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?

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:

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:

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.

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.