A UCLA-led research team has developed what they say is a faster and more accurate way to determine where the many bacteria that live in, and on, humans come from, and have made the computational tool available on a software sharing platform.
The tool, called “FEAST,” can analyze large amounts of genetic information in just a few hours, compared to tools that take days or weeks, according to the university, which reported that the software program could be used in health care, public health, environmental studies and agriculture.
The tool can deduce the origins of any microbiome, which typically contains hundreds to thousands of microbial species.
“Microbiomes are found everywhere, from the digestive tracts of humans to lakes and rivers that feed water supplies. The microorganisms that make up these communities can originate from their surrounding environment, including food,” according to a UCLA statement released Monday. “Knowing where these organisms come from and how these communities form can give scientists a more detailed picture of the unseen ecological processes that affect human health. The researchers developed the program to give doctors and scientists a more effective tool to investigate these phenomena.”
“My hope is that scientists will use FEAST to diagnose bacteria-related health conditions,” said UCLA computer science graduate student Liat Shenhav, the study’s first author. “For example, if a particular cancer has a microbial signature, FEAST can potentially be utilized for early diagnosis.”
The source-tracking program gives the percentage of the microbiome that came from somewhere else. For example, using the tool on a kitchen counter sample can indicate how much of that sample came from humans, how much came from food, and specifically which types of food.
“Armed with this information, doctors will be able to distinguish a healthy person from one who has a particular disease by simply analyzing their microbiome,” according to UCLA. “Scientists could use the tool to detect contamination in water resources or in food supply chains”.
Eran Halperin, the study’s principal investigator,holds UCLA faculty appointments in the Samueli School of Engineering and in the David Geffen School of Medicine.
“The microbiome has been linked to many aspects of human physiology and health, yet we are just in the early stages of understanding the clinical implications of this dynamic web of many species and how they interact with each other,” Halperin said. “There has been an unprecedented expansion of microbiome data, which has rapidly increased our knowledge of the diverse functions and distributions of microbial life. Nonetheless, such big and complex datasets pose statistical and computational challenges.”
According to the researchers, who include scholars from Columbia University and Ben-Gurion University, Israel, FEAST is up to 300 times faster, and significantly more accurate, than other source-tracking tools and can process much larger datasets.
The study, which was supported by the National Science Foundation, was published online in the journal Nature Methods.