Which foods are actually healthy for your individual gut microbiome? Several companies are offering personalized dietary guidance based on your test results, but their answers in one experiment turned up with some conflicting advice.
I recently got on the scale to weigh myself, thinking I've got to eat better. With so many trendy diets today claiming to improve health, from Keto to Paleo to Whole30, it can be confusing to figure out what we should and shouldn't eat for optimal nutrition.
A number of companies are now selling the concept of "personalized" nutrition based on the genetic makeup of your individual gut bugs.
My next thought was: I've got to lose a few pounds.
Consider a weird factoid: In addition to my fat, skin, bone and muscle, I'm carrying around two or three pounds of straight-up bacteria. Like you, I am the host to trillions of micro-organisms that live in my gut and are collectively known as my microbiome. An explosion of research has occurred in the last decade to try to understand exactly how these microbial populations, which are unique to each of us, may influence our overall health and potentially even our brains and behavior.
Lots of mysteries still remain, but it is established that these "bugs" are crucial to keeping our body running smoothly, performing functions like stimulating the immune system, synthesizing important vitamins, and aiding digestion. The field of microbiome science is evolving rapidly, and a number of companies are now selling the concept of "personalized" nutrition based on the genetic makeup of your individual gut bugs. The two leading players are Viome and DayTwo, but the landscape includes the newly launched startup Onegevity Health and others like Thryve, which offers customized probiotic supplements in addition to dietary recommendations.
The idea has immediate appeal – if science could tell you exactly what to make for lunch and what to avoid, you could forget about the fad diets and go with your own bespoke food pyramid. Wondering if the promise might be too good to be true, I decided to perform my own experiment.
Last fall, I sent the identical fecal sample to both Viome (I paid $425, but the price has since dropped to $299) and DayTwo ($349). A couple of months later, both reports finally arrived, and I eagerly opened each app to compare their recommendations.
First, I examined my results from Viome, which was founded in 2016 in Cupertino, Calif., and declares without irony on its website that "conflicting food advice is now obsolete."
I learned I have "average" metabolic fitness and "average" inflammatory activity in my gut, which are scores that the company defines based on a proprietary algorithm. But I have "low" microbial richness, with only 62 active species of bacteria identified in my sample, compared with the mean of 157 in their test population. I also received a list of the specific species in my gut, with names like Lactococcus and Romboutsia.
But none of it meant anything to me without actionable food advice, so I clicked through to the Recommendations page and found a list of My Superfoods (cranberry, garlic, kale, salmon, turmeric, watermelon, and bone broth) and My Foods to Avoid (chickpeas, kombucha, lentils, and rice noodles). There was also a searchable database of many foods that had been categorized for me, like "bell pepper; minimize" and "beef; enjoy."
"I just don't think sufficient data is yet available to make reliable personalized dietary recommendations based on one's microbiome."
Next, I looked at my results from DayTwo, which was founded in 2015 from research out of the Weizmann Institute of Science in Israel, and whose pitch to consumers is, "Blood sugar made easy. The algorithm diet personalized to you."
This app had some notable differences. There was no result about my metabolic fitness, microbial richness, or list of the species in my sample. There was also no list of superfoods or foods to avoid. Instead, the app encouraged me to build a meal by searching for foods in their database and combining them in beneficial ways for my blood sugar. Two slices of whole wheat bread received a score of 2.7 out of 10 ("Avoid"), but if combined with one cup of large curd cottage cheese, the score improved to 6.8 ("Limit"), and if I added two hard-boiled eggs, the score went up to 7.5 ("Good").
Perusing my list of foods with "Excellent" scores, I noticed some troubling conflicts with the other app. Lentils, which had been a no-no according to Viome, received high marks from DayTwo. Ditto for Kombucha. My purported superfood of cranberry received low marks. Almonds got an almost perfect score (9.7) while Viome told me to minimize them. I found similarly contradictory advice for foods I regularly eat, including navel oranges, peanuts, pork, and beets.
Contradictory dietary guidance that Kira Peikoff received from Viome (left) and DayTwo from an identical sample.
To be sure, there was some overlap. Both apps agreed on rice noodles (bad), chickpeas (bad), honey (bad), carrots (good), and avocado (good), among other foods.
But still, I was left scratching my head. Which set of recommendations should I trust, if either? And what did my results mean for the accuracy of this nascent field?
I called a couple of experts to find out.
"I have worked on the microbiome and nutrition for the last 20 years and I would be absolutely incapable of finding you evidence in the scientific literature that lentils have a detrimental effect based on the microbiome," said Dr. Jens Walter, an Associate Professor and chair for Nutrition, Microbes, and Gastrointestinal Health at the University of Alberta. "I just don't think sufficient data is yet available to make reliable personalized dietary recommendations based on one's microbiome. And even if they would have proprietary algorithms, at least one of them is not doing it right."
There is definite potential for personalized nutrition based on the microbiome, he said, but first, predictive models must be built and standardized, then linked to clinical endpoints, and tested in a large sample of healthy volunteers in order to enable extrapolations for the general population.
"It is mindboggling what you would need to do to make this work," he observed. "There are probably hundreds of relevant dietary compounds, then the microbiome has at least a hundred relevant species with a hundred or more relevant genes each, then you'd have to put all this together with relevant clinical outcomes. And there's a hundred-fold variation in that information between individuals."
However, Walter did acknowledge that the companies might be basing their algorithms on proprietary data that could potentially connect all the dots. I reached out to them to find out.
Amir Golan, the Chief Commercial Officer of DayTwo, told me, "It's important to emphasize this is a prediction, as the microbiome field is in a very early stage of research." But he added, "I believe we are the only company that has very solid science published in top journals and we can bring very actionable evidence and benefit to our uses."
He was referring to pioneering work out of the Weizmann Institute that was published in 2015 in the journal Cell, which logged the glycemic responses of 800 people in response to nearly 50,000 meals; adding information about the subjects' microbiomes enabled more accurate glycemic response predictions. Since then, Golan said, additional trials have been conducted, most recently with the Mayo Clinic, to duplicate the results, and other studies are ongoing whose results have not yet been published.
He also pointed out that the microbiome was merely one component that goes into building a client's profile, in addition to medical records, including blood glucose levels. (I provided my HbA1c levels, a measure of average blood sugar over the previous several months.)
"We are not saying we want to improve your gut microbiome. We provide a dynamic tool to help guide what you should eat to control your blood sugar and think about combinations," he said. "If you eat one thing, or with another, it will affect you in a different way."
Viome acknowledged that the two companies are taking very different approaches.
"DayTwo is primarily focused on the glycemic response," Naveen Jain, the CEO, told me. "If you can only eat butter for rest of your life, you will have no glycemic response but will probably die of a heart attack." He laughed. "Whereas we came from very different angle – what is happening inside the gut at a microbial level? When you eat food like spinach, how will that be metabolized in the gut? Will it produce the nutrients you need or cause inflammation?"
He said his team studied 1000 people who were on continuous glucose monitoring and fed them 45,000 meals, then built a proprietary data prediction model, looking at which microbes existed and how they actively broke down the food.
Jain pointed out that DayTwo sequences the DNA of the microbes, while Viome sequences the RNA – the active expression of DNA. That difference, in his opinion, is key to making accurate predictions.
"DNA is extremely stable, so when you eat any food and measure the DNA [in a fecal sample], you get all these false positives--you get DNA from plant food and meat, and you have no idea if those organisms are dead and simply transient, or actually exist. With RNA, you see what is actually alive in the gut."
More contradictory food advice from Viome (left) and DayTwo.
Note that controversy exists over how it is possible with a fecal sample to effectively measure RNA, which degrades within minutes, though Jain said that his company has the technology to keep RNA stable for fourteen days.
Viome's approach, Jain maintains, is 90 percent accurate, based on as-yet unpublished data; a patent was filed just last week. DayTwo's approach is 66 percent accurate according to the latest published research.
Natasha Haskey, a registered dietician and doctoral student conducting research in the field of microbiome science and nutrition, is skeptical of both companies. "We can make broad statements, like eat more fruits and vegetables and fiber, but when it comes to specific foods, the science is just not there yet," she said. "I think there is a future, and we will be doing that someday, but not yet. Maybe we will be closer in ten years."
Professor Walter wholeheartedly agrees with Haskey, and suggested that if people want to eat a gut-healthy diet, they should focus on beneficial oils, fruits and vegetables, fish, a variety of whole grains, poultry and beans, and limit red meat and cheese, as well as avoid processed meats.
"These services are far over the tips of their science skis," Arthur Caplan, the founding head of New York University's Division of Medical Ethics, said in an email. "We simply don't know enough about the gut microbiome, its fluctuations and variability from person to person to support general [direct-to-consumer] testing. This is simply premature. We need standards for accuracy, specificity, and sensitivity, plus mandatory competent counseling for all such testing. They don't exist. Neither should DTC testing—yet."
Meanwhile, it's time for lunch. I close out my Viome and DayTwo apps and head to the kitchen to prepare a peanut butter sandwich. My gut tells me I'll be just fine.
The U.S. has the highest incarceration rate in the world, costing $182 billion per year, partly because its antiquated data systems often fail to identify people who should be released. A tech nonprofit is trying to change that.
Recidiviz has built a platform that connects the different databases, with the goal of identifying people who are already qualified for release but remain behind bars or on supervision. “Think of Recidiviz like Google Maps,” says Jacoby, who worked on Maps when she was at the tech giant. Google Maps takes in data from different sources – satellite images, street maps, local business data — and organizes it into one easy view. “Recidiviz does something similar with criminal justice data,” Jacoby explains, “making it easy to identify people eligible to come home or to move to less intensive levels of supervision.”
People like Jacoby’s uncle. His experience with incarceration is what inspired her passion for criminal justice reform in the first place.
The problems are vast
The U.S. has the highest incarceration rate in the world — 2 million people according to the watchdog group, Prison Policy Initiative — at a cost of $182 billion a year. The numbers could be a lot lower if not for an array of problems including inaccurate sentencing calculations, flawed algorithms and parole violations laws.
Sentencing miscalculations
To determine eligibility for release, the current system requires corrections officers to check 21 different requirements spread across five different databases for each of the 90 to 100 people under their supervision. These manual calculations are time prohibitive, says Jacoby, and fall victim to human error.
In addition, Recidiviz found that policies aimed at helping to reduce the prison population don’t always work correctly. A key example is time off for good behavior laws that allow inmates to earn one day off for every 30 days of good behavior. Some states' data systems are built to calculate time off as one day per month of good behavior, rather than per day. Over the course of a decade-long sentence, Jacoby says these miscalculations can lead to a huge discrepancy in the calculated release data and the actual release date.
Algorithms
Commercial algorithm-based software systems for risk assessment continue to be widely used in the criminal justice system, even though a 2018 study published in Science Advances exposed their limitations. After the study went viral, it took three years for the Justice Department to issue a report on their own flawed algorithms used to reduce the federal prison population as part of the 2018 First Step Act. The program, it was determined, overestimated the risk of putting inmates of color into early-release programs.
Despite its name, Recidiviz does not build these types of algorithms for predicting recidivism, or whether someone will commit another crime after being released from prison. Rather, Jacoby says the company’s "descriptive analytics” approach is specifically intended to weed out incarceration inequalities and avoid algorithmic pitfalls.
Parole violation laws
Research shows that 350,000 people a year — about a quarter of the total prison population — are sent back not because they’ve committed another crime, but because they’ve broken a specific rule of their probation. “Things that wouldn't send you or I to prison, but would send someone on parole,” such as crossing county lines or being in the presence of alcohol when they shouldn’t be, are inflating the prison population, says Jacoby.
It’s personal for the co-founder and CEO
“I grew up with an uncle who went into the prison system,” Jacoby says. At 19, he was sentenced to ten years in prison for a non-violent crime. A few months after being released from jail, he was sent back for a non-violent parole violation.
“For my family, the fact that one in four prison admissions are driven not by a crime but by someone who's broken a rule on probation and parole was really profound because that happened to my uncle,” Jacoby says. The experience led her to begin studying criminal justice in high school, then college. She continued her dive into how the criminal justice system works as part of her Passion Project while at Google, a program that allows employees to spend 20 percent of their time on pro-bono work. Two colleagues whose family members had also been stuck in the system joined her.
As part of the project, Jacoby interviewed hundreds of people involved in the criminal justice system. “Those on the right, those on the left, agreed that bad data was slowing down reform,” she says. Their research brought them to North Dakota where they began to understand the root of the problem. The corrections department is making “huge, consequential decisions every day [without] … the data,” Jacoby says. In a new video by Recidiviz not yet released, Jacoby recounts her exchange with the state’s director of corrections who told her, “‘It’s not that we have the data and we just don’t know how to make it public; we don’t have the information you think we have.'"
A mock-up (with fake data) of the types of dashboards and insights that Recidiviz provides to state governments.
Recidiviz
As a software engineer, Jacoby says the comment made no sense to her — until she witnessed it first-hand. “We spent a lot of time driving around in cars with corrections directors and parole officers watching them use these incredibly taxing, frankly terrible, old data systems,” Jacoby says.
As they weeded through thousands of files — some computerized, some on paper — they unearthed the consequences of bad data: Hundreds of people in prison well past their release date and thousands more whose release from parole was delayed because of minor paperwork issues. They found individuals stuck in parole because they hadn’t checked one last item off their eligibility list — like simply failing to provide their parole officer with a paystub. And, even when parolees advocated for themselves, the archaic system made it difficult for their parole officers to confirm their eligibility, so they remained in the system. Jacoby and her team also unpacked specific policies that drive racial disparities — such as fines and fees.
The Solution
It’s more than a trivial technical challenge to bring the incomplete, fragmented data onto a 21st century data platform. It takes months for Recidiviz to sift through a state’s information systems to connect databases “with the goal of tracking a person all the way through their journey and find out what’s working for 18- to 25-year-old men, what’s working for new mothers,” explains Jacoby in the video.
TED Talk: How bad data traps people in the U.S. justice system
TED Fellow Clementine Jacoby's TED Talk went live on Jan. 13. It describes how we can fix bad data in the criminal justice system, "bringing thousands of people home, reducing costs and improving public safety along the way."
Clementine Jacoby • TED2022
Ojmarrh Mitchell, an associate professor in the School of Criminology and Criminal Justice at Arizona State University, who is not involved with the company, says what Recidiviz is doing is “remarkable.” His perspective goes beyond academic analysis. In his pre-academic years, Mitchell was a probation officer, working within the framework of the “well known, but invisible” information sharing issues that plague criminal justice departments. The flexibility of Recidiviz’s approach is what makes it especially innovative, he says. “They identify the specific gaps in each jurisdiction and tailor a solution for that jurisdiction.”
On the downside, the process used by Recidiviz is “a bit opaque,” Mitchell says, with few details available on how Recidiviz designs its tools and tracks outcomes. By sharing more information about how its actions lead to progress in a given jurisdiction, Recidiviz could help reformers in other places figure out which programs have the best potential to work well.
The eleven states in which Recidiviz is working include California, Colorado, Maine, Michigan, Missouri, Pennsylvania and Tennessee. And a pilot program launched last year in Idaho, if scaled nationally, with could reduce the number of people in the criminal justice system by a quarter of a million people, Jacoby says. As part of the pilot, rather than relying on manual calculations, Recidiviz is equipping leaders and the probation officers with actionable information with a few clicks of an app that Recidiviz built.
Mitchell is disappointed that there’s even the need for Recidiviz. “This is a problem that government agencies have a responsibility to address,” he says. “But they haven’t.” For one company to come along and fill such a large gap is “remarkable.”
