JUN 11, 2019 3:43 PM PDT

Tracking the Source of Bacteria in a Microbiome

WRITTEN BY: Carmen Leitch

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.

Image credit: Public Domain Pictures

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.


Sources: UCLA, Nature Methods

About the Author
  • Experienced research scientist and technical expert with authorships on over 30 peer-reviewed publications, traveler to over 70 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
JAN 31, 2021
Microbiology
Does a Strain of Gut Bacteria Cause Parental Neglect?
JAN 31, 2021
Does a Strain of Gut Bacteria Cause Parental Neglect?
The gut microbiome is made up of a huge number of different microbial species, and scientists are learning more about ho ...
FEB 02, 2021
Immunology
Tumors Under Seige by Cancer-Killing Salmonella
FEB 02, 2021
Tumors Under Seige by Cancer-Killing Salmonella
Salmonella is a genus of rod-shaped bacteria, often given a bad rap thanks to its association with food poisoning. But c ...
MAR 25, 2021
Microbiology
Good Microbes Can Help Plants Withstand Heat
MAR 25, 2021
Good Microbes Can Help Plants Withstand Heat
Bacteria live everywhere, and we're starting to understand how they affect the biology of animals and plants. This comes ...
MAR 29, 2021
Microbiology
High-Fiber Diets Can Alter the Microbiome Quickly & Significantly
MAR 29, 2021
High-Fiber Diets Can Alter the Microbiome Quickly & Significantly
We know that the microbes in the gut have a significant effect on human biology, and researchers are starting to learn m ...
APR 02, 2021
Drug Discovery & Development
Anti-Parasitic Medication Could Be Therapy for COVID19
APR 02, 2021
Anti-Parasitic Medication Could Be Therapy for COVID19
What are tropical and neglected diseases? Chronic infections that plague developing nations with often little financial ...
APR 19, 2021
Microbiology
Small Differences Enable Some Microbes To Persist in the Gut
APR 19, 2021
Small Differences Enable Some Microbes To Persist in the Gut
The world is full of microbes that have colonized nearly every environment including the human body. The vast majority o ...
Loading Comments...