Viral Host Range Database: an online tool for recording, analyzing and disseminating virus-host interactions

Issue 131 | June 18, 2021
9 min read
Capsid and Tail

Last month in our PHAVES series, Quentin Lamy-Besnier, a PhD student in the Debarbieux lab, introduced the Viral Host Range Database their group has developed. This online resource lets you find, document, analyze and distribute information on hosts that a virus can infect. Here’s the recording, along with a recap by Stephanie Lynch!

What’s New

Apurva Virmani Johri (Vitalis Phage Therapy, India) and colleagues published a case report in Frontiers in Pharmacology on phage therapy for treatment of chronic bacterial prostatitis. Significant improvements in symptoms and re-testing of samples after phage treatment indicated a reduction in bacterial load and resolution of the infection.

This paper is extra notable because it represents Vitalis Phage Therapy’s first published case report! (It’s also a great example of collaboration with the Eliava Phage Therapy Center!)

Antibiotic resistanceCase studyPhage Therapy

Joshua Borin (University of California San Diego) and colleagues published a new paper in PNAS showing that coevolutionary phage training leads to greater bacterial suppression and delays the evolution of phage resistance. For example, they found that a phage trained for 28 days suppressed bacteria ∼1,000-fold for 3-8x longer than its untrained ancestor. Interestingly, one way that this phage improved was by recombining with a defunct prophage gene in the host genome, which doubled its fitness.

EvolutionPhage trainingPhage-host interactionsResearch paper

Clément Coclet and Simon Roux (DOE Joint Genome Institute) published a review in Current Opinion in Virology on major challenges of host prediction methods for uncultivated phages. They highlight different approaches, giving their distinct strengths and limitations. They also outline complementary experimental assays which are being proposed to validate and refine these bioinformatic predictions.

Bioinformatics ToolHost predictionResearch paperUncultivated phages

Eleanor Townsend (University of Warwick) and colleagues published a new review in Frontiers in Cellular and Infection Microbiology on the origins and roles of phages in the human gut microbiome. They review phageome development in infancy and adulthood, and consider the phageome’s role both biologically and in the context of health and disease.

Gut phageomeReview

Stephan Tetter (ETH Zurich) and colleagues published a report in Science on developing virus-like ‘artificial nucleocapsid’ carriers for diverse vaccine and delivery applications. They evolved a protein that forms multimeric, spherical cages into a highly efficient capsid that selectively packages its own encoding RNA. Additionally, directed evolution resulted in changes to the encoding RNA structure that enabled efficient uptake versus other cellular RNAs.

Non-viral carriersResearch paperVaccine delivery

Latest Jobs

Lab CoordinatorSEA-PHAGESSoil viruses
Gonzaga University (Spokane, WA) is hiring a biology lab coordinator to prepare lab facilities for teaching multi-section lab courses. The labs are the first semester component of the HHMI SEA-PHAGES program, where students use microbiology and molecular techniques to discover, purify, and characterize phages from the soil.
Horizontal gene transferPhD projectPhage evolution
Jagiellonian University (Poland) is recruiting a PhD student to work on a project related to quantifying evolutionary dynamics of tails in phages infecting bacteria of Klebsiella pneumoniae and the role of horizontal gene transfer in the evolution of phages.
AnaerobesMolecular biology toolsTechnician
The Institute of Virology at the German Research Centre for Environmental Health is looking for a research technician to propagate and isolate bacteria and phages (aerobic and anaerobic), coordinate and conduct in vivo preclinical studies, and process and analyze samples using molecular biology tools.
Pathogenicity islandsResearch Assistant
The National University of Singapore is hiring a research assistant to work on Staphylococcus aureus, phages, and pathogenicity islands.
AnaerobesResearch Assistant
The National University of Singapore is hiring a research assistant to study the microbiology of anaerobes and phages.
MicrobiomeResearch Technician
Delaware State University is looking for a Research Technician (Part-time) in Molecular Biology and Bioinformatics to study microbiome and phage derived from various samples and its application using molecular biological techniques and bioinformatics.

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Sign up here to be part of the longest running phage meeting.

Phagebiotics Research Foundation and Phage Directory present the 24th biennial Evergreen International Phage Meeting August 2-5th 2021. This year you can participate in person or virtually. The meeting will include primary session talks, live and virtual poster sessions, daily flash talks and Q&A for all participants.

Please submit abstracts by July 2nd if you would like to be considered for oral presentations.

We would love to see your posters! Please submit by July 16th.

As always, we look forward to hearing about all the exciting phage work going on worldwide!

ConferenceHybrid

Dear current & future members of ISVM (International Society for Viruses of Microorganisms)

Please take 4 min to fill out this survey to keep your membership active or to join our society. Stay up-to-date with exciting events that await the Viruses of Microbes community! And don’t forget, basic membership is free!

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PHAVES #19 will be a seminar by Dr. Ameneh Khatami, who is a senior lecturer in Child and Adolescent Health for the University of Sydney, based at The Children’s Hospital at Westmead, where she also works as a paediatric infectious diseases physician.

Ameneh’s talk is entitled ‘Phage therapy for difficult-to-treat infections in children’, and will take place July 1, 9 AM Sydney time (June 30, 4 PM Pacific Time).

Small group networking to follow! Register here for this event or future PHAVES events!

Virtual EventPHAVESPhage Therapy

Viral Host Range Database: an online tool for recording, analyzing and disseminating virus-host interactions

Profile Image
PhD Candidate
La Trobe University

I am a third year PhD student from La Trobe University, Melbourne, currently isolating and researching the use of bacteriophages for skin infections in animals. I have a background in Animal & Veterinary Bioscience and hope to continue research of bacteriophages as therapeutics within the veterinary or livestock sector. I am also currently developing and optimising the use of animal-alternative models for safety and efficacy trials of phage therapy. I am always willing to chat about phage research and would like to connect with phage biotech companies as I am interested in jobs within the industry sector.

PHAVES #17, a seminar & tutorial by Quentin Lamy-Besnier (May 18, 2021)

YouTube video

Overview and highlights

Phages usually infect more than one bacterial host, and the phage host range is a dynamic value based on the number of strains it can infect.

Challenges in phage host range data

  1. Finding the host of a phage

Many public repositories only have species-level information. Publications generally don’t have a universal key for host range data collection/visualization and usually key information about the phage, bacterial host or methods is missing. This information is important for downstream applications such as phage therapy, where we want to know the host range as fast and accurately as possible.

  1. Combining host range data

It is tedious to merge data across various experiments or publications. We need a platform that gathers, manages and visualizes that host range data across datasets, for a quick overview!

  1. Leveraging host range data

For the community, most host range data is unavailable. This limits the knowledge and the potential development of phage therapy without knowing the phage ecology, identifying potential receptors and therefore good phage candidates.

What is the solution? ‘Viral Host Range Database (VHRdb)’

A web-based tool to search, explore and contribute experimental host range data for viruses infecting archaea, bacteria and eukaryotes! Allows user-based searches, uploads and provides tools for quick analysis. (Read the paper describing VHRdb here!)

Tutorial for VHRdb

Tutorial begins at 11:02 of the recording

Search function

  • Option to explore phages or bacterial hosts based on their name (eg. if you have a bacterial isolate in your collection that you would like to find a phage for, search the name of your bacterial host and VHRdb will display all phages that infect this strain).
  • In the search function you can also find contact information for who the strain or phage belongs to, along with information specifically about the phage, bacterial host or methods of host range testing.
  • Option to further explore the bacterial host or phage via the linked NCBI information.

Contribute function

  • Create a free account today to contribute your data!
  • Upload the excel spreadsheet containing the phage host range data (phage name in column, bacterial host in rows, and numeric system for no infection, intermediate or infection).
  • You can choose to keep the data private (not added to the public database), and there is an option to add collaborators to your private database.
  • You can always edit data later after uploading (eg. add a related publication, add more phages, etc.)

Explore function

  • After uploading your data through the ‘contribute’ function, you can now explore (eg. visualize and analyze) your data.
  • Filter which phage or bacterial hosts are included in your visualization.
  • Add other phages or bacterial hosts from the public database to your data for quick and simple comparisons
  • Add infection percentage (%) and sort based on host susceptibility/resistance or narrow/broad phages.
  • Easily share the table view via the share button, or download as a CSV file.

Conclusion

VHRdb provides a convenient way to find, store and compare phage host range data. This allows science to be more ‘open’ and paves a road for future applications such as phage therapy.

Want to learn more, or cite the VHRdb? Here’s the reference:

Quentin Lamy-Besnier, Bryan Brancotte, Hervé Ménager, Laurent Debarbieux, Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions, Bioinformatics, 2021, https://doi.org/10.1093/bioinformatics/btab070


Many thanks to Atif Khan for help finding and summarizing this week’s phage news and jobs posts!

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