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Have you ever spent a really long time looking at a diagram of butanoate metabolism? Or wondered if your Firmicutes are producing butyrate? I’ve been having all kinds of thoughts like this since sending my intestinal microbes to verified labs for identification and testing. I’m a food writer, not a science writer. But as I explain to my husband while googling “how to identify your microbiota,” it’s a logical professional evolution from food to digestion.
I’ve long been preoccupied by my colon. My father died of colon cancer when I was a teenager; mine is of the utmost concern. Digestive health has always been rather niche—not to mention private. But suddenly, everyone talks about “gut health.” We talk, specifically, about our microbiomes—the trillions of bacteria that inhabit us, which have been linked to sleep, heart health, mental health, aging. I read aloud to my husband from the medical journal The Lancet: “The expectation that sequencing one’s gut microbiome might be the key to diagnosis and treatment where conventional approaches have failed is now fairly commonplace within gastroenterology clinics and beyond.”
According to a publication called Nutrition in Clinical Practice, these days, internet searches for “gut microbiome” and “gut microbiota” generate millions of results. Amazon teems with microbiome books, including microbiome books for kids—Meena and the Microbiome (forthcoming in 2025)—and dogs—Healthy Gut, Healthy Dog. Gut health is taking over TikTok. Scan your refrigerator for the word “probiotic.” Brands are shilling directly to your bacteria!
Roshini Raj, MD—associate professor at NYU Grossman School of Medicine, frequent guest on the Today show and CNN, and author (Gut Renovation: Unlock the Age-Defying Power of the Microbiome to Remodel Your Health from the Inside Out)—tells me that in rodents, specific microbiomes have been linked to different personalities. It’s like getting a star chart reading—but scientific!
Apparently, one can’t (yet) go to your internist for a microbiome checkup. But in our age of at-home health tests, I can have my microbiome evaluated from the comfort of home. Four tests I read about—DayTwo, Genova, Labcorp, and Carbiotix—need a doctor’s prescription. But others are sold direct-to-consumer. It’s an embarrassment of riches. Cross-referencing reviews, I choose two, Viome and Zoe. Speaking of embarrassment: to test one’s microbiome, one must provide a sample of what comes from one’s microbiome. At a dinner party, I workshopped several euphemisms and found them all lacking in poetry.
Waiting for the tests to arrive, I read. The belief that bacteria are bad is as outdated as bloodletting. The field of microbiology focused on pathogenic—i.e., disease-
causing—bacteria for over a century because the connection between disease and bacteria had just been established. In the last 25 years, however, we’ve seen that our guts are brimming with beneficial bacteria. (Also: viruses, fungi, archaea, and eukaryotes.) The role of microbiota in the gut-brain axis, an active network of communication between the intestinal nervous system and the central nervous system, was discovered by two women in 1986. Research in the last decade has revealed ever more intimate links between our microbiomes and all our bodily functions. We’ve currently identified one thousandth of one percent of all the microbes on earth. Each microbiome is as unique as a fingerprint. They’re also catching: Research says our microbiomes can resemble those of the people we live with.
My test kits arrive in sleekly designed boxes emblazoned with slogans. Zoe’s declares: “It’s time to start understanding your body.” In Viome’s instruction manual, I read: “Welcome to the next step on your health journey!” I buzz with anticipation. These boxes contain smaller boxes, containing finger prickers and pipettes—both Viome and Zoe require you to take your own blood. It’s when I pull a tape measure out of the Viome box that I wonder if I’m in too deep. (You can exhale. It’s for measuring one’s stomach bloat.)
Zoe’s test requires clients to eat two glucose-heavy cookies before testing. They are awful. The first I forgo after two bites, deeming no internal astrology worth it. The other is robin’s-egg blue. I pretend it’s Play-Doh—which I used to enjoy—and choke it down. As I proceed with my sample collection, I’m reminded that some enterprises tend to elude you the instant you focus on them. Like sneezing, and getting pregnant. And…other things.
But let us skim nimbly past such details. Eventually, two inconspicuous padded envelopes filled with relevant samples are dropped off to be mailed. For Zoe, I wear a blood sugar monitor for two weeks—gathering information that will help dictate my personalized recommendations. I find this engrossing, checking it every 15 minutes, which, according to my husband, makes me look like I’m investigating my armpit. But then, my test results arrive, first from Viome, then Zoe, and it’s time for me to meet my trillions of tenants.
According to Viome, my active gut microbes include Akkermansia muciniphila and Bifidobacterium adolescentis ATCC 15703—which are both generally considered “good”—as well as Bubaline alphaherpesvirus 1, a virus native to water buffalo. There are dozens of others, sequenced and identified. Though I keep reviewing my lists, I can’t find any additional description of my microbes as “good” or “bad.” It’s just a neutral list of Latin names which, after I’ve waited so expectantly, is a bit of a letdown.
I call Grant Antoine, Viome’s supplement lead, and Viome CEO Naveen Jain, for help navigating my results. I read Antoine my list of microbes, hoping for some thumbs-up or down. He repudiates me. Apparently, microbes can’t be clearly defined as good or bad. But wasn’t that the whole point? What about the rodents? “Those are just associations,” says Antoine. “There’s no causal relationship there that we’re aware of.” Bacterial diversity should be high. Otherwise, the list of microbes is just a courtesy.
Viome’s technology focuses on RNA, providing insight into the actual function of my microbes. Viome then rates this functioning—delivering 63 qualitative scores, including Digestive Efficiency (41, “Average”) and TMA Production (“Good”). I have a lot of “Average.” My biological age is two years younger than my actual age. I have red “Suboptimal” scores for Cognitive Health, Digestive Efficiency, and Gut Lining Health, among others. My microbes, it seems, are falling asleep on the job. Antoine tries to reassure me. “Your results were pretty good. You had a couple of areas to work on.” Jain disagrees: “Anything that’s ‘Average’ requires improvement.”
Zoe sequences my microbiome using a technology called shotgun metagenomics, which maps DNA. I prefer Viome’s app and what my husband calls “user experience.” But I prefer my results from Zoe. Zoe divides my microbes into “good” and “bad”—though I now have Antoine’s voice in my head reminding me it’s just association. My Blood Sugar Control is “Excellent.” My Blood Fat Control and Microbiome Biodiversity are “Good.”
I compare the two lists of microbes. There’s some overlap, and some divergence. Maybe my microbiome changed. Maybe the companies use different datasets for identification. Looking back and forth, it occurs to me that there’s no standardized dataset against which to compare results. There’s no universal terminology, no consensus about which variables matter and what causes them to vary.
More perplexing is what to do next. Viome instructs all clients to avoid sugar, flour, soda, and cured meat. My personalized list of “avoid” and “minimize” foods from Viome is short: cassava, couscous, barley, maple syrup, molasses, white rice, and breadfruit—plus red bell peppers because, apparently, my gut hosts a red bell pepper virus I’m obliged to starve out. Otherwise, I’m supposed to eat “superfoods”—like cabbage, fennel, and bamboo shoots—and take $199 worth of custom formulated precision supplements, prebiotics, probiotics, and oral lozenges, each month. (Each supplement pack arrives with my name printed on it, which is oddly flattering.)
Zoe doesn’t sell supplements. Its researchers advise me to avoid my “gut suppressors”—which include canned soup and cheese-flavored corn puffs—and eat “gut boosters,” including avocados, lentils, kale, collards, peas, chickpeas, kidney beans…and bell peppers. Zoe’s lead nutritionist, Federica Amati, tells me that this will provide a beneficial substrate for my good bacteria and ideally starve “the bad guys.” When I review all the recommendations side by side, they amount to avoiding processed foods and eating lots of plants. “I just don’t know that the science is quite there yet for recommendations to be that accurate on an individual basis,” is Raj’s assessment. Suzanne Devkota, director of the Cedars Sinai Human Microbiome Research Institute, is even less ambiguous. “The sequencing part of most of these tests is probably fine, but the recommendations they give you are all crap.” She recognizes the value in Viome’s data. “But what to do about it? We still don’t know.”
Because they aren’t FDA regulated, at-home microbiome tests can’t diagnose anything really worrisome. Even if there were an accepted microbial fingerprint for leaky gut, or depression, or insomnia, neither Viome nor Zoe would have been legally allowed to identify it to me. Devkota, who’s advocated for FDA oversight of at-home microbiome tests, believes the tests have a place in health assessment—she tells me: “I think everyone should have a healthy baseline, and that includes the microbiome. What I recommend is to only use one company, and buy a few of the kits and test yourself every six months. And only compare your data to yourself, and totally ignore where they put you on a plot.” I ask Alessio Fasano, MD, professor of nutrition at Harvard T.H. Chan School of Public Health and director of the Mucosal Immunology and Biology Research Center at MassGeneral Hospital for Children (he also sits on Viome’s advisory board), how science knows that if I follow my recommendations my microbes will move in the right direction. “That’s the $30 million question,” he says with a laugh. “And to make a long and complicated story short: It’s definitely a work in progress.”
One of the most quietly revolutionary developments to come from the field of microbiome research is a further dismantling of the orthodoxy of “calories in, calories out.” A 2015 study published in Cell found wide variation in blood sugar response to the same foods based on participants’ “lifestyle, medical background, and the composition and function of his or her microbiome.” Whether or not my own personalized recommendations are helpful, the underlying scientific fact—that one man’s meat is another man’s poison—is potentially life changing, on a population level.
It’s been several weeks since I started eating “superfoods” and “gut boosters” and (mostly) skipping “avoid” foods. I’m unquestionably healthier. I refuse to log meals, and I plan to cancel my supplement subscription. But, conscious that I’m feeding my vast internal populations and seeking to starve bad actors, I’ve been eating differently. There’s solid data showing that eating 30 different plants a week results in a more resilient microbiome, a number I hold in the back of my mind. I’m certain that my internal star map would look better if I tested it today.