New Pipeline Studies Viruses in Humans and Coral Reefs

Tens of millions of still-unknown or poorly understood viruses have the potential to cause diseases, including new pandemics, and impact the health of valuable terrestrial and marine environments.

An international collaboration led by Flinders University has developed a new pipeline to investigate the ‘virosphere,’ encompassing all the genomes of viruses and bacteriophages (viruses that attack bacteria) worldwide.

In a project described in the GigaScience journal, researchers from the Flinders Accelerator for Microbiome Exploration (FAME) have collaborated with Professor Scott Handley from Washington University and colleagues to analyze viruses in human populations and on coral reefs.

Their goal is to develop a robust method for identifying viruses in all animals, plants, and environments, demonstrating the pipeline's flexibility for future research.

With the help of FAME directors Professors Elizabeth Dinsdale, a marine microbial biologist, and Robert Edwards, a microbiologist, the project conducted deep metagenome testing on viruses discovered in a sizable collection of fecal samples from the UK community.

The study examined anomalies in the data, such as differences in the viral genome between different households, using a sizable UK database.

The approach's tractability was then put to the test by the researchers looking into a variety of viral data from an entirely different environment: the mucus coatings removed from Bermuda's coral reefs.

Viruses are by far the most diverse organisms on the planet and yet accurate identification and annotation of viral sequencing is still in its early stages.

Robert Edwards, Professor, Bioinformatics and Human Microbiology, Flinders University

Edward said, “This new pipeline seeks to rule out or ‘sacrifice’ thousands of genomic sequences to remove irregularities and find novel viruses that are characteristic of each virome to find a disease ‘signature’.”

The project is called "Hecatomb," after an animal sacrifice or killing custom from Ancient Greece.

Now we have a new software platform for viral metagenomics that can find the viruses in the sequence haystack to better understand the actions of these new or existing viruses.

Robert A Edwards, Professor, Bioinformatics and Human Microbiology, Flinders University

The Hecatomb project, according to Dr. Scott Handley, Professor of Pathology and Immunology at Washington University's School of Medicine, offers a chance to study viruses and bacteriophages linked to illnesses like inflammatory bowel diseases.

I am involved in projects devoted to advancing understanding of how microbial and viral ecology and invasive pathogens operate and impact human health. To do this, we needed to produce the hecatomb pipeline to utilize high-throughput sequencing technology, and integrate computational tools enabling viral community analysis. We use the hecatomb pipeline to classify and test how alterations in viral community membership and function contribute to disease.

Dr. Scott Handley, Professor, Pathology and Immunology, School of Medicine, Washington University

According to Dr. Michael Roach, a bioinformatician from South Australia and the project’s first author, the research identified several novel viruses and provides a solid foundation for future research on the potential effects of viruses on common ailments like irritable bowel syndrome or even as a means of protecting coral reefs from bleaching or pollution.

“From our pipeline of viruses studied in our metagenome samples, we can now look for viral or bacteriophage signatures which explains the disease states, including when the samples vary between households,” said Flinders University academic Dr. Roach, who is based at the Adelaide Centre for Epigenetics, at the University of Adelaide.

Professor Dinsdale notes that metagenomes extracted from reef protective mucus in Bermuda's open ocean and nearshore reefs offer an additional opportunity to further the understanding of the genomic makeup of viruses in healthy marine environments.

“More exact metagenome databases and analysis pipelines are vital to understand the virosphere and preserve species in the face of climate change and biodiversity loss. The prevalence of virus infections and microbiome imbalance can affect humans, animals, and plant populations alike,” said Professor Dinsdale.