Tuesday, December 29, 2015

Reflections on 2015

Where did it go?

I hope 2015 treated you all well, and that 2016 brings great health and prosperity to everyone. I've tried to keep the blog light and informative and I've really enjoyed interacting with all of the commenters. We talked about some great stuff, looking back through the posts, and I can kind of see my thinking has changed quite a bit from 2014.

I'm now more than half-way through my master's courses in biotechnology, classes start back up in February. I'm hoping to maintain my 4.0 grade point average, and if all goes as planned, I'll be done in November 2016.

Gut Microbiome - I have been quite disappointed that the research and discussion still revolves around identifying the bacteria responsible for different diseases and less emphasis is placed on the diet. I think it is becoming apparent to all that each person is unique and carries a unique set of gut microbes. Fecal transplants get little mention anymore, despite the great promise shown. For each of us, I think all we can do is experiment with the foods we eat and try to find a great mixture of fruits, veggies, fungi, nuts, seeds, grains, etc... foods that keeps our digestive system working well. I have not lost my passion for using potato starch and inulin as a supplement when fiber intake is low, but they should not be a sole source of fiber. I keep trying to expand my repertoire of fibrous foods as I come across new sources (my latest is spelt).

Gut Testing - The various companies offering gut tests have been the biggest let-down of 2015 for me. I've spent a lot of time in the black box of bioinformatics this year, and I've looked at hundreds of gut reports. I'm afraid there are simply too many variables both in the tests themselves and in the individuality of the guts to use these tests for anything more than amusement value. Now I see that some of these companies are even offering health predictions based on your sample.  I stand firmly that a gut test generated using 16s rRNA profiling is in no way useful as a diagnostic tool. For one thing, I do not trust any of the results or percentages generated by 16s rRNA sampling, and for another, the gut biome changes so rapidly after a single meal that a snap-shot of your flora based on a simple swab of poo is meaningless in the grand scheme of gut health. While it is fun to see the species/genera named in a report, they are not worth the paper they are printed on in terms of diagnostic potential. Culture-based sampling is more reliable, but cannot be used to identify an entire microbiome, only certain species. If I suspected a pathogen, I would have a real doctor use a culture-based platform to discover if it exists. Additionally, the bacteria in your gut is only half the story. The fungal/yeast inhabitants are quite likely just as responsible for maintaining good gut (and overall) health as the bacteria identified through standard gut tests.

Dieting Trends - I think the tide has shifted away from low carb diets and more towards vegetables and grains. At present, "Paleo" just seems to be a keyword to direct internet searches and sell diet books. How anyone ever thought that crispy bacon strips emulate ancestral eating is beyond me. Potatoes are "bags of sugar" and all grains are evil. The reality is, almost any whole plant food is healthy for us. Refined grains are not whole foods. We do not require pounds of meat per day. In my mind's eye, the biggest dangers in eating are the over-processed, refined foods we choose for convenience. In that respect, "paleo" steered us away from the worst offenders, but never really taught us to eat a human-appropriate diet. I'm hoping that the diet fads of 2016 and beyond all include plenty of whole grains, beans, potatoes, and heavy-hitter fibers.

The Future of Vegetable Pharm - For 2016, I'm going to be talking a lot more about potatoes and the potato hack. Since the beginning, more visitors have found this blog searching for "potato diet" than any other search terms. It's fun to talk about, and I think it's a worthwhile topic. As we discuss through the year, I'll try to capture everything and present it as an ebook later on. Throughout the year, feel free to comment as you like on older posts if you find any new and exciting research on RS, fiber and gut health. Blog post frequency will depend mostly on how much free time I have between classes, gardening, raising bees and chickens, and fishing.

To the future!


  1. Well, for me, 2015 was another year of continued experimentation to make my gut happy, but it was not entirely successful.

    You may recall that I tried a semi-monotonous diet that included large amounts of several (consistent) fibers, as detailed in a comment on this post:

    It did not particularly work, and I abandoned it a few weeks after starting due to pretty severe gut discomfort. I wonder if this was simply 'too much, too soon', for a dysfunctional gut.

    I have come around to a position not dissimilar to what I believe yours is. That is, we all have exposure to large amounts of bacteria, and so the right approach is to modulate the gut biome by proper fiber intake.

    I am just beginning a new experiment that combines the following hypotheses:

    a) Eating a low-fiber diet may temporarily suppress dysbiosis symptoms (see Kempner's rice diet; the relief many people get during water fasting).

    b) Consistently eating a small set of prebiotics may help establish a strong, durable microbiome optimized for those prebiotics (perhaps one of the benefits of the potato hack; traditional cultures typically eat large amounts of 'staple' plant foods).

    Basically, I'm going to eat very-low-fiber, except that I'll take a small supplemental amount of raw potato starch (RPS). As tolerated, I'll slowly ramp up the RPS amount over time. I'll also eat very small quantities (~1 Tsp / day) of probiotic foods; mainly sauerkraut and kimchi. I doubt this latter part is particularly relevant.

    The hope is that after several weeks of this, the microbiome becomes quite good at dealing with the RPS, so I can take reasonably large amounts of it daily (> 30g/day), and my gut becomes accustomed to (and happy with) the strains present. At that point, additional fibers shouldn't be a problem, and I can widen intake to other fiber sources without disturbing gut health. RPS will always be taken in this program in non-trivial amounts -- it's the staple that ensures the continued well-being of the key species that formed during the early phase.

    Who knows if it'll work. If not, I may try a similar program, but with different 'starter' fibers (oatmeal, cooked/cooled rice, etc). RPS is attractive as a foundation fiber because it's just so easy to consistently take.

  2. Tim, thank you for posting a most enlightened and honest view, and stating it clearly and unequivocally. I suppose I enjoyed this post so much because my views have morphed in that same direction over the past few years. I find your writing is often that ray of sanity in an otherwise tumultuous nutritional blogosphere. All the best for 2016.

  3. In addition, I think a person needs to find what their 'sweet spot' is for dietary fibre. There's all sorts of recommendations in grams per 1000 kcal. But fibre varies from the solubles to the insolubles.

    My view, ahem, is 'do you poop once a day? Twice? Is it easy to pass?' And what I've noticed is that quantity is not necessary for quality. Some days it's a clear out and some days it's a 'sample'. Why? How the hex do I know? I could eat the same damn thing for days (and sometimes I do) and end up with a variable result. That's just the way it goes but so long as it's not hard and difficult, it's all fine. After all, wasn't one of the touted benefits, initially, of consuming resistant starch that the bacterial fermentation products feed the colonocytes and keep the colon healthy?

    A combo of beans or 'root veg' like spuds, eddoes, taro... plus other root veg (you guys know what they are), and greenstuff, 'shrooms, all work out fine. Just fine.

    I hope everyone who travels the internet highway and ends up over here and learns a lot about keeping the old guts moving along nicely has a happy, healthy, poopy New Year!

    Eat real food! Booyah!

    1. The thing is, it doesn't appear to be a simple relationship for many people. For some, the more fiber (up to reasonable limits), the more regular and better they feel.

      For others, myself included, it is often the case that the more fiber I eat, the worse I feel. No one knows exactly why this is. And that seems to include fibers from real foods that we know are healthy for many people (beans, cabbage, lentils). Studies have shown conflicting results when additional fiber is tried for digestion problems.

      But we also know that some folks who used to have digestive issues have solved them by eating more fiber. So it should be possible, via some combination of diet and lifestyle (e.g. daily walks, etc), to reboot the gut and get it to be healthy.

      I'm trying to figure out the right way to do that, but I haven't yet.

    2. Because, as Tim says above, there is just sooo much we still don't know about the micrbiome, It seems to me that a safer way to heal would be using whole foods, prepared carefully and ramping up in teeny tiny increments. I suspect that by focussung on one fiber you are more likely to cause further unbalance. I bet that the people who do well with R PS already have a fairly robust assortment of bugs. Or, like Wilbur, take a huge variety of powders along with a huge variety of whole food fibers.

      These things would probably help

      Drinking bone broth with as many meals as possible.

      Drinking the juice of fermented vegestables till you can hand the veggies themsevles...but do continue to drnk the juice.

      Here is booklet with simple recipes for Intestinal Recovery that includes the hands down easiest way to make sauerkraut

      More work than just taking a Powder, but may be necessary

      Happy New Year Tim and everyone.

    3. +1 Ellibelly, that is *excellent* advice.

    4. I don't like to complicate things too much. A few fermented cucumbers per week, some dried weird brown unsulfured apricots...(that's what Costco had), green stuff every day, other fresh vegetables in whatever form (usually soup), beans almost every day (got used to this now), a slice of sourdough whole rye most days and I'm done in the 'good for the microbiome department'.

      I think it's easiest when a person can fall back on their hereditary food culture with modifications. However, must admit, I do some 'cultural appropriation'.... the 'in thing' to accuse people of these days.

      Which I was considering the other day: if it's Fusion Cuisine and expensive somehow it's not 'cultural appropriation'.

    5. @elliebelly, the motivation for a simple fiber supplement (raw potato starch) was twofold:

      - A previous experiment I tried that involved more complex, real foods was a disaster. I ate a veggie soup composed of cabbage, pinto beans, garlic, stock and onions (all fresh and organic) for about 2 weeks straight, and ended up feeling as bad as I can remember. Terrible gut bloat, insomnia, and all-around feeling like garbage. Sure, it may have been too much, too fast.

      - Both Tim and Art Ayers have written articles that indicate simpler diets may, at least in some cases, lead to increased gut diversity. See:



      It's a fair point that any processed food may be missing the important bits from the original, so maybe raw potato starch is incomplete. But it's also fair to say that RPS isn't a synthesized, isolated compound.

      Incidentally, I eat lots of broth and have done the fermented veggies thing for months at a time, and neither seems to do much for me.

    6. Zogby, As I am sure you have noticed, while just one of those things (RPS, simple diets, complex diets, bone broth, fermented veggies) by themselves have had almost miraculous benfits for some people, there are plenty like you who don't improve so easily. Clearly there is no one answer.

      But I would encourage you to not drop things like bone broth and fermented vegs (or just their brine). I suspect that there is a mix of things that, over time can help create the right conditions. Each person has to keep experimenting. And as long as something with time tested benefits is not causing harm, I would advocate keeping it n the mix. Art Ayers, by the way, is a huge proponent of fermented vegs. Go slow and in small increments and don't give up! Best wishes.

    7. Zogby

      I see things a bit differently. Ayers says the SAD diet is complex. I think it's reasonable to infer that he thinks a diet of raw, unprocessed and fermented veggies is simple, because it promotes diversity. I see a difference between the complexity of the diet and the complexity of the foods that make it up.

      In Tim's potato hack, the diet is very simple. But the potato is a very complex food that goes far beyond the RPS it produces.

      The SAD diet is complex because there's no consistency in what the gut bugs eat, aside from perhaps the gut lining. The have to be generalists.

      A diet that includes just RPS as the sole source of gut food can be a complex diet in this view, especially if it is difficult to be consistent because of issues that arise.

      My fiber mix, I think, makes ,y diet simple. My gut bugs get nearly the same thing every day from my mix. It's a big part of my diet - 80% or so of my fiber intake. I am very consistent. It's a complex drink composed of about 20 powders.

    8. I think we're mainly in agreement in principle -- I used 'simple' perhaps when I should say consistent (see my original comment).

      I tend to believe, as I believe you and Art do, that the gut will do best when it receives the same types, and perhaps amounts, of fiber every day, because the organization of the biome will optimize to handle that fiber.

      But the fact of the matter is that when I've tried any type of consistent fiber in previous experiments, either as whole foods (cabbage/bean/onion soup), or via a fiber mix (for example, RPS/psyllium/FOS), it has always ended up very badly for me within a few days.

      Why? Here are some possibilities:

      - The non-fiber portion of the meal is relevant, and I'm eating poor or not consistent enough choices.
      - I really simply lack important gut species, or have unfortunately persistent pathogenic species. This would be a bummer.
      - I didn't give it enough time, or I ramped up too quickly.

      In any event, I'm going to try to use the potato hack with a small amount of RPS (probably in chicken stock, as per one of Tim's alternatives in his latest post). And if I can tolerate that, ramp up the consistent fiber to higher amounts and more sources. I'd love to build up to being able to take a 'fiber-smoothie' every day. I think it's an elegant and simple way in the modern world to provide a consistent set of fibers for our gut.

    9. Oh, and @elliebelly -- I still eat a lot of stock, and occasionally eat fermented veggies. As you might imagine, you can't continue to do everything you've ever tried, since you can only do/eat so much in a day!

      But I agree those two appear to be time-tested and reasonable to retain.

    10. We were talking with Dr. Ayers a couple weeks ago, and he commented that simpler diets could lead to more diversity due to the evolutionary pathways that a simple, consistent diet would allow. Continually changing fiber types and then eating no fiber for periods of time, as the SAD diet provides, would lead to evolutionary dead-ends whereas a diet filled with consistent fiber types would allow bacteria to flourish and create new subspecies to fill every available niche.

      Presenting your gut with a wide array of fibers should be no problem as long as it's consistent. But a very diverse diet that changes daily would lead to a stunting of the microbiome.

      Oh, zogby - The potato starch gravy is cooked, don't forget, so almost zero RS. You could, however, sprinkle some on top after it has cooled, if you wanted to add back in some RS. A slice or two of raw potato as you are cooking is an even better way to get the RS, though.

    11. zogby

      I this A) is right "The non-fiber portion of the meal is relevant"

      But I admit I have forgotten what your issues are.

    12. Zogby

      My impression from what I've read of your posts (I grant that it might not be accurate) is that you are jumping from extreme to extreme. My gut has been perfect for at least two years, and even I would not attempt two weeks of cabbage and bean soup. I wouldn't expect any problems, but I think it would suck and my gut would be screaming for more variety. For someone with your issues, I think the potato hack is extreme.

      I think too that you are expecting too much too soon. Fixing my gut took at least 15 months. I felt MUCH better within about 6 months, but there were foods that I could not eat and less frequent but still occasional diarrhea. I can now eat everything, and my stools are wonderfully consistent 100% of the time.

      A few days of this and a week of that won't, I think, matter much.

      What I did - and when I did it there was far less info - was continue to eat what I normally ate, but with every meal add something new that fed the gut. Really, this just amounted to making sure I ate my veggies with every meal. Then eventually I tried making veggies a higher percentage. At some point, I started my fiber mix, but by then things were working better. This was at least 6 months.

      I did go through periods of high gas. I slept in the basement for a while. It was occasionally painful.

      I recently saw some stuff about "contrabiotics." Plantains and broccoli have specially shaped sugars that prevent pathogens from attaching to the intestine. If I were starting over, I'd be eating a few raw broccoli florets and/or plantains (dehydrated chips, powder) with most meals. But just a little. View this as a long term project, with things working very slowly at the beginning but then exponentially faster as you progress.

    13. That's an excellent point about evolution. An important aspect of evolution is cumulative natural selection. A complex thing like a human eye does arise spontaneously. Instead it is the product of many small changes occurring over many generations. Diet simplicity and time together promote gut complexity through evolution. That's further suggestion that this is not a short term process.

      I think this answers a question I've had for a long time. Can I ever stop? I think the answer is no. I've created an environment that has evolved to provide what I need. If I stop, I'll likely starve out species that have functions special to me.

      I agree with Gemma about A.

    14. @Wilbur, that's actually really useful to know that it took you a while (months) to adapt to a high-fiber diet. I do tend to try 'accelerated' experiments to get results faster, and perhaps that's caused problems. I'll try to move much slower, and be more patient, with this current experiment.

      As always, thanks all for sharing your thoughts!

    15. zogby, beans and onion in soup with carrots, celery, okay. But don't add the cabbage. That's too much variety in the scope of insoluble fibre.

      Some things just don't mix all that well. You can make cabbage and beet borscht but no beans in it. For example. Or cabbage soup that contains potatoes.

      You need to look up traditional soup recipes because the old folks knew what they were doing.

      Sometimes soups made from only one main ingredient, like fresh green peas or green beans or mushrooms etc. are the best things to start with. Don't mix things up too much thinking that more is better when in fact it's not.

      I'm not sure here with Gemma (being Czech) but as a Hungarian, the soup traditions are usually quite simple. Partly from 'eating seasonally' but also because it just works better in the 'happy stomach' department. Any other vegetables added to the basic soup ingredient, be it peas or beans or whatever,are included to add some nuance of flavour and not as a major ingredient.

      You can't just throw the contents of the refrigerator and pantry into a big pot and end up with a good result (flavour or gut happiness wise).

      Cabbage soup is usually mixed with potatoes.

      There's all sorts of bizarre vegan combo recipes on the web, but these are recent inventions borrowing on old themes. Again, this quasi religious cult group are convince that if they make up something that looks like slops for pigs, it's healthy for humans. bahhh.

    16. Zogby Yes on the time scale. I misspoke. My gut has been perfect for about a year. It has been really good for about two years. It still seems to get better and better. It's a long process. Keep your perspective. I've fixed problems I've had for over 30 years - in about two years. That's fast.

      Listen to Gabriella. I've gotten to listen to my gut, and it has bad things to say about cabbage and beans. Can't explain. But cabbage and potatoes sounds really good. In fact, it's a favorite with vinegar.

      Simple is awesome. I bought a package of shiitake mushrooms the other day, and sautéed those in butter with smoked salt. It was a fantastic lunch, and gut friendly to boot. It could have very easily gone into a quick miso broth.

  4. Zogby, I agree with you wholeheartedly. I have the same problem as you, if I increase my fibre too quickly my constipation comes back. From day to day, I don't know if I will be "regular" or not. So any advice given does not fit all.

    Ellybelly, I have also found out that sticking to one source of RS, makes me sluggish. At the height of the RS "hype" I found out the potato starch did not agree with me, so started looking for alternatives. And someone on another blog admonished me for for dragging my heals, and not jumping straight in. As it turned out, I was right for being cautious and trying to add as many different sources of RS to my diet.

    To Tim and all readers and contributors of this blog, I wish you all an inspiring 2016.

    Jo tB

    1. Yeah, I've found that increasing fiber, for me, has a delayed effect. I'll feel fine for a few days, and then worse after that -- particularly if I keep eating lots of fiber. This delayed effect makes it harder to figure out exactly what's going on.

      The best I've felt over the past few years was during fasting experiments. Maybe some of the benefit was just the reduced fiber intake.

      But it's nearly impossible to avoid fiber, and I tend to believe that a _healthy_, well-fed biome is better than simply avoiding fiber, in the long run. So I'm keen to fix the problem rather than merely avoid it.

    2. Maybe rather than being a delayed effect, it is a cumulative one...try just a small amount and stay at that level for a few weeks. Then add another tiny ncrement for another few weeks.

  5. Wishing you A Happy 2016..! Tim
    Yours is a rare, honest and fine blog. May you be blessed with all you need to keep it going..!!

  6. I plan on doing the potato hack the first week of January. I did it for 2 weeks way back when it was first being discussed at FTA and found it tough going and when I finished thought "Why would I ever want to do this again?" but am now looking forward to it.

    1. Perfect timing! Funny how something about the holidays and the first of the year bring out people looking for an extreme diet hack, lol.

      Some advice: get some really good potatoes of different varieties. Try as many different ways of cooking as you can. There are some really nasty potatoes in the supermarket as well as some really great ones. The big Russets are made for baking, cooking them any other way will result in some mighty unpalatable spuds.

      Let us know how it goes.

  7. Just read this yesterday - Mainstream medicine says the next 20 years will look like this: http://www.medscape.com/features/slideshow/20-years-ahead?nlid=94503_785
    The first five have to do with the microbiome.

  8. Elliebelly: Is the beet kvass recipe you used the one that is in the Intestinal Recovery book?

    1. Alis,

      Ha! i am not exactly sure how I made that. What I have been doing for a while now ( so probably what I served you) is to ferment beet chunks and an onion or two in an air lock with a 2% brine. It sits on the counter for 3 -5 days. And continues to develop flavor in The fridge after that. I eat the beets and drink the brine.

      There are a zillion variations on beet kvass. The one I liked best used a long fermenting period. But I find the above recipe just as tasty and quicker so don't bother making kvass per se. I haven't tried her recipe, but it is a very quick one, ready to drink in two days. So probably has a very mild flavor, but may be very good for someone with gut problems.

      Sent from my iPad

  9. Congratulations Tim for your critical comments on the commercial microbiome kit providers. They have to sell their product even though the only good side effect is raising interest towards real whole foods.

    The next step for whistle blowing could be companies offering SNP analysis (or even sequencing) and giving recommendations for your diet and exercise. Well, they have a niche as long as real biochemical laboratory testing is more expensive.

    My dream is a bathroom analyser. You pee, poop, spit and breathe (nothing invasive) and it gives you your daily recommendation for diet, exercise, stress reduction, sleep and social connection. Well, I will dream on and on the mean time listen to my body and a selection of metabolic testing.

    Productive new year!


  10. keep up the great work Tim,,all the best for 2016

  11. Happy New Year! I hope you are feeling great! Nice post, although I still think it's hard to catch pathogens even by culture. Thrive up there in Alaska!

    1. Agreed! Pathogens are very hard to detect, even seemingly simple ones like Lyme disease. It makes me cringe to see websites claiming to be able to fix your gut with a uBiome or Doctor's Data test.
      I've been privy to several uBiome tests that showed high numbers of certain bacterial pathogens, but when asked, uBiome "re-examined" the report and could not find the pathogens any longer.
      At least the science is getting better as more focus is placed on the importance of the gut biome.

  12. Maybe not the right place to put it, but I've come across 2 articles of great interest. I have the feeling that our microbiome is getting ever more attention in the scientific world.



    Jo tB

  13. Ah it's disappointing as I got so excited about uBiome and its potential for a while but I agree with you that really it can only be used for a bit of fun. Hopefully in the not too distant future there will be something more reliable!

    1. It will be fun to keep an eye on all this as the science evolves.

    2. I would be interested to know your thoughts on this science...



    3. Having looked at the site, I'd be leery of taking this type of thing. Helminths are also a leading cause of stomach ulcers. I'm not convinced that just every will benefit from helminth therapy, just as everyone does not benefit the same from probiotics, prebiotics, and even food.

    4. Thanks! It seems crazy to me and I would sooner have a fecal matter transplant... But what do I know? Not much! Thanks again!