Creating a searchable directory of phages

Issue 74 | May 8, 2020
12 min read
Capsid and Tail

Imagining what searching for a phage on Phage Directory could look like.

We’re excited to share a sneak-peek into our progress toward creating a global phage catalogue and search tool!

Also in this issue: more new phage defense findings, prophages doing more strange and exciting things, more money for phage therapy clinical trials, and lots of upcoming virtual phage events!

What’s New

US biotech company Intralytix was just awarded a multimillion dollar grant from NIAID to perform a phase 1/2a clinicial trial to assess safety and efficacy of phage therapy against Shigella.

Clinical TrialGrant funding newsPhage Therapy

Artem Isaev (Skolkovo Institute of Science and Technology, Russia) and colleagues have published an article in Nucleic Acids Research on how the T7 phage DNA mimic protein Ocr inhibits the host BREX defense system. Ocr, which had been previously shown to protect against type I R-M systems, associates with methyltransferase BrxX and blocks methylation as well as exclusion of external phage DNA. Paper | Press release.

Research paperPhage defense

Katherine Wetzel (University of Pittsburgh) and colleagues recently published their work on protein-mediated and RNA-based origins of replication of extrachromosomal mycobacterial prophages in mBio. The study highlights the diversity of lysogeny maintenance systems and describes a set of phage-based plasmids with varying features, such as copy number and compatibility, that opens new avenues for actinobacterial genetics.

Research paperLysogeny

Flavia Squeglia (National Research Council of Italy) and colleagues published a paper in Structure that describes a new structural and functional study of a Klebsiella phage tailspike protein with capsular polysaccharide depolymerase activity. This study points to new mechanistic insights into capsular degradation by Klebsiella phages.

Research paperStructural Biology

Wenyuan Chen (Hunan Normal University, China) and colleagues published a letter in Protein & Cell describing a cryo-EM study into the structural changes the T7 phage capsid undergoes upon DNA packaging and maturation.

Research paperStructural Biology

The French Phage Network (Phages.fr) has published its annual conference report, which summarizes what was discussed at the 5th annual conference, which took place in Grenoble, France, in October 2019. This meeting attracted about 100 participants from academia, hospitals and industry from France and beyond.

Conference Report

Dr. Hany Anany of Agri-Food Canada was interviewed in this piece on phage use in agriculture. He gives an overview of how phages are currently used in the global food industry, how phages are seen by Health Canada, and how phages could be adopted throughout an integrated food production system.

InterviewPhage in agriculture

Congratulations to Cesar de la Fuente, one of our early Phage Directory community members (check out his impressive collection of phages!), who was just awarded the 2020 ACS Infectious Diseases Young Investigator Award.

Award

Latest Jobs

The David Braley Centre for Antibiotic Discovery at McMaster University has three faculty positions open in the areas of antimicrobial discovery and resistance.
Armata Pharmaceuticals, a Los Angeles-based phage therapy company, has several openings in R&D, process development, DNA sequencing, genetic engineering, project management, quality assurance and quality control.

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!

May 8, 2020

Seeking European collaborator

Emmanuel Nnadi, Plateau State University, Bokkos, Nigeria

Would you be interested in collaborating on a grant fellowship application? I plan to apply for the EDCTP-TMA2020CDF - Career Development Fellowships on poverty-related diseases particularly evaluating the role of phage therapy in diarrhoeal infections with particular emphasis on E. coli. This will require a European partner to collaborate on this project.

If you would be interested in collaborating on this project please freely reach me via email [email protected].

Seeking collaborator
May 8, 2020

Seeking Norwegian collaborator

Jesca Lukanga Nakavuma (BVM, PhD), Makerere University

We are applying for NORHED II grants and we wish to actualize the Eastern Africa phage research consortium aimed at establishing/upgrading a lab for in-depth characterization of phages, establishing a phage bank, and developing regional policies for phage applications. I am spearheading a proposal on phages against zoonotic pathogens from animal production systems.

We plan to have Makerere University as the lead applicant for the Southern partners with others including someone from Ethiopia, Tanzania and Institute of primate research in Kenya. We must have a Norwegian collaborator. Establishing linkages with biological product companies for production at commercial scale is also important.

Please contact [email protected] if you are interested.

Seeking collaborator
May 8, 2020

Let’s get some virtual phage events going!

Phage Directory

We’ve heard from many of you that you’re missing out on hearing about each other’s phage work! So we’re putting together a plan for a series of virtual phage events.

Let us know your topic suggestions, nominate a speaker (maybe yourself!), and share virtual event tips in our Slack group: https://phage.directory/slack.

Phage DirectoryVirtual Event
May 8, 2020

Upcoming Virtual Event: Phages for aquaculture

Aquatic Biologicals

We are excited to announce and share with you the forthcoming talk of the CEO and founder of Aquatic Biologicals, Dr. Pantelis Katharios, who is going to give a webinar through #EAStalk on “Phage therapy as an alternative treatment in aquaculture. Applications in fish hatcheries”. If you are interested in getting further insights about bacteriophages and the great potential of phage therapy, make sure you mark your calendars for 26th May at 14.00 CET/Brussels time.

AquacultureVirtual Event
May 8, 2020

Upcoming Virtual Series: All About Phage Therapy

Vitalis Phage Therapy

In these difficult times of pandemic lockdowns and quarantine, we bring you a series of discussions called “All About Phage Therapy”. For the first discussion, senior microbiologist Prof. Sanjay Chhibber from Panjab University will be joining us on Facebook Live on Sunday, 10th May at 11 am Indian Standard Time. Join at https://facebook.com/VitalisPhageTherapy.

Phage TherapyVirtual Event

Creating a searchable directory of phages

Profile Image
Product designer and co-founder of Phage Directory
Co-founder
Phage Directory, Atlanta, GA, United States
Twitter @yawnxyz
Skills

Bioinformatics, Data Science, UX Design, Full-stack Engineering

Jan Zheng is a co-founder of Phage Directory and has a Master of Human-Computer Interaction degree from Carnegie Mellon University, and a computer science and psychology background from UMBC.

For Phage Directory, he takes care of the product design, engineering, and business / operations aspects.

Profile Image
Phage microbiologist and co-founder of Phage Directory
Co-founder
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’re excited to share a sneak-peek into our progress toward creating a global phage catalogue and search tool! At the start of 2020, we laid out our goals for helping the phage community manage and mine its phage data. Since then, we’ve been working hard to build a comprehensive, searchable directory of phages that can streamline access to phages and phage data.

We’re building a system that can index the phages available at existing phage collections, like DSMZ and NCTC, as well as the phages available at research labs, and the phages published in the literature. Our goal is to make it easier for you, phage researchers and phage professionals, to find the information and the phages you need.

Collaborating with the phage community

Over the past few months, we’ve started to collaborate with labs and phage collections around the world to establish a schema, which helps us understand how each collection manages the data around their phages (shoutout to BCM Tailor Labs, NCTC, and the Felix d’Herelle Center for sending us your phage metadata so far—thank you!).

Today, we’d like to share an update on how things are going, and to gather feedback from the wider phage community! Since our tool is meant to help phage researchers and professionals quickly access phages and phage data from around the world, we’d like to know what phage attributes matter to you.

Why are we doing this?

We want to make it less cumbersome and time-consuming to work with phages. We want to make it easier to find the right phage for any application or research question, and we want anyone to eventually be able to mine the database to get new phage insights.

By streamlining access to phage data, we hope to take some of the burden off of you, so you don’t have to waste hours looking up phages through reading dozens of papers and writing dozens of emails that take weeks of back and forth. An up-to-date, searchable phage tool that lets you find and reference phages quickly, and lets you order the phage from a reputable phage collection to boot, should save many hours of drudgery.

Imagining what a universal phage search tool might look like

Here’s a mock-up of what we’re envisioning a phage search might look like on the next version of Phage Directory. Many details still need to be worked out, and a lot of that will depend on the feedback we get from community members. How can we make our database and interface maximally useful for the phage community?

Wireframe showing a future Phage Directory search result.
This wireframe shows an example of what we’re envisioning for the next version of Phage Directory, where we’ll be able to support searching for phages across labs and phage collections around the world using a single system. (High-resolution version.)

Building the back-end: a structured database that accepts data from any collection

To build a universal search system for phages, we need to establish a way to place each phage collection’s data side-by-side and match up one collection’s attributes to the equivalent collected by another. Because although many collections collect overlapping data, each collection/organization is driven by a different mission, and thus cares about slightly different aspects of a phage. And even when the same attribute is collected by two different collections, it’s almost certain that each will have its own name for that attribute.

For example, a piece of information like “Isolation Source” could go by many different names, like “Original source”, “Isolation”, “Source (type of sample)” or “Discovery notes”. These kinds of differences makes it really hard to make a universal phage search tool user-friendly.

Creating a master list of phage attributes

While we could build a rudimentary text-parsing system to try to tie data together, we decided to create a schema, or dictionary, that defines all the types of data that could be useful to phage research, phage therapy and other applications. Then, by mapping each collection’s list of attributes to this schema, we’ll essentially be able to translate the terms into one language. In the end, a single search term will “speak the language” of many different collections, and will bring back the relevant search results.

After combing through the metadata for several phage collections, we’ve created the beginning of our schema. We’ve divided the list into a few major categories, and given a bit of insight into what fits into each:

  • Phage Identification (this one’s “easy”: what’s the phage’s name?)
  • Phage Isolation (what were the circumstances of this phage’s initial isolation?)
  • Phage Propagation (how should you propagate this phage?)
  • Physical Characteristics (what does the phage look like? what about its plaques? how stable is it?)
  • Genomic Characteristics (is the genome sequenced? what does it show?)
  • Phylogenetic Characteristics (where does this phage fit taxonomically?)
  • Biological Characteristics (burst size, host range, etc.)
  • Reference Publications (original reference and others that build on it)

We’d love your input on what we’re collecting

We want to ensure that when we make our phage search tool publicly available, that it is actually useful for people. So we’d like to know:

  • When you buy a phage or request a phage from a lab, what do you wish to know about it?
  • Is there an attribute you wish labs or collections would track about a phage, but don’t?
  • What aspect of the process of requesting or buying phages could be improved?
  • What questions should we be asking you that we aren’t?

To share your answers, please join our Slack group, where we’ve set up a channel called #phage-metadata just for this discussion. Or, you can always email us at [email protected]

Ready to add your phage collection’s metadata?

For those of you in a position to share your lab or organization’s phage metadata with us, we really want to hear from you!

Send us an email at [email protected], and we’ll invite you to complete the phage attribute mapping exercise we’ve set up.


Rohit Kongari helped us produce this week’s article by helping us source and write the What’s New and Jobs sections. Thanks Rohit!!

Interested in becoming a Phage Directory volunteer?
Email [email protected].

Capsid & Tail

Follow Capsid & Tail, the periodical that reports the latest news in phage therapy and the phage community.

We send Phage Alerts to the community when doctors require phages to treat their patient’s infections. If you need phages, please email us.

Supported by

Leona M. and Harry B. Helmsley Charitable Trust

Crossref Member Badge