UW associate professor Elhanan Borenstein recently published a research paper alongside Ohad Manor, a post-doctoral fellow in the Borenstein lab, focusing on a computational technique called “FishTaco,” an acronym for Functional Shifts’ Taxonomic Contributors. There are no fish or tacos otherwise involved.
The crux of the FishTaco is that it combines two datasets about the gut microbiome: the composition and abundance of species, and the different types of genes encoded for activities like vitamin synthesis and breaking down carbs.
“When researchers are using this data, it’s a lot of comparative analysis,” Borenstein said. “You really have to go beyond just making a list of species, which is a lot of what the field is doing. You have to analyze this system as a system. You have to really try to think about it as a complex network of interactions.”
That’s just what Borenstein’s lab is trying to do.
Their study analyzes public data from previously published papers. By applying FishTaco to these data sets, Borenstein and Manor were able to identify species in the gut microbiome that drive functional imbalances observed in diseases.
“It’s a constantly changing system. For example, if you change your diet, you change your microbiome, [or] if you take antibiotics,” Borenstein said. “This is to some degree one of the opportunities of microbiome research: [The gut is] an organ in your body that you can actually change. If you understand an association between a microbiome and a specific disease, maybe we can determine intervention.”
The motivation behind Borenstein and Manor’s work revels in the potential for future microbiome-based interventions. While functional imbalances are driven by the collection of genes in the gut, microbiome-based interventions will likely occur at the species level, according to Borenstein.
The hope is to add or remove a species to create a certain health outcome, which can be done through either shaping a person’s diet or the intake of pharmaceutical drugs.
“FishTaco will quantify exactly what is the [bacterial] species driving this shift,” Borenstein said.
The computational tool was made publically available by Borenstein’s lab before the paper was published so other researchers could run it on their own data. The field, according to the professor, tends to promote data- and tool-sharing.
Even though the paper recently came out, the team developed the software tool over two years ago. In addition to FishTaco, the Borenstein lab has developed a variety of other tools for studying the gut microbiome.
“Another big line of work is trying to build models of the microbiome,” Borenstein said. “[Like] being able to put forward a complete computation model of the microbiome that would allow us to predict how a microbiome would respond to specific perturbations [dietary changes].”
An important thing to note, however: While microbiome compositions are associated with certain diseases, that doesn’t mean the link is causal.