Review: Jona Microbiome Test

We hear a lot about the microbiome, also known as the zoo of different bacteria living in your digestive system. We know some are good and some are bad. Some strains are associated with longevity, while others are associated with scary diseases.

In fact, virtually every aspect of our health has been linked to the microbiome, in one way or another, including cancer, mental health, and diabetes. There are also thousands of companies out there that want you to spend your entire paycheck on supplements, which may or may not be right for your body’s specific needs. Meanwhile, thousands of studies on the microbiome are published each month. Even the world’s geekiest gastroenterologist can’t keep up with all of that.

That’s where a new company called Jona comes in. It uses AI to analyze the hundreds of bacterial strains in your gut, cross-reference them with all the latest and highest-quality research, then give you a breakdown of your results and an action plan you can follow to theoretically improve your health outcomes. While AI gets shoehorned into virtually every product these days, whether we want it or not, this implementation actually makes sense.

How It Works

To use Jona, order a kit online. The kit is the same gold-standard kit that your GI doctor would give you, which is known as a shotgun test. It scans for every strain of bacteria, as well as pathogens like parasites and viruses. It’s a home stool-sample kit which—while strange—is easy to use. You ship your sample off to a lab using the included self-paid packaging. The lab is also independent of Jona (and again, it’s probably the same one your doctor would use); it just sends the results to Jona.

Those results are likely to contain hundreds of different bacteria and their relative abundance in your system. It would take you years to research the significance of each one, and by the time you got to the end, enough new research would be out that you’d have to start all over.

The service that Jona provides is that it has an LLM constantly reading new studies as they are published. It ranks the quality and applicability as it goes, too. For example, a study with a large sample size of humans, studied over time, from a reputable institution would likely be rated a 3 (the highest), while a small study that only used mice or petri dishes would likely be rated a 1.

Roughly two to three weeks after you send in your sample, you get a detailed, interactive report that highlights your health associations (i.e. if there’s anything to look out for), as well as the things you might do to improve them. If you want to read the study or studies that led the AI to that conclusion, they will be linked there, too.

Critically, Jona does not sell any supplements or probiotics, nor does it recommend brands of supplements or probiotics for an affiliate kickback. I really like that a lot. There are other home gut tests that are cheaper than Jona’s, but they rarely use shotgun testing, and most have their own stores and drive their customers toward buying expensive supplements. The only product Jona sells is the test and analysis, which basically eliminates conflict of interest.

In More Detail

Courtesy of Jona

When you first purchase your kit, you fill out an intake form. This has basic questions about your diet, lifestyle, and exercise habits, as well as your family medical history. This is where you put in any concerns you or your doctor may have. Have you been super gassy lately? Lots of fatigue? ADHD? Does your doctor say you’re prediabetic? Put all that in there. These are the things that Jona will keep an eye out for when it analyzes your test later (though it will show plenty more than that, as I’d soon find out). My home test kit arrived about three days after I purchased it.

Look, there’s nothing quite like starting your day by pooping on a little paper hammock affixed to your toilet seat and then poking it a bunch of times with a cotton swab. It was more of a mental hurdle than a practical one, though, as the collection and disposal (you just flush the hammock down when you’re done) was easy enough. You then swish the stick around in a solution, cap it, and send it off. Twenty days later, I got an email that my results were in.

On the website, your results are broken down into a few sections: Summary (with tabs for Brain Health, GI Health, Metabolic Health, Skin Health, and Physical Performance), Action Plan (with tabs for Highest Impact, Diet, Lifestyle, and Probiotics), and the Organisms page, which shows you every single organism it found in your sample, and their relative abundance. Mine held some surprises.

On the positive side, my Microbiome Diversity came in at 4.19, which is above average (normal range is 2.80–3.99, as measured by the Shannon Index), which it says is a sign of a healthy microbiome, and it didn’t find any pathogens or parasites. It says I digest lactose well (thank goodness). It didn’t find any associations for things like depression, celiac disease, IBS, ulcerative colitis, leaky gut, hypertension, eczema, or a bunch of other things that I’m thankful to not have. Some of these were actually a bit puzzling, frankly, as I’ve struggled with insomnia pretty much my entire life, but it didn’t find any associations there, or for fatigue, and I am most assuredly a tired human.

As far as associations that it did find, some were things I suspected, while others were total surprises. Under Brain Health, I had a moderate association for stress and a low association for ADHD, neither of which shocked me. Under Metabolic health was a “very low” association for prediabetes, which I actually thought would be higher, unfortunately. I had a moderate association with osteoarthritis, which made sense, given my family history.

But here's something strange: Under Metabolic Health it showed a moderate association with Hashimoto’s disease. That wasn’t something that was on my radar at all. I checked my bloodwork from my most recent physical, and my thyroid numbers looked normal, but I had a doctor’s appointment the next week anyway, so we ran some additional bloodwork that looked specifically at the thyroid. Sure enough, my thyroglobulin antibodies were almost double what they should be.

I quickly made an appointment with an endocrinologist who said I shouldn’t worry about it much for now, but it’s something to keep an eye on going forward. I’m so glad that I now know to stay up to date on it, and I wouldn’t have known at all if I hadn’t taken this test. Hopefully it will end up being nothing, but early detection could go a long way.

On the other side, it also found a moderate association for alopecia areata, an autoimmune disorder that causes large distinct patches of hair to fall out. And that’s very weird, because I demonstrably do not have that. So, it’s important to note that while some of elements of your microbiome might be associated with a condition, it’s by no means definitive, nor does it mean there’s causation there, necessarily.

It was also interesting to see what it didn’t find. For instance, on my intake I put that bloating was something I’d been experiencing, but my test results showed no associations with bloating. When I asked Jona’s team about it later, they noted that obviously that doesn’t mean that the issue isn’t happening, but they don’t have evidence for a link to the microbiome specifically. Of all the things that would be directly linked to the microbiome, you’d think bloating would be right up at the top, but evidently not in my case. I was actually a bit disappointed to find that, because I was hoping it would reveal that long elusive fix. Oh well.

What to Do

Courtesy of Jona

For each of the conditions listed, it would give me my top recommendations. For example, my top three for Hashimoto’s was to increase omega-3 fatty acids and magnesium (both based on established research) and to up my step count (limited research). You can also see the specific organisms you have that are associated with it and click References to see the associated studies. Even with this distillation, it’s still a lot of information to sort through, and it’s not always immediately clear how the linked studies pertain to your situation (at least for the layperson).

The next tab is the Action Plan. It features recommendations for Diet, Lifestyle, and Probiotics, but it also has a High Impact list which takes the top suggestions and gives you just a handful to focus on. For me it was increase aerobic exercise, vitamins C, D, and B2, and magnesium. Easy enough! I thought that helped it feel less overwhelming. It even auto-generates a downloadable grocery list, which I found helpful.

While the AI generally puts things together in a way that makes sense, there are definitely some head-scratchers. For instance, for Hashimoto’s, it says to avoid “probiotic containing Lacticaseibacillus paracasei strain Shirota.” But for prediabetes recommendations, I'm supposed to increase my consumption of this probiotic.

Elsewhere, polyphenols is one of my recommendations. It highlights foods that are good sources and suggests avoiding dark Chocolate and coffee, because these may conflict with other recommendations or self-reported food sensitivities. If I’m going to give up dark chocolate or coffee, I’d better have a good reason. It also recommended I consume more arabinoxylan, which is a starch found in cereal grains. I should eat more oats, barley, rye bread, and corn but not wheat nor rye. Why would it tell me to eat rye bread, but not rye?

I broke this down with Jona’s chief medical officer, Lawrence Kosinski. You may need to break down these results with your own doctor. In fact, Jona’s kit is the only one that’s available both to doctors and to consumers. Doctors typically won’t use anything that doesn’t use shotgun sequencing, and the analysis in the Jona report is a lot easier for doctors to understand. Since Jona is already an AI company, though, it would be nice for it to have a public-facing LLM chatbot that allows you to ask questions directly.

Interpretation

Courtesy of Jona

My call with Dr. Kosinski was interesting, not just for clarifying my results but for understanding Jona’s recommendations. Think of the gut like a petri dish. There are different types of petri dishes containing different substrates (i.e. foods), depending on what they want to grow. “So you need to create the right milieu to create the right microbiome,” Kosinski said. "The number one thing I want you to get into peoples' heads: Prebiotics are more important than probiotics. What you eat is the most important thing. That’s why Jona gives recommendations for what to eat.”

His bottom line was that a diverse diet is really important, which I have, so I should effectively keep eating the way I’m eating but try to integrate more of the foods Jona recommended. So that’s what I did. I added supplements for vitamins C, D, and B2 (via a B complex), as well as magnesium, since those were the top recommendations on my Action Items list (though Jona listed the foods containing those, not supplements).

Four months later, I took the test again. I’d been trying to exercise more, de-stress, and eat more of the things. When Dr. Kosinski saw the results, he told me that I’d taken my healthy microbiome and made it even healthier. My diversity had dropped from 4.19 to 4.0, but he wasn’t worried about that, because I’d boosted a lot of my good bacteria even higher. There were some good things in my results, too. My stress had gone from moderate to Very Low, and my prediabetes had gone from Very Low association to None.

But then there were some disturbing changes, too. On my first test it showed Very Low for my association with Parkinson’s disease, which I’d been nervous enough about. On the second test it had jumped up to Moderate. Obviously, not what I wanted to see. Over at Skin Health, my association for alopecia areata had gone from Moderate all the way to High! Which is especially weird, because again as far as I or anyone else can tell, I don’t have that.

So I got Dr. Kosinski back on the phone. We clicked on the Parkinson’s results and then the Organisms tab within it. The first thing that stood out was that one bacteria called Akkermansia had taken a massive jump. The normal range is 0.12–1.96 percent, and in my first test I came in at 0.73 percent. In my second test I clocked in at a whopping 5.35 percent. Digging into the references, we found that vitamin D could be associated with an overabundance of Akkermansia, so it was possible that taking the daily vitamin D supplement was way more than I needed. He reminded me that that’s why Jona generally recommends foods, not pills. A similar thing had happened with my alopecia areata.

If this sounds frustrating, you would be right. It's like playing whack-a-mole inside my gut, and indeed all of the High Impact items in my Action Plan were now different. But that’s just kind of life in the microbiome. It’s an ever-changing slurry. Ultimately, while sometimes troubling, I’m glad to have these health concerns on my radar that otherwise wouldn’t have been. It’s encouraged me to eat healthier, exercise more, and make sure I have my medical team checking certain things regularly. All of that is net positive.

Since I took the test, there are a couple of new features. The first launched in late September and is the Digital Twin. Jona has the data to make a replica of your microbiome, and you can run experiments on it. For example, if I just wanted to zero in on Hashimoto’s and Parkinson’s, it would zero in on the top eight actions you could take to help those associations, and it shows you how the relevant organisms are likely to go up or town as a result. Of course, your body is an organic system, and there are always a million confounding factors, so I wouldn’t expect everything to go exactly to plan.

The other feature, launching by the end of 2025, is one I really wished it had after my second test. It's a track-changes page. Basically, if you have taken multiple tests, it will have a visual overlay, making it easier for you to see what has gone up and what has gone down. This should make it easier for the average consumer to see trends within their microbiome.

Of course, multiple tests means paying multiple times, and Jona’s kit isn’t cheap, coming in at $485. If you’ve shopped around for microbiome tests online, that may be shocking to you, as many of them are in the $200 to $300 range. Virtually all of the cheaper ones are using lower-quality tests that might look at 20 or 30 types of bacteria and then recommend supplements that they sell. The shotgun test Jona uses is the medical standard, and it looks at tens of thousands of organisms at a deep, DNA-sequencing level. Jona’s AI has also digested (no pun intended) more than 220,000 studies related to the microbiome, and it continues to ingest 2,000 more each month, with your results updating as new, quality research comes to light.

Certainly, this test isn’t for everyone, and there are places where it could be improved from a usability standpoint. It would still be best to share you results with your doctor and a gastroenterologist. It gave me a lot of insight into one of the most complex systems in my body, and it provided guidance on how I could make improvements. Too much information can fuel hypochondria, but it’s also true that early detection can be crucial when combating certain diseases or conditions. I’m really glad I did it, and I would absolutely do it again.