Evidence is growing that the 100 trillion organisms in the human gut play a role in individuals’ differing responses to food. PHOTO: WEIZMANN INSTITUTE

For almost a decade, researchers have been sequencing the bacteria that live in the human gut. Now, some startups are claiming they can use that technology to help people diet more effectively—and in at least one case, scientists say the approach is showing some promise.

The companies are aiming to address a problem identified in recent years: Standard nutritional advice doesn’t work for everyone. Research shows that people fed identical foods can have vastly different blood-glucose responses, which may explain why one person can eat doughnuts daily without gaining weight and another can’t.

While some of this variability is due to genetics, there is growing evidence that the 100 trillion organisms that live in the human gut—known as the microbiome—also play a role. Composed of more than 8,000 different types of bacteria, viruses and fungi living together in a complex ecosystem, the gut microbiome varies from person to person and is affected by a variety of factors, such as sleep, exercise, antibiotics use and, most important, diet.

The glucose response
Thanks to advances in genetic sequencing, researchers increasingly believe that these bacteria affect the body’s ability to harvest energy from food, a measure known as the postprandial glucose response, or PPGR. If untreated, high blood glucose is a risk factor for a host of metabolic conditions, including obesity and diabetes.

DayTwo Inc., an Israeli startup, and Viome Inc., a company backed by Silicon Valley entrepreneur Naveen Jain, say they can help people normalize their blood sugar by analyzing the mix of bacteria that influence their glucose response. Customers send in a stool sample, from which their microbiome is sequenced, along with other information, including a brief medical history, daily activity levels and blood-test results. The companies send back individually tailored diets via an app designed to keep each person’s blood-sugar levels balanced.

Until now, most diets have been based on the glycemic index, a half-century-old list that ranks foods based on how they affect blood sugar. While this index is widely used by doctors to provide dietary advice, it is based on an average response and has been found wanting because many people aren’t average.

DayTwo, which charges $329 for its kit, bases its dietary recommendations on research at the Weizmann Institute of Science in Rehovot, Israel. In 2015 the institute produced a double-blind, peer-reviewed study that showed that individual glucose responses to the same exact meals varied dramatically. Using a test group of 800 people, the study showed that some people produce less glucose after eating a bowl of ice cream than they do after eating a portion of sushi, a food most people would consider to be more healthful.

“We did a dietary intervention that showed that for different people, even people who were prediabetic, we could significantly lower their PPGR,” says Eran Segal, one of the Israeli researchers and a consultant to DayTwo.

Doctors’ views
Until very recently, many doctors were hesitant to base any nutritional advice on the microbiome, saying researchers still didn’t know what each type of micro-organism does exactly, how they interact with other bacteria, and whether they cause disease or are only a biomarker of disease.

But Jack Gilbert, faculty director of the University of Chicago’s Microbiome Center, says he now believes it’s possible to give some dietary advice based on microbiome analysis, even though the microbiome’s role isn’t fully understood. “This is less about trying to identify the particular mechanisms of the microbes and more about identifying the potential correlated association between the microbial communities and how they positively associate with blood-glucose levels and response to different types of food,” he says. Dr. Gilbert, who isn’t connected to DayTwo, says he has put his own father, who is prediabetic, on the program.

The American Academy of Nutrition and Dietetics, which as recently as last year expressed reservations about microbiome-based diets, also has “evolved” its position, says Sonya Angelone, a San Francisco nutritionist and a spokeswoman for the academy. “I think this is the future of really good health care,” says Ms. Angelone, though she suggests pairing such data with advice from a dietitian.

Rob Knight, a professor of pediatrics at the University of California, San Diego, and faculty director of the university’s Center for Microbiome Innovation, says the Weizmann research underlying DayTwo is “very solid and rigorous, which puts them ahead of the curve.” But, he adds, “I think it is still very challenging to extend results like that beyond the population you have studied directly.”

Perhaps because of these concerns, DayTwo, which bases its dietary advice on an algorithm licensed from the Weizmann Institute that connects microbiome composition with predicted glucose responses, has joined with Mayo Clinic to duplicate the Israeli study on 329 people in the U.S. The goal is to ensure that the diet advice works as well for Americans, whose genetics and diet are different from many Israelis.

Nicholas Chia, assistant director of the Center for the Individualized Medicine Microbiome Program at Mayo Clinic, says the results of the follow-up study were close to the Weizmann’s Institute’s findings. “That’s a pretty good sign that we’ve replicated the Israeli study and that it continues to work,” he says.

A competing approach
Viome, meanwhile, uses gene-sequencing technology to analyze not only bacteria but also viruses and fungi in the gut. The Bellevue, Wash., firm, which charges $399 for its analysis, compares users’ microbiomes with 800 individuals the company has preselected as healthy specimens. It gives broad advice on foods to eat or avoid to improve glucose response, enhance sleep and focus, and reduce anxiety.

Though Mr. Jain says Viome’s sequencing technology, licensed from the Los Alamos National Laboratory in New Mexico, is superior to other technologies, Viome’s dietary advice isn’t yet based on peer-reviewed research. Mr. Jain says Viome is conducting a microbiome study on 2,000 people that should be completed later this year.

Drs. Gilbert and Knight and Ms. Angelone declined to discuss Viome, saying they hadn’t seen its studies. A spokesman for Viome says hundreds of testimonials are evidence that Viome’s service is working.

Other companies, including uBiome Inc., the American Gut project and Biohm also offer sequencing of the microbiome, but they focus on how an individual’s gut bacteria differ from the average, not on helping people understand which foods elevate their blood glucose. Some sell probiotics that they say improve the mix of bacteria, though many experts caution that the rapid growth in marketing and use of probiotics may have outpaced scientific research for many of their proposed uses and benefits.

“Although some probiotics have shown promise in research studies, strong scientific evidence to support specific uses of probiotics for most health conditions is lacking,” the National Institutes of Health says.

As for microbiome-based diets, questions remain. Can these eating plans change a person’s gut bacteria for the better, and if so, do people need to measure how much it has changed? “The right diet might change over time as the bacteria change,” says Dr. Knight at UC San Diego.

Viome includes a follow-up analysis as part of its annual fee; DayTwo has decided to wait for further studies to determine whether the changes in the microbiome are so significant that the microbiome needs to be assessed once more.