Are Microbiome Food Recommendations Real or Hype?

Thomas David Kehoe
11 min readMar 16, 2018

Microbiomes influence physical and mental health. Two companies, Viome and DayTwo, tell you what foods to eat and what foods to avoid, based on your gut microbiota. DayTwo is $499; Viome is $119. I did DayTwo once and Viome twice.

I’m a super-healthy 57-year-old with no gastrointestinal (GI) disorders. I’ve taken antibiotics only once in my life. I can eat anything. I ate out of Whole Foods dumpsters for three years without ill effects.

I’ve been bitten by dogs three times and never been infected. A few months ago I stepped on a nail sticking out of a board. I cleaned the wound and checked that my last tetanus booster was less than five years ago. The wound became infected and hurt for about ten hours. After that the infection went down and was gone in a week.

The typical American kid takes twenty courses of antibiotics by his or her 18th birthday; adults take antibiotics every two years. I believe that old people are healthier than young people because we grew up without so many antibiotics.

I believe that antibiotics are overprescribed by doctors, that antibiotics damage one’s microbiome, and that this is causing or contributing to the epidemic I’m seeing of combined GI disorders, metabolic disorders (e.g., obesity), and mental health issues. (The people I see with these three conditions don’t have a specific mental illness, they just have nonspecific mental health problems.)

My Winning Microbiome

Outside magazine recently had an article comparing the microbiomes of seven top outdoor athletes. Sponsored obstacle course racer Amelia Boone, who advertises for the Tough Mudder races, was declared to have the “winning microbiome.”

“Amelia Boone Has a Winning Microbiome”

I didn’t realize that competitive microbiomes are a sport now. Ms. Boone’s secret to winning the microbiome competition is that half the bacteria in her gut is Acinetobacter, a rare bacteria found in soil. None of the other competitors had any Acinetobacter, and I don’t have any either. Apparently crawling through mud pits involves eating a lot of dirt.

Here’s the data visualization of the seven athletes’ microbiomes:

Microbiomes of seven outdoor athletes

The takeaway is, different people have different microbiomes. My microbiome looks like none of the seven athletes.

My First Viome Gut Bacteria

My gut bacteria (“Activity” is me), according to Viome.

Viome no longer tells you the percentages of each bacteria. Now you just get a list of microbes.

My DayTwo Gut Bacteria

My gut bacteria, according to DayTwo.

The Viome and DayTwo results don’t match. They’re not even close. Only four of the 23 bacteria in Viome’s results were found in DayTwo’s results, and all four were down the list, in the 1% bracket or less. The C. difficile that was #2 in Viome’s analysis wasn’t even found by DayTwo. I did the two analyses a year apart, but my diet, health, etc. didn’t change.

The “population” numbers don’t match either.

Viome doesn’t tell you what each bacterium does. DayTwo gives you a little biographical sketch of each bug:


I asked DayTwo why the two companies don’t match. Tread Childs responded immeadiately:

This is not very surprising.

Viome is using RNA sequencing which is different (and not superior) from our sequencing method by showing the microbiome actual gene expression (which means that you measure which bacteria are active and what do they do) instead of the microbiome genetic potential in our shotgun DNA sequencing.

However, RNA is far less stable and requires much more delicate lab protocols, especially when extracted from harsh environments like stool samples, it provides very noisy measurements. Any mishandling of the sample by the client may increase this noise significantly. This is unlike DNA, which is relatively stable.

DayTwo Scientific Basis

DayTwo’s customer service is outstanding. When I inquired about the scientific basis of their recommendations, an employee quickly sent me a study in Cell, Personalized Nutrition by Prediction of Glycemic Responses. The five-year study was conducted at Isreal’s Weizmann Insitute of Science. The resulting technology was then licensed to DayTwo.

The investigation followed blood glucose responses in 800 subjects, measuring responses to 46,898 meals. The investigators developed software to predict blood glucose responses to meals based on gut microbiota and other parameters.

Next, 26 subjects were divided into two groups. 12 subjects ate diets based on the software’s recommendations; 10 out of 12 had improved outcomes. 14 subjects ate diets based on expert dieticians’ recommendation; 8 out of 14 had improved outcomes. In other words, the software was as good as or better then the experts.

Finally, the 26 subjects’ microbiomes were analyzed, before and after the dietary changes; increases in “good” bacteria were seen, and decreases in “bad” bacteria.

Viome hasn’t published a similar study. I don’t know where they got their food recommendations from, but the phrase “pulled out of their ass” comes to mind.

DayTwo Procedure and Customer Service

When sending in my poop sample, DayTwo also asks for standard blood test results. I’d just had my annual checkup so I copied the results over to DayTwo’s forms.

When my results were ready I received an email from DayTwo, plus a real person called me and said that I could schedule a free consultation with a nutritionist.

DayTwo’s Food Recommendations

DayTwo’s focus is on diabetes and glycemic control. I don’t have diabetes so I’m not their target customer.

DayTwo’s food recommendations were uncanny. Blackberries were on of my top recommended fruits. When I lived (in poverty) in Oregon, I picked blackberries during the summers. I never got tired of eating blackberries three times a day. DayTwo recommended other fruits that I eat as much as I can (in season) including peaches, melons, and pomegranates.

The fruits DayTwo told me to avoid, I’ve never liked. Red and green grapes taste like they were made in a factory. When I was a kid we got good apples from farm stands in Wisconsin, but apples have been bred into tastelessness. I don’t like guavas. DayTwo’s fruit recommendations felt dead on.

It’s possible that my microbiome is tuned for blackberries, peaches, melons, and pomegranates because these are the fruit I eat most often; and that my microbiome isn’t tuned for grapes because I don’t eat grapes.

DayTwo’s vegie recommendations were good too. My top vegies included asparagus, which I’ve always eaten lots of in season. Roasted brussel sprouts were my always-bought deli items when I shopped at Whole Foods. My vegies to avoid are potatoes, yams, and sweet potatoes, which I’ve never eaten much of.

In the dairy section, DayTwo recommended cheese for me. Cheese is my favorite food. I was born in Canada and grew up in Wisconsin. Check out my blog post about scoring 200 kg ($7000) of European cheeses from the Whole Foods dumpster. Yogurt is also recommended. I eat yogurt every morning with blackberries.

The breads and cereals section says that whole grain breads are OK for me, on a limited basis. I’ve never eaten much bread, and I only like whole grain breads. My DayTwo “avoid” list includes bagels and cream cheese, which I’ve never liked. I’ll rate this section as accurate too.

In the meat, fish, and eggs section, eggs are recommended at the top. I like eggs and eat them regularly. Tuna, steak, salmon, I love all these and eat them often. (Organic, grass-fed steaks, frozen and vacuum-packed, are an item that Whole Foods throws out in large quantities, which my dog and I ate almost daily.) Tilipia is on my “limit” list. It’s not my favorite fish. Squid is further down the list. I don’t like squid. (Learning that much calimari sold in American restaurants is actually pork bung didn’t increase my appetite for squid.) This section feels right to me, except that salmon sashimi is on my “avoid” list. I love salmon sashimi. It could be that suchi is mostly white rice.

In the legumes and nuts section, walnuts are at the top of my recommended list. I eat lots of walnuts. I make pesto every week, and I’ve tried cashews, pine nuts, and sunflower seeds, but walnuts make the best pesto. Peanut butter is high on my list, which I love. Chia and flax seeds are high on my recommendations, and I put these in my protein shakes. I just like them, and how they make me feel for hours afterwards. On my avoid list are veggie burgers, of all types. I’ve never liked veggie burgers. Plus, as a Boulder Jew, I never eat a veggie burger when I’m drinking soy milk. :-) This section feels right.

Moving to snacks and sweets, brownies are recommended. Well, I like brownies, but I hardly ever eat them. OK, when we’d get pounds of carmelita bars from the Whole Foods dumpster, I couldn’t resist them. Cinnamon rolls are also good for me, according to DayTwo. Cheesecake is recommended further down the list, and I hate cheesecake. There are lots of desserts on the “avoid” list that I like but rarely eat. The “recommended desserts” list doesn’t make any sense to me, so I asked Tread Childs to explain it:

a cinnamon roll will spike your blood sugar less than the specific amount represented for beans or kale. This does not mean we encourage you to have cinnamon rolls for 3 meals a day — but maybe the cinnamon roll is a better option on “cheat day” than the spiking French Toast Meal, for example. Conversely, while kale is considered to be healthy, we can see that it can spike your blood sugar and therefore we would advise to eat it with something such as a kale salad with an olive oil based dressing, rather than on its own.

The last list is beverages. It recommends that I drink alcohol and coffee, neither of which I drink. Juices are on the “avoid” list, and I don’t drink much juice either.

All in all, the DayTwo food recommendations feel right. They’re not going to make me change my diet, as the foods I eat often are recommended and the foods I don’t eat are on the “avoid” list, but I’ll feel justified when making my shopping choices.

Viome Results

Viome’s website doesn’t indicate that their recommendations are based on a published scientific study.

Instead of telling you how much of various microbes you have in your poop, Viome tells you your scores on 19 pathways and other activity. My results said that I had five poor areas, eight good areas, and six acceptable areas.

Topping my “scores to focus on” was “Overall Gas Production.” Viome got that right! My grandmother farted frequently and my mom’s fart storms left my ex-wife incredulous. My farting led to my ex-wife’s nickname for me, which I will decline to share. Viome further tells you whether your gas problem is oderless methane (my problem) or stinky hydrogen sulfide (I’m good on that). I’ll ask my friends to verify that my farts are oderless!

Another area of concern was “Butyrate Production Pathways.” Butyrate is a beneficial nutrient (a short-chain fatty acid) “known to beneficially affect many wellness areas from gut lining to insulin sensitivity and satiety (feeling full).” I do have problems feeling full. After eating a meal I often continue to feel hungry for an hour or so. I never really feel full, the best I can do is to not feel hungry. DayTwo also found that I lack the bacteria that produces butyrate. I took a probiotic that provides this bacteria but I guess it didn’t do anything.

My other areas of concern are “Oxalate Metabolism Pathways,” which contribute to kidney stones, which I’ve never had; and “uric acid production pathways,” which leads to gout, which I’ve also never had.

If Viome’s diet recommendations work for me, I should fart less, feel more full, and not develop kidney stones or gout.

My good scores were for:

  • Protein Fermentation. I crave protein for breakfast and lunch.
  • Flagellar Assembly Pathways, which indicate “unrest in your microbiome as flagellar structures are helping beneficial organisms move away from a perceived threat.”
  • Salt Stress Pathways, which indicate too much salt in your diet. I don’t eat much salt.
  • Bile Acid Metabolism Pathways. A poor score indicates an “inability to break down fat or absorb nutrients properly.”
  • LPS Biosynthesis Pathways, which relates to inflammatory activity.
  • Ammonia Production Pathways. A poor score indicates that proteins aren’t digesting properly and food isn’t moving adequately down one’s GI tract.
  • Biofilm, Chemotaxis, and Virulence Pathways. A poor score indicates a “microbial war zone” or “a pro-inflammatory or hostile environment in the gut….some threat in the environment and your microbes are trying to either defend themselves, attack each other, or move.”
  • TMA Production Pathways. A poor score indicates “unfavorable metabolic and cardiovascular effects.”

My acceptable scores included:

  • Metabolic Fitness. A poor score indicates problems with “blood sugar, insulin resistance, or weight control.” I’ve never had these issues.
  • Digestive Efficiency.
  • Inflammatory Activity.
  • Intestinal Barrier Health. This indicates the health of your gut lining and the possibility of toxins and harmful bacteria leaving your GI tract and entering your bloodstream, i.e., a “leaky gut.”
  • Sulfide Gas Production Pathways. The stinky part of farts.
  • Putrescine Production Pathways. A poor score indicates that you’re eating too much protein and not digesting it properly.

Overall, these results feel right, and they are consistent with each other.

Viome’s Food Recommendations

Viome recommended that I take four supplements: a probiotic, a prebiotic, curcumin (I already take turmeric), and butyrate supplement. The first three are likely general good advice that they tell everyone.

Viome’s food recommendations match DayTwo’s recommendations. I should eat:

  • asparagus
  • Brussels sprouts
  • blackberries
  • cheese
  • yogurt
  • eggs
  • beef
  • salmon
  • walnuts
  • peanuts
  • chia
  • flax

I should avoid:

  • grapes

Viome and DayTwo disagree on tuna.

Viome only listed eleven foods for me to avoid. Four I don’t eat: crab, goat, haddock, and hemp hearts. The other seven I eat: bell peppers, blueberries, green beans, navy beans, pinto beans, spinach, and trout. Changing my diet to avoid these foods won’t be difficult.

There’s also a “minimize” list of about 60 foods. The changes I’ll have to make are almonds (I’ll switch from almond milk to oat milk), cabbage (I love cabbage in salads), cherries (I eat cherries every day when they’re in season), chickpeas, cranberries, dates, honeydew, lentils, mangos, maple syrup (no, please, I love maple syrup!), miso, nectarines, oranges, papayas, pears (I eat a pear every morning in the winter), peppermint and spearmint, plums, pumpkin, rice (including rice milk and rice noodles), salt, soybeans (including soy milk, tofu, and tempeh), stevia (I hate it), sweet potatoes and yams, tuna, and watermelon. Minimizing these foods will be harder. When I was in Montreal I ate breakfast at a restaurant that had a “sugar shack” breakfast: crepes with maple syrup, ham cooked with maple syrup, beans cooked with maple syrup, eggs, and potatoes. I’m starting to cry…


Both Viome and DayTwo seem to be legitimate. I like that Viome presents their results as 19 pathways, instead of percentages of individual microbes. The food recommendations of both companies more or less match, even though the microbes each found don’t match. If diabetes is your concern, go for DayTwo. If you’re more interested in general health, Viome is less expensive.

The Podcast I Recommend

After I wrote this blog post Damien Blenkinsopp suggested that I listen to his interview with Richard Sprague, on his podcast The Quantified Body. I’d searched for reviews comparing DayTwo and Viome before going with Viome, but found nothing. This podcast is two hours long and super detailed about microbiome testing, comparing many labs and services.



Thomas David Kehoe

I make technology for speech clinics to treat stuttering and other disorders. I like backpacking with my dog, competitive running, and Russian jokes.