Interview with Mr. Heisenbug

Although the blog Mr. Heisenbug (“Respect the microbiota”) is quite new, I have learned a lot from it, especially about the importance of fiber. I interviewed the blogger:

SETH Tell me about yourself, such as your background relevant to your blog.

HEISENBUG  My name is Shant Mesrobian. My professional/academic background has no relation to the content of the blog. My background is in tech/politics/publishing. The blog is just a side hobby and is produced from independent research. (I’m a “non-expert” as you might call it.)

SETH When did you start your blog? What led you to start it? Have you blogged before?

HEISENBUG I started the blog about a month ago. I have not blogged before. I started it because the topic interests and excites me a lot. I anticipated a surge in microbiome experimentation and “hacking” and felt I could help direct that conversation in a productive direction. In digging through the research, there seemed to be a lot of dots that needed connecting.

SETH What do you mean, “dots that needed connecting”?

HEISENBUG  Certain clusters of bacteria, and certain mechanisms (butyrate production, endotoxemia) kept surfacing in the studies I came across. For instance in the smoking post, it was sort of staring at you in the face that smoking clearly reduces levels of bacterial groups that are implicated in health and disease. Yet the study didn’t seem to find that interesting, so there was a gap that needed to be filled. But the pattern could only be detected by someone who reads a bunch of disparate studies. Same with the obesity/transplant study — many people are trying to help themselves because they vaguely know that potato starch can elevate butyrate (perhaps not even that much) — so here is a study showing directly that a different microbiota can achieve that, and it is particularly by elevating levels of bacteria that I had previously implicated as being prime starch degraders + butyrate producers. It’s been a series of eerie coincidences that has kept me posting material.

In general, I think there is a bit of an information gap about how to alter gut biota — there isn’t a real understanding of what “fiber” is.

SETH What do people fail to understand about fiber?

HEISENBUG First, that fiber is an overly broad and useless term. The only definition you can assign to the term is “a food that, when consumed, is not digested and is transported directly to the large intestine.” But what happens to the fiber when it gets there is completely dependent on what type of fiber it is. The type of fiber most people are familiar with is the mechanical kind that is just a bulking agent. Insoluble. No fermentation or microbial impact. Comes out the other end. The fibers we’re interested in are the bioactive type that are not only fermentable by gut bacteria, but preferentially fermented by good, commensal bacteria. But this isn’t what people think of when they hear “fiber.”

The other thing that’s not understood is that fiber can make a significant impact on the microbiome. People are just very primed by the germ theory aspect of bacteria — that they’re “bugs” you have to “catch.” So while people have begun to accept the idea that there are good bacteria that you want, the understanding is still very stuck in the “you have to eat the bacteria to get good bacteria.” I’m a big fan of fermented foods (making & eating), but I don’t believe it’s the primary way to tend to one’s microbiome.

SETH How have your ideas/beliefs about fiber changed over the years?

HEISENBUG I currently consume a paleo/ancestral type of diet. Before then, I regarded fiber as most people do: a necessary, functional component of food that you need in order to “stay regular”. I sought it out mostly from whole grain foods. I did not realize there were different types of fiber, or that they had anything to do with gut flora.

Then, when I went paleo, I adopted the general paleo attitude toward fiber: fiber comes from grains and grains are bad, that fiber is an unnecessary bandage that covers up for a bad diet, and that good digestive health can be had by simply eating nutritionally dense, non-toxic foods that people are evolved to eat. Fermented/probiotic food being a helpful addition.

Then I came to my current position once I learned more about the microbiome. What I’ve realized is that while paleo/ancestral eating goes a long way toward correcting the modern standard American diet, it still retains one common feature with it (at least in the way most people seem to practice it), which is that it focuses primarily on feeding the upper GI, while starving the lower GI (ie, your large intestinal microbiota).

And the ironic twist is that by dropping wheat, paleo may in fact have LESS fermentable fiber than the standard American diet. That’s because, while it contains mostly insoluble fiber, wheat does contain a small amount of fermentable fiber, which means that wheat constitutes the primary source of fermentable prebiotic fiber for the average American. So drop wheat, and you probably just lost your predominant source of fermentable fiber for your gut flora.

SETH The most interesting idea I’ve seen on your blog is that smoking is associated with heart disease (and other diseases) because it reduces microbial diversity. Because of this idea, I’ve become a lot more interested in fiber. Is this your idea? As you say, because smoking is such a big risk factor, it is a good place to start to understand heart disease (and other diseases). What are other explanations of why smoking is such a big risk factor?

HEISENBUG I’ve never seen anyone else make the connection between smoking -> microbial diversity -> heart disease. Smoking’s high (#1) correlation has always intrigued me, especially since there have never been solid explanations for it. Separately, I’ve been reading about endotoxemia-induced inflammation and its effect on chronic metabolic disease. So when I came upon this study, it was sort of a smoking gun.

As I said, the explanations for smoking being a big risk factor, if you really read them, aren’t saying anything. They are generalities. “Smoking contributes to heart disease because it contributes to atherosclerosis.” Well of course. Atherosclerosis IS heart disease. The question is how? Smoking raises LDL cholesterol. Ok, but how?

The inflammatory cascade that results from loss of microbial diversity, a bloom in “bad” bacteria, and a decrease in “good” bacteria, is an explanation for all of those.

SETH Could the importance of fiber explain that famous failed beta-carotene trial? There had been plenty of correlations between beta-carotene and better health. Yet in an experiment, people taking beta-carotene if anything did worse than the control group. Maybe beta-carotene consumption was a marker for fiber (e.g., people who ate more beta-carotene ate more carrots).

HEISENBUG If the epidemiology that inspired the trial was based on high carrot consumption, then I think that’s definitely a possibility — carrots are fairly high in pectin, a type of fiber with decent prebiotic activity. But since the trial subjects did even worse than placebo, I find another explanation convincing — that unusually high doses of beta-carotene, which is a precursor to vitamin A, blocks actual Vitamin A.

SETH Has your better understanding of fiber improved your own health?

HEISENBUG My health is already pretty good, and I think I’m probably too young for metabolic and chronic disease symptoms to make themselves evident, so I “unfortunately” can’t report on those types of markers. So for me this is all preventative at the moment. And I have yet to experiment with some more potent, high-dose prebiotic sources. I plan to soon. But I have noticed a significant improvement in sleep and a next-day feeling of well-being, relaxation, and clarity after a day when my fiber intake is higher and I consume yogurt cultured with lactobacillus and bifidobacteria, and I suspect it has something specifically to do with the bifidobacteria. That’s just a hypothesis now and something I’m currently exploring on the blog. Figuring out the ideal sourcing, combination, and amount of fiber is really still a work in progress as far as I’m concerned. There’s no real handbook, and people are just starting to figure all of this out. Lots of people experimenting with resistant starch (in the form of potato starch) are reporting dramatic stabilization in blood sugar and weight, digestive improvements, and greatly improved sleep. I’m hoping that a lot of personal experimentation and self reporting, combined with gut sequencing services like American Gut and uBiome, will get us closer to figuring it out.

18 Replies to “Interview with Mr. Heisenbug”

  1. Great interview Seth. I had found his blog (probably from a link here?) and only begun to read through it but it looks fascinating. Improving gut health is looking more like a new year’s resolution for me.

  2. This is a great interview, Seth, thanks.

    @MrHeisenbug, thank you. I hope you have time to answer several questions.

    1) You say that honey is rich in scFOS. How does one determine which foods contain decent prebiotic capabilities?

    2) I find that a rounded teaspoon of honey, taken just before bedtime, significantly improves my sleep. Does that contain enough scFOS to alter the microbiome?

    3) What is the transit time, from ingestion to when scFOS starts to be fermented? I know that my sleep is improved by the 3-hour mark, because that’s when I historically have woken up from my initial sleep. On the honey protocol I sleep deeply until the 5-hour mark. So whatever it is in honey which makes me sleep better, it is being used by the body/mind within 3 hours.

    4) Others suggest it is the sugars in the honey which cause the improved sleep. Or perhaps some of the other 200+ factors in honey. Can you suggest designs for experiments which would tease out the true causes of improved sleep? For example, ingesting a certain type of sugar, or ingesting an isolated fermentable fiber.

    5) How long do prebiotics stay in the gut? Are they consumed within a 24-hour cycle or do they stay around longer? So could somebody eat a food with scFOS one day and it would not only improve sleep that night but the next night as well?

    In conclusion, many thanks for bringing your knowledge and enthusiasm to this fascinating subject.

  3. Hi Seth and Heisenbug (love your name!)

    The famed NEJM beta carotene was a failure in not just that trial but ALL synthetic Lurotin beta-carotene trials like HATS, Physicians health, and CARET. It is factory made from benzene petroleum derivatives by the chemical company BASF AG. These are not bio-identical to mammalian receptors. The fact that synthetic non-bioidentical hormones like PROVERA in the Women’s Health Initiative where record numbers of women died of strokes, cancer and heart risks are inherently dangerous cannot be overstated, I think.

    Natural, food-based carotenoids are not only safe but extremely efficacious.

    Great post and interview!

    Seth: Thanks. That’s a good point. Which I never heard Bruce Ames make.

  4. Mr Heisenbug have you considered that the differences in bacterial groups in smokers are due to other causes rather than cigarettes? Smokers may not be as health conscious and may be less likely to eat vegetables for example. Perhaps the positive changes in microbial composition after smoking cessation may be due to other lifestyle changes (improved diet). Quite often smoking cessation is accompanied by an overall effort to improve health in other ways also.

    I would be interested in seeing the microbial composition of someone who ate more like Michael Pollan but smoked regularly.

  5. Kirk,

    Foods high in fermentable prebiotic fiber are pretty easy to find provided you know what to look for. Fructooligosaccharides/inulin/resistant starch/mucilage/pectin is a good list and should direct you to plenty of foods.

    Honey contains many oligosaccharides that have all been shown to have prebotic activity. The FOS in honey (kestose, nystose, inulobiose) are among those. The oligosaccharides are formed from honey’s simple sugars by the activity of enzymes provided by bees.

    The amount of fermentable fiber in a teaspoon of honey would be well below 1 gram. If honey has outsized prebiotic activity, it is likely due its unique combination of oligosaccharides. Trying to isolate/duplicate this somehow in an experiment would be quite difficult outside of a lab setting. But I still think it would be worthwhile to test for a prebiotic effect, and a pure formulation of FOS would probably be the closest substrate (something like:

    I guess coincidentally, the 3 hour mark is probably a good general marker for when you’d expect fermentation to begin. That’s when the small intestine would be mostly emptied, and this is also confirmed by breath tests which test for malabsorption and small intestine bacterial overgrowth. The cutoff for these tests is 2.5 to 3 hours — anything detected before then is considered premature fermentation. After 3 hours is considered to be normal colonic fermentation. Among fibers, oligosaccharides/FOS are known to ferment very rapidly and preferentially.

  6. Stuart,

    The smoking study did not just pick random people off the street who had already quit smoking. It was a controlled cessation study.

    Your second point is a good one. I too wonder if certain dietary or other factors are protective from smoking’s microbial impact. After all, tobacco smoking is ancient and has existed for a long time. But the very high levels of the diseases it is strongly associated with are not.

  7. Great post/interview.

    A few things. I know that people who have heart problems are required to take antibiotics before having dental work…I assume that there are some studies out there showing the connection between these two problems. Might make for some good reading/future posts on Heisenbug. This might also help confirm your theory about heart disease, bacteria, and smoking.

    Also to Kirk, because I have a toddler at home, I have learned more than I wanted to know about sleep cycles. The three hour mark is the end of a typical sleep cycle. I am wondering if something at 3 hours is waking you up because that is when you are most wake-able…Conversely, I am wondering if the honey somehow extends the sleep cycle to 5 hours making everyone more rested.

  8. from that suppversity post, “There is “natural” lactulose in milk: Due to the fact that lactulose can be produced by the heat-induced isomerization of lactose (see inset in figure to the left for a reaction curve for milk that’s heated at 130°C), all varieties of heat treated milk, even the low-temperature pasteurized variety will contain a certain, albeit low amount of lactulose (see figure to the left)”

    warm milk before bed anyone…

  9. Adam,

    Lactulose is definitely shown to be potently prebiotic/bifidogenic. In fact, it’s what they use in those breath tests I mentioned in the comment above.

    My only issue with it is that it’s not really something found in food. It’s commercially produced from lactose as a food ingredient and for medical purposes. As the article says, you can find lactulose in milk, but only because of the pasteurization process. As such, I don’t see a reason to go out of one’s way to obtain lactulose (it isn’t very practically obtained) when there are other good options that have more of a basis in human dietary patterns.

    Daz: I was just thinking that myself.

  10. I was talking with a friend about using honey. He said that several years ago he asked his Avurpedic physician how to improve his sleep. The physician said to drink warm milk with honey just before bedtime.

    Seth: very interesting!

  11. Heisenbug, I wondered why UHT milk in Tetrapacks tastes different, sweeter, than regular milk. Also it is a bit of a quandary: some moderately lactose intolerant people report that they can consume SOME UHT milk without catastrophe. I suppose eventually the laxative action of the lactulose will get them if the lactose doesn’t again depending on volume ingested.

  12. hi Mr. H,

    i was just looking at an old list i quickly put together quite a while back,
    in the doc i listed fibres that i did not want to go looking for ie. may be best for me to avoid.
    & fibres that probably worth getting ie. may be good for me.
    i should clarify that at the time i probably put things on the ‘avoid list’ if i read some ‘bad press’ about it…eg. low fodmap diets?

    anyway at the time, my list went like this,
    ‘avoid/bad’: Insoluble (roughage), FOS, fructan, Inulin,
    ‘good’: RS (resistant starch), Pectin, GOS?,

    the list is likely way over-simplified, if it makes any sense at all…?

    anyway just wondered if you may have some sort of list of your own, possibly ordering ‘good’ to ‘bad’ dietary fibre.
    &/or comment on my list.

    i seem to recall at the time that pectin look interesting, & i was already on the RS ‘bandwagon’. not sure why i thought GOS may be a good one.

  13. Daz,

    The only reason to actively avoid any specific type of fiber, as far as I know, is if you have a specific intolerance for it and it gives you gastrointestinal problems. Even insoluble fiber isn’t necessarily “bad.” But it can come in a package, like wheat, that may give you separate issues.

    The only reason you’d put FOS or Inulin in the “avoid” bucket is because they are both fructans and belong to the “FODMAP” group — types of carbohydrates that some people do not absorb properly and thus experience gastrointestinal issues. The “FODMAP Diet” is specifically designed for those people. In this case, I think GOS would probably have to be on that list too.

    The question in my mind about this is that, since that kind of intolerance may be caused by small intestine bacterial overgrowth (ie, fermentation happening where it shouldn’t), then presumably any type of fermentable fiber would be an issue, not just FODMAPs. Also, I’m curious as to whether FODMAP intolerant people have a problem with FOS, since it’s shorter chain and known to cause less issues than something like inulin.

    For now, only your personal experimentation can answer these questions.

  14. One of the best, if not THE best source of resistant starch (RS) is potato starch. It’s almost pure RS, with no additional carb effects. Bob’s Red Mill Potato Starch is the one most people are now using to get more fermentable fiber. Most natural food sections have it, or you can get it on Amazon.

    Note: it’s NOT simply potato flour. It’s potato STARCH. Potato flour is just dried and powdered potatoes. It contains almost zero RS.

    A few hundred people have been experimenting with it, to almost universal positive effect. Check out the Free the Animal blog to get some more info. There are dozens of posts and hundreds of comments.

    Unnecessary disclaimer: I don’t work for Bob’s Red Mill :=)

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