Gut Testing Services

The Potato Hack is a quick weight loss diet, but it works primarily by altering your gut flora. The connection between the bacteria in our gut, weight loss, immune system, and even brain function is well-documented in medical literature. A couple years ago, several companies appeared that offer advanced testing of the bacteria that inhabit your gut. The testing is fairly cheap, and you get a nice report showing the resident bacteria that were found in a tiny sample of poop that you send them in the mail.  These same companies are now offering advanced gut testing services.  Let’s look at some:

UBiome SmartGut

UBiome just launched this pilot program. Gut testing ordered by a doctor and covered by your insurance. Their website says that if your insurance will not cover it, you won’t be billed.

The services look very much like what you can do yourself with an $89 test kit, but a doctor will help you decipher the results. This could be great for most people who have no idea how to interpret the results of a uBiome dashboard report.

I can see where uBiome is going with this…many people are reluctant to spend $89 for a test of their microbiome. Perhaps if there was a network of doctors willing to order this test, uBiome would make more money. If they can get insurance companies on board, and offer incentives to the prescribing doctors, then they are in for a real windfall.

Color me skeptical, but I find it hard to believe there are doctors out there who would feel comfortable offering advice based on a single uBiome test. If I was in a position to order such a test, I would insist on three samples from the same stool and ask that they be tested blind, that is, the lab doing the tests are not aware the three samples are identical. I would also want multiple tests over a week or two. A single test can be extremely misleading and contain numerous errors.

UBiome offers the following disclaimer on their website:

Statements made on​ http://www.ubiome.com have not been evaluated by the Food and Drug Administration, and are not intended to diagnose, treat, cure, or prevent any disease. The information on the uBiome website is provided for informational purposes only and with the understanding that uBiome is not engaged in rendering medical advice or recommendations. You should not rely on any information on the website to diagnose or treat a health problem or condition, or replace consultations with qualified health care professionals to meet  your individual needs. Always check with your doctor before changing your diet, altering your sleep habits, taking supplements, starting a new fitness routine, or for answers to your personal medical questions.

These statements are mandatory. I have one in my book that looks similar. Everyone ignores disclaimers. But in this case, I’d say it’s spot-on. I’m not sure how a doctor gets around this disclaimer to offer you advice, but I have a feeling that the doctors using SmartGut™ will have a similar disclaimer.

Bottom line – Use uBiome for your amusement only. For $89 you can get a wealth of information about the condition of your gut flora, but you must be aware that the information you get from uBiome might be completely wrong.  If you use SmartGut™, know your doctor! Preferably a medical doctor, and not an internet “gut guru” who has a PhD in basket weaving and a naturopathy practice. The SmartGut™ program could easily be abused by “doctors” who are only interested in selling you expensive supplements and more tests.

MapMyGut

MapMyGut is based at King’s College in London. This new company is a collaboration with the Human Food Project, the folks who brought us American Gut. MapMyGut is intended to be a “high end service,” (translation: expensive).

This high-end offering is very similar to uBiome’s SmartGut program. It’s only available through a network of “accredited health professionals” who will be able to translate the results of a single stool sample:

From your results Map My Gut scientists at the forefront of microbiome research will deliver a comprehensive constructive report on improving your personal gut microbe diversity for better health and longevity.

Again, I’m skeptical.

Available only in the UK, but soon coming to America.

Bottom line – I would not recommend this service unless I knew the doctor well. The doctor should have a background in bioinformatics, microbiome research, and be a medical doctor, not an “accredited” naturopath that you have never met.

VIOME

Viome is the brainchild of Naveen Jain. Jain has an impressive resume of high-dollar ideas, including his current venture of mining minerals on the moon. Some even blame Jain for the dotcom bubble crashing in 2000 due to his company InfoSpace imploding.

Viome costs $999 for a year’s worth of testing, or $99 a month on payments. For this hefty price tag, you send 4 stool samples over a year to Viome and they will provide an app and personalized recommendations for your diet.

The difference between Viome and uBiome or MapMyGut is that Viome uses a super-advanced method to test your gut bacteria:

Large changes in your gut microbiome can’t be measured  by commonly used technologies (16S), due to their poor resolution (genus level and higher). Viome’s proprietary technology accurately measures all changes in your gut microbiome and quantifies its biochemical activities. Imagine the resolution of the hubble telescope being applied to your inner universe! At this ultra-high resolution your gut microbiome is only 5% similar to others unlike the analysis from commonly available technologies indicating 97% similarity. Since, you are so unique, you and your 40 trillion microbial friends deserve personalized nutrition!

Perhaps Jain has invented a better way to test gut flora than the world’s standard, 16S. But if he has, he’s not talking about it and there are no papers describing it, that I can find. And after 2 years of biotech graduate studies, I can tell you that I have not heard of anything better than 16S for analyzing gut bacteria. Or anything else. Period.

Bottom line – Perhaps if you are an enlightened biohacker and want to get in on the leading edge of something new, this is for you. But if you just want to know why your tummy hurts, look elsewhere.

Thryve

Thryve is a team of young scientists who’ve recently gotten into the gut health business.  It appears that they use a process similar to uBiome and MapMyGut to analyze your gut flora. The twist with Thryve is that they offer a “Repair Plan” ($79.99/mo) and a “Maintain Plan” ($59.99/mo) that The Repair Plan consists of four annual tests and the Maintain Plan, two. In addition, they will get you on a course of probiotics containing Bifidobacteria, Lactobacillus, Bacillus, and Streptococcus to ensure that your gut is healthy.

Thryve also promises that mycobiome and phage [really good articles at these links!]  testing will be available by late 2017 or 2018.

Bottom line – This is a really new company, very expensive, and they probably have a lot of bugs to work out of their process before they are ready to sell four gut tests for almost $1000. You could get the same from uBiome for under $400 and buying a couple rounds of Elixa.

My Thoughts on Gut Testing

I was excited a couple years ago with the launch of American Gut and uBiome. These companies offered affordable ways to analyze the bacteria in your gut. However, after nearly 5 years of looking at hundreds of gut reports, and doing dozens of my own, I am sad to say that we are not there yet.

Gut testing companies have several hurdles to overcome:

Sampling – Almost all companies use a swab kit. Users are instructed to swab a piece of used toilet paper and quickly immerse the swab in a preservative liquid. This leads to problems.

  • The skin area around your “hind end” contains its own bacterial populations which will contaminate the sample.
  • Samples taken from different parts of a turd will contain different bacteria, only a thoroughly mixed bowel evacuation would contain all of the bacteria in your sample.
  • Time delays from mailing may cause certain bacteria to bloom and give inaccurate results.

The Gut Flora – Your gut flora is more than a collection of bacteria found in poop. Within your gut, many species of bacteria reside deep withing the mucous layer or hidden in your appendix. Additionally, there are fungi and yeast which may be even more important than the bacteria. Also found in a gut microbiome are bacteriophages and viruses. A disruption in any of these populations can lead to dysbiosis.

Analysis Methods – There are basically two ways to analyze gut bacteria, live cultures and 16S rRNA. Live cultures are perfect for a clinical setting where a specific pathogen is suspected, but this method cannot be used to give a complete listing of all the bacteria in your gut. 16S rRNA is a proven method to name all of the bacteria found in a sample, but it has limitations. 16S is only as good as the machines and databases. This method makes a digital representation of your bacteria based on the traits of each bacteria found in a specific genetic region (16S). The digital output is then matched against several databases and given a name based on the percentage of matching features. The biggest limitation is that 16S cannot accurately predict to the species level, so only genera can be determined. This would be like saying, “we know it’s a dog, but not which type of dog. But at least we know it’s not a cat.” 16S is a reliable method, with many limitations when used in whole genome gut analysis. Unless Viome has a better method up their sleeve, it’s all we really have at this point.

Gut Bacteria – No one knows what a healthy microbiome looks like, what species need to be present and which ones are universally harmful to our health. We can only make associations. This, I believe, is the true goal of uBiome, MapMyGut, Thryve, and Viome – to develop extensive databases of gut profiles matched with patient information and sell this data to people who are trying to develop gut protocols and therapies. Eventually, enough data will be available to show that X bacteria is always present in Chrohn’s Disease, for instance, and Y is not.  But gut bacteria do not play by anyone’s rules.  They have genes and epigenetic “switches” they can flip to change how they eat, live, and die. Bacteria also reside amongst fungi and viruses that might be more important than the bacteria themselves.

What To Do?

The only gut test I recommend is uBiome’s basic kit. It’s $85 and they give you a boatload of data about your sample on their free website dashboard. It’s fun to look at, and compare if you want to learn about your gut flora, but don’t expect much out of a single test. I’ve seen reports loaded with errors that escaped their quality controls. But it’s fun and helps you learn.

Forget all these advanced testing protocols. If you want the healthiest gut you can possibly have, just live right. Eat real food, lots of fiber. Exercise. Get good sleep. Give up bad habits (smoking, drinking, bad relationships). Get plenty of sunshine.

Once gut dysbiosis sets in, it’s hard to overcome. Some may never overcome serious gut issues. I suspect it is the most gut-challenged people that will flock to these gut analysis services and pay $1000s only to be told, “Eat more fiber!” or “Buy these supplements!” There is no other outcome…there are no drugs to remove a single species of bacteria, so what’s the point?  All you can do is control the feeding of bacteria, and your own health.  Sometimes it takes a lot of experimentation and guessing…and that’s all that any “accredited professional” can do, too.

Questions, comments?

Tim Steele

53 Comments on “Gut Testing Services”

  1. Wilbur May 8, 2017 at 1:03 pm #

    Tim –

    This is a great summary of the many points that you’ve made for years. I myself have never had any interest in getting my gut tested. And it seems the companies are moving toward money rather than knowledge (addressing the shortcomings).

    I only learned recently learned something about sponges. I might have known once, but forgot, that they are animals.

    http://bit.ly/2qTviKL

    Complex intertwined collections of all sorts of things that work together to work as a digestive system. These gut tests, to me, seem to be the equivalent of sampling the water coming out at the “butt” (there is a name, but forgot it) to say something about the beautiful, complex structure. Moreover, sponges might be made of similar constituent parts, but vary wildly in shape, size, habitat, ability to digest certain foods, etc.

    For me, sponges are a great metaphor for seeing how difficult the problem is, and how far we are from understanding it.

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  2. Debbie May 8, 2017 at 1:13 pm #

    This was a fascinating read. I love that there isn’t something we have to spend money and time on that will give us absolute results – this way I can just eat as healthily as I can, and keep experimenting on myself. Since I’ve been having excellent results in the bowel movement department, I’m going to stick with my current plan for now. Thanks, Tim.

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    • Tim Steele May 9, 2017 at 6:55 am #

      Yep. Everyone should strive to have normal digestive patterns, feel great, and live a stress-free life. There is no one-size-fits-all approach, for sure. I was looking into the enzymes you mentioned. Great that they are helping you! Perhaps digestive enzymes are a big part of the puzzle we have been overlooking, allowing undigested foods to enter the colon where they create turmoil. Good on you for trying different things!

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  3. Rob May 8, 2017 at 9:15 pm #

    “just live right. Eat real food, lots of fiber. Exercise. Get good sleep. Give up bad habits (smoking, drinking, bad relationships). Get plenty of sunshine”

    that pretty much sums it up for me. I’ve had other issues to sort (methylation has been massive), but it has just been a matter of consistency, persistence and trial and error.

    Also – I’m still doing the weekly fasts (39 hours usually) and these have also brought about slow, but consistent improvements.

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    • Tim Steele May 9, 2017 at 6:57 am #

      I’ve been trying to do a weekly fast, but sometimes I just don’t “feel it” and eat. Other times it feels right and I’ll skip eating for a day. I think there is value in periodic fasting, but perhaps not on a set schedule.

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      • Rob May 9, 2017 at 11:32 pm #

        I think I’m too logical for ‘spontaneity’! If I know I need to do something and when – I’m good to go. If I need to ‘play be ear’ I get too scared I’ll just take the easy route! This has caused problems in the past mind – especially with regards to developing a connection and listening to your gut (Wilbur always talks about the importance of this).

        Maybe a little moderation is called for! I must admit I do enjoy the fasts – especially the feeling and improvements afterwards. One thing I have learnt though is to avoid the cold showers on fast days – its just too much for me (well at the minute!)

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  4. kbseddon May 8, 2017 at 9:33 pm #

    Your ‘My Thoughts on Gut Testing’ section is a really good summary of the current state of the art.
    This was a good read.
    Thanks Tim.
    -Karl

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  5. Gemma May 8, 2017 at 10:43 pm #

    Great write-up, Tim.

    I love seeing remarks and links on the importance of fungi and that they “might” be beneficial.

    This is worth highlighting this as well:

    “This, I believe, is the true goal… to develop extensive databases of gut profiles matched with patient information and sell this data…”

    Or, misuse the data.

    So, it’s clear “What to do.”

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    • Tim Steele May 9, 2017 at 6:48 am #

      Yes, this data could easily be sold and misused. In these days of concern about ObamaCare, TrumpCare, and pre-existing conditions, it’s probably not wise to give out much personal health information to a company who relies on sharing your data for profit.

      As to the fungi, you’ll notice I said, “there are fungi and yeast which may be even more important than the bacteria.” I never said that they might be beneficial, we have known for a long time there is definitely a beneficial aspect of fungi. It’s a shame no one is doing much testing, focusing on the more easy target of bacteria. But in the gut, everything can be good or bad depending on the circumstances, influenced mainly by diet.

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      • Gemma May 9, 2017 at 8:00 am #

        Tim

        “I never said that they might be beneficial,”

        It was mentioned in the mycobiome article you linked, that’s why I commented on it:

        “If the communities are undisturbed, however, the fungal inhabitants appear to be harmless or perhaps even beneficial.”

        Perhaps even beneficial… Good grief!

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        • Tim Steele May 9, 2017 at 9:08 am #

          Good grief, indeed! lol

          It is scary to think about antibiotics. They wipe out most bacteria, and let the fungi have free-range over the gut. And like I keep saying, once dysbiosis sets in, it’s really hard to turn it around.

          Like

          • Gemma May 9, 2017 at 9:53 am #

            Tim

            Wait, didn’t you mean to say ” “I never said that they might NOT be beneficial,”?

            Not that people think that fungi are evil, you know.

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            • Tim Steele May 9, 2017 at 10:58 am #

              lol, no, I was playing off the words “might be” in that sentence. I would never say “Fungi might be beneficial” because I know they are. It may be a stretch to say “more beneficial,” though. But the reality is probably that all of it needs to there, in balance, to be considered beneficial. A fine balancing act, but it’s been around for millions of years…trust the gut. Feed it right and let it do what it’s supposed to.

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              • Gemma May 9, 2017 at 11:12 am #

                “because I know they are”

                Then stop playing with words and say it loud! Fungi are vital, essential, or some such.

                I’m waiting… 🙂

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          • Barney May 9, 2017 at 11:08 am #

            “They wipe out most bacteria, and let the fungi have free-range over the gut.”

            So, does preferential feeding of bacteria (prebiotics) allow their populations to increase to the point that they end up with “free-range over the gut”? In soil, the balance matters and changes as the soil and plant life “matures”.

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            • Tim Steele May 9, 2017 at 11:17 am #

              If you took some potent anti-fungals and killed off the fungi, then the bacteria might have free-range. Like you said, “balance matters.” Fungi are vital and essential! Same as bacteria and phages in the gut. And to tie it all back to the blog post, there has not been a test devised yet that can accurately capture the true essence of a gut biome. We can peer into the bacteria involved, but it is quite meaningless in context.

              On another note, this just out about how fecal transplants work against C. diff infections: Bile acid metabolism. https://www.medpagetoday.com/meetingcoverage/ddw/65141

              Like

  6. Robert May 9, 2017 at 5:46 am #

    Thank you for a great summary, it’s great info for anyone looking to get better gut health.

    I personally made a funny mistake. This autumn I started to get interested in leaky gut, which quickly led to resistant starch. I read all the articles on FTA, including the 1000s of comments. Then on to Vegetablepharm, and I’ve read all articles there too, plus the comments. It’s taken many months.

    The thing is, I read all of them in chronological order, started from the beginning. Therefore, a few months ago I was as hyped up as most of you back in 2014, it almost seemed RPS would make you immortal from all the articles and comments. Also there was a lot of conclusions made from individual gut tests.

    But of course now I’ve gotten to the end, and there is a more balanced approach, like your article above. I now see it would have been wiser to have started with the most recent information 🙂

    Anyhow, it was a fun experiment, the first time on RPS. The dreams, gasses, all of it. It sort of transforms your view on fermentable fibers. I still do potato starch occasionally, but try to get as much fiber from whole foods as possible. But interestingly, even with long breaks from RPS, for example a 10-day vacation on Cyprus eating mostly at restaurants, the original effects doesn’t come back from RPS. It appears to have made a long term change in my microbiome, adding it back after some time produces no gas, nothing strange.

    I would like to thank you, and all the commenters here for all your help and interesting thoughts.

    Next on my list is serious probiotics. I’m going to get some Elixa, possibly Prescript-Assist too when budget allows for it.

    The only prebiotics I can find locally (I’m Swedish, but live in Lithuania) is potato starch, flax seeds and oat brans. There is also wheat and rye brans, but I don’t know if they have value for the gut. Anyone knows?

    Thanks Jo TB for the tip about amazon.de, they ship to Lithuania. I thought I would be stuck with only these prebiotics, but I’ll now be able to get inulin, GOS, and even baobab. It would be fun to try it out.

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    • Tim Steele May 9, 2017 at 6:41 am #

      Thanks, Robert – It’s been a journey for all of us, and requires lots of personal experimentation as each person starts with a different gut flora and a different set of problems. Wheat and rye bran contain mostly cellulose fibers…valuable to the gut, but easily found in most of the other vegetables you are eating, not much value in supplementing. Oat bran is much more beneficial due to its high levels of beta glucans which are proven to be good for gut health. Good luck!

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    • Wilbur May 9, 2017 at 12:12 pm #

      Robert –

      Try to think more broadly about prebiotics. Sure, you can make a special drink or smoothie with added fibers, seeds, and such. But there’s lots of stuff that’s prebiotic. Or maybe virtually everything is, but some are bad. Vegetables are prebiotics (and probiotics unless irradiated). Generally speaking, dark green or colorful have lots of good stuff like antioxidants that are utilized. Tea and coffee. Good crafted beer and red wine. Dark chocolate. Even meat gristle. Dried figs and apricots. Potatoes! Other roots like radishes, burdock, dandelion, sunchoke, etc. Fruits. Heck, super al dente pasta (crunchy). Of course, garlic and onion. Spices, like cumin, fenugreek, black peppercorn, etc.

      I’ve always viewed the above as primary prebiotics.

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      • Robert May 10, 2017 at 9:25 pm #

        Thank you Wilbur,

        Fresh radishes are starting to appear at the farmers market now, they are delicious. And is beer really good for gut bugs as well? That’s good news!

        I also have access to sunchokes, but somehow I haven’t found a way to incorporate them in my diet. Anyone has a suggestion how to eat them?

        I guess powders have their place because of my laziness, or because of our society making healthy eating difficult.

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        • Gemma May 10, 2017 at 9:32 pm #

          Robert

          you are in Lithuania. Do not forget to eat some local mushrooms.

          Like

          • Robert May 10, 2017 at 9:53 pm #

            Thanks, they contain beta glucans right? We did pick lots of chantarelles last summer and autumn, might still be some left in the freezer. This year the goal is to find boletus mushrooms, they are so tasty. Also to pick lots of wild blueberries and freeze them.

            Like

        • Wilbur May 11, 2017 at 7:57 am #

          The right kind of beer, yes! I’m not sure about, say, Miller Lite though. It’s probably like processed food. Here’s an interesting article:

          https://aapsblog.aaps.org/2016/03/17/cheers-to-gut-health-beer-and-your-microbiome/

          I love sunchokes! For starters, you can use them similar to potatoes. Make a sunchoke-radish-carrot hash. Or sunchokes-potato hash. Both are great with fish. Cut into cubes, cover with your choice of oil (I use either butter or olive), and roast. Or sauté. You can them raw. Believe it or not, they are excellent when diced small and put into lasagna. It makes a great meat substitute.

          I hear you on the benefits of fibers. I just like to keep the frame right.

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          • Robert May 11, 2017 at 9:28 pm #

            Interesting with the beer. It’s fascinating that all those traditional foods have benefits. It’s possible to find unfiltered and/or unpasteurized beer over here, I’ll go for that.

            Good suggestions for sunchokes also, thanks a lot!

            Like

  7. Barney May 9, 2017 at 8:31 am #

    Good job Tim. You mentioned numerous issues with this type of analysis, but could some of these points also be raised when referring to the “accepted” research studies and papers?

    Another part of the collected data is the self reported profile. I would question the accuracy of that data and therefore any conclusions based on it. For example, does everyone answer accurately about their health? Or I wonder how many have sent in a sample from a family pet just to see what might be reported. I don’t doubt your conclusions about the ultimate goals for the data. I just wonder if anyone would ever be able to use it for legitimate scientific research.

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    • Tim Steele May 9, 2017 at 9:14 am #

      For sure! But with lots of data, anything is possible. I’m not sure the tools exist for such deep data mining at present, but when they do, this information will be very valuable.

      Yes, I question the legitimacy of most research studies that use whole genomic analysis of the gut microbiome. I’m a data geek, in real life single points of data are mostly meaningless unless they are part of a trend you can view. The temperature in my house might be 72F right now, which seems fine. But if it was 150F three minutes ago, something strange is happening and it won’t stay comfortable for long. This is the problem with bloodwork labs of all type, though. A single fasting blood glucose reading or cholesterol reading is all that a doctor needs to prescribe a medication with a long list of side effects.

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  8. Robert May 11, 2017 at 9:51 pm #

    Since gut testing is unreliable, perhaps the brilliant​ minds over here can help with a question: I sometimes suspect that my gut bugs responsible for the suppressive immune system is not working well, or even are missing completely. I read about this on Art Ayers blog. I haven’t been sick for a long time, I can’t even remember when, and that despite the people around me dropping like flies this winter. I used to think this was a good thing until reading some comments indicating the opposite on vegetablepharm.

    This “problem” started when I had antibiotics, and especially after getting vaccinated against swine flu 7-8 years ago. I then didn’t catch a cold for three years despite crappy diet. Before that I would get sick like most people, once or twice in the winter. Art claims antibiotics can wipe out those immunity suppressive gut bugs.

    Since starting potato starch I’ve had benefits, but also sometimes feelings of more inflammation. And I thought perhaps the starch was feeding the bugs I have, the aggressive immune system bugs.

    Could that be the case, or am I just imagining? If it’s true, what could be done to get the immunomodulatory bugs back, or if they’re there, how to feed them?

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    • Wilbur May 12, 2017 at 6:14 am #

      I’m not an expert on this, but I have given it some thought.

      Regarding colds: There are two aspects to a cold, catching one and the severity of the symptoms. I thought I had gone long periods of time without catching colds. Recently, however, my daughter had a very bad cold and I was taking care of her. A day or so in, I felt a little weird. Can’t describe. Since the thermometer was already out, I took my temp. It was almost 102 F! It stayed there until the next morning. That little weird feeling was the only thing I felt. Had I not taken my temp, I would’ve probably thought I just needed more sleep.

      Another time my wife and daughter both got stomach viruses. 18 hours of misery. At 1 pm the following day I got sick to my stomach and felt very tired. I lied down on the couch. By 5 pm I was fine. We ate an early dinner and went to a hockey game.

      Many stories like that.

      From what I’ve read, higher chronic inflammation can cause the symptoms to be worse. In my case, the symptoms are so mild that the deviation from normal is not noticeable.

      Have you tried Elixa?

      I was a typical person when I started out. There was nothing special about me. Except that I did not stress out over what bugs I might or might not have. There wasn’t much information available then, which probably helped. I knew my plan was right, so I stuck to it. Sometimes my, say, bowel movements would seem worse. But then I’d remember they weren’t good before I started. Gradually things turned around. Some things took several months. Some things years.

      You’ve seen Tim’s advice, so you know what to do there. There’s another aspect to it that I believe is also important, something that Tim does too. The best I can explain it is as an “artisan” aspect. Do it the real way. For example, many eat yogurt for probiotics. It seems like a real food. But the bacteria are very carefully controlled to give consistent texture and taste, to give precise culture times, and to make the product safe. It is not designed to provide a complex, robust self-sustaining colony of bacteria. I cannot eat commercial yogurt. Many people make their own yogurt but still use commercial as a starter.

      As an experiment, I made my own using chile stems as a starter, as is apparently traditional in India. That is artisan – the real way. It is a different product. Now I eat at least a spoonful every day. I’ve lost count of which generation I’m on, but it seems to get stronger each time.

      Tim eats artisan stuff too. He brews his own beer, makes his own birch syrup, at one point produced his own honey, grows his own vegetables, etc.

      We’ve both done our own vegetable ferments. I’ve gotten lazy, but I know the people I buy from and that they do it the right way. I believe that is important. Using culture starters or whey might reduce failed ferments, but your gut is cheated of enzymes and diversity from the soil the vegetables were grown in.

      I would love to have access to lots of good unfiltered beer! I can get a little here, but it’s a straggle.

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      • Tim Steele May 13, 2017 at 6:06 am #

        Here’s another article (hattip JotB) from Tim Spector, Chief Scientist of the MapMyGut project: http://www.dailymail.co.uk/health/article-3405567/Do-bug-tum-makes-Bacteria-gut-reveal-astonishing-secrets-health.html

        Note that everything they mention points to “eat less junk/more fiber.”

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      • Robert May 14, 2017 at 10:34 pm #

        Thank you Wilbur, this is good advice. It’s also similar to what Art Ayer recommends on his blog, just giving it time and eating a good diet. I’ll try to be patient.

        I too have had days when I feel weird, “maybe I’m catching something”, but then the next day it’s gone.

        I’m about to try Elixa actually, who knows, it might prove to be a “shortcut” to better microbiome. Before I’ve just had some weak local probiotics.

        The artisan aspect has been emphasized many times in comments on this blog, and I believe in it. I don’t grow my own veggies, but many around me do, and we get for free or buy from them. Sauerkraut we buy from locals, kimchi we make our own. Raw honey and milk is also readily available.

        That sounds like a crazy yogurt, I’ll look into it. We use commercial ones as a starter, but it would be nice to get something more “wild”.

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      • Robert May 28, 2017 at 6:01 pm #

        Wilbur,

        I tried the chili stems for making yogurt – wow! That is some powerful bugs. I used to use store bought yogurt as a starter, but once I got the chili stem starter going, it ferments much faster and gets thicker. And it appears not to be so temperature sensitive (good, since I don’t have a yogurt maker). The consistency is almost like whipped cream after draining. The taste is different, milder, not so tangy. I think it could be used more broadly in both foods and desserts. And it’s funny not knowing what kind of bugs are hiding in there.

        I have access to raw milk, do you think it’s safe or any benefits from not boiling that raw milk before starting the fermentation?

        I’ve also been thinking about your comments regarding cravings. It’s definitely true that cravings change when you feed your microbiome. I’ve always had cravings for sugar, it didn’t go away even when doing low carb. But when I did RPS those cravings disappeared for the first time, I just couldn’t be bothered to eat candy. The last three months I’ve cut down on the potato starch though, trying to just get it from natural foods, and slowly those candies are getting more attractive again. I might try to increase the RPS again, but first I will try Elixa.

        Instead other cravings have arisen. Most prominently cravings for raw onion. I get this a lot. Also garlic, sometimes chili peppers. Even fresh radishes.

        All this is very strange, I’m 34 years old, and for 33 years I was craving only junk food. Candies, McDonald’s, pizzas, white bread etc was something I really liked, and it took constant will-power not to give in to. As soon as I let my guard down, felt I deserved some comfort or fun, this is where I turned.

        Now, even the thought of going to McD is revolting. Buying a pizza seems like a crazy idea. Picking up a processed food in the store, looking at the label, seeing all those horrible stabilizers, emulsifiers and other killers of gut bugs, fills me with disgust. And I used to just love buying some frozen burger patties and some burger buns to make a quick yet very rewarding dinner.

        Granted, knowledge could be a factor. I know more now about the harm of vegetable oils, emulsifiers etc, this influences too, a Big Mac isn’t just 1000 empty calories, it’s way more harmful than that.

        But nevertheless, I do feel that changing your gut microbiome is certainly affecting your cravings. If that is true, it’s huge. Everyone knows that junk food is bad for you, it’s just that we can’t resist the cravings. Here could be the key to a healthier diet, and a subsequently a healthier population.

        Like

    • Tim Steele May 12, 2017 at 10:16 am #

      That’s the million dollar question, Robert. Case in point, read today’s “Poop Scoop” the blog of MapMyGut: https://mapmygut.com/whats-love-got-to-do-with-it/?utm_campaign=shareaholic&utm_medium=facebook&utm_source=socialnetwork

      You’ll quickly figure out that all they are doing is guessing and grasping at straws. No one mentioned that maybe the differences were due to a faulty test, or variations of stool sampling. There seemed to be no correlation to the health of Meera and Aryan, just differences in gut flora.

      I think that this type of gut testing service will fizzle out fast. The only advice that can come of any gut test is: Don’t eat SAD. Eat lots of fiber. Eat real foods. Beyond that, one just has to hope they attract the right microbes through diet and interactions with nature. Perhaps one day there will be more we can do…fecal transplants or probiotics that contain human digestive bacteria, ie. Akkermansia, Roseburia, F. prausntzii.

      Like

      • Robert May 14, 2017 at 11:31 pm #

        Thank you Tim, eating real foods, much fiber seems to be what it all boils down to. I find it to be quite calming, knowing you are doing the right thing. But I’m glad I don’t have the horrible health problems connected to severe dysbiosis many suffer from. It can be quite sad to look for information about gut health on various blogs and forums. People get desperate searching for a solution.

        I won’t eat SAD, and not even SSD (Standard Swedish Diet). I guess the standard European junk food diet is similar to the american in many ways, just less antibiotics and GMO’s. Stuff gets rejected on the border here because of too much toxins or pesticides, and then they sell it in the US instead…

        Like

  9. Robert May 14, 2017 at 11:24 pm #

    This was an interesting article (via MDA):

    Wine And Coffee May Be Good For Your Gut Bacteria, Helping To Diversify Your Microbiome

    I don’t have access to the full scientific paper, but this article made some interesting conclusions, and some odd ones. Too much carbs was bad for the microbiome, and a high fat diet too! So what are we left with then? A high protein diet I guess…

    Like

    • Tim Steele May 15, 2017 at 7:24 am #

      I think they are confusing “carbs” and “fat” with “junk food.” Eating real food is rarely wrong when it comes to the gut.

      Like

  10. Jo tB May 15, 2017 at 10:13 am #

    Robert, I see that the article is already over a year old. I could contact the lead author in Groningen (I live in Holland) for further clarification. I’m sure they would be willing to comment. Groningen is doing a lot of research into paleo / evolutionary diets, so this avenue of research definitely fits into the overall picture. I personally think the author of the article is giving her own interpretation into what is going on.

    Like

    • Robert May 17, 2017 at 9:35 pm #

      Jo, that would be kind of you. I personally thought it seemed like an interesting study, and probably other ones too would enjoy more information.

      Like

  11. Richard Lin June 9, 2017 at 5:33 pm #

    Hi Tim – I’m Richard the CEO of Thryve. I didn’t even realize you had done such an intensive write up about the commercial enterprises coming out in the microbiome space. Very comprehensive and I’m impressed. Thanks for doing contributing in this way – consumers should receive an unbiased review of offerings in the market.

    Couple of points I’d like to address:

    We noticed an increasing amount of collection methods that prevented accurate data during the sampling process. For instance, some companies used a dry swab or antibiotics in their liquid buffer to lyse the microbial cells. As you know, based on these methods bacteria could change based on their environment due to temperature and shipping methods. Furthermore, by using antibiotics the microbial cell walls burst and the DNA that falls out degrades the sample – thereby, resulting in an inaccurate picture of the microbiome. We did many internal tests to figure out exactly how to provide the most accurate picture so we developed our own proprietary liquid buffer that keeps the cells in stasis and prevents overgrowth or degradation of fecal samples. You can see our report here on the higher yield of diversity we were able to pick up using 16s rRNA sampling: https://drive.google.com/drive/u/0/folders/0B8FBMq0yFrClNVlqSmFKOEExM2c

    Furthermore, most other microbiome companies claiming to offer “Artificial Intelligence and Machine-learning” are most likely on the buzzword bandwagon and not truly offering machine generated insights and summaries. We are partnered exclusively with a leading quantum computing machine intelligence software company that is working with us to develop our machine-learning algorithms to deliver true insights into thousands of microbiome research articles and utilizing natural language processing to summarize said research into our own microbiome ontology. In short, our software brings in the specific bacteria, their inputs (prebiotics), and outputs (chemicals, enzymes, etc…) into an easy to read and acted upon format in our user interface.

    Finally, our probiotics are co-developed with one of the world’s leading probiotic research and manufacturing partners, Synbiotech. We’ve scouted for the best probiotic partner to work with so that our customers receive the highest quality product for a low price. Together, we chosen the strongest blend to create our 100B CFU and 15 strain probiotic that have shown to be acid and bile salt tolerant, higher intestinal adherence / adhesion yield, improved immunity, and longer lasting storage stability. What this means is our probiotics actually have research behind them surviving gut transit conditions. We also ship our probiotics on ice, bottling in glass amber (to block out harmful UV rays and keep moisture out), double test at manufacturing and bottling to ensure accurate CFU counts and no pathogenic microorganisms, and put it all together in a vegan, Non-GMO Hydroxy-propyl-methyl-cellulose capsule to ensure it bypasses stomach acids. We manufacture our probiotics in a GMP, ISO 9001/20002, SGS, and FDA compliant facility to ensure the highest quality. If you’d like to see our probiotics whitepaper by our partnered lab, please see here: https://drive.google.com/file/d/0B-bzApZXCpbjRGtCeGNjRXdiZWs/view?usp=sharing

    As you mentioned, we are planning to launch yeast and phage protocols for our sequencing using ITS for yeast and a proprietary reagent for phages. Furthermore, we are aiming also to offer truly custom and personalized probiotic blends based on customers intolerances, goals, and microbiome results. There is a lot to be excited about in this space and we look forward to what the future holds.

    We stand behind our product and would be happy to give the first month completely free to anyone who is interested to see that our product is truly one of a kind and not vapor ware or smoke & mirrors.

    Cheers,
    Richard
    CEO
    Thryve

    Like

    • Tim Steele June 10, 2017 at 7:27 am #

      Hello Richard – Thank you for this great comment! How exciting it must be for you to be working with such cutting-edge technology. It’s great that you have developed a better preservative, I hope it works out for you. When American Gut first started, their samples were returned to the lab in a dry test tube causing all sorts of problems. But this is the second step, I still wonder how accurate it is to use a swipe from toilet paper to gather the sample. I think the only way to get a thorough look at feces would be to have the entire homogenized bowel movement, but I’m sure that would turn customers off. I’d be interested in seeing a study where you looked at the results of a single stool test, one with a bacterial sample collected from toilet paper residue, and another collected from a sample of the well-mixed feces. My guess is that they would look vastly different.

      On the bioinformatics end, do you also give the customers the fasta/fastq files generated? Which database are you using to create your reports? We spent a lot of time here analyzing the raw data provided by UBiome and AmGut with MG-Rast and some others. I felt that MG-Rast gives the best results since it matches against all of the metagenomic repositories (SSU, LSU, Greengenes, etc.). No one has yet been able to promise accurate species-level identification…do you intend to try, or are you also roadblocked at genus-level identification? I do not understand proprietary bacterial prediction as uBiome claims to have mastered. Why not use the standard libraries and allow for third-party verification of the test results? When someone tells me that their Illumina predictions cannot be verified by any means, it throws up a huge red flag.

      While I hope you get lots of customers and collect many megabytes of data, we all know that you have a lot of work to do. For example, here are two studies showing that stool consistency and activity level have profound effects on the outcomes of 16SrRNA sampling (http://gut.bmj.com/content/65/1/57 ) (http://gut.bmj.com/content/63/12/1913 ).

      In regards to phages and fungi, I look forward to seeing what you find, but I caution you to act carefully. It’s been shown that the fungal communities are far more important than the bacterial and upsetting this balance because we do not yet understand the complex relationships between bacteria, phage, and fungi could be disastrous.

      And I have not even mentioned the bacteria found in mucous or fibers that influence gene expression.
      Best of luck,
      Tim

      Like

      • Richard Lin June 10, 2017 at 9:18 am #

        Totally agree. A sample from toilet paper vs. homogenized stool will look drastically different. That said, the biggest issue (like you mentioned) is the overall customer experience. It’s more palatable from a consumers point vs. buying a separate blender to mix poo. Unfortunately, it’s one of the compromises we take to make it easier for customers to contribute to this area of science. Ideally, the most accurate view into the gut ecosystem to get scoped and grab a biopsy – talk about next level commitment to the science. I believe many of the current players in the market know this issue but aren’t necessarily publishing those studies because it would make make all their current data, erroneous… That’s where true machine-learning algorithms can reduce the noise from a collection method like toilet paper and provide an accurate depiction of your sample. At Thryve, we are working on solving this very problem – amongst many others.

        The other thing you would have to consider is the entire lab process. From extraction, library prep, sequencing, etc… could tamper the sensitive ecosystem that is contained in each customer sample. For example, even the infrared lights used in the Illumina HiSeq machine could tamper the microbes in any given sample. SecondGenome is (for lack of a better word) killing it here on the front office lab work required to have tamper-free samples. Unfortunately, they are b2b and aren’t offered to consumer. That said, there’s always room for partnerships on our end to offer the highest quality test to our customers ;).

        In terms of FastQ files, we always make this readily available as long as customers reach out through support@thryveinside.com. We currently store it in our s3 bucket but it can’t be accessed yet via the UI – it’s in our backlog and we are getting to it soon :). We’ve built out own proprietary bioinformatics pipeline and very similar to MG-RAST our reference database calls all known public microbiome domains (SSU, LSU, NCBI, etc…) to keep the most up to date information for our NGS DB.

        We generally only put 25-50 samples per run which gives us more reads in a run. This adds way more costs for us but provides mode depth and accuracy to get species level microbes. This also gives our customers a quicker turnaround time of 2-3 weeks vs. others at 3-6 months. This factors into our higher costs as well. Most “proprietary” software (including the bioinformatics offered) are probably constructed 80% from open-source libraries and 20% unique. We’ve been exploring how to be more transparent with our code so customers have an understanding of what we claim. For instance, our pipeline uses Kraken, Luigi (Spotify originally created this for batch jobs), and several other pieces of software.

        Otherwise, hope this was helpful. Cheers!

        Like

        • Tim Steele June 10, 2017 at 10:16 am #

          Yes, very helpful. If I were in charge of QC at a company like yours, I’d want to run the samples through the pipeline several times, then match the results and establish a confidence score. I’ve seen many, many reports from uBiome and AmGut that were obviously flawed. These companies do not seem to have a good QC system in place to toss out bad reports.

          Like

        • Barney June 11, 2017 at 2:39 am #

          Hi Richard,

          Can you provide some more context for this statement : “We generally only put 25-50 samples per run which gives us more reads in a run. This adds way more costs for us but provides mode depth and accuracy to get species level microbes. This also gives our customers a quicker turnaround time of 2-3 weeks vs. others at 3-6 months.” How does fewer samples and more reads result in faster turnaround. Also, how many reads per run and how long are the sequences?

          You mentioned direct access to the FastQ files is in the pipeline. What else is in your backlog?

          Thanks.

          Like

          • Richard Lin June 11, 2017 at 7:23 am #

            Hi Barney – thanks for your comment. The way to speed up the processing time with the machines are to lower the threshold of demand it requires to save on costs. You can imagine every run is a separate cartridge that can hold up to 700 samples. If you wait for 700 samples it could take a while to fulfill, but on a per unit basis it’s much cheaper. We run the machines at 25-50 samples so the turnaround time gets much faster. Usually the extraction, processing, library prep, and sequencing take around 7 or less days to complete. This is more a business problem as fundamentally if you offer one-time kit purchases it’s much harder to reach profitability and offer these types of quicker results without taking a large hit on your revs.

            We run about 17M reads per run on the v4-v5 regions.

            We have a couple of larger features regarding how to interpret your microbiome data that I can’t disclose at the moment. Also we are continuing to improve on our ML training set which is a large effort in it in itself. Operationally, we are setting ourselves up for custom probiotics within the next year so stay tuned for that as well!

            Like

        • Tim Steele June 11, 2017 at 12:23 pm #

          Richard, I was just checking out your website and found this: “Thryve is an open and connected way to share your microbiome data, knowledge and interest with other citizen scientists.”

          Does this mean you will freely share all the data you collect from paying customers? American Gut has made all of their data available through the European Nucleotide Archive. They blinded the names, but all of the metadata is available. Will you be doing something similar?

          Like

          • Richard Lin June 13, 2017 at 11:57 am #

            Hi Tim – great question. I don’t think we’ll necessarily go down the route that American Gut has done. However, we’d like to make anonymized opt-in data more easily accessible than a download from an FTP server. Still figuring out the best course of action with the optimal user experience. Probably a long the lines of a social network for the biome.

            Like

  12. Sam August 22, 2017 at 4:31 pm #

    I used Genova Diagnostics: GI Effects Comprehensive Stool Testing, twice. It is the lab I chose and my ND uses them too. The test is cheaper if you can ask you Doc to order for you about $150, the rest insurance picks up.

    Like

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