C&T Round Up for May 2020

Issue 77 | May 29, 2020
6 min read
Capsid and Tail

Extra phage news from the month of May!

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.

What’s New

Alita Burmeister (Yale University) and colleagues published a new paper in PNAS describing how pleiotropy complicates trade-offs between phage resistance and antibiotic resistance for a bacterial host, which has implications for phage therapy and other phage applications.

EvolutionPhage-host interactionsResearch paper

Evgenii Rubalskii (Hannover Medical School) and colleagues published a new paper in Antibiotics presenting their findings on using phage therapy to treat critical infections related to cardiothoracic surgery. They showed that phages (in combination with antibiotics) led to eradication of bacterial infections in 7/8 patients, with no adverse side effects.

Phage TherapyResearch paper

Sean Carim (UC Berkeley) and colleagues published a new preprint on the systematic discovery of pseudomonad genetic factors involved in tailocin sensitivity. Tailocins are essentially headless phages that likely evolved from defective prophages; check out Sean’s Twitter thread explaining tailocins and their work here!

PreprintTailocins

Ruimin Gao (Canadian Food Inspection Agency) and colleagues published a new paper in BMC Genomics showing a comparative genomic analysis of 142 bacteriophages infecting Salmonella enterica subsp. enterica (the full complement of the prophages available in public databases for this host). 90 of the genomes grouped into 17 clusters, while 52 had no close relationships to other phages.

Phage genomicsResearch paper

For some interdisciplinary research news, Rachel Yoon Kyung Chang, Philip Chi Lip Kwok (University of Sydney) and colleagues published a new paper in Bioengineering and Translational Medicine on the stabilization mechanism of inhalable phage formulations. Their findings support the hypothesis that spray-dried phages are stabilized by immobilization inside a rigid glassy sugar matrix.

Phage TherapyResearch paper

Mahboubeh Soleimani Sasani & Fereshteh Eftekhar (Shahid Beheshti University, Iran) published a new paper in Current Microbiology discussing the findings from their phage therapy study to treat lobar pneumonia infection induced by Klebsiella pneumoniae in mice. The saw that treatment with a single phage reduced bacterial counts in the lung by 7 logs.

Phage TherapyResearch paper

Maciej Konopacki (West Pomeranian University of Technology, Poland) and colleagues published a new paper in Biochemical Engineering Journal describing PhageScore, a new approach for comparative evaluation of phage lytic activity.

Phage methodsResearch paper

Dmitry Antipov (Institute for Translational Biomedicine, Russia) and colleagues published a new paper in Bioinformatics on metaviralSPAdes, a tool for viral assembly from metagenomic data.

Bioinformatics ToolResearch paper

Ruoshi Zhang (Max Planck Institute for Biophysical Chemistry, Germany) and colleagues published a new preprint on SpacePHARER, a tool that predicts phage-host relationships by identifying phage genomes that match CRISPR spacers in genomic or metagenomic data.

Bioinformatics ToolResearch paper

Anti-CRISPRs are widespread among phages, but it’s been hard to screen for them. Jiawei Wang and colleagues at Monash University have developed an ensemble learning based predictor, PaCRISPR, to accurately identify anti-CRISPRs from protein datasets derived from genome and metagenome sequencing projects.

BioinformaticsBioinformatics ToolResearch paper

Check out how the US Army’s Combat Capabilities Development Command (CCDC) Chemical Biological Center is making use of a polymerized phage in biomanufacturing of BioCNFs, a black carbon material like charcoal that can help break up mustard gas and nerve agents. The CCDC has received seed funding to scale its phage-polymer production through DARPA’s Living Foundries Program.

Biotech newsMaterials SciencePress Release

Register for an upcoming virtual event on AMR and the requirement for a new business model for antimicrobials, hosted by members of European Parliament (June 4 at 12pm CET). Includes a talk by Jean-Paul Pirnay (Queen Astrid Military Hospital) on phages to combat AMR!

AMRPhage TherapyVirtual Event

Check out these two new phage-related podcast episodes: Dr. Steffanie Strathdee, Co-Director of the Center for Innovative Phage Applications and Therapeutics (IPATH) discusses AMR on “This Podcast Will Kill You”, and “The Bio Report” talks with Greg Merril, CEO of Adaptive Phage Therapeutics, about modernizing phage therapy.

Biotech newsPhage TherapyPodcast

Latest Jobs

A postdoc position (funded by ERC Research) on virus-virus interactions and experimental evolution is available in the Sanjuan Lab at the University of Valencia, Spain. Contact [email protected].
A PhD position on modulation of virion stability is available at the Institute of Physical Chemistry (Polish Academy of Sciences) in Warsaw, Poland.
A postdoc position is available at APC Microbiome Ireland in the Gut Phageomics Laboratory.
A bioinformatician/data steward position related to metagenomics and phage-host interactions is available at the University of Utrecht, Netherlands.

Community Board

Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

May 29, 2020

Update to Capsid & Tail: Could phages cure asthma?

Phage Directory

We learned that the CURE project partner from Sweden, which we wrote about in last week’s Capsid & Tail article, “Could phages cure asthma?”, is no longer part of the CURE team. Thanks very much to Sofia Romagosa at the European Federation of Allergy and Airways Diseases Patients’ Associations (EFA) for bringing this to our attention!

CorrectionPhage Directory
May 29, 2020

Episode 4 of “All About Phage Therapy”

Vitalis Phage Therapy

In the 4th ed. of #AllAboutPhageTherapy we’re honored to have Dr Elizabeth ‘Betty’ Kutter live in discussion. Lovingly referred to as “The First Lady of #PhageResearch”, Betty is one of the most experienced & respected phage experts worldwide. Make sure to tune in: May [email protected] IST.

Phage TherapyVirtual Event

C&T Round Up for May 2020

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Phage microbiologist and co-founder of Phage Directory
Co-founder
Phage Directory, Atlanta, GA, United States

Jessica Sacher is a co-founder of Phage Directory and has a Ph.D in Microbiology and Biotechnology from the University of Alberta.

For Phage Directory, she takes care of the science, writing, communications, and business aspects.

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Postdoctoral Researcher
Skills

Bioinformatics, Biotechnology, Molecular Biology, Phage isolation, Phage Therapy, Phage-host interactions, Teaching, Phage Genomics, RNA Sequencing

I am a Phage Biologist at heart with a strong technical background in Biochemistry, Bioinformatics, Phage Genomics, Microbiology and Molecular Biology. I worked on the role of phage spanins in host lysis for my PhD under the guidance of Dr. Ryland Young at Texas A&M University. I am currently working on understanding the host-phage interactions between Staphylococcus aureus and phage K towards use in phage therapy applications.

In place of a feature article this week, we’re highlighting the three features we published this month. Be sure to check them out if you missed them, and let us know if you have thoughts, comments or questions! Reach us anytime by email or Slack!

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