PhageCast

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.com⁠⁠www.phagenomics.net⁠Contact 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.com⁠⁠www.phagenomics.net⁠Contact 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.com⁠⁠www.phagenomics.net⁠Contact 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.com⁠⁠www.phagenomics.net⁠Contact 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.com⁠⁠www.phagenomics.net⁠Contact 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 Gut36:55 - 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: phagetherapy@ceb.uminho.ptEpisode Chapters:00:03 - IntroductionWelcome to Phage Cast! Brief overview of today’s guest and topic.00:12 - Guest Introduction: Professor JoanaBackground 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 SupportHow Portugal’s public hospitals finance phage therapy and accessibility considerations.14:41 - How to Push for Phage Therapy in Other CountriesProf. Joana shares insights into the regulatory approval process and public advocacy strategies.19:16 - Safety of Non-GMP PhagesWhy the Belgian model ensures high safety and quality standards without GMP certification.23:05 - Importance of Public AwarenessHow media exposure led to public support and political action in Portugal.25:19 - Treating Patients Since 2022Success 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 EngineeringExploring how engineered phages can enhance treatment effectiveness and regulatory challenges.31:57 - Phage Adaptation StrategiesHow phages can be evolved to improve efficacy in chronic infections.32:59 - Closing Remarks & Symposium InvitationDetails on the International Symposium on Advances in Phage Therapeutics in Braga.34:20 - OutroFinal 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?

Today we speak with Hugo Oliveira, researcher in the Center of Biological Engineering in Braga, Portugal. We discussed how depolymerases work, how to identify them in your phages, how to isolate phages with more than one depo, and what could be the secret to a cocktail that works against Acinetobacter baumanii. Enjoy the episode!Episode chapters:What is your research focus?Why Acinetobacter as a target?What are depolymerases? Where are they located in the genome?What are the enzymatic activities? What is the main use of this depolymerases in a context of application?Do the phages have several depolymerases?How can we isolate a phage with several depolymerases?How can we detect the depolymerases in the genome?How did you start in the world of phages?Do you have advice for people starting on the field?

Today we speak with Frenk Smrekar, the Founder and CEO of JAFRAL and the Vice-President of PhageEU, he has been working in the field of bacteriophage production since he started his PhD in 2005.On this episode we cover his work in Jafral and much more: he gives his thoughts and experience on phage production, manufacturing and GMP production; on whether we need GMP for phage therapy and we also cover the mission of PhageEU (https://phageurope.eu) We also did not miss the chance to ask him about the transition from academia to industry. A must listen for anyone interested in the field of phage therapy! Enjoy!Episode chapters: What is Jafral doing?What is GMP production?In which case would it make sense to have phage produced under GMP? What is the real cost of GMP?What about phage cocktails?What do you look for in production strains?What about endotoxins?How do you purify phages?Should labs be purifying the phages before running their tests?What is phage EU?How did you get introduced to the world of phages? What were the challenges in your entrepreneurial journey?What skills do you look for in industry in people after their PhDs?Would you have any advice for someone looking into entrepreneurship?What are you most excited about the future of the field?

Today we interview Evelien Adriaenssens, researcher and group leader at the Quadram Institute. We speak about the minimum bioinformatic skillset that a phage researcher should have and what tools you can use to get there. Stay till the end of the episode to hear some of the work she is doing on Gut Viromics and the challenges this work entails. At the very end we ask some personal questions and career advice,Enjoy!Episode chapters:What is the minimum bioinformatic skillset for a phage researcher?How to decide between short read vs long read sequencing to sequence your phage?What are the tools to assemble and annotate your phage without command lines?Why you should learn to use open source software early in your career.The reason behind the abolishment of the morphology taxonomic classification. How do I know what is my phage taxonomy?Submitting your genome to GenBank.Are all phage genomes linear? How do I choose where my phage genome starts? What is the gut virome? What is a healthy virome? Does it play a role in the immunity of babies?Phages as probiotics. What are the major challenges when analyzing viromes? How do you know if your phage genomes are integrated in bacteria or if they are free phages?How did you get introduced in the phage world?What’s your favorite failure?What’s your advice for PhD students? What do you like the most in your job today?What are you most excited for the future of the phage field?

In this episode we interview Luis Melo, a researcher in the Centre of Biological Engineering in Portugal, he develops his research in the Phage Biotechnology group also known as Azeredo lab. Luis tells us about his research focus, Coagulase-negative staphylococcus phages, and how phage replicates in cells of different metabolic states (biofilms). We talk about RNA seq workflow, its challenges and analysis. We also dive into a recent publication of his team where they explore the use of transcriptomics to understand phage-host interactions: Phage SEP1 hijacks Staphylococcus epidermidis stationary cells’ metabolism to replicate (link here) Some things you can hear:00:37 What is your research focus? 01:30 Why coagulase-negative staphylococci?02:55 What is the relationship between coagulase-negative staphylococci and biofilms?03:39 Are dormant cells important?05:45 Where did this story begin for you?08:10 What is the aim of this study? Why is it important to understand the phage-dormant cells interaction?10:02 When you did the transcriptomic analysis of the phage infecting exponential and stationary cells: what did you find?13:40 What is the exact workflow for RNA seq? What is the analysis like?19:49 Is there going to be any follow-up of this study?20:56 How did you start in the world of phages?21:58 What is your advice for PhD students or early career researchers? 24:37 Was there any failure that helped you succeed later in your career? 25:55 What do you like the most in your job?26:27 What do you think is coming on the phage field?

Today we interview Steven de Soir, postdoctoral researcher at uvain Drug Research Institute (UCLouvain) & LabMCT of the Queen Astrid Military Hospital. We cover his work with phages and antibiotics against Pseudomonas aeruginosa biofilms, which was covered in his article Exploiting phage-antibiotic synergies to disrupt Pseudomonas aeruginosa PAO1 biofilms in the context of orthopedic infections (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10783084/) . Some things you can hear: What is Steven’s research focus? Why do we need phages in orthopedic infections? How do you find a balance between phages and antibiotics in a patient? Why did you choose certain specific antibiotics? Did you find synergies between phage and antibiotics? What about your phage cocktails? Combined treatment or sequential treatment? What is the biofilm respiratory rate? This and much more on the science and some personal opinions and advice in the episode!

Today we are happy to welcome Yves Briers. He is Professor in Ghent University, well known for his work in endolysins, funder of Obulytix and Chair of the Belgian Society of Viruses of Microbes. In this episode you can hear all on endolysins: What are endolysins? What is their mode of action? How do bacteria develop resistance? How can we target gram negative bacteria? How far are we in research? How did we get to the 3rd generation of endolysins? On the last part you will also hear the reason behind the fubding of Obulytix and why Belgium has decided to create the Belgian Society of Viruses of Microbes. Stay till the end to hear Yves’ recommendations for researchers! Enjoy!

In this special episode, Jeremy Barr, from the organizing committee of Viruses of Microbes 2024 (VoM) walks us through the Scientific Program highlights of VoM. Jeremy gives an overview of the conference and of the field… On top of that, you can hear his tips on how to network when going to conferences. Enjoy!

In this short episode of phage bites, we talk to Daan van der Berg, a PhD student at TU Delft. Why do phages carry their own tRNA? He explains what tRNAs are and how phage uses them, and in turn how bacteria cleave and downregulate them to counterattack phage infections. In the second part of the conversation, we also talk about his experience as a PhD student. We hope you find it useful, enjoy! Find the article below for more details: Phage tRNAs evade tRNA-targeting host defenses through anticodon loop mutations

Today we are interviewing Graham Hatfull: Graham Hatfull is Professor of Biological Sciences at the University of Pittsburgh, USA. He is well-known in the phage field for his work in mycobacteriophages. Why are mycobacteriophages important? Why do we need those phages? You will learn about phage therapy efforts against Mycobacterium tuberculosis (TB) and M. abscessus, how endolysins work against these pathogens… and much more. Graham also told us about the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, which covers almost 150 participating institutions and over 5,000 student researchers each year: curious about what it takes to start it? In the last part of the episode, you can hear some advice from him for people entering on the phage field. Enjoy the episode!

In this episode of phage bites, we talk to Enea Maffei, a recent-graduate, Postdoctoral researcher at D-HEST in ETH Zurich. He explains how he isolated phage Paride against dormant cells of P. aeruginosa and he explains us a bit more about the story, combination with antibiotics, how he isolated the phage, how the phage performed in animal models and much more... tune in to hear the details! In the second part of the conversation, we also talk about his experience as a PhD student and the struggles he faced and overcame before starting his new position as a Postdoctoral researcher. Find the article below for more details: Phage Paride can kill dormant, antibiotic-tolerant cells of Pseudomonas aeruginosa by direct lytic replication

In our conversation with Paul Turner we covered his research on phage evolution and how he has applied his findings to treating Cystic fibrosis patients against MDR Pseudomonas aeruginosa with phage therapy. Phages have the power to select on certain bacterial treats, thus, the understanding of how bacteria develop resistance to phage can make us be better prepared to respond to this resistance. Paul Turner´s lab is applying this knowledge, predicting the trade-offs of bacterial resistance to phage, to achieve bacterial killing reversing the antibiotic resistance. He talked about ongoing work in this matter, how these findings are translated from in vitro to in vivo, and he also gave really inspiring and insightful advice for the people in the field. More on Paul Turner: https://turnerlab.yale.edu/publications/personalized-inhaled-bacteriophage-therapy-decreases-multidrug-resistant-pseudomonas Dr. Paul Turner is the Rachel Carson Professor of Ecology and Evolutionary Biology at Yale University, and Microbiology faculty member at Yale School of Medicine. his research focuses on the evolutionary genetics of viruses, particularly RNA viruses, and phages that infect bacterial pathogens & the use of phages to treat antibiotic-resistant bacterial diseases. He is also quite active in science-communication and outreach to the general public, and he has a TED talk that you can find online on the use of phages to treat antibiotic resistant bacteria.