Bioinformatics software paves the way for phage therapy

A new bioinformatics software program is paving the way for a rapid expansion of research into bacteriophages (phages) — the viruses that play key roles in controlling bacteria — through more accurate genome sequencing.

Developed at the Flinders University College of Science and Engineering and described in the journal Bioinformatics, the Phables computational tool can identify and characterise 49% more complete phage genomes compared to existing viral identification tools. Research into isolating and harnessing bacteriophages paves the way for progress in the emerging field of ‘phage therapy’ — a more natural way to target specific bacteria which post a constant risk to immune-compromised, young and elderly patients, as well as ‘super’ bacteria which have become resistant to regular antibiotics.

“Understanding phages is essential because they can influence everything from the health of ecosystems to the treatment of bacterial infections in humans,” said Dr Vijini Mallawaarachchi, from the Flinders Accelerator for Microbiome Exploration (FAME) lab.

“Traditional methods of studying phages from environmental sequencing data have been limited, often failing to fully capture the complete genetic information of phages. This incomplete picture has been a barrier to fully understanding their roles and impacts.”

By contrast, the Phables software uses a new, more effective approach to computationally reconstruct the genetic content of phages from environmental sequencing data, with tests on various datasets showing it can identify more complete contiguous genomes of phages than existing state-of-the-art software tools. As noted by Professor Robert Edwards, Director of Bioinformatics and Human Microbiology for FAME, “This marks a major advancement in phage bioinformatics, allowing us to computationally reconstruct complete phage genomes.

“It will facilitate the discovery of novel phages and enable their laboratory isolation, which will lead to advancements in medical treatments, environmental management and a deeper understanding of microbial life,” Edwards continued.

“This revolutionary tool not only enhances our understanding of the microbial world but also paves the way for innovative solutions to some of the most pressing health and environmental challenges of our time.”

Phables was launched at the Australian Society for Microbiology Annual National Meeting 2023 and the Australian Bioinformatics and Computational Biology Society Conference 2023, and already has almost 9000 downloads across different software repositories. This year, the Flinders University research team aims to use the tool to discover novel phages and to potentially use these isolated phages in therapies, including new treatment options for individuals with conditions such as cystic fibrosis and inflammatory bowel disease.

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