Abstract
It is with great pleasure that we bring you this special edition of PHAGE. One of the joys of bacteriophage biology is that we are still very much in the discovery phase—a little akin to Victorian zoology and botany where we traversed the world finding new species or families even of animals and plants. In the case of bacteriophages, we often travel to much less glamorous places than our predecessors did, and to reveal the true beauty of our finds, we need genomics and other omics tools.
We need to sequence, annotate, and compare our newly isolated bacteriophages at their genome level, a set of tasks that are not totally straightforward. Such information however is enormously rewarding and exciting to gather, and allows us to classify, understand, and select bacteriophages for practical purposes. Fitting with this issue, inPhocus comes not from a specific part of the world but provides insights into the overall landscape of phage collections as surveyed by Phage Directory.
We are pleased to present a series of articles within this special edition that will allow researchers to obtain a state-of-the-art overview on the principles of “calling” phage genes, annotating and retrieving genomes, a practical guide as to how to do this, and a new tool on how to quickly and easily compare your newly isolated phages however you please. There is also a way to accurately enumerate phage plaques making use of state-of-the-art machine learning algorithms. We hope that this set of articles will inform current research within this field, and also provide the background information needed for clinical practitioners to understand the biology of these organisms.
The first of these research articles has been penned by Evelien Addriassens, Dan Turner, and Andrew Kropinski and it presents a series of questions on why we should annotate our phage genomes and on the importance of doing this well before depositing genomes in public databases. Several programs and packages are available for all the different aspects of phage genome annotation and like the organisms themselves, the packages and programs available to us are endlessly evolving and often some are entirely replaced by others. This article reviews the benefits of several different packages for each of the major steps in understanding phage genomes.
There is more than one way to skin a goat as the saying goes, and this article is followed by an article by Andy Millard and Nastya Shen who have written a practical guide on how to take raw sequence reads to fully fledged genomes ready to submit, using a subset of the packages listed in the preceding article. Of note, Andy has annotated hundreds of phages and helped many other researchers annotate theirs, but Nastya Shen is new to this field and has worked closely with Andy to compile a protocol and carry out full test runs of the specific programs that are listed. We are confident, therefore, that with little previous expertise—this should present you with the key skill sets that you need to go from your sequence data to having a phage that you can start to understand.
For the third of the articles in this issue—we are pleased to present an article by Guillemo Rangel and authors who describe a graph-based way of visualizing phage genomes that will allow the reader to contextualize their genome(s) of interest in the context of other phages that target that organism, or are related to the genome in question.
The other articles in this special issue also provide valuable tools for phage researchers; PhageCommander from Matt Lazerof and colleagues combines nine different genome identification programs to make robust phage gene calling. INPHARE by Ryan Cook and team have made an automatic retrieval and analysis system so as to automatically retrieve phage genomes from databases so they can be efficiently curated and analyzed. Finally OnePetri by Michael Shamash and colleagues have developed a collection of machine learning models to create a new tool that accurately counts phage plaques on petri dishes. This tool has a very user-friendly interface that can be used through a mobile phone.
So our next issue will be a general issue and we very much welcome submissions from all corners of the globe. If you need a little help with any aspect of drafting the article, we highly recommend you engage with Phage Directory's new structured peer feedback platform, [Instill Science] (https://instill.xyz). Instill is an initiative created to improve the quality and quantity of scientific output, through fostering inclusivity and peer-led collaboration in the science community.
One of my overall hypotheses is that phages always attract collegial researchers! We are, therefore, confident that the phage community will benefit from and enjoy this free service. Furthermore, if you like scientific writing and wish to contribute to this process, become an Instill member by going through the same weblink.
Finally—phage biologist and artist Ellie Jamison currently at the University of Warwick in the United Kingdom has agreed to be our cartoonist in residence and provide a cartoon for each issue! We hope you like her first picture that captures cloud-based thinking of phage genomes as much as we do!
Martha R.J. Clokie, PhD
Editor-in-Chief
PHAGE