How to analyze your phage genomes, and stories from a multi-decade phage career: triple webinar recap issue!
Issue 114 |
February 19, 2021
15 min read
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!
A year ago on Twitter, Jeremy Barr (Monash University) shared a picture of several 40-year old phage stocks, and asked “what should we do with them?” People said ‘check titre!’ ‘get WGS’ and ‘are they the same as the stock phages we’ve all been using?’ Now, his lab has published the results in a new paper in MSystems (led by Dinesh Subedi) showing temporal stability and genetic diversity of 48-year-old T-series phages. Check out Jeremy’s Twitter thread for an explainer!
Phage stabilityResearch paper
Phages are generally described as species-specific or even strain-specific, but how often do we really check? Daniel Cazares (Universidad Nacional Autónoma de México, Mexico) and colleagues pitted phages against a diverse collection of 600 bacteria and found more host promiscuity than you’d expect! Their new MSystems paper describes a novel group of promiscuous podophages infecting diverse Gammaproteobacteria.
Quentin Lamy-Besnier (Institut Pasteur) and colleagues have created a Viral Host Range database, a tool that they built to gather, analyze and search experimental host-range information. They hope this will help leverage the experimental host-range data produced over the years by the phage community. The phage community is invited to contribute!
The Turner Lab at Yale is hiring a research assistant to work on phage microbiology and phage therapy research projects.
PhD project
The Wilhelm lab is seeking a post-doctoral research associate to study the genetics of viruses that infect microalgae. The post-doc will work in a collaborative team and perform experiments that develop tools used to genetically engineer viruses in the Mimiviridae and their hosts, focusing on viruses of photosynthetic plankton.
Post Doc
The Buchan lab is seeking a post-doc to study viruses (phages) that infect a member of the Roseobacter lineage of marine bacteria. The candidate will work to investigate host-phage interactions and influence on competitiveness in marine niches and perform experiments designed to understand novel interactions between phage and host extrachromosomal elements (plasmids).
PhD projectPost Doc
The Vardi lab is seeking a PhD and postdoc candidates w/expertise in metabolomics to join a new project funded by the Simons Foundation in the field of chemical ecology, focusing on alga-virus interactions & chemical communication in the ocean. Our laboratory employs state-of-the-art mass spectrometry to investigate the metabolic landscape produced by microbial interactions at sea. The project will involve diverse microbial, physiological & analytical chemistry tools.
PhD projectPost DocResearch Assistant
The Lindell lab is seeking PhD students and Post-docs to study horizontal gene transfer in cyanophage using experimental evolution, Cyanophage ecology in the North Pacific Ocean, and Synechococcus genome adaptation in the Red Sea. Also seeking a Research Assistant to study infection properties of cyanophages.
Scientist
Computercraft is hiring a scientist to work with a team of virologists and computer scientists to improve viral sequence resources at the National Center for Biotechnology Information (NCBI).
PhD project
The Environmental Microbial Genomics (EMG) group at the University of Copenhagen is offering a PhD scholarship in phage biocontrol of the phyllosphere microbiome.
Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!
The 3rd Bacteriophage Therapy Summit is taking place virtually on March 23-25. With expert speakers from the FDA, BiomX, Cytophage, Loughborough University and Eligo Bioscience, join us online to progress fundamental bacteriophage research into clinically-significant products and overcome the global antibiotic resistance crisis.
Virtual EventPhage TherapySponsor
Next week is Phage Futures 2021 (Feb 24-26)! Jessica and Jan of Phage Directory will be there, along with two dedicated social media assistants, Curtis Hoffmann and Atif Khan, to help keep you all in the loop via Twitter! (Another of our volunteers, Steph Lynch, will be in attendance too!)
And on day 1 of the conference, Jessica will moderate a panel on translation of in vitro phage results to in vivo, and understanding phage pharmacology. Panelists will be Dr. Paul Turner, Dr. Bob Blasdel, and Dr. Martha Clokie. Beyond this there will be tons more — hope to see many of you there!
Registration is open for (online) VEGA, Viral EcoGenomics & Applications, 2021. Hosted by the JGI, the goal of this series of online seminars is to bring together a “Viral Ecogenomics” community to foster discussion on how to best capture and characterize uncultivated viruses, understand the role of viruses in natural ecosystems, and functionally explore viral genetic diversity toward innovative biotechnological and industrial applications. This will be a series that runs through April and May.
Viral ecologyVirtual Event
Phage/Virus Assembly 2021 will take place online July 27-30. Register here!
Phage assemblyVirtual Event
[Date change!] The sixth iVoM event will be Thursday, Mar 4, 11AM GMT (note earlier time than usual too!), and the theme will be “Biotechnology applications in health care”.
It will feature talks by:
Laurent Debarbieux: Phages (in)action in the gut
Krystyna Dabrowska: A study that went wrong: phage engineering and phage pharmacokinetics
Tristan Ferry: Phage therapy experience in France in the field of Bone and Joint infection
I am M R Madhav pursuing M.Tech by Research under the guidance of Dr N Ramesh at the Antibiotic Resistance and Phage Therapy laboratory in the School of BioSciences and Technology at Vellore Institute of Technology, Vellore, Tamilnadu, India. I will be completing this degree by early 2020. I have been working in the field of clinical microbiology and infectious disease for the past two years, wherein I have isolated eight phages and have characterised two of them. Majority of my studies focuses on combating the aquaculture infections. While I have also experience on isolating phages against MDR Pseudomonas aeruginosa and Klebsiella pneumoniae. I want to pursue my higher studies (PhD) in deciphering the role of phages for utilisation in diagnosis, prognosis and therapeutic strategies. I am continually working towards learning and sharing knowledge about the quintessence of phage therapy.
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.
Skurnik Lab, University of Helsinki, Helsinki, Finland
I’m a MSc researcher and phage enthusiast, with background of Translational medicine. Working at Phage Therapy laboratory, University of Helsinki, Finland. My current projects include development of high-throughput phage screening assay to enhance phage diagnostics, and working with Phage Therapy for patients.
Highlights of Evelien’s talk, by Madhav Madurantakam Royam
Noutin Fernand, a PhD student from Pan African University, Kenya, introduced the speaker
First Evelien gave an overview of what the overall process looks like from the reads to the assembly: once we get our sequenced phage genomes, from there we annotate the genome and submit it to the databases, and all along the way we identify the genome ends & organisations, gene predictions, special features, regulatory elements and gene functional predictions.
A few concepts on the assembly, read mapping and annotation were introduced. She further explained the phage genome structure with circularly permutated and defined ends along with its implications.
Most of the phages have coding sequences on both the strands, but there are possibilities to have coding sequence in one strand alone. In case of any gap between the coding sequences, each frame must be analysed, and the start codon along with the ribosome binding site such as Shine-Dalgarno sequence must be examined.
After delineating the coding sequences, the functional annotation is performed using tools for protein function such as BLASTp, HHPred and structural prediction using the PHYRE2.
An essential criterion is the knowledge of the database in use because, for examples, RefSeq is a curated database while not all phages are present.
If you are unsure of the function, general rules for functional annotation is to label them as “hypothetical protein”.
She also gave a brief introduction on ICTV (how to name and classify a phage), explained how to assign a new subfamily or family, and how the basic phage classification workflow works.
Phage-term predicts terminal repeats based on read mapping and is accurate in most cases. However, Sanger sequencing can be used to verify the exact location and start/stop endpoints of the repeats.
Genome circularity works as a good measure for completeness reliably for phages with headful packaging or long terminal repeats, but not for phages with cos-sites/short overlaps or genomes that have been Nexterra-prepped.
Prokka can be a very helpful manual annotation tool while handling metagenomic datasets.
The viral clusters produced by the tool V-contact are related at the sub-family level according to the latest ICTV reorganization of species and genus levels.
Prophages predictions from bacterial genomes are not sufficient to submit them as complete genomes for the phage.
Showing evidence that the phage can be induced and verifying the completeness through whole genome sequencing should help avoid polluting viral databases with bacterial sequences.
Phage Bioinformatics Series #1, by IBRC and Phage Directory: Tuesday, Feb 16
Highlights of Deborah’s talk, by Madhav Madurantakam Royam
Dr. Urmi Bajpai, an Associate Professor from Acharya Narendra Dev College, University of Delhi India, one of the leaders of IBRC (International Bacteriophage Research Consortium), introduced the speaker, Deborah Jacobs-Sera, who oversees PHIRE (Phage Hunters Integrating Research and Education) and SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science) programs.
In Dr. Hatfull’s lab they have a collection of about 18,000 phages and they have sequenced around 3700 of them, almost all of the phages were isolated by the students through the PHIRE and SEA-PHAGES program.
The first steps for the students are: initial collection samples, purification, DNA extraction and archiving and the sequencing. - They use Illumina for sequencing, as they get good enough coverage and experience to analyse the genome without additional technology.
Dan Russell from their laboratory has written tutorials on how to finish an orientation and it is available in PhagesDB (http://www.phagesdb.org).
Most annotation is done manually as there are possibility to miss certain genes as phages don’t follows the rules of programming parameters.
An important skill for the bioinformatic analysis is pattern recognition.
The predictive coding potential is done using Glimmer and GeneMark tools which used the 4 nucleotide patterns using the Hidden Markov models.
Some of her guiding principles for phage genome annotation are (i) Only one frame in one strand for a protein coding gene, (ii) Genes do not overlap but less than few bp eg. 30 bp, (iii) Phages have high gene density with tightly packed genes, (iv) Most protein-coding genes will have coding potential, (v) Many phage genes are unique and will not have any homologues in the databases (and many more!)
She talked through a genome representation of Zizzle phage in the DNA Master software and how the data are represented. - She explained how to investigate a gene or ORF that has overlap and how the data should be read.
She briefed us on the Phamerator software using two phages Zizzles & LilMoolah and concluded with some tips on the DNA Master files.
Want more phage bioinformatics? Join our Slack Community, and check out our new page!
As a companion to this series, we’ve launched a Slack channel called #phage-bioinformatics within the Phage Directory Slack (https://phage.directory/slack). In our community, you can share your questions and work through issues together with the community.
We also created a Phage Bioinformatics resources page!, where you’ll find the PDFs, slideshows, links, resources, video recordings etc. collected throughout our webinars and Slack conversations.
Dr. Elizabeth (Betty) Kutter talked about her journey from mathematics to phage research and her love for phages which has lasted for 60 years and is still counting. A true inspiration for young/future phage researchers!
She shared stories of how she’s balanced life between research/academia and family as a woman researcher.
She discussed her take on transition of using phages for therapeutic purposes and experiences in Tbilisi, Georgia.
She discussed her experiences and thoughts on how to approach physicians for using phages as alternative treatment.
Note: Betty has asked for those who attended (or wanted to) to please feel free to email her at [email protected]. She would love to hear about who you are, where you’re from, and what you’re working on!
Register for upcoming PHAVES seminars — not only do we host speakers, interviews and AMAs, but we host breakout rooms after the talks to encourage casual socializing/networking among the phage community!
Thanks to Jessica Irons (Georgia Institute of Technology) for her work writing summaries for the Jobs section this week!
