses that lack robust genetic tools, such as agricultural pathogens and bacteriophages, and to develop modified viruses for therapeutic applications. The position requires a candidate with proficiency in microbiology and molecular biology.
Academic Faculty Phage biotechnology

Tenure-track Assistant Professor: Biotechnological Utilization of Microbial Viruses

University of Copenhagen, Copenhagen, Denmark

The Department of Plant and Environmental Science invites applications for a tenure-track assistant professor position within the field of bacteriophage biology with start 1 May 2020, or as soon as possible thereafter.

The impact of microbes on the health of eukaryotes is increasingly recognized in both human-, animal- and plant-related research. Surrounding- and regulating the distribution of the microbes are the bacteriophages, often outnumbering the bacteria 10:1. The bacteriophages thereby act as modulators of bacterial communities and may have great future biotechnological potential as both biocontrol agents and as a source of new biotechnological enzymes.

The position is advertised in connection to a newly established Environmental Microbial Genomics (EMG) group headed by Professor Lars Hestbjerg Hansen to address this major knowledge gap within phage biology.

Industry Scientist PharmaResearch and development

Scientist II, Bayside Solutions

Pleasanton, California

Bayside Solutions is seeking a Scientist II to be part of our client’s team in the East Bay Area. This is an opportunity to work with the largest privately held pharmaceutical corporation in the world and ranks among the world’s 20 leading pharmaceutical corporations.

The individual will work in a small team of individuals in the design and early development. Experience working with bacteriophage, viruses, or Smarticles technology is preferred.

Academic Faculty Host-microbiome interactionsEvolution of microbiomes

Two tenure-track assistant professorships in microbiome research

University of California, Irvine

The Departments of Molecular Biology and Biochemistry (MBB) and of Ecology and Evolutionary Biology (EEB) at the University of California, Irvine, invite applications for two tenure-track assistant professorships in microbiome research.

1. Host-microbiome interactions. Our goal is to hire a researcher who is not focused on a particular disease, but rather investigates how to disentangle host-microbiome interactions broadly across diseases or animal hosts. Potential research areas for the position include (but are not limited to) investigating how the microbiome mediates host responses to pathogen infection, chemical challenge or injury, altering host metabolism or influencing host development or homeostasis.

2. Evolution of microbiomes. Microbial evolution within a community context is key to understanding how microbiomes respond to disturbance. Within humans or other hosts, a disturbance might be a change in diet, disease progression, or administration of a treatment or probiotic. Potential research areas for the position include (but are not limited to) the evolution of antibiotic resistance in a community context, the evolution of microbiomes in response to global change, the evolution of drug metabolism, host-microbiome coevolution, or the comparative evolution of microbiomes across hosts.

The researchers would join an actively growing and collaborative group of campus faculty studying the microbiomes of hosts and the environment, organized and facilitated by the UCI Microbiome Initiative.

Community Board

Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

Questions about E. coli and phages

Michelle Yang

How are strain B and UPEC strains of E. coli similar?
How do you select phages for a phage cocktail?
Please email me at [email protected].

Phage cocktail

Year One of Capsid & Tail

Profile Image
Phage microbiologist and co-founder of Phage Directory
Phage Directory, Atlanta, GA, United States

Jessica Sacher is a co-founder of Phage Directory and has a Ph.D in Microbiology and Biotechnology from the University of Alberta.

For Phage Directory, she takes care of the science, writing, communications, and business aspects.

We’ve been publishing Capsid & Tail for a year now, and while some of you have been here since the early days, we know many of you have found us relatively recently. So this week, we’ve gone through our archive to dig up some of our favourite issues (and some of our audience’s!) from some key categories we’ve covered over the past year.

When patients need phages

Phage Directory started as a way to help source phages for compassionate use cases. We’re proud of the work we’ve done to help physicians and researchers access phages for patients (our policy on this here). You can read about one of these cases in the two-part series we wrote here: part 1 and part 2. If you want to know what it’s like to help, we also interviewed some of the labs that offered phages in response to one of our alerts. Outside of what we do to source phages, we also covered phage access in India in an interview with Pranav Johri of Vitalis Phage Therapy, and how the Queen Astrid Military Hospital in Belgium processes requests for phages.

Phage therapy case reports

We’ve covered a few different phage therapy case studies, and plan to continue doing so. So far we’ve covered polymicrobial musculoskeletal infections (four patients in Belgium, a patient in Israel) and a patient with a disseminated Mycobacterium infection in the UK.

Phages and intellectual property

A popular topic we’ve covered several times has been intellectual property and phages. We did a four-part series on phage IP, including patents (part one, part two), trade secrets and government incentives.

Regulating phage therapy

We’ve published two guest articles so far on the regulatory landscape when it comes to phages (this one by Dan Evans, and this one by Ruby Lin and colleagues). We also gave a rundown of Belgium’s new way of regulating phage therapy (the magistral framework) and how the US regulates compassionate phage therapy. We broke down the Declaration of Helsinki as it applies to treating people with phages compassionately, and got into the rules governing who owns phages in an article on the Nagoya Protocol.

Commercializing phages

We’ve covered this topic through recaps of the Phage Futures US conference (here’s an overview and here’s an in-depth report). (Stay tuned for our Phage Futures Europe recap, coming soon!). In addition, guest author Cathy Nguyen covered phage diagnostics, we interviewed Assaf Oran of BiomX on their company’s progress toward making phage products to tweak the microbiome, guest author Panos Kalatzis covered phages in aquaculture and we covered a phage trial done in poultry.

Phage banks

A topic we’re really excited about is phage banks; how does phage sharing work, and who’s facilitating it? We published an overview of what the main phage banks around the world are doing, interviewed a group of NCTC scientists about their phage bank re-launch, and dove into how the DSMZ in Germany is navigating the Nagoya protocol, which governs how phages can be shared.

Phage research

We’ve enjoyed covering phage research papers, especially those that cover useful methods that might help other labs, like this one on using zebrafish as a phage therapy model and this one on evaluating phage-host coevolution. If you want a rundown on current avenues in phage research, our Evergreen phage conference recap is a good place to start.

Phage bioinformatics

Bioinformatics is something we’d like to get into more in the future (prospective guest authors, we’d love your help!). So far, we’ve covered a paper on standards for reporting uncultivated viral genomes and published recaps on two phage ‘omics-related workshops: the OSU Viromics workshop 2019 (by Anushila Chatterjee) and a phage annotation workshop with Galaxy.

Emerging areas for phages

We’ve had a couple of excellent intros to new fields where phages are becoming part of the conversation: phage therapy in the gut (by Sabrina Green) and phage therapy for pregnant and new mothers (by Lucy Furfaro). We hope to have more articles like these, both in the sense of looking at emerging areas of research and development for phages, and because we love when guest authors give a window into their fields/projects!

Conference and workshop recaps

We really like doing conference recaps, and especially love when others report back on the events we have to miss! This year, we published recaps of Phage Futures Congress 2019, the OSU Viromics workshop 2019 (by Anushila Chatterjee), ASM Microbe 2019 (by Sian Owen), PhageUGAL Summer School (by Colin Buttimer and colleagues), the Evergreen Phage Conference 2019, and a pre-Evergreen workshop on phage annotation with Galaxy.

Fan favourites

Some of our most-read articles (based on open rates of emails on that week) have been Issue 8: Belgium’s new brand of phage therapy, Issue 22: Collaboration leads to phage therapy success, Issue 35: Regulating phage therapy: Let’s build a foundation for our future, and Issue 41: Finding a phage community on Twitter. That said, we see the open rates of past articles gradually creeping up over time, so people do seem to be going back and reading past articles!

Can you teach the phage community something? Want to highlight an aspect of your research?

We love short, conversational articles that dive into a topic that’s relevant to the phage community. If you’d like to sign up for a slot, do so here! We’d love to have you as a guest writer.

Many thanks to our guest writers so far!

Picture of guest writers
Thanks to all our guest writers to date! To read their articles, visit our Capsid & Tail archive.

Capsid & Tail

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In collaboration with

Mary Ann Liebert PHAGE

Supported by

Leona M. and Harry B. Helmsley Charitable Trust

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