qPCR as a window into phage therapy

This week, Jan takes another detour into data-land, playing around with spreadsheets and tabular data, exploring VLOOKUP, pivot tables, and other formulas.

This week we introduce a new guest writer, Thomas Hunt, who will write about his experiences in lab automation.

Adam Yang, an intern at Shanghai Institute of Phage, interviewed the co-founder of CreatiPhage, Nannan Wu. CreatiPhage is the first company applying phage therapy to humans in China, and seeks to promote the overall development of phage therapy regionally and globally.

This month, we featured a new UK Phage Therapy initiative and wrote about lessons in scaling bio and how to think about data.

This week, Jan goes meta about data. Everyone throws around the term data, but what is it exactly? Jan explores the different kinds of data, how to work with data, and shares some ideas for keeping data neat and tidy.

This week, Jessica Sacher shares learnings from setting up a pipeline for phage production/purification/QC at Phage Australia, and using it to provide phage therapy for our first 3 patients in 2022! Biggest learning: the hardest part about scaling phage therapy has little to do with phages and mostly everything to do with communication and process.

This week, Dr. Josh Jones from UK Phage Therapy drops an announcement on the establishment of a new UK-based phage therapy screening and manufacturing initiative, which will function as the UK’s national clinical phage centre.

This month, we wrote an article for GARDP about phage therapy business models. For this issue, we’re also revisiting a couple of gems from Dr. Paul Jaschke’s lab!

This week, we’re republishing an article Dr. Jon Iredell and Jessica Sacher wrote for GARDP Revive, the Global Antibiotic Research & Development Partnership.

Well hello there, 2023! We’ve made great strides in the past year, gotten our hands wet in the lab (Jessica at least 😉), built data systems, and even delivered phages for patients. This year we aim to do a whole lot more of that! This week, we’re also re-launching the Instill experimental community forum, so come check it out.

We’re at the end of the year again, and what a whirlwind of a 2022 it’s been! Here’s our annual end-of-year reflection on what we’re most proud of, what we’ve accomplished, & those who’ve helped us along the way!

This week, Jan takes a detour into data analytics! This follows up on the last informal Data Series post designing an auditable, replicable, and accessible phage data system. This time, Jan delves a bit deeper into what data analytics is, what tools are used, and connects it back to the phage realm.

Happy December, everyone. I hope you’ve all enjoyed your Thanksgiving! Jessica and I took a short break in New Zealand and it was sublime. This past month, we featured an article by Adam Yang that explored COVID-19 and phages. We also featured a series by Ruby Lin, thoroughly exploring what a sustainable phage therapy ecosystem could look like.

This week, Adam Yang of Lake Forest Academy explores secondary bacterial infections behind COVID-19 deaths, and discusses how phage therapy may be used as a solution.

This week, Ruby CY Lin of Phage Australia dives further into commercialization pathways and opportunities for Phage Australia, and the phage industry as a whole.

This week, Ruby CY Lin of Phage Australia dives further into commercialization pathways and opportunities for Phage Australia, and the phage industry as a whole.

In Part Two of this three-part series, she explores possible phage therapy income streams.

This week, we highlight our October feature articles: Dive down the rabbit hole with us on designing phage data systems, building sustainable phage therapy, and get excited for this year’s World Phage Week!

This week, Ruby CY Lin of Phage Australia dives deep into commercialization pathways and opportunities for Phage Australia, and the phage industry as a whole.

In Part One of this three-part series, she explains the importance of phage manufacturing at scale, and explores streamlined regulations and health economics and reimbursement pathways.

This week, Oluwasegun Isaac Daramola and Williams Timilehin Owoeye explain why you should join them in celebrating another spooky World Phage Week!

This week Jan Zheng explores a few design decisions and considerations behind building a system for collecting data from every part of the phage therapy pipeline.

This week, we highlight the feature articles we published in September! Learn about main themes from Phage Futures Europe 2022, MetaPhage: a new pipeline for turning raw reads into phage insights, and how to set up a basic phage QC system in the lab.

Patients need safe phages, but most regulators don’t yet have official positions on what makes a phage batch safe. This week, Jessica Sacher (Iredell lab, Phage Australia) shares her recent foray into learning about phage quality control and working toward setting up a basic phage QC system in the lab.

MetaPhage is a new pipeline for turning raw reads into phage insights. It’s a massive step in the right direction towards one-click phage analysis. Here’s my trying (and failing) to run MetaPhage on a laptop, and a short tutorial to get you started.

Phage Futures Europe was recently held in Amsterdam, where the phage biotech field came together to discuss recent progress in clinical phage therapy and commercialization. Jessica Neubauer and Madhav Madurantakam Royam are back this week with their coverage of day 2 of the event!

This week, we highlight the feature articles we published in August! Learn about phage+AI and how you can get involved, what happened at Phage Futures this year, how phage-making is going at Phage Australia, and meet Phage Directory’s stellar brigade of volunteers!

This week Marcin Lubocki and Piotr Tynecki explain how AI tools like PhageAI can help us characterize our phages faster and more accurately (but only with the help of the phage community!).

Last month Madhav Madurantakam Royam and Jessica Neubauer attended Phage Futures Europe in Amsterdam, and they’ve brought us a sneak-peek into what they learned!

This week Jessica Sacher shares an update on her work toward setting up a new phage-making system in the Iredell lab (part of Phage Australia).

Our lovely phage community would not exist without the hard work of some incredible phage enthusiasts! This week, we’re recognizing a few of our Phage Directory volunteers for some great stuff they’ve done lately.

This week, we highlight the feature articles we published in July! Learn about Intralytix’s past and present, navigating complexity when you start making phages for therapy, and the new phage-bacteria interaction atlas the Gates Foundation is funding.

There’s still too little data on phage-bacteria biology to support scalable therapeutic phage development. This week, Kayla Young of Phase Genomics tells us how proximity ligation-based metagenomic sequencing is enabling the world’s first comprehensive phage-bacteria interactome atlas.

This week Jessica Sacher takes us through her process for setting up a new phage-making system in the lab, including making sense of a dizzying array of options, managing overwhelm, and resisting ‘optimization creep’.

This week Madhav Madurantakam Royam, a PhD student at the University of Warwick, talks to Dr. Alexander Sulakvelidze, founder and CEO of Intralytix, one of the first modern phage companies to have products on the market.

This week, we highlight the feature articles we published in June! Learn about what happened when the Phage Australia team shipped a phage around the country, Jean-Paul Pirnay’s views on phage therapy, and how producing phages has changed over the years.

This week, Kyle Jackson tackles phage manufacturing. He first enlightens us on how phages have historically been produced and preserved. Then, through a chat with Frenk Smrekar and Barbara Hubad, we learn how JAFRAL helps companies and university labs consistently produce safe phages today.

This week, Madhav Madurantakam Royam, a PhD student at the University of Warwick, talks to Dr. Jean-Paul Pirnay about how the Queen Astrid Military Hospital in Belgium is advancing phage therapy.

The Phage Australia network recently shipped a purified phage to collaborators across the country, and had everyone titre it and report back. Stephanie Lynch, who spearheaded this effort, tells us what was done and what the team learned.

This week, we highlight the feature articles we published in May! Learn about the latest Mycobacterium phage treatment, how we might make our spot tests less subjective, how to get involved in DeSci, and what a phage biologist thought of this year’s ECCMID.

You may have heard people (especially on Twitter) talking about DeSci, or decentralized science. Today Jessica Sacher shares her experience diving into LabDAO, a new DeSci initiative enabling science through a lab space/experiment sharing network.

This week, we highlight a new case report published last week in Cell. It documents the successful phage therapy of a Mycobacterium abscessus infection, which led a 26-year old in Colorado with cystic fibrosis to receive a lung transplant one year after phage therapy.

For the first time since 2019 the yearly European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) took place in-person. Jessica Neubauer, MSc student and Phage Directory volunteer, was there to report on all phings phage!

How do you turn subjective observations into a quantified, somewhat-less-subjective observations? This week Jan Zheng continues his phage data series, delving into how (and why) the well-known ‘Net Promotor Score’ used by software companies might be adapted to score phage plaque assays. (Net Phage Score…?)

This week, we highlight the features we published in April! Catch up on what happened at the last Phage Futures Europe, and learn how to organize your phage biobank data!

Now that we’ve covered tracking phage metadata and building identities for our phages, it’s time to consider how our phages fit into our biobanks. This week in Capsid and Tail, Jan Zheng explains his thinking on how to organize phage biobank data.

What’s the state of phage commercialization? Longtime Phage Directory volunteers Sheetal Patpatia and Aël Hardy, who attended the last Phage Futures event, report on their key takeaways.

This week, we highlight the features we published in March! Learn about how to name your phage, how to track your phages, and how to get pheedback from phage peers!

With feedback from users, the Instill platform is evolving. This week Katharine Muscat, phage PhD student and volunteer Instill coordinator, shares how members have benefited from and contributed to Instill, and what they’ve learned from testing it out!

What’s in a phage name, and how can we make it count? Should we give phages pet names or serial numbers? This week Jan Zheng continues his informal blog series on phage data, with a new post on how he’s thinking about naming phages.

As your phage collection grows, keeping track of your phages and associated data becomes increasingly important. This week, Jan Zheng explores how to rein in all that data before it gets out of control.

Did you know there are over 500 phage phriends who hang out in the Phage Directory Slack community? Today, undergraduate phage enthusiast Sayde Perry shares info about the Slack, how to get involved, and what to expect.

This week, we highlight the features we published in Feb — learn about digital phagograms, phageSuisse and the recently held Bacteriophage Therapy Summit!

phageSuisse is a nonprofit founded to bring together health actors working or wishing to work with phages in Switzerland. This week, Vera Neumeier shares a recap of four recent phageSuisse webinars.

As the field of phage research is increasingly becoming data-driven and intertwined with artificial intelligence (AI), predicting phage-host interactions can provide new biological insights and support the development of personalized phage therapies. This week Dimi Boeckaerts, Ghent University doctoral researcher, shares his views on this exciting topic!

From Feb 14th-16th, the who’s who of the phage world is getting together to discuss everything from isolating phages from hospital wastewater to the role of the immune system in phage therapy!

This week, University of Vienna MSc student Jessica Neubauer explains why you should spend your Valentine’s day cultivating your love of phages at the upcoming (virtual) Bacteriophage Therapy Summit!

This week, we highlight the features we published in Dec & Jan! Learn about combining phages with antibiotics, scaling up phage production, the new Web3 x science movement, and catch Phage Directory’s 2021 reflection and 2022 outlook!

Phage Directory started because Jan (a ‘tech person’) saw how his skills could help fix inefficiencies in Jessica’s field: phage biology. Now, more people like Jan are getting excited to focus on solving problems in science/biology/biotech (accelerated by COVID and the new Web3/blockchain era). Some are even looking at Phage Directory as an example of what success can look like!

A bioreactor should provide the ideal environment for cells (and by extension, phages!). But choosing your setup can be tough. This week, Robert Matthew from Cellexus provides a nice explainer to help you understand your options!

Good morning, 2022! We’re extremely proud of our work empowering the community, running events like Evergreen and building Instill. This year, we’ll be focused on building the “operating system” for phage therapy. From lab workflows to web portals and complex databases, we’ll build infrastructure to scale phage therapy from tens to thousands of treatments.

It’s our last issue of the year! We reflect on what we’re especially proud of from this year, and highlight some stats on where we’re at as a community! Also: a giant thanks to each of our amazing volunteers!

In our PHAVES series this fall, Aël Hardy, PhD student at Forschungszentrum Jülich, Germany, spoke about his research into the inhibition of phage infection by aminoglycoside antibiotics. Here’s the recording, along with a recap by Sayde Perry!

This week, we highlight the feature articles we published in November! Learn about optimizing the route for phage delivery, single use bioreactor technologies vs. traditional solutions, and phage therapy to combat a shell infection in a sea turtle!

Remember when Shelley the sea turtle got phage therapy, thanks to the phage community? This week, Stephanie Lynch distills main learnings from the paper and shares her interview with Shelley’s vet, plus a webinar/Q&A that dives deeper!

This week, we’ve got a discussion on the advantages, disadvantages and comparative costs of single use bioreactors vs. traditional solutions, written by Adam Ostrowski, Technical Application Specialist at Cellexus.

This week, Lizzie Richardson brings us a guest post on optimising the route for phage delivery.

This week, we highlight the feature articles we published in October! Learn about the phages being collected around the world, a doctor-patient experience with phage therapy, successful use of phage to treat bacterial prostatitis, and Cytophage and BiomX’s thoughts on overcoming barriers to phage commercialization.

This week, McMaster University PhD student Kyle Jackson interviews Cytophage and BiomX executives, who share phage therapy commercialization challenges and progress and a sneak peek into what they’ll present at Phage Futures.

You can also read this article on the Phage Futures Europe 2021 website here!

This week, Apurva Virmani Johri and Pranav Johri of Vitalis Phage Therapy take us behind their recently published phage therapy case report, which describes the successful treatment of a patient with prostatitis using phages (done at the Eliava Phage Therapy Center).

In our PHAVES series this summer, Dr. Gina Suh, an infectious disease physician at the Mayo Clinic, and John Haverty, a phage therapy patient, spoke about phage therapy from a doctor’s and patient’s perspective. Here’s the recording, along with a recap by Rohit Kongari!

We’re compiling the results of our State of Phage 2020 Survey, and we’re excited to show you a third snapshot of the findings! Today we’re focusing on phage collections; which phages are labs collecting, how many do they have of each, and where did they get them from?

This week, we highlight the four feature articles we published in September! Learn about a new plaque counting app by Michael Shamash, a new plaque sizing tool by Ellina Trofimova, how Australian pediatrician Ameneh Khatami is treating kids with phages, and highlights of student- and postdoc-selected talks from Evergreen 2021!

This week, we’re featuring an article co-published with PHAGE Journal highlighting a selection of talks from the Evergreen 2021 conference, written by a group of phage-enthusiastic students and postdocs who attended!

This week’s feature article was co-conceived and co-produced alongside the PHAGE Journal editorial team, led by Martha Clokie and Thomas Sicheritz-Ponten.

This week, we’re featuring a post by Ellina Trofimova, software engineer-turned-MSc student at Macquarie University in Australia. She tells us about the Plaque Size Tool she’s developed, including how it came about and what it can do!

In our July PHAVES series, Dr. Ameneh Khatami, a paediatric infectious disease physician and senior lecturer at the University of Sydney, spoke about phage therapy for difficult to treat infections in children. Here’s the recording, along with a recap by Sayde Perry & Stephanie Lynch!

This week, we’re featuring a post by Michael Shamash, a graduate student at McGill University in Canada, who developed the new phage plaque counting app OnePetri! He takes us through the story behind the app, how it works, and what its future holds!

This week, we’re highlighting the three features we published in August! We’ve got a reflection on African phage scientists’ challenges and progress by Raphael Hans Lwesya, a reflection (plus stats!) on Evergreen 2021 (including how to access >100 talks and posters), and a behind-the-paper on coevolutionary phage training by Joshua Borin!

This week, we’re featuring a guest post by Joshua Borin, a UC San Diego PhD Candidate. Joshua takes us behind his recent PNAS paper on how coevolutionary phage training leads to improved phage infectivity.

Last week, in collaboration with Dr. Betty Kutter and her unstoppable team, we helped run the iconic Evergreen International Phage Meeting — but with a twist — this time it was a hybrid virtual/in-person event! We are overjoyed with how it went, and so grateful for the incredible engagement of the phage community. Over 500 registrants, 64 of which attended in person!

In this week’s feature article, we’ve got a thank-you letter from Betty, as well as directions on accessing the >100 videos you can watch (as nearly everything was recorded), plus a giant poster & abstract library for you to peruse!

This week, we’re featuring a guest post by Raphael Hans Lwesya, MSc student at Makerere University in Uganda and founder of thephage.xyz, a new phage-related info hub. Raphael shares his thoughts on phage technology development in Africa, highlighting challenges, progress and initiatives led by African phage scientists.

This week, we’re highlighting the four features we published in July! We’ve got a sneak-peek into the upcoming Evergreen Phage Meeting, a blog post on Phage Directory’s new phage research feedback exchange initiative, ‘Instill’, an interview with Branko Rihtman and Richard Puxty about strange things roseophages do with their DNA, and a profile of Adaptive Phage Therapeutics by Kyle Jackson, who’s recently come on board to help keep us all updated on phage companies!

This week, Kyle Jackson (PhD student at McMaster University) brings us a profile of Adaptive Phage Therapeutics, the clinical-stage phage biotech company commercializing the US Navy’s phage collection. This is the first in a new column Kyle will be writing, to help us keep up with the phage companies bringing phages closer to the clinic!

This week, Madhav Madurantakam Royam interviewed Dr. Branko Rihtman and Dr. Richard Puxty about their new paper describing an unusual nucleotide substitution from deoxythymidine to deoxyuridine in a novel family of phages belonging to Naomiviridae.

Are your manuscripts meeting their potential? We’re launching a new community initiative called Instill Science to help you raise your impact (and get credit for helping your fellow phage community members do the same).

In case you haven’t heard, the Evergreen Phage Meeting is happening both in person and online this year in Olympia, Washington from Aug 1-6. This week, we’re highlighting what to expect from this meeting (via a letter from Betty Kutter) and why you should join us!

This week, we’re highlighting the three feature articles we published in June: a guest blog post by David Sáez and Lorenzo Corsini on breeding better phages, a recap of a clinical phage therapy case presented in PHAVES by Dr. Laura Damioli and Dr. Greg Canfield, and a recap of the Viral Host Range database presented in PHAVES by Quentin Lamy-Besnier.

Last month in our PHAVES series, Quentin Lamy-Besnier, a PhD student in the Debarbieux lab, introduced the Viral Host Range Database their group has developed. This online resource lets you find, document, analyze and distribute information on hosts that a virus can infect. Here’s the recording, along with a recap by Stephanie Lynch!

In our PHAVES seminar series last month, Dr. Laura Damioli and Dr. Greg Canfield (University of Colorado Anschutz) shared their experience treating their first patient with phage therapy for a spinal hardware infection. Here’s the recording, along with a recap by Stephanie Lynch!

This week, we’re featuring a guest blog post by David Sáez and Lorenzo Corsini of PhagoMed; they dive into their recent paper describing how they’re breeding phages to be better for therapy using a modified Appelman’s protocol.

This week, we’re highlighting the three feature articles we published in May: a ‘behind-the-paper’ guest post by Steven Sutcliffe and Michael Shamash, a full recap of all six iVoM webinars by Ivone Martins and Luis Melo, and an interview with Dr. David Harper on phage therapy, past and future, by Curtis Hoffmann.

What brought phage therapy to where it is today? This week, we’re featuring an interview with Dr. David Harper, CEO of Evolution Biotechnologies, by Curtis Hoffmann, a longtime Phage Directory volunteer. They discuss David’s thoughts on historical and modern phage therapy.

This week, we’ve got highlights and recordings for the six “iVoM” webinars we co-hosted with the VoM/ISVM team from Sept 2020 to March 2021! These webinars included talks by 18 expert speakers and brought together more than 1000 unique virus-of-microbe enthusiasts!

This week, we’re featuring a ‘behind the paper’ article by Steven Sutcliffe and Michael Shamash, graduate students in the Maurice Lab at McGill University. They dive into their new paper on what happens to gut phages when common oral medications (e.g. painkillers) are taken.

This week, we’re highlighting the four feature articles we published in April: virtual event recaps by volunteers Rohit Kongari and Stephanie Lynch, a guide on responding to phage therapy requests, and an opinion piece by Mert Selimoglu on phage cocktail-based COVID-19 vaccines.

This week, we’ve got highlights and recordings for 3 webinars we hosted this month: An interview with Dr. Randy Fish on clinical phage therapy for diabetic foot wounds, a talk by Dr. Clara Torres-Barceló on plant pathogen phage research, and a phage bioinformatics workshop with Dr. Jason Gill!

This week, we’re featuring an opinion piece by Dr. Mert Selimoglu (Pakmaya, Turkey) on phage-based COVID vaccines, and the opportunity he sees for using a phage library/cocktail approach to make more effective vaccines.

Are you getting phage therapy requests from the public, and wondering how to respond? We’ve put together a guide + resources you can use (short version: send them our way)!

Bonus: we’ve included resources for physicians too, including how you can use our Phage Alert service to source phages for patients.

For the 2nd webinar of the Phage Bioinformatics Webinar Series jointly organized by IBRC and Phage Directory, we hosted Katelyn McNair, a research scholar at the University of California, Irvine and San Diego State University. This week, we bring you a recap of her talk (written by Dr. Rohit Kongari) and the recording!

This week, we’re highlighting the three feature articles we published in March: a quick dive into phage and diabetic foot ulcers, a recap of the Phage Futures conference last month, and a recap of Jon Iredell’s PHAVES seminar this month on the Australian experience with phage therapy.

Earlier this month we hosted PHAVES #13, a talk by Prof. Jonathan Iredell, who shared his group’s experience with phage therapy at the Westmead Institute for Medical Research in Sydney, Australia. Here’s the recording, along with a recap by Stephanie Lynch!

We attended Kisaco Research’s Phage Futures Congress 2021 at the end of February, and now present our recap of the event. We hope to provide a window into what you missed, and/or a refresher if you were there!

Today we’re doing a quick dive into diabetic foot ulcers and phages. What’s the problem, what are some ways phages have been used to date, and what’s the current status of clinical trials?

This week, we’re highlighting the four feature articles we published in February: an interview with Richard Alm of CARB-X, part two of our State of Phage survey results, and a recap of the three phage events we hosted last week, written by three of our amazing volunteers!

This week, we (co-)hosted three webinars: Africa Phage Forum #2 with Dr. Evelien Adriaenssens, the first event of a new IBRC Phage Bioinformatics Series with Deborah Jacobs-Sera, and PHAVES #12 with Dr. Betty Kutter. Here are the recordings, and highlights of each, written by three of our volunteers!

We’re compiling the results of our State of Phage 2020 Survey, and we’re excited to show you a second snapshot of the findings! Today we’re focusing on strain collections; which bacterial species are phage labs collecting, how many do they have of each, and where did they get them from?

This week, we bring you an interview with Dr. Richard Alm, Alliance Director at CARB-X, a major current funder of new antimicrobials, including phage! Richard shares how he sees phages fitting into the clinical landscape, and shares his advice for phage biotech companies.

This week, we’re highlighting the four feature articles we published in January: Phage Directory’s 2021 outlook, a guest blog post, an interview, and a first look at our State of Phage survey results! Enjoy!

It’s been almost three months since we launched our State of Phage 2020 Survey! We’re excited to show you a snapshot of the data coming in. Today we’re focusing on who responded to the survey: where are they from, what’s their career stage, and how much phage experience do they have?

For this week’s feature article, we interviewed Dr. Arkadiusz Wojtasik, a Production Director at Proteon Pharmaceuticals, about how his team uses the Cellexus CellMaker to produce phage for livestock farming.

The NCTC in England has freshly re-characterized 100 phages originally collected for bacterial typing in the 1950s-1990s. If you want your phages to last as long as these, this is a great place to deposit!

Hello 2021!! This year, we’re focusing on empowering the phage community with the knowledge and tools it needs to overcome phage research challenges & help others do the same.

For our last issue of 2020, we’re reflecting back on Phage Directory’s 2020 progress, and the incredible collaborators who have made it possible. We’re really proud of the ways we’ve been able to connect and work with the phage community virtually this year, and can’t wait for the next one!

Pranav and Apurva Johri, founders of Vitalis Phage Therapy, recently set up a new framework that allows patients in India to get phage susceptibility testing done locally. We sat down with Pranav and Apurva to learn more about what this milestone means, how they achieved it, and what the response has been so far.

This week, we’re highlighting the four feature articles we published in November: two interviews, a guest blog post, and a recap of the month’s PHAVES event!

This month, we hosted episode 10 of PHAVES, a talk on phage engineering by Dr. Paul Jaschke, Lecturer at Macquarie University! Here’s the recording, along with a recap written by Stephanie Lynch, PhD candidate at La Trobe University (and our amazing volunteer PHAVES coordinator)!

This week, Tolulope Oduselu and Olubusuyi Adewumi of the Ibadan Bacteriophage Research Team describe their recently-launched initiative to foster research participation for undergraduate students at the University of Ibadan in Nigeria.

For this week’s feature article, Rodrigo Monteiro and Graça Pinto interviewed University of Wroclaw Professor Zuzanna Drulis-Kawa about her phage therapy and phage depolymerase enzyme research. She shares how she navigates complex grant projects along with the challenges of hosting conferences, such as Viruses of Microbes 2018.

💯 It’s our 100th issue and 2nd birthday!! Thanks so much to all of you for reading and sharing Capsid & Tail; we wouldn’t have gotten this far without your support!

This week, we’re highlighting the three feature articles we published in October: an interview, a guest blog post, and a recap of the two PHAVES events we hosted this month. Enjoy!

This month, we hosted two episodes of PHAVES! Here are the recordings, along with brief summaries. Thanks very much to our special guests, Gordon Smith (Fixed Phage), Chloe Jerrold-Jones (Cellexus), and Dr. Rodrigo Ibarra-Chavez (University of Copenhagen).

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.

For this week’s feature article, Dr. Rohit Kongari interviewed Dr. Ben Burrowes, Senior Scientist at the Center for Phage Technology at Texas A&M University, about his path from phage PhD to industry scientist, to running his own consultancy, to his recent transition back to academia.

This week, we’re highlighting the four feature articles we published in September: two guest blog posts, an interview, and a recap of the two PHAVES events we hosted this month. Enjoy!

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, Dr. Sabrina Green and Dr. Panos Kalatzis.

This week, Fatma Abdelrahman, a research assistant at Zewail City of Science and Technology in Egypt, announces the launch of her new initiative for supporting women who work with phage.

This week, we interviewed Dr. Manuel Garrido, a Production Specialist at TechnoPhage, about how they’ve scaled their phage manufacturing with the help of the Cellexus CellMaker.

This week, two PharmD students from different countries, Christine Thompson (USA) and Yasmine Bendimrad (Morocco), share their views on pharmacists’ roles in antimicrobial stewardship and how phages could fit into their scope as future infectious disease pharmacists.

This week, we’re highlighting the three feature articles we published in August: two interviews and a recap of the two PHAVES events we hosted this month. Enjoy!

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.

This week, Dr. Rohit Kongari interviewed Dr. Vivek Mutalik of Lawrence Berkeley National Laboratory about his journey to become a phage researcher, and how he’s using his engineering background and penchant to develop tools to answer questions in phage biology.

Since 2003, Denise Tremblay has managed the phage collection at the Félix d’Hérelle Reference Center for Bacterial Viruses at the Université Laval in Quebec City, Canada. We interviewed Denise about how the center collects, stores and distributes its phages, and why COVID-19 researchers are requesting their phages.

This week, we’re rounding up an extra helping of July 2020’s phage news and research.

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, Dr. Elyse Stachler and Piotr Tynecki!

This week, we interviewed Gavin Hands, CEO of Cellexus, about the company’s history of helping phage researchers and biotech companies scale up their phage production.

This week, Donna May Papa, Assistant Professor at the University of Santo Tomas in Manila, Philippines, tells us about her lab’s journey into phage research, and their plans for the future.

This week, Jess Friedersdorff of Aberystwyth University in Wales tells us about her fascinating research into phages of the rumen microbiome.

This week, we’re rounding up an extra helping of June 2020’s phage news and research.

We kicked off PHAVES this Tuesday! We discussed Phage Directory’s origin story and future directions, answered questions from the community, and hosted a series of small-group breakout sessions. Here’s how it all went!

This week, Prof. Yves Briers of Ghent University in Belgium takes us behind the scenes of his group’s new paper on an efficient new way of engineering thousands of phage lysins at once.

Dr. Ritah Nakayinga attended the 4th Phages for Global Health workshop in Tanzania this year. This week she shares her experience at the workshop, its impact on her research, and the importance of phage training like this in East Africa.

Continuing the new, once-monthly Capsid & Tail format we started in April, this week we’re rounding up an extra helping of May 2020’s phage news.

This week, we’re spotlighting CURE, a multidisciplinary project laying the foundation for treating and curing asthma with phages.

This week, Capsid & Tail’s volunteer editor Dr. Rohit Kongari talks to UCSF’s Dr. Adair Borges about the unexpected connection she’s uncovered between phage anti-CRISPRs and the Pseudomonas alginate pathway.

We’re excited to share a sneak-peek into our progress toward creating a global phage catalogue and search tool!

It’s a challenge to pick from so many exciting phage-related developments each week, and our backlog is overflowing! So in place of a Feature Article, we’re dedicating this week’s issue to sharing an extra helping of phage news and articles from April 2020.

Phages for dogs too? This week, Stephanie Lynch, a PhD candidate at La Trobe University in Melbourne, Australia, tells us about her research into phages and endolysins to treat multidrug-resistant Staphylococcus pseudintermedius infections in dogs.

This week, Graça Pinto and Rodrigo Monteiro bring us a Q&A with Dr. Evelien Adriaenssens about her career studying phages and viromes, her thoughts on manipulating microbiomes with viruses, and how viral classification is changing.

The last time we were at a conference, it was Phage Futures Congress 2020 (Feb 5-6, 2020). Since we’re all working from home, it’s a perfect time to reflect back on the phage development community’s recent progress.

Can phages help COVID patients? We’ve been hearing chatter about this subject from the phage community over the last few days, so we’ve decided to start the conversation here and keep it going. What, if anything, can the phage community do to help with the COVID-19 crisis?

Attention student and postdoctoral phage biologists planning to attend Viruses of Microbes 2020 in Portugal this year! Phage Directory will be sponsoring two cash awards in collaboration with the Viruses of Microbes organizing committee, and applications are now open!

In the spirit of social distancing and working from home, this week we’re exploring some ideas and tools that enable online communities and allow teams to collaborate from around the world and to work from home.

This week, a group of researchers led by Dr. Anthony Maresso at Baylor College of Medicine describe their new initiative, TAILΦR, which makes phages tailored to patients’ infections.

Need phages for your research? This week, we bring you a guide on how to use Phage Directory to find the phages you need.

This week, Julie Callanan, a PhD student at APC Microbiome Ireland and University College Cork, introduces us to RNA phages, why they’re so elusive, and how her research is beginning to unravel their secrets.

This week, Dr. Ramesh Nachimuthu reflects on the ICBRAMR conference, which took place in Vellore, India in December 2019 and focused on the promise of phages in the fight against antimicrobial resistance.

This week, Ella Balasa, a cystic fibrosis patient who received phage therapy from Yale researchers in 2019, tells her story.

This week, we bring you an interview with Danish Malik, Senior Lecturer at Loughborough University. He tells us about current challenges with phage manufacturing, including what phage companies need to think about, and how academic-commercial collaborations in this area can be key.

This week, we bring you an interview with Michele Wales, founder of the legal firm InHouse Patent Counsel. She tells us about the unique challenges phage companies face in protecting their IP, and why she’s optimistic about what’s to come.

Last Fall, we attended the Phage Futures Europe conference, which covered phage commercialization with a focus on how European regulators are thinking about phage therapy.

This week, we present our full recap of that event, just in time to get everyone excited for the upcoming Phage Futures Congress, set to take place in Washington, DC Feb 5-6, 2020. Hope to see you there!

Happy New Year, phage enthusiasts! This week, we share how we plan to help the phage research community systematize and standardize phage data collection in 2020.

This week, Dr. Michela Gambino, a postdoc in the PHAGEBio group at the University of Copenhagen, tells us about the importance of pork in Denmark, and about their group’s search for phages against E. coli in pigs.

This week, Aël Hardy, an MD-PhD student at Forschungszentrum Jülich in Germany, explores physicians’ awareness about phages and how it could be improved. He interviewed two French physicians who recently used phages to treat some of their most desperate patients.

This week, Dr. Urmi Bajpai, a phage researcher in New Delhi, India and co-creator of the International Bacteriophage Research Consortium, tells us about a public phage therapy lecture her Consortium held last month to raise awareness of phage therapy and antibiotic resistance in India.

This week, Dr. Atunga Nyachieo and Ivy Mutai of the Institute of Primate Research in Nairobi, Kenya tell us about how phage research training began at their institute in 2017, how it continues to grow, and the impact it’s had so far.

This week, we’re highlighting a paper published by Shelley Gibson and colleagues at Baylor College of Medicine and the VA Medical Center in Houston, Texas. They’ve constructed and characterized phage libraries against three pathogens, and made them available for phage therapy.

This week, we provide an overview of two major new antibiotic resistance reports: one from the US (CDC) and one from Canada. We provide a few takeaways, briefly compare the reports, and hope to inspire you to dive in to learn more about the magnitude of the antibiotic resistance problem.

This week, Nnaemeka Emmanuel Nnadi, a Lecturer at Plateau State University in Bokkos, Nigeria, shares some of the challenges his phage research lab faces due to their resource-limited setting.

This week, Milan Buňata of MB Pharma, a Czech company that’s recently gotten into phage, tells us about phage therapy traditions in the Czech Republic, what their company is working toward, and their interest in collaborating with the phage community.

We’ve been publishing Capsid & Tail for a year now, and while some of you have been here since the early days, we know many of you have found us relatively recently. So this week, we’ve gone through our archive to dig up some of our favourite issues (and some of our audience’s!) from some key categories we’ve covered over the past year.

This week we highlight a recent paper on using phage therapy to treat severe musculoskeletal infections (osteomyelitis). A multidisciplinary group in Belgium made up of surgeons, infectious disease physicians, pharmacists, microbiologists and phage scientists treated four patients with phages, and in the process the team came up with a set of standards for treating this type of infection with phages.

You may have heard of the Nagoya Protocol in the context of isolating or sharing phages or bacteria. But what is the Nagoya Protocol, and how does it apply to phage research and development? This week, we’ve put together a primer to help explain it, and a bunch of resources that should help you navigate it.

This week, we’re covering an introductory phage genome annotation workshop that was taught at the 2019 Evergreen Phage Conference. The workshop, Phage Genomics with Galaxy and Apollo, was taught by Jason Gill, a professor at the Center for Phage Technology at Texas A&M University.

Are you a company or lab that needs to produce phages in high quantities? This week, Craig Loftus of Cellexus tells us about how their CellMaker system can help you get higher phage titres in less time and with less cleaning.

Hello phage people! It’s been about a month since Evergreen, and we’re ready with our wrap-up post. We’ve covered highlights, themes, and what really excited us about the conference!

How close are we to being able to treat chickens with phages? This week, we cover a recent study published by Viviana Clavijo and colleagues from the Universidad de los Andes in Colombia. They tested a 6-phage cocktail on chickens in a commercial farm setting and showed control of Salmonella incidence without affecting chicken productivity metrics.

This week, Colin Buttimer and colleagues from APC Microbiome in Ireland and the University of Galati in Romania share their inspiring experience organizing and teaching Romania’s first phage summer school. Because of their success, a food safety research group in Romania will now be pursuing its own line of phage research!

This week, Paulina Deptula, a postdoctoral researcher at the University of Copenhagen, shares her experience using Twitter to find both phages for her research and a supportive community ready to help.

This week, phage researchers and clinicians from the Westmead Institute and Westmead Hospital brief us on how phage therapy is regulated in Australia, through the lens of their experience treating 14 patients with IV phage therapy.

NCTC, a culture collection that supplies bacterial strains around the world, is re-launching its phage collection. How did this come about, and what does this mean for the phage community? We interviewed a group of NCTC microbiologists to find out.

This week is a special, exciting week for Phage Directory! We’ve got big news pertaining to funding, new directions, and a website makeover! And to balance out all the NEW, our feature article this week focuses on something that’s staying the same: how we handle phage therapy requests, and what we do and don’t do when it comes to helping with compassionate phage therapy cases.

This week, Sabrina Green, a graduate student at Baylor College of Medicine, tells us how gut pathogens like ExPEC could be treated with phages, describes the challenges, and highlights her own research on the topic.

This week, Siân Owen, a postdoctoral fellow studying prophage biology at Harvard University, gives us the scoop on the phage side of this year’s ASM Microbe conference.

This week, Dan Evans, a research technician in the Van Tyne lab at the University of Pittsburgh, takes us through the regulatory challenges keeping phage therapy out of the mainstream, highlights ways to overcome these hurdles, and suggests tangible action items for the phage community that could make a difference.

This week, we’re showcasing a story we received from Karen Adler, an MSc student in Dr. Ronen Hazan’s lab at the Hebrew University of Jerusalem. She tells us about the phage work their lab is doing with high school students, some of the results the students have achieved, and provides her tips on inspiring these students. Thanks Karen!

Bacterial diseases cause significant losses in the global fish farming (aquaculture) industry, and phages are being explored as a solution.

When compassionate phage therapy case reports are described in published works, the Declaration of Helsinki often gets mentioned. But where did this declaration come from, why is it referenced so often, and how does it apply to phage therapy?

The Queen Astrid Military Hospital in Brussels has treated patients with phages since 2007, but lately, they’ve had a lot more phage therapy requests. This week, we’re highlighting a recent report describing who’s doing the requesting, what kinds of infections they’re seeing, and how they handle all these requests.

We interviewed Pranav Johri, a former phage therapy patient who founded Vitalis Phage Therapy to help others access phage therapy, especially in his home country of India.

UC Denver postdoc Dr. Anushila Chatterjee attended this year’s Ohio State University Viromics Workshop. Here’s her report on what was covered!

Where can you buy phages, and where can you deposit yours? This week, we take a tour of phage banks around the world.

This week, we highlight a new paper documenting the first use of engineered phages in human therapy, published yesterday by Rebekah Dedrick, Carlos Guerrero-Bustamante, and colleagues in Nature Medicine.

What love, community, and phages can do: this week, we bring you a review of Steffanie Strathdee and Tom Patterson’s phage therapy memoir, The Perfect Predator.

Beyond therapeutics, phage-based diagnostics show the versatility of phages in biotech. This week, guest writer Cathy Nguyen takes us through three examples of phage-based diagnostics.

Where is the world at with compassionate phage therapy? This week, Dr. Shawna McCallin highlights a new review (co-authored with us at Phage Directory and with Dr. Ben Chan at Yale) of phage case reports published to date.

Should phage therapy be considered for pregnant women? This week, Dr. Lucy Furfaro introduces the field of perinatal phage research.

The first case of phage therapy in Israel shows how patients can benefit from collaborations between academia, medicine, military and biotech.

This week, we highlight a useful new animal model for the phage therapy community.

We attended Phage Futures 2019 at the end of January, and now present our full recap of the event.

To understand what it’s like to take part in phage crowdsourcing, we interviewed five labs who’ve contributed phages on behalf of a patient.

How is phage-host coevolution studied in the lab, and what can it tell us?

A look into government incentives for antimicrobial development, and how they apply to phage therapeutic development.

In past issues, we covered what it means to patent something & whether patenting works for phages. In this issue, we dive into an alternative to patenting: trade secrecy.

This week, we attended Phage Futures Congress 2019, which we found to be a huge success!

Simply having a patent on something doesn’t actually protect your invention. That patent has to actually hold up in court. How is this determined, and what kind of chance do phages stand?

You may have heard through the grapevine that “phages can’t be patented”, but several phage patents exist, and biotech and pharma are investing in phage-based therapeutics. What’s the deal?

People are starting to ask questions about phage therapy. We need your help to put together an FAQ. Do they qualify? How can they get it, and where do they get it?

Have you submitted genome sequences for phages that haven’t been cultured yet? Here’s what you should report if and when you do.

This week, we’re sharing insights from our experience talking to middle school kids about phages, phage therapy, and Phage Directory.

This week, we bring you a Q&A with BiomX CBO Assaf Oron.

This week, we explore Belgium’s unique new way of treating patients with phages…

To provide a window into what happens during a phage hunt, we’re devoting this issue to showing some of what’s happened over the last three weeks. We’ve put together an infographic to help illustrate how labs across the globe have come together in support of this cause.

We’re incredibly humbled by all the wonderful feedback and for your help in spreading the word about Capsid & Tail and Phage Directory. Thank you!!

For this week’s issue, we’d like to reflect on our first year as Phage Directory. We’re one year old this week!

This is the second post in a series on how patients are being treated with phages outside of traditional clinical trials.

This is the first of a series of posts about how patients are being treated with phages outside of traditional clinical trials.

Welcome to the first issue of Capsid & Tail, a mini-periodical of links, topics, and commentary that covers the ins and outs of the phage world.