State of Phage #1: A wide diversity of backgrounds & phage experience

Issue 110 | January 22, 2021
18 min read
Capsid and Tail

State of Phage logo courtesy of Kema Malki (@kemamalki)

It’s been almost three months since we launched our State of Phage 2020 Survey! We’re excited to show you a snapshot of the data coming in. Today we’re focusing on who responded to the survey: where are they from, what’s their career stage, and how much phage experience do they have?

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Add your voice to the State of Phage 2020 Survey!

State of Phage 2020 logo

In celebration of our 100th issue of Capsid & Tail, we launched a survey called State of Phage 2020! We created this survey to help us all better understand the phage research community globally, including what kind of phages people are collecting, what methods they’re using, and more. If you work with phages, please fill it out! We’ll compile and share the results in Capsid & Tail in 2021, and repeat the survey annually so we can all follow and share our community’s exciting growth over time.

Thanks so much to the 120 labs who’ve completed the survey, and to those who have shared it!! We’ll be shutting down the survey in 2 weeks, so if you’ve started but haven’t finished the survey (52 of you — your browser should have saved your progress if you want to finish where you left off!) or you want to take it from the beginning, please fill it out by Feb 5!

We’d love if you continued sharing it with friends! https://survey.phage.directory/

Take the State of Phage 2020 Survey

What’s New

BBC Future has published a great in-depth feature called ‘The viruses that prey on human diseases’, featuring interviews with directors of the Eliava Institute (Mzia Kutateladze) and Queen Astrid Military Hospital phage therapy unit (Jean-Paul Pirnay), and more!

NewsPhage Therapy

Yuping Li and Joseph Bondy-Denomy (University of California San Francisco) published a new review in Cell Host & Microbe discussing how anti-CRISPRs affect the ecology and evolution of bacteria and phage.

Anti-CRISPRCRISPRReview

Carly Davis (University of Alberta, Canada) and colleagues published a new paper in Microorganisms showing that aztreonam lysine (an antibiotic) increases the activity of phages E79 and phiKZ against Pseudomonas aeruginosa PA01.

Phage-antibiotic synergyResearch paper

Amjad Khan (Western University, Canada) and colleagues published a paper in PLOS Computational Biology showing that evolution along the parasitism-mutualism continuum determines the genetic repertoire of prophages.

Computational biologyProphageResearch paper

In light of the COVID crisis, there seems to be renewed interest in using phages to deliver genetic material in the body. Matthew Tridgett (University of Warwick) and colleagues published a new paper detailing their method for engineering bacteria to produce pure phage-like particles for gene delivery.

Phage delivery systemsResearch paper

Latest Jobs

PhD projectPost Doc
Rafal Mostowy (Jagiellonian University, Krakow, Poland) will soon be looking for a postdoc and a PhD student to work on microbial genomics and structural bioinformatics to study the role of HGT in phage evolution.
Lecturer
Nottingham Trent University (Clifton Campus, UK) is hiring a Lecturer or Senior Lecturer in Microbiology. Seeking expertise in expertise in clinical microbiology, medical microbiology, molecular microbiology, virology, and/or public health microbiology.

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!

BCM Tailor labs has posted a video tutorial on how to do a quick phage precipitation. In this video you will learn how to precipitate your phage in 10 to 15 minutes. This is in order to concentrate your phage from a solution. This can be modified for other viruses too.

Phage methodsVideo

Dr. Pilar García Suárez is editing a Special Issue of the journal Antibiotics called “Benefits of Bacteriophages to Combat Antibiotic-Resistant Bacteria”.

AMRSpecial Issue

RATIO PRESENTS: BACTERIOPHAGES: Join us on 2nd Feb when we will talk about merciless killers – the bacteriophages, small biological machines designed to kill bacteria.

This event will give an overview of the main principles of the bacteriophage ecology and discuss the implications in the phage therapy.

About the speaker: Andrey Letarov is the head of the laboratory of Microbial viruses at Winogradsky Institute of Microbiology RC Biotechnology RAS, Moscow, Russia. He is also a professor at Virology department of the faculty of biology of Lomonosov Moscow State University. During his whole scientific career he was studying various aspect of bacteriophage biology, including organization and folding of phage proteins, bacteriophage evolution, bacteriophage diversity and ecology.

Virtual Event

The Africa Phage Forum is hosting its next phage webinar in its series, Feb 15 at 4pm GMT / 11am Eastern with special guest Dr. Evelien Adriaenssens, who will give a talk entitled Basics of phage genome annotation and classification - how to get started. Register now for this event and/or the whole series at https://apf.phage.directory.

Virtual Event

State of Phage #1: A wide diversity of backgrounds & phage experience

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.

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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.

It’s been almost three months since we launched our State of Phage 2020 Survey! We’re excited to show you a snapshot of the data coming in. For this snapshot, we’re focusing on the ‘who’, ie. who responded to the survey? What stage of career are they at, where are they located, and what level of phage experience do they have? In future issues, we’ll release more data, digging into the specific phage work being done, the methods being used, the phages and host strains people are collecting, where they get their strains and phages, where they like to publish, their thoughts on sharing and commercializing phages, and more!

A refresher: why we did this survey

The phage field is clearly growing around the world, but we realized that no one has collected a bird’s eye view of what everyone is working on. From our conversations with researchers, we believe that phage research activity and diversity of approaches is greater than the published literature would suggest. We created the State of Phage 2020 survey to fill this gap.

We hope it will help researchers learn more about how their phage research approaches compare with others around the world, and that it will help establish a baseline for the current state of phage research so we can collectively track how it grows and evolves over time. Check out https://survey.phage.directory for more info on the ‘why’ behind State of Phage 2020!

Our plans & hopes

This issue marks the beginning of a series that will wade through the data, looking at a different theme or two each time, but we’ll also publish a full report at the end of it all. We hope researchers will read it, learn lots about the field, and share it with others to inspire them to join the community and pursue their own phage research (or maybe fund it!).

Now, let’s dive in!

Who’s responded to the survey to date?

We’re thrilled to have received 120 full responses to our survey. Filling this thing out was no small feat, so thank you all so much for taking the time to let us know about the kind of phage work you’re doing!

Also, 52 people filled out part of the survey, but not the whole thing (yet) — a reminder; if this is you, you should still be able to head to https://survey.phage.directory and complete your responses! (Your browser should have saved your progress). There’s still time for you to be included in the final counts.

Phage labs are highly spread out, and phage ‘hotspots’ are emerging in at least a dozen countries

Of the 120 responses, we rarely had the same lab or organization respond twice! A whopping 117 came from unique labs, and 102 came from unique organizations (university, institute or company). This really gives a picture of how spread out phages labs are around the world, and it also points to phage being a priority at a huge number of separate organizations. 18 organizations did have two or more labs represented in our results, suggesting possible phage research “hotspots” beginning to form (or at least pockets of extra enthusiasm!). Our data points to these kinds of phage hotspots in the UK, France, Denmark, Belgium, India, Australia, Singapore, USA, Canada, Pakistan, Uganda, and Nigeria. Amazing!

Responses came in across all career stages

We asked about career stage, and found that about 1/3 are students (across undergrad, masters and PhD programs), with PhD students representing the majority (77% of all students). We had 17 postdocs respond to the survey, and 47 professors. Among professors, about half were early career professors, while the other half were senior professors. We also had 5 responses from government, and 7 responses from industry.

Career Stage #
Undergraduate 4
Masters 6
PhD 34
Post-doctorate 17
Early-career Professors 27
Senior Professors 20
Government 5
Industry 7

88% of respondents do academic research

We asked respondents about their job responsibilities. Most are performing academic research (105/120), while half report teaching (60/120). About 10% report industry research (13/120), and about a quarter reported that their responsibility was to be a student (29/120).

Phage research is being done on six continents

We asked where respondents’ phage research was predominantly being conducted (so this is not a nationality question; rather, it’s to show where phage labs are physically located).

Our 120 respondents are doing their phage research in 44 countries, shown here as a heat map showing relative number from each: a darker colour indicates more respondents from that country. We can see that the USA had the most respondents, followed by India, but that the rest of the respondents were spread out across the globe, covering all continents (except Antarctica — anyone want to head over there and start a phage lab?).

Map of responses

60% have 1-6 years experience, and 10% have been working on phage for 20-46 years!

We asked how many years people have been working with phages, and got quite a spread of answers! Here’s a graph showing number of responses for each number of years. We found that the bulk of respondents were relatively new to phage work, with 60% of respondents (73/120) having between 1-6 years phage experience. About 30% of respondents (35/120) had between 7 and 18 years phage experience, while around 10% (11/120) had worked with phage for 20-46 years! Incredible!

Years of experience

Isolating, characterizing, publishing on, and sharing phages

We wanted to get a sense of how many labs had taken part in isolating, characterizing, publishing on, and sharing phages (for research, for therapy, and commercially).

90% have isolated a phage, labs do a healthy mix of wet lab and bioinformatics, 70% have published

We found that isolating phages was the most commonly reported activity, with 88% reporting they’d isolated phages in their lab. Characterizing phages in the wet lab was also a popular activity (84%), with almost as many reporting genetically characterizing phages with bioinformatics (76%). 70% of respondents reported having published at least one phage paper or preprint.

Experience %
Isolated phages 88%
Characterized phages in a wet lab 84%
Characterized or analyzed phages genetically with bioinformatics 76%
Published a phage paper in a peer-reviewed journal or on a preprint server 70%
Sent phages to other researchers 52%
Prepared and purified phages for clinical / therapeutic use 23%
Tested or shared your phages on behalf of a prospective phage therapy patient 22%
Taught an undergraduate phage course that isn’t SEA-PHAGES 18%
Deposited phages into a phage repository like ATCC or NCTC 15%
Sold or licensed phages 8%
Participated in SEA-PHAGES as a student 6%
Taught SEA-PHAGES 5%

Half have shared phages with other researchers, nearly a quarter for phage therapy cases, and only 15% with repositories

As for sharing phages, the most popular type of sharing was sending phages to other researchers; half of respondents had done so. As for sharing phages for therapeutic use in a patient, we were very surprised to see that more than two dozen labs had tested, shared, and prepared their phages for clinical use. Contrary to our expectations, about the same number of labs that reported having tested their phages and shared them on behalf of a patient had actually also done the work of purifying their phages for clinical use. (Normally when we send phage alerts, far more labs volunteer to help in the initial phage host range testing phase than in the clinical purification phase, whereas this data suggests many more labs than we thought may be preparing purified clinical preps of their phages). Interesting!

Lastly, when it comes to depositing phages into repositories, like ATCC or NCTC, only 15% reporting having done so. This reflects what we’ve heard from those who manage these types of repositories; getting researchers to deposit their phages is a constant battle for them. (We’re working on ways to incentivize this in collaboration with repositories around the world, so stay tuned for that!)

Phage hunting courses: beyond SEA-PHAGES

We asked about the undergrad phage hunting courses respondents had taught. Surprisingly, far more labs report having taught a non-SEA-PHAGES undergraduate phage hunting course (22 respondents) than a SEA-PHAGES course (6 respondents). We didn’t realize there was so much phage hunting being taught outside of SEA-PHAGES — this is really exciting! (If anyone wants to email us and share more about the way they’re teaching their course, and which phage hosts they’re using in the classroom, we’d love to hear about the undergrad phage hunting operations you’re running! We’d love to better understand this area, and do what we can to support what you’re doing!)

Stay tuned for more!

That’s it for now! Stay tuned for future Capsid & Tail issues, where we’ll continue delving into the data that’s come in. We’re learning a lot about the phage field, confirming some suspicions of ours, and very much enjoying the surprises!

Your thoughts are always welcome

Anything you found surprising about this data? Do you have questions about how we’ve done our analysis? Do you think we’ve missed any interesting interpretations? Email us and share — we’d love to hear from you!


Thanks to Sheetal Patpatia for her work writing summaries for the What’s New and Jobs sections this week! It’s Sheetal’s first week as a volunteer, so she’s off to a great start! Welcome Sheetal!

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