Phage evolution: an ancient solution to a modern problem

Issue 97 | October 16, 2020
9 min read
Capsid and Tail

Schematic of the CAVE pipeline for phage directed evolution, with iterative cycles of mutagenesis and thermal selection. Image source: Favor et al., Scientific Reports, 2020.

This week’s feature article was written by Andrew Favor, Nextbiotics bioinformatics advisor and University of Washington PhD student. He takes us behind his recent Scientific Reports paper on a rapid in vitro platform for enhancing phage characteristics.

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What’s New

Ever wondered about the biological function of genes that overlap with other genes? Bradley Wright (Macquarie University, Australia) and colleagues engineered the gene overlaps out of the φX174 phage genome and found that gene overlap was critical to the phage’s ability to function and replicate normally.

Phage engineeringResearch paper

Charles Bernard (CNRS, France) and colleagues published a new paper in the ISME Journal describing their identification of a new communication system that may regulate host defense mechanisms (similar to the arbitrium system) in Bacillus phage phi3T.

Phage defense systemsResearch paper

Emma Guerin and Colin Hill (APC Microbiome Ireland and University College Cork) published a new review on human gut phages in Frontiers in Cellular and Infection Microbiology. They discuss the main human gut phageome findings to date (incl. composition, phage-host interactions, and persistence of virulent phages) as well as current methods, bottlenecks, and ways to overcome hurdles in this field.

Gut phageReview

Sensei Biotherapeutics has raised $28.5 million to advance their pipeline of personalized cancer drugs, one of which is an immunophage therapy that involves engineering lambda phage to display tumor-associated antigens, leading activated T cells to target the tumor.

Biotech news

UMass is expanding its SEA-PHAGES undergraduate phage hunting program, with a goal of eventually replacing its traditional intro biology lab course with the SEA-PHAGES curriculum for all 1,200 students who participate each academic year.

NewsUndergraduate phage research

Latest Jobs

The Scanlan lab at the University of Warwick is hiring a research fellow to undertake laboratory based biochemistry/microbiology/molecular biology research work to assess how photosynthesis in a marine cyanobacterium can be controlled. Phage experience desired.
The University of Tennessee (Knoxville, Tennessee) is hiring a postdoc to study phages that infect a member of the Roseobacter lineage of marine bacteria.

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!

The next rendition of PHAVES will be a seminar with Rodrigo Ibarra Chavez on Oct 20 at 11AM Eastern / 5PM CEST. He’ll tell us about phage-inducible chromosomal islands (PICIs), piracy in the phage-world, and insights on their application in biotechnology. Small group networking to follow! Register here!

PHAVESVirtual Event

The Ibadan Bacteriophage Research Team is hosting a series of webinars to celebrate International Phage Week at the end of the month! Talks will take place Oct 26 and 27. The theme will be “Early Career Research in Bacteriophage Studies: A leverage for Bacteriophage Therapy Advancement”. Speakers will be Prof. Urmi Bajpai, Dr. Nnadi Nnaemeka, Stephanie Lynch and Dr. Sabrina Green. Save the dates and register here.

Virtual Event

Proteon Pharmaceuticals is hosting a webinar Oct 28 (16:30 to 17:30 IST) on E. coli phages to treat poultry flocks. Register here.

Virtual Event

I am looking for a collaborative research grant under INDIA-EU Cooperation on research & innovation Green Deal: Building a low-carbon, climate resilient future sponsored by Department of Biotechnology, New Delhi. I would like to develop phage cocktail as a Biocontrol agent in Food Industry and Veterinary purpose. Please contact me at [email protected]

Seeking collaborator

Frontiers in Cellular and Infection Microbiology has a new research topic open, The Application of Phages Against Infectious Diseases. Editors: Pan Tao, Jeremy Barr, Jingmin Gu.

Special Issue

Phage evolution: an ancient solution to a modern problem

Profile Image
Scientist
Bardales Lab,
Nextbiotics, Oakland, CA, USA
Skills

Bioinformatics, Data Analytics, Machine Learning / AI, Biotechnology, Molecular Biology

I am a bioinformatics advisor for Nextbiotics, a biotechnology company that utilizes synthetic biology approaches to provide solutions to the emergence of antibiotic-resistant bacteria. My research focuses on protein design, machine learning, and the use of computational tools to develop new types of materials and medicines. In my previous research experience, in academia and industry, I focused on utilizing modified bacteriophage proteins to create drug-delivery vehicles and antimicrobial agents. I hold a B.S. in Chemical Biology and M.S. in Materials Science and Engineering from the University of California, Berkeley, and am currently a Molecular Engineering PhD student at the University of Washington.

Over the years, as researchers have worked to bring phage therapy to fruition, a variety of barriers have stood in the way of adopting phage-based interventions as an alternative to conventional antibiotics. In clinical trials, phage formulations have been shown to quickly lose activity after being administered to test subjects, largely due to the innate structural fragility of these viruses. Additionally, beyond limitations in stability, the root issue of bacterial resistance remains a central limitation; just as bacteria develop resistance to conventional antibiotics, they can, and will, eventually develop resistance to the phages that they are being targeted by. It then stands to reason that switching to phage-based approaches merely changes the participants within the scheme of treatment-resistant bacterial infections, rather than overcoming the core issues themselves.

Origins of a solution

In our recent Scientific Reports article, Optimizing Bacteriophage Engineering Through an Accelerated Evolution Platform, we showcased a new methodology: Chemically Accelerated Viral Evolution (CAVE). This can be used to produce phages with enhanced thermal stability. The inspiration for this technique came about when our team faced issues involving the rapid loss of activity by phages that were being stored at even lenient temperatures (25-35 degrees Celsius). Our motivation for improving the survival rate of phages was threefold: we needed to find ways to extend the shelf life of phage-based products, promote their retention of activity at physiological temperatures during therapeutic applications, and ensure their stability during manufacturing processes. As we looked for ways to achieve this, we were drawn towards simple methods that had stood the test of time.

While scoping out various potential approaches, we stumbled upon some relatively old papers, from the 1950s and 60s, which described how alkylating agents like ethyl methanesulfonate (EMS) could induce random mutations in phages without inhibiting their activity. We decided to re-frame such observations in the context of a directed evolution scheme by developing an iterative protocol wherein each evolutionary cycle included a selection step so that the diversified phage gene pool would be gradually be guided towards the enrichment of desired traits.

Improving phage survival

In our initial efforts to improve the structural stability of our phages, we applied thermal-tolerance screenings as the selection steps, where mutant phages were incubated at high temperatures, only allowing variants with enhanced heat-resistance to survive. This method actually ended up being extremely effective in improving phage stability, and the innate simplicity of the platform suggested great versatility; the mutagenesis protocol could work on virtually any phage, and the selection steps could easily be modified in order to create phages with different sets of desired properties. Additionally, by studying the mutation patterns that arose over the course of evolution, we could gain great insight regarding the structural biology of phages. As we continued to characterize the properties of our newly produced phages, it became apparent that this simple method had provided an effective way to overcome one of the most significant limitations of phage therapy: the ability of phages to survive and retain their activity.

Changing host preferences

Since our initial experiments, we have refined high-throughput methods for producing evolved phages to meet a variety of needs. In addition to evolving thermally tolerant phages from a diverse range of families, we have used our technology to change host preferences from those of wild type phages. This technique has led us to develop new phages to target emergent strains of pathogenic bacteria in an efficient manner. This allows us to avoid the classic struggle of finding candidate phages in the wild that might possess activity against such hosts. One example of this application’s value was seen when we received samples of antibiotic-resistant Salmonella. Starting with wild type phages that initially displayed little or no lytic activity against these hosts, we were able to successfully evolve novel phages that could effectively target a majority of the provided strains. These results have revealed some of this technique’s most exciting potential, and we look forward to presenting them in greater detail in a forthcoming publication.

Conclusion

In the world’s efforts to develop antimicrobial agents, it has consistently been difficult to keep up with the rate at which bacteria develop resistance to the antimicrobial agents to which they are subjected. However, by having a rapid in vitro platform for enhancing phage characteristics, we have found a way to evolve phages in a manner that improves their therapeutic efficacy and expands their host ranges. With an ability to produce effective and diverse phages when needed, we finally have the necessary tools to keep up with this evolutionary arms race in a way that is aligned with the natural dynamics of phage-host systems. Ultimately, we see this technology as a powerful method for overcoming the barriers of phage therapy, and its effectiveness and flexibility provide great promise in actualizing the potential for phages to meet the needs of our modern world.

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