Novel ‘FishTaco’ computational method links gut microbes with disease

Microbiome
University of Washington scientists have developed a computational method for linking microbiome species to specific diseases.

The last few years have seen an avalanche of research focused on the microbiome—the community of tiny microbes that live in our bodies and are believed to influence many diseases, including diabetes, obesity and cancer. But linking individual bacterium with particular disorders has proven to be challenging.

Researchers at the University of Washington have developed a novel computational method that they believe can be used to determine the influence of individual bacterial species in the microbiome to particular disorders. They dubbed their technique FishTaco, a nickname for “Functional Shifts' Taxonomic Contributors,” according to a press release from the university.

FishTaco combines two approaches to scrutinizing the microbiome: one that examines the species, or taxa, within the microbiome and the other that examines all the genes in the bacterial population. "FishTaco integrates the taxonomic and functional approaches, linking shifts in the microbiome's species and gene compositions and identifying the taxa that drive functional imbalances observed in different diseases," said Elhanan Borenstein an associate professor of genome sciences at the University of Washington School of Medicine and a senior author on a new paper published in the journal Cell Host & Microbe.

In the study, Borenstein and his colleagues analyzed the microbiomes of people with Type 2 diabetes and inflammatory bowel disease. They used FishTaco to describe how particular microbes create functional imbalances that have been observed in the diseases. They found that disease-specific links vary widely from one condition to the next, suggesting that their method could point to therapies designed to manipulate the microbiome.

Several ongoing studies are aimed at unlocking the mysteries of the microbiome in the hopes of finding innovative therapies. Last summer, researchers at Brigham and Women’s Hospital used a type of RNA sequencing to uncover two types of bacteria that are significantly elevated in patients with multiple sclerosis. Gut bacteria have been shown to boost the effectiveness of the cancer drug cyclophosphamide, and Vedanta Biosciences recently teamed up with NYU to research ways of combining microbiome-based immunotherapies with checkpoint inhibitors to treat the disease.

The developers of FishTaco hope to prove the value of their computational method in the burgeoning field of microbiome research. The technique, they say, not only pinpoints which bacteria are present in particular diseases but also what exactly those bugs are doing—two key pieces of information that will be needed to effectively change the composition of the microbiome with diet, drugs or other therapeutic approaches.