There are trillions of microbes in the human microbiome, which has been linked to a wide array of health conditions. It has become clear that researchers and clinicians have to know more about the microbiome if we are to understand and treat many diseases. Doing so will mean characterizing the many microbes that come be a part of this vast microbial community. Researchers at UCLA have now created a tool that can quickly find the origins of a microbiome, which can help in the effort to understand them.
The human gut microbiome has received intense research attention in recent years, but microbiomes are found everywhere. The tool created by the UCLA researchers is called FEAST, and it will apply to many research areas. They have made it publicly available here, and it can be used by scientists assessing microbiomes in the environment, clinic, gut of an organism, and everywhere else that bacteria live.
“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,” said the principal investigator of this study Eran Halperin, who holds UCLA faculty appointments in the Samueli School of Engineering and in the David Geffen School of Medicine.
Understanding where the microbes in a microbiome come from can provide a variety of different insights. For example, it can help researchers identify the source of contamination; it can also aid in our study of the human gut microbiome, how it’s built and altered by disease, our environment, the food we eat, or anything else. It can show how much of a gut microbiome is native to an organism and how much comes from other sources.
With more information about bacterial strains in the microbiome, scientists or clinicians might be able to diagnose a disease using this new tool and a sample of a patient’s microbiome.
“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.”
FEAST is estimated to be about 300 times faster than current tools that trace the origins of microbiota. It can also handle larger amounts of data and assess a wider range of microbes, both of which are vital for painting a complete picture, the scientists 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,” Halperin added. “Nonetheless, such big and complex datasets pose statistical and computational challenges.”
The researchers tested their tool by comparing the microbiomes of infants born vaginally or by caesarean, and analyzed microbes living on a kitchen counter.