Building on the shoulders of phage giants

Issue 272 | July 5, 2024
7 min read
Capsid and Tail

This week, we feature Bishoy Maher Zaki, a PhD researcher who transitioned from phage isolation to phage bioinformatics. He’s currently streamlining phage genome analysis tools for the research community — and is asking for help from the phage bioinformatics community!

Urgent July 5, 2024

Urgent need for Enterococcus phages for a patient in the UK

Phage Therapy

We are urgently seeking Enterococcus phages for a patient in the UK.

Ways to help at this stage:

  • By sending your phages for testing on the patient’s strains
  • By receiving the patient’s strain and testing your phages
  • By helping spread the word about this request
  • By providing us with names/email addresses of labs you think we should contact

Please email [email protected] if you can help in any way, or if you would like further details/clarification.

Let’s make a difference,
Phage Directory

Urgent June 30, 2024

Urgent need for Proteus mirabilis phages for a patient in Belgium

Phage Therapy

We are urgently seeking Proteus mirabilis phages for a patient in Belgium.

Ways to help at this stage:

  • By sending your phages for testing on the patient’s strains
  • By receiving the patient’s strain and testing your phages
  • By helping spread the word about this request
  • By providing us with names/email addresses of labs you think we should contact

Please email [email protected] if you can help in any way, or if you would like further details/clarification.

Let’s make a difference,
Phage Directory

What’s New

Chantel Trost (University of Toronto) and colleagues found that the anti-CRISPR protein AcrIF25 disrupts the type I-F CRISPR-Cas system by pulling apart Cas7 from its guide RNA, one subunit at a time. (And it does this with no apparent enzymatic activity!)

Anti-CRISPRResearch paper

Dinesh Subedi (Monash University) and colleagues have developed a five-phage cocktail, Entelli-02 against 156 clinical Enterobacter cloacae complex strains from the Alfred Hospital in Melbourne. They show that Entelli-02 exhibits broad host coverage (99%) and efficacy (92%), and have produced it as a therapeutic-grade product, verified and endotoxin unit-compliant, ready for use.

Phage therapyEnterobacter cloacaePhage cocktail

Hadil Onallah (Hebrew University of Jerusalem) and colleagues have laid out a step-by-step protocol for compassionate phage therapy outlining phage matching, treatment, and monitoring for non-resolving infections.

ProtocolPhage therapyCompassionate use

Enterotoxigenic Escherichia coli (ETEC)-induced diarrhea in piglets can lead to weight loss and death. Michela Gambino (University of Copenhagen) and colleagues characterized a collection of phages infecting porcine ETEC, and a collection of 79 diverse host strains. Their work points toward multifactorial resistance mechanisms of ETEC to phage infection.

Phage sensitivityE. coliPorcine

The (NIH Division of Microbiology and Infectious Diseases) recently discussed a new suggested funding solicitation for phage therapy centers — here’s the recording of the council meeting!

Grant funding newsPhage therapyVideo

Latest Jobs

Research FellowPhage biocontrol
The University of Otago’s Phi laboratory (led by Peter Fineran) in Dunedin, New Zealand is hiring an Assistant Research Fellow to develop phage-based biocontrols for bacterial pathogens in primary industries.
PostdocPhage biologyRNA
The Helmholtz Institute for RNA-based Infection Research (HIRI) in Würzburg, Germany is hiring for multiple positions to study RNA phage defense mechanisms and molecular biology.

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!

Tobi Nagel and Francesca Hodges have organized a hybrid meeting to discuss therapeutic phage bank recommendations.

The meeting is scheduled for July 15th in Cairns, Australia from 1-2:30 PM Australian Eastern Standard Time (GMT+10) (5-10 min walk from VoM convention center in Cairns, which will begin at 3pm that day).

The goal is to address differing opinions within the phage community on key topics identified through their global survey.

Please register your interest above if you’ll be coming!

Phage banksSurveyHybrid meetingVoM

The DOE Joint Genome Institute (JGI) is hosting the “VEGA 2024: Viral EcoGenomics and Applications” symposium, taking place on November 12-13, 2024, in Berkeley, California. The symposium aims to bring together the viral ecogenomics community to discuss capturing and characterizing uncultivated viruses, understanding their ecological roles, and exploring their biotechnological potential.

Viral EcoGenomicsPhage ApplicationsIMG/VR

In an upcoming course in Lyon, France (Nov 12-13 2024), the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) will explore current clinical experiences, compassionate use protocols, cohort studies, and ongoing clinical trials in phage therapy, emphasizing global regulatory navigation and implementation.

Course coordinator: Tristan Ferry.

Register by Oct 27, and apply for an attendance grant by Sept 20.

Clinical EvidencePhage TherapyClinical Practice

PHAGE: Therapy, Applications, and Research Journal has announced an impact factor increase to 3.5.

JournalImpact factor

A recent episode of BBC Sounds’ “In Our Time” interviewed Martha Clokie and James Ebdon about how phages can be used to track and cure bacterial illnesses.

Phage therapyPodcast

Building on the shoulders of phage giants

Profile Image
LecturerPostdoctoral Researcher
Skills

Molecular Biology, Teaching, Phage isolation, Bioinformatics, Microbiology, Biofilms

My passion for phages sparked after attending a seminar back in 2014, hosted by Prof. Ramy Aziz at the Faculty of Pharmacy, Cairo University in Egypt. In that seminar, I enjoyed the sessions of Prof. Hany Anany and Prof. Martha Clokie, which opened my eyes to the potential of phage research in the fight against antibiotic-resistant bacteria. Soon after, I was lucky to join a short internship at Prof. Clokie’s lab at the University of Leicester. Capsid and Tail readers must know that phages literally and figuratively “grow on you.” Totally smitten, I chose a PhD project focused on hunting and characterizing phages against multidrug-resistant pathogens of the respiratory tract, particularly Acinetobacter baumannii and Klebsiella pneumoniae. I was fortunate enough to be supervised by a trio of experts, each in a different area of the topic: Dr. Reham Samir, a microbiologist, Prof. Aziz, a phage genomics expert, and Prof. El-shibiny, a master of phage therapy. Their combined expertise and guidance incredibly helped me manage the complexities of phage research and maintain high standards in my work.

I isolated some phages and characterized them at the Center of Microbiology and Phage Therapy (CMP), Zewail City, Egypt. Then, in the late stage of my PhD, I focused on bioinformatics analysis of the obtained genomic sequences: Analyzing phage genomes is crucial for understanding their biology and therapeutic potential! In this phase, I felt totally lost without a roadmap1 and did not know where to begin and end2 (I am quoting the titles of the cited papers below). It was my first experience handling a genomic sequence, from assembly to annotation and phylogenetic analysis, turned out to be a treasure cove for me.

Prof. Aziz advised me to learn from Prof. Kropinski’s publications and check his workshop material. From there, I started to learn and understand the basics of phage genomics, followed by annotation and phylogeny. The published articles by ICTV members regarding the taxonomy updates and the abolishment of morphological taxonomy were super helpful in building my knowledge and following them to do proper phylogenetic analysis.

I had a roadmap to what was needed to comprehensively analyze my phage genomes, which directed me to build  my own list of tools (particularly web-based tools) This list was very helpful and facilitated my work as it was categorized based on the tools’ functions. Then, I started to share it with my colleagues in Egypt who work on phage biology. Prof. Aziz liked the way I organized my analysis tools and, Prof. El-shibiny gave me the floor to train and share my learning experience with his students at CMP, and they were happy with the tool list. Literally, with what I learned and collected in more than six months, they were able to kick off with genomic analysis within a few days of training and using this list.

Recognizing the need for a more comprehensive and inclusive resource, Prof. Aziz and I launched a survey, entitled “Phage Bioinformatics Wish List: From Sequence to Knowledge!” to gather valuable input from the phage research community on their preferred bioinformatics tools. By collecting this data, we hope to create a robust and user-friendly resource that empowers researchers of all experience levels in the bioinformatics analysis of their phages’ genomes.

This survey is open to all researchers interested in phage bioinformatics. We encourage you to participate and contribute your expertise. By working together, we can build a valuable resource that accelerates phage research and facilitates the way for phage beginners.

Please take the Survey: Phage Bioinformatics Wish List:  From Sequence to Knowledge!

Bishoy Zaki, PhD, a phage biologist from Egypt

  1. Shen, Anastasiya, and Andrew Millard. “Phage Genome Annotation: Where to Begin and End.” PHAGE (New Rochelle, N.Y.) vol. 2,4 (2021): 183-193. doi:10.1089/phage.2021.0015.
  2. Turner, Dann et al. “A Roadmap for Genome-Based Phage Taxonomy.” Viruses vol. 13,3 506. 18 Mar. 2021, doi:10.3390/v13030506.
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