From phage therapy to viromics and phage careers: a recap of August’s PHAVES

Issue 89 | August 21, 2020
8 min read
Capsid and Tail

This month, we hosted two episodes of PHAVES! Here’s your recap of both, along with links to the recordings. Thanks very much to our special guests, Pranav Johri, Apurva Virmani Johri, and Dr. Evelien Adriaenssens.

Urgent August 21, 2020

Urgent need for Chryseobacterium indologenes phages for a patient

Phage Therapy

We are urgently seeking Chryseobacterium indologenes phages for a patient in Europe.

Ways to help at this stage:

  • By receiving the strain and testing your phages
  • By sending your phages for testing on the patient’s strain
  • By helping spread the word about this request
  • By providing us with names/email addresses of labs you think we should contact

Please email [email protected] if you can help in any way, or if you would like further details/clarification.

Let’s make a difference,
Phage Directory

What’s New

Catherine Mageeney (Sandia National Labs, Livermore, California) and colleagues published a new paper in MSystems on their development of a new technology platform that enables on-demand phage production through computationally identifying prophages in near-neighbour bacterial strains and then engineering them to be non-lysogenic.

Computational biologyPhage TherapyPhage-host interactionsResearch paper

Menglu Li (Anhui University, China) and colleagues published a new paper in IEEE/ACM Transactions on Computational Biology and Bioinformatics describing PredPHI (Predicting Phage-Host Interactions), a new deep learning-based tool for predicting the host of phages from sequence data.

AIResearch paper

Aurélie Fluckiger (Gustave Roussy Cancer Campus, France) and colleagues published a new paper in Science showing cross-reactivity between tumor antigens and the tape measure protein encoded by an Enterococcus hirae prophage. Administering enterococci expressing the phage gene improved anti-tumor immunotherapy in mice, and in human cancer patients, phage presence was associated with improved survival after immunotherapy.

Phage-immune interactionsPhages and cancerResearch paper

US phage therapy company Adaptive Phage Therapeutics has received a $9.8-million Department of Defense Award to develop phage-based vaccine candidates against SARS-CoV-2.

Biotech newsCOVIDGrant funding news

The Austrian phage therapy company PhagoMed has been selected as a Gold Track company (one of 5) by EIT Health, the premier biotech acceleration program in Europe.

Biotech news

Latest Jobs

The Lieberman lab at MIT (which studies human microbiome colonization, phages included) is hiring a research scientist to develop in-house genomic pipelines into widely-used community resources, conduct original research, and build systems for data tracking of high-throughput experiments.
Lawrence Berkeley National Lab’s Joint Genome Institute Division has an opening for a computational biologist postdoctoral scholar to lead comparative analyses of multi ‘omics datasets to address questions regarding microbial and viral genomic diversity, metabolic activity of key populations in microbiomes of interest, and virus-host interactions in the environment.
The Malik lab at the University of Loughborough (Loughborough, UK) is hiring a PhD student to work on microencapsulation of biological food additives to improve animal nutrition. (The Malik lab works on phage manufacturing and formulation (read more here), making this a great opportunity for a phage-enthusiast!)

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!

Phage Directory is exploring a new opportunity related to phage sharing, and we’re looking to hear from the phage community! Phage biotech companies are seeking to expand their phage collections (for therapeutics and biocontrol), and we’re helping them identify research labs interested in sharing/licensing their phages. Do you collect phages? If so, I’d love to talk to you about this new opportunity. Email [email protected].

Funding opportunityPhage Directory

Save the date for PHAVES, which continues Sep 1 at 6 PM EST (GMT-4), 8 AM Sept 2 AEST. (Welcome Australia and NZ! We moved the time for this one, so you won’t be asleep!) Dr. Sabrina Green of Baylor College of Medicine and BCM TAILOR Labs will tell us about her gut phage research (she defended her PhD just yesterday!! Congrats Sabrina!!) and about her work co-founding TAILOR labs, which produces therapeutic phages for patients. Small-group networking session to follow!

PHAVESVirtual Event

The 2nd Hanson Wade Bacteriophage Therapy Summit takes place (virtually) Aug 27-28, and registration is open! On the Thursday afternoon of the conference, we’ll present our vision of how to use technology to scale up phage therapy.

The KITP Bacteriophage Forum continues (virtually) Aug 25 at noon Pacific: Luciano Marrafini (Rockefeller/HHMI) and Paul Turner (Yale) will speak. Register here.

Virtual Event

The Pathogens journal has opened a Special Issue about “host-pathogens interactions and phage therapy”. — Gabriel Almeida

Host-pathogen interactionsPhage TherapySpecial Issue

From phage therapy to viromics and phage careers: a recap of August’s PHAVES

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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.

This month, we hosted two PHAVES events; here’s your recap of both!

PHAVES 4

Pranav Johri and Apurva Virmani Johri described their work improving access to phage therapy in India through Vitalis Phage Therapy, the organization they founded after Pranav himself went through the process of phage therapy.

Youtube video of PHAVES 4 (45:25)

Here are some of the questions Pranav and Apurva answered

  • What was the bacteria causing the infection?
  • Did you faced any side effects after phage therapy?
  • Were these bacteria resistant in vitro?
  • Did you receive one of the “premixed” Phage cocktails from Eliava or a personalised one?
  • Are you done with treatment or need to continue other courses?
  • Was there an official collaboration between the hospital in Indian administering the phage and Eliava?
  • Did you need any kind of approvals from ICMR or other organizational body to get phage treatment in India going? Are their compassionate use regulations in place already or something that needs to be worked on?
  • A lot of doctors criticize the lack of double blind studies in phage therapy and don’t think the case reports are enough. Are you aware of any double blind studies being done in India at the moment?
  • I know you’ve now set up a collaboration with diagnostic testing centers, at least one in India. How is that going?
  • How many doctors in India are now treating patients with phages?
  • How many patients have been treated?
  • How much does phage therapy cost through Vitalis, and who pays?

PHAVES 5

Ask Me Anything: Dr. Evelien Adriaenssens answered questions about phage taxonomy, viromics, and her transcontinental career progression from PhD student to postdoc to new PI.

Youtube video of PHAVES 5 (54:12)

Here are some of the questions Evelien answered

  • The ICTV seems to have been really productive in creating new taxa — what’s that like getting buy-in from NCBI, and have you been getting a lot of push-back from other researchers?
  • hello from Edinburgh, Scotland! Evelien, what would be your recommendation for someone who finds a (pro)phage in a bacterial genome? How do you know if it’s unique? Would you recommend uploading it to GenBank? If so, how to name/classify it? Thanks!
  • Hello from Pretoria (Cowan’s lab). What do you think about working on virus communities from viromics or from metagenomics datasets? What are the benefits and disadvantages of these two methods?
  • Hello Dr. Evelien, Greetings from India, I am little bit confused on the Myoviridae and Siphoviridae classification, can you enlighten us on some of the quite specific features for distinguishing them? In case where sequencing is not available can we distinguish based on tail size or other features based on TEM morphology?
  • What is the ICTV guideline identity threshold to classify 2 phages as 2 different phages? Are the guidelines the same for metaviromes?
  • Hello, greetings from Mexico, I have a question about phylogeny, while some people use the amino acid sequence of the DNA Polymerase or Capside with tools like VICTOR, what do you recommend?
  • More of a career question - did I understand correctly that you did multiple postdocs before starting your own research group? How did you decide when you were ready to start on your own and when it was better to try a different postdoc?

Want to continue the conversation?

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