Capsid and Tail
A weekly phage periodical
May 23, 2019
Issue 29: OSU Viromics Workshop

Exploring viral ecology tools at the OSU Viromics Workshop

UC Denver postdoc Dr. Anushila Chatterjee attended this year's Ohio State University Viromics Workshop. Here's her report on what was covered!

Excited to attend the OSU Viromics workshop in 2020? Get on the mailing list for next year!

Check out the Sullivan Lab on Twitter for some key tweets from the event, which took place May 8-10, 2019. Also, find yourself some new viral ecologists to follow!

What’s New

A 13-month old infant was successfully treated with phage therapy (English article | Dutch article) post-liver transplant at the Saint-Luc University Hospital in Brussels. Phages were obtained from the Queen Astrid Military Hospital—read more about how the Queen Astrid now processes and responds to patient requests for phage therapy for patients like this one in their recent paper by Sarah Djebara and colleagues.

Phage TherapyQueen Astrid Military HospitalMagistral PhageNews

The BBC’s CrowdScience has done a fantastic podcast interview on phage therapy and phage hunting (31 min), where they travel to Tbilisi, Georgia, visit the Eliava Phage Therapy Center, and go phage-hunting with the scientists there. They even drink some phage! This is a great piece that really takes the listener into the world of phages.

PodcastEliava Institute

The Cystic Fibrosis Foundation, a world-leading non-profit that drives CF research and development, has teamed up with CARB-X, a global partnership investing in antibacterial innovation, in pursuit of a new Infection Research Initiative. They will host a live webinar June 11, 10-11 am ET, to introduce this initiative.

WebinarFundingCystic Fibrosis

A new phage pharmacokinetics paper by Katarzyna Hodyra-Stefaniak and colleagues in Krystyna Dabrowska’s group at the Polish Academy of Sciences has demonstrated a “short-circulating phage” phenotype that has implications for engineered phage therapy. Contrary to expectations, T4 phages engineered to display tissue-homing peptides (including lung, prostate, and brain-targeting peptides) were cleared more rapidly from mice (likely via complement) compared to unmodified T4.

Phage PharmacokineticsResearch

The Society for Bacteriophage Research and Therapy, SBRT, a new society in Varanasi, India, is accepting new members. Their goal is to work together as a team for the betterment of bacteriophages and their positive global impact. Find them on Twitter @PhageIndia.

Phage Society

Latest Jobs

Technician: Bacteriophages
Texas A&M University, Texas Agricultural Experiment, College Station, TX

The Technician I, under general supervision, assists in planning research on support laboratory methods and techniques, carrying out procedures, and recording results for a series of closely-controlled experiments.

Preferred Education And Experience:

  • B.S. in Biochemistry or Microbiology
  • Research experience in microbiology laboratories.
  • Independent research experience in bacteriophage projects.

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  • Knowledge of standard microbiology and molecular biology laboratory skills.
  • Skills working with bacteriophage, including isolation, culturing and characterization. Skills in bioinformatics analysis of bacteriophage genomes.
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Community Board

May 23, 2019
IBRC Community Update: New web design, a documentary, and new members welcome!
Organization: International Bacteriophage Research Consortium

The IBRC portal is inspired by the global antibiotic resistance situation & the promising potential phages offer as credible antimicrobial therapeutics.

Launched in October 2018, IBRC is a joint effort by Acharya Narendra Dev College (ANDC), University of Delhi, India and Open Health Systems Laboratory (OHSL), USA to build a consortium of scientists working on phages and lysins.

If you’re a phage scientist/scholar, a medical or industry professional, or a phage therapy supporter interested in joining the consortium, contact Dr. Urmi Bajpai at [email protected] or at [email protected], or tweet @phageconsortium.

To help promote AMR awareness, and prior to launching the IBRC, Dr. Bajpai created a short docu-drama film on AMR and phage therapy (10 min), which will be soon dubbed in other languages too. In it, you’ll hear from Pranav Johri of Vitalis Phage Therapy and Mzia Kutateladze, the director of Eliava Institute.

Collaboration Request Phage Consortium

Exploring viral ecology tools at the OSU Viromics Workshop

Anushila Chatterjee, PhD
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Exploring the virus world, inside out

Did you know that your body contains 100-fold more viruses than your own cells? Luckily, majority of these viruses infect only microbes, including archaea, bacteria and fungi. In fact, these natural predators of the microbial world are the most dominant biological entities found on earth and are increasingly recognized as key enablers in soil, ocean and human ecosystems.

Scientists are investigating contributions of microbe associated viruses in modulating microbial community structure, function and evolution, pathogen limitation, mammalian immunity and global biogeochemical cycles.

Viromics: revolutionizing our understanding of viral impact

Viromics leverage high-throughput sequence-based tools to study viral genomic content in an environment and have revolutionized our understanding of the impact of microbial viruses on mammalian health and environment.

The 2019 OSU Viromics Workshop

Recently, nearly 60 research trainees from across the world attended a viromics workshop hosted by leading marine virologist Prof. Matthew B. Sullivan at Ohio State University to learn about the computational tools available to identify viruses in complex genomic datasets and predict their biological functions.

During this interactive training with instructors Ben Bolduc (OSU), Simon Roux (JGI), Arvind Varsani (ASU), Bonnie Hurwitz (U Arizona), and Ben Temperton (U Exeter), the trainees were exposed to resources like iVirus and IMG/VR.

iVirus: a set of bioinformatics apps geared toward viruses

iVirus, developed by the collaborative efforts of Sullivan and Hurwitz labs, offers diverse bioinformatic applications or “apps” through the CyVerse Discovery Environment cyberinfrastructure, geared to facilitate virus discovery in diverse environmental specimens.

The OSU viromics workshop trainees gained first-hand experience in using iVirus apps to assemble and annotate virus genomes, predict structure, composition and relative abundance of viral communities in metagenomic datasets.

Making bioinformatics friendlier to non-computational biologists

The availability of community-friendly apps in iVirus and accessibility to CyVerse supercomputing nodes allow wet-lab scientists to analyze viral ecological datasets without necessarily learning to write command line codes from scratch or completely rely on computational biologists to analyze high-throughput sequencing data.

Additionally, the workshop participants also learned how use IMG/VR’s interactive virus database to detect viruses in their own data and predict host specificity of those viruses.

Concluding remarks

Together, the OSU viromics mini-symposium provided an exciting opportunity to the next-generation viral ecologists to get well-acquainted with the state-of-the-art tools in viral ecology, inspired them to leverage apps in iVirus to customize their own viromics data analysis pipeline and opened doors for future collaborations to build and improve resources to explore biological functions of environmental viruses.

References

  1. Mokili JL, Rohwer F, Dutilh BE. 2012. Metagenomics and future perspectives in virus discovery. Curr Opin Virol 2:63-77. https://doi.org/10.1016/j.coviro.2011.12.004
  2. Bolduc B, Youens-Clark K, Roux S, Hurwitz BL, Sullivan MB. 2017. iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure. ISME J 11:7-14. https://doi.org/10.1038/ismej.2016.89
  3. Goff SA, Vaughn M, McKay S, Lyons E, Stapleton AE, Gessler D, Matasci N, Wang L, Hanlon M, Lenards A, Muir A, Merchant N, Lowry S, Mock S, Helmke M, Kubach A, Narro M, Hopkins N, Micklos D, Hilgert U, Gonzales M, Jordan C, Skidmore E, Dooley R, Cazes J, McLay R, Lu Z, Pasternak S, Koesterke L, Piel WH, Grene R, Noutsos C, Gendler K, Feng X, Tang C, Lent M, Kim SJ, Kvilekval K, Manjunath BS, Tannen V, Stamatakis A, Sanderson M, Welch SM, Cranston KA, Soltis P, Soltis D, O’Meara B, Ane C, Brutnell T, Kleibenstein DJ, et al. 2011. The iPlant Collaborative: Cyberinfrastructure for Plant Biology. Front Plant Sci 2:34. https://doi.org/10.3389/fpls.2011.00034
  4. Paez-Espino D, Pavlopoulos GA, Ivanova NN, Kyrpides NC. 2017. Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data. Nat Protoc 12:1673-1682. https://doi.org/10.1038/nprot.2017.063
  5. Paez-Espino D, Eloe-Fadrosh EA, Pavlopoulos GA, Thomas AD, Huntemann M, Mikhailova N, Rubin E, Ivanova NN, Kyrpides NC. 2016. Uncovering Earth’s virome. Nature 536:425. https://doi.org/10.1038/nature19094

Anushila Chatterjee, PhD

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Anushila Chatterjee is a postdoctoral fellow in Breck Duerkop’s laboratory at the Department of Immunology and Microbiology, University of Colorado, Denver/Anschutz Medical Campus. Her research focuses on phages and understanding dynamics of phage-bacteria interactions in the context of mammalian gut.

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