PhageCast

In today’s episode we interview Rafael Pinilla-Redondo, Group Leader of the Bacterial Immunity research group at the Section of Microbiology, University of Copenhagen.

We start the conversation with an overview of his research, he tells us how his team looks into the interplay between phages and bacterial defense systems.

We also talk about the different approaches to uncover and characterize bacterial immunity, from bioinformatic predictions to experimental phage–bacteria interactions, insights into CRISPR-Cas systems—particularly Type IV CRISPRs, CRISPRi systems and their counter-defenses like RNA-based anti-CRISPRs.

The current big questions in bacterial immunity and what impacts this research could have on biotechnology and translational applications.

Finally, Rafael shares his personal journey into the phage field, what excites him most about current research, his reflections on setbacks that turned into opportunities, and his advice for PhD students and early-career researchers.

PhageCast 2025 is sponsored by PrecisionPhage:

⁠www.precisionphage.com

⁠⁠www.phagenomics.net⁠

Contact PrecisionPhage on LinkedIn! 

PrecisionPhage is a Finland-based phage biotech, providing services worldwide:

 🔹phage laboratory R&D services such as on-demand phage isolation

 🔹licensing of bacteriophages against WHO priority pathogens

 🔹ready-to-use and custom-made bioinformatics software for phage and host genome analysis. 

Are you new to phage genome assembly and functional analysis, and would you like to be able to get them done using the latest methods but without the burden of coding or manual work? 

PrecisionPhage welcomes you to get familiar with Phagenomics!

Phagenomics is a web-based software providing automated phage genome assembly, annotation & analysis, as well as comparative genomics. The tool bundles phage bioinformatics in a user-friendly online platform, performing the work of a seasoned phage bioinformatician in an automated manner.

Phagenomics is developed in-house by PrecisionPhage. 

Try Phagenomics for free at ⁠www.phagenomics.net⁠ and sign up for a pro subscription trial.

In today´s episode we interview Greg Resch, Senior Lecturer and Head of the laboratory of bacteriophages at the Lausanne University Hospital (CHUV), and PI in the NCCR Microbiomes.

We started the conversation asking about the latest results regarding the detection of single phage lysis using microfluidics.

We also cover in this episode:

- Some of his work with phage-antibiotic combinations against infective endocarditis, targeting staphylococcus aureus.

- The effect of different antibiotics and phages in MSSA or MRSA strains from their studies, we cover how they also studied phage resistance of several bacteria recovered from those treatments...

- Many more details on how glycosylation and its regulation affect phage susceptibility.

Finally we also talk about regulations of phage therapy in Switzerland and Greg gave us an impressive overview of his career and gave some interesting tips and suggestions for people starting in the phage field.

PhageCast 2025 is sponsored by PrecisionPhage:

⁠www.precisionphage.com

⁠⁠www.phagenomics.net⁠

Contact PrecisionPhage on LinkedIn! 

PrecisionPhage is a Finland-based phage biotech, providing services worldwide:

 🔹phage laboratory R&D services such as on-demand phage isolation

 🔹licensing of bacteriophages against WHO priority pathogens

 🔹ready-to-use and custom-made bioinformatics software for phage and host genome analysis. 

Are you new to phage genome assembly and functional analysis, and would you like to be able to get them done using the latest methods but without the burden of coding or manual work? 

PrecisionPhage welcomes you to get familiar with Phagenomics!

Phagenomics is a web-based software providing automated phage genome assembly, annotation & analysis, as well as comparative genomics. The tool bundles phage bioinformatics in a user-friendly online platform, performing the work of a seasoned phage bioinformatician in an automated manner.

Phagenomics is developed in-house by PrecisionPhage. 

Try Phagenomics for free at ⁠www.phagenomics.net⁠ and sign up for a pro subscription trial.

In this episode we speak with Tristan Ferry, one of the main drivers of Phage Therapy in France. We talk about how phage therapy is managed in France, we focus on how phages are used against implant associated infections, what are the pathogens involved and what is the best administration route, what they look for in phages and failed treatments and learnings.

On the personal side we could hear a more personal view of his work, how it is to manage such responsibilities, financial pressures of the scientific system and one of the best pieces of advice for PhD students.

Enjoy!

PhageCast 2025 is sponsored by PrecisionPhage:

⁠www.precisionphage.com

⁠⁠www.phagenomics.net⁠

Contact PrecisionPhage on LinkedIn! 

PrecisionPhage is a Finland-based phage biotech, providing services worldwide:

 🔹phage laboratory R&D services such as on-demand phage isolation

 🔹licensing of bacteriophages against WHO priority pathogens

 🔹ready-to-use and custom-made bioinformatics software for phage and host genome analysis. 

Are you new to phage genome assembly and functional analysis, and would you like to be able to get them done using the latest methods but without the burden of coding or manual work? 

PrecisionPhage welcomes you to get familiar with Phagenomics!

Phagenomics is a web-based software providing automated phage genome assembly, annotation & analysis, as well as comparative genomics. The tool bundles phage bioinformatics in a user-friendly online platform, performing the work of a seasoned phage bioinformatician in an automated manner.

Phagenomics is developed in-house by PrecisionPhage. 

Try Phagenomics for free at ⁠www.phagenomics.net⁠ and sign up for a pro subscription trial.

22.- Expert opinion on phage therapy | Round table from the First International Symposium on Advances in Phage Therapeutics

We are sharing one of the sessions of the 1st International Symposium on Advances in Phage Therapeutics that was held in Braga, Portugal during the month of June. You will hear a round table focused in challenge and frontiers for phage therapy.Martin Loessner from ETH Zúrich, moderating the discussion with Rob Lavigne, from KU leuven, Jean Paul Pirnay and Sara Djebara from Queen Astrid Military Hospital and Mzia Kutateladze from Eliava Phage Therapy Center.

Topics such as: clinical improvement vs bacterial eradication, phage and antibiotic combination or resensitation, is it more important to have 2-3 really good phages or a big collection that you can go to?, can we move from a simplistic reductionist to a systems, more complex view?, what is the advantage of using phage mixtures?, is AI the way forward?, what should be the future of phage therapy?, is phage resistance necessarily a bad thing, if used long-term?,should there be last-resort phages?, do we need to train phages?, What about engineering bacteriophages? These and much more in this hour of conversation packed with food for thought! Enjoy!

PhageCast 2025 is sponsored by PrecisionPhage:

⁠www.precisionphage.com

⁠⁠www.phagenomics.net⁠

Contact PrecisionPhage on LinkedIn! 

PrecisionPhage is a Finland-based phage biotech, providing services worldwide:

 🔹phage laboratory R&D services such as on-demand phage isolation

 🔹licensing of bacteriophages against WHO priority pathogens

 🔹ready-to-use and custom-made bioinformatics software for phage and host genome analysis. 

Are you new to phage genome assembly and functional analysis, and would you like to be able to get them done using the latest methods but without the burden of coding or manual work? 

PrecisionPhage welcomes you to get familiar with Phagenomics!

Phagenomics is a web-based software providing automated phage genome assembly, annotation & analysis, as well as comparative genomics. The tool bundles phage bioinformatics in a user-friendly online platform, performing the work of a seasoned phage bioinformatician in an automated manner.

Phagenomics is developed in-house by PrecisionPhage. 

Try Phagenomics for free at ⁠www.phagenomics.net⁠ and sign up for a pro subscription trial.

In this episode we talk to Alexander Harms, researcher and proffesor from ETH Zürich. We asked him about the Basel Phage Collection. Lots of basic science covered and many curiosities and insights from E.coli phages that give us certain predictive power towards phage traits.

Some of the questions we cover:

What is your research focus nowadays?

What is the Basel phage collection exactly?

Why K12 as the host?

What are the main learnings from the work of characterization?

Are E coli phages normally broad host range?

What drives this host range?

What do we know about anti-phage defense systems in bacteria?

Could it inform therapeutic selection of E. coli phages?

Can AI build on the learnings from the collection?

Is this collection helping do rational phage engineering?

What are the basic phage characterization assays one should do on phages?

How did you get introduced to the world of phages?

Do you have any favorite failure?

Any advice for PhD students?

What do you like the most in your job?

What are you most excited for in the future of the field?

Where can people find more about you and your work?

PhageCast 2025 is sponsored by PrecisionPhage:

⁠www.precisionphage.com

⁠⁠www.phagenomics.net⁠

Contact PrecisionPhage on LinkedIn! 

PrecisionPhage is a Finland-based phage biotech, providing services worldwide:

 🔹phage laboratory R&D services such as on-demand phage isolation

 🔹licensing of bacteriophages against WHO priority pathogens

 🔹ready-to-use and custom-made bioinformatics software for phage and host genome analysis. 

Are you new to phage genome assembly and functional analysis, and would you like to be able to get them done using the latest methods but without the burden of coding or manual work? 

PrecisionPhage welcomes you to get familiar with Phagenomics!

Phagenomics is a web-based software providing automated phage genome assembly, annotation & analysis, as well as comparative genomics. The tool bundles phage bioinformatics in a user-friendly online platform, performing the work of a seasoned phage bioinformatician in an automated manner.

Phagenomics is developed in-house by PrecisionPhage. 

Try Phagenomics for free at ⁠www.phagenomics.net⁠ and sign up for a pro subscription trial.

Science is a road of failure, however those failures can also bring lessons. In this episode we re-visit the best answers to one of our career questions: Was there any failure that set you up for future success? Do you have a favourite failure?

You can hear phage researchers explaining what failure means for them in many different contexts (Paul Bollyky, Yves briers, Luis Melo, Colin Hill, Evelien Adriaenssens, Paul Turner, Lorenzo Corsini and Rob Lavigne).

This episode is one of our ways to celebrate our 2 year anniversary and to thank you for your support over this time.

PhageCast 2025 is sponsored by PrecisionPhage:

⁠www.precisionphage.com

⁠⁠www.phagenomics.net⁠

Contact PrecisionPhage on LinkedIn! 

PrecisionPhage is a Finland-based phage biotech, providing services worldwide:

 🔹phage laboratory R&D services such as on-demand phage isolation

 🔹licensing of bacteriophages against WHO priority pathogens

 🔹ready-to-use and custom-made bioinformatics software for phage and host genome analysis. 

Are you new to phage genome assembly and functional analysis, and would you like to be able to get them done using the latest methods but without the burden of coding or manual work? 

PrecisionPhage welcomes you to get familiar with Phagenomics!

Phagenomics is a web-based software providing automated phage genome assembly, annotation & analysis, as well as comparative genomics. The tool bundles phage bioinformatics in a user-friendly online platform, performing the work of a seasoned phage bioinformatician in an automated manner.

Phagenomics is developed in-house by PrecisionPhage. 

Try Phagenomics for free at ⁠www.phagenomics.net⁠ and sign up for a pro subscription trial.

On todays´ episode we get to chat with Colin Hill, Professor at University College Cork, APC microbiome, and we discuss his research on the gut microbiome and phages.

He explains the coexistence of phages and bacteria in the gut, we speak about the discovery of crAssphages, the knowledge and the potential of phages in manipulating microbiomes for health benefits and he shared his career journey and great advice for researchers.

Enjoy the episode!

Timestamps & Chapters:

00:00 - Introduction – Welcome & Colin Hill’s background.

03:15 - Colin’s research journey.

07:40 - What Makes a Healthy Microbiome? – Why defining gut health isn’t so simple.

12:20 - How phages shape bacterial communities.

18:05 - CrAssphages - The discovery of one of the most abundant phages.

24:30 - Can Phages Replace Antibiotics? – A new, more precise approach to treating infections.

30:10 - Experiments in the Gut

36:55 - Advice for Young Scientists – Colin’s lessons on research, career, and taking ownership.

42:20 - The Future of Phage Therapy – What’s next for microbiome science?

48:00 - Closing Thoughts – Final takeaways.

In this episode we interview Dr. Paul Bollyky, MD, PhD, and PI of the Bollyky Lab at Stanford University School of Medicine.

You can hear his lab’s research on phage biology and translational applications: how phages interact with bacterial infections, particularly Pseudomonas aeruginosa and their role in immune responses.

He explained the role of filamentous phages in biofilms, how phages influence immune system activity, and the mechanisms involved in phage clearance from the body.

Episode chapters:

What is your lab research focus?

Why is the immune system important in phage research?

Why are there few in vivo bacteriophage pharmacokinetics studies?

Can phages regulate infections by influencing immune responses?

What typically happens to exogenously administered phages?

How do filamentous phages work and how are they isolated?

Are filamentous phages found as free particles or integrated in bacterial genomes?

Do filamentous phages play similar roles in biofilms of other pathogens?

What role do neutrophils play in clearing phages?

What advice would you give to labs starting in phage therapy research regarding immune system and clearance studies?

Do you think that something else needs to be studied other than neutrophils and phagocytes?

What is your view on phage therapy?

What about the regulations for engineered phages?

How did you get introduced to the phage world?

Do you have a favorite failure?

Any advice for PhD students starting in the field?

In this episode, we welcome back Prof. Joana Azeredo a leading researcher at the Center of Biological Engineering. She played a crucial role in the recent approval of phage therapy in Portugal. We discuss the regulatory framework, phage production challenges, hospital applications, and how Portugal’s model compares to Belgium’s.

We also explore the impact of public awareness on regulatory changes, engineered phages, and Joana’s insights into future advancements in phage therapy.

At the end, we talk about the upcoming International Symposium on Advances in Phage Therapeutics happening in Braga this June.

Enjoy the episode!

Check the 1st International Symposium on Advances in Phage Therapeutics, set to take place, between the 16-17th of June 2025, in Braga (Portugal) . Deadline for abstracts 15th February. symposium: https://skyros-congressos.pt/PhageTherapy/

Phage therapy requests and email contact: [email protected]

Episode Chapters:

00:03 - Introduction

Welcome to Phage Cast! Brief overview of today’s guest and topic.

00:12 - Guest Introduction: Professor Joana

Background on Prof. Joana’s research in bacteriophages, biofilms, and genetic engineering.

02:05 - What Was Approved in Portugal?

A breakdown of the phage therapy approval in hospitals and its regulatory framework.

03:30 - How Will Phage Therapy Work?

Explaining the hospital process, prescription guidelines, and phage production standards.

06:42 - Are Hospitals Ready for Phage Therapy?

Discussion on hospital infrastructure, required equipment, and production logistics.

08:40 - Who Can Produce Phages?

Explaining quality control standards and the differences between GMP and non-GMP production.

12:06 - Funding & Public Healthcare Support

How Portugal’s public hospitals finance phage therapy and accessibility considerations.

14:41 - How to Push for Phage Therapy in Other Countries

Prof. Joana shares insights into the regulatory approval process and public advocacy strategies.

19:16 - Safety of Non-GMP Phages

Why the Belgian model ensures high safety and quality standards without GMP certification.

23:05 - Importance of Public Awareness

How media exposure led to public support and political action in Portugal.

25:19 - Treating Patients Since 2022

Success stories from phage therapy cases, including a notable Mycobacterium abscessus patient.

28:26 - Can International Patients Be Treated in Portugal?

Discussion on access for non-Portuguese patients under the new regulation.

29:09 - Future of Phage Engineering

Exploring how engineered phages can enhance treatment effectiveness and regulatory challenges.

31:57 - Phage Adaptation Strategies

How phages can be evolved to improve efficacy in chronic infections.

32:59 - Closing Remarks & Symposium Invitation

Details on the International Symposium on Advances in Phage Therapeutics in Braga.

34:20 - Outro

Final thoughts

In this episode we interviewed Peter Braun, Head of Molecular Biotechnology at Fraunhofer Institute for Translational Medicine and Pharmacology in München, Germany.

We talked about his experience using phages as biotechnological tools: engineering phage RBPs and whole phage particles for detection of highly pathogenic bacteria of interest in the army, such as Bacillus anthracis, Yersinia pestis and Klebsiella pneumoniae.

You can hear about the detection tools and their challenges to identify Bacillus anthracis, and how they compare to phages. You will learn how they developed diagnostic phage proteins, a clever assay for antibiotic sensitivity testing and how they developed diagnostic phages.

We also touch briefly on phage engineering and one of the challenges they faced, and how they solved it.

On the personal side you will hear about Peter’s exotic career and wise advice and inspiration.

Enjoy!

Episode chapters:

What is your research focus?

What kind of infectious diseases are you interested in?

Can you tell us a bit more about your background?

Why do we need a new method for detection? (For bacillus anthracis)

Which proteins did you choose and how did you compose this toolbox?

Are phage RBPs really so specific?

Why using GFP and not NanoLuc for example?

What was your aim with these phages to detect Klebsiella?

What about the clinical samples? Which ones did you test?

Is there any limit of detection?

Do you imagine this application in the clinic?

We saw you needed to delete some phage genes, why?

You got introduced to phages during your PhD, how was this?

Was there any failure in your career that set you up for future success?

Do you have any advice for PhD students or early career researchers starting in the field?

What do you like the most about the position you are in right now?

What are you most excited about in the phage field?