Squinting At A Specifically General View of the Gut Microbiome

This was my very first post of more than 100 by now, April of 2013, that began my evolution in thinking about the gut microbiome: Prepare for the “Resistant Starch” Assimilation; Resistance is Futile. Yes, the narrative was initially somewhat hyperbolic, silver-bullet, miracle cure and all. I’ll cop to all of it.

I am primarily an integrator, synthesizer, and promoter of things that make evolutionary sense to me and I always kick off with a bang. But I’m also the least intransigent blogger you’ll ever meet. I expect being half or more wrong from the outset. Rather than spend endless hours, days, weeks and months checking all my jots and tittles in a self-deluded effort to not be wrong about anything (completely futile, because you’re always wrong about something), I go full shotgun and brace for the criticism and constructive critique:


(^ Wash, Rinse, Repeat—ad infinitum)

This manner of dialectic saves time, teaches more people faster—in fact, we all learn together, collaboratively—is an honest process, and seems to me to be the most natural way to build increasingly complex and closer-to-truth hierarchies of quality* knowledge (* See my AHS12 presentation: Paleo Epistemology and Sociology).

It is for this reason that in terms of most of my posts, I do not delve into “excruciating” detail. For instance, I’m typically not talking about a specific 1-in-1,000 species of a gut bacteria, unless it’s a well identified pathogen run amok like C. diff, after a round of antibiotics (the antibiotics being the general issue—specific, to highlight general). Similarly, I don’t dwell on deeply dysfunctional guts but rather, on the vast majority of guts, some better than others, but always with the idea of improving whatever you begin with—never achieving perfection.

Shotguns usually hit the bullseye, too.

I’ve done a number of podcast interviews over this last year or so, most about Resistant Starch. The truth is, I didn’t have any idea at the outset whether RS would pan out at all, be the Next Big Thing, or more likely, be a very important specific piece of the general puzzle. I now believe it’s the latter.

So, with that, here’s my latest podcast interview. It’s with Will Barron of Upgraded Ape, one of of those biohacking folks. Upgrade your gut biome for improved brain performance. Talking resistant starches and fish with Richard Nikoley. While RS is in the title, I can assure you that I took a far more general track with it.

  1. I take pains to emphasize that whatever devils are in details, it’s the enormous complexity of the gut microbiome that’s the important thing.
  2. That focussing on very specific things in terms of specific pathogens, overgrowths, etc., is the province of clinicians with clinical experience that builds with practice and is applied to more and more specific and identifiable problems.
  3. That while experimenting and supplementing with RS and dirt-based probiotics is fine, not generally harmful (suggestions that it is, are bullshit), it is nonetheless likely best to get most prebiotics from various foods, and probiotics from being less sanitary, a bit more dirty. But supplementation, while not ideal, is better than nothing.

Alright, take a listen, and if you’ve heard some of my earlier interviews that focussed primarily on resistant starch, tell me if I haven’t upgraded my specific views in general.

Now, let’s squint some more. This post was formulated only an hour ago, when I read Jeff Leach’s account of taking it up the butt for science, over morning coffee and an American Spirit ciggie: (Re)Becoming Human: what happened the day I replaced 99% of the genes in my body with that of a hunter-gatherer.

When he announced his planned DIY fecal transplant some while back on the Human Food Project’s Facebook, I thought he was deeply confounding variables. I suggested that a better first step would be to bed down and swap bodily fluids and microbes with a Hadza woman for some months as a first step (interest of science, y’know?) and only then take some Hadza guy’s shit up his butt. ‘Butt’ it is what it is.

Anyway, take a good read at that post. I was going to do some excerpts and comment on them, but I don’t want anyone to miss the forrest through the trees. In short, I’m now a much bigger fan of Leach, and it’s this bit of writing that did it for me. Take particular note of the vast differences between a Hadza gut and an American gut.

Keep squinting, Jeff. Good work, anxious to see the ultimate results.

…To wrap it up, it’s easy, in hindsight, to say that supplementing RS in forms like potato starch is “bad.” It’s complete bullshit, and I’ll tell you why.

  1. It’s not harmful. How can it be harmful to ingest a real food fraction?
  2. People in general Paleo/RealFood have been talking about prebiotics for-fucking-ever. Onions, Garlic, Jerusalem artichokes, bla bla bla.
  3. Nobody really listened and when they did, it was chest beating over a coupla grams. It was only ever predominately about bacon, grilled meat, and added spoonfuls of coconut fat and grassfed butter.
  4. SAD dieters get way more fermentable fibers than “paleo” peeps (which isn’t saying a lot in an H-G scenario not even ridiculously and fantastically focussed on the way outlier Inuit). And H-Gers get way more than SAD.

But for my last point, it goes back to the way above. Nobody has any tolerance for being only half right. This is always a mistake. Always. Prebiotics have been jerked off about forever, but nobody paid real attention.

Until fucking potato starch and suddenly, there are many thousands worldwide doing so. But that’s a specific thing. What’s the general thing they learned is that when they took some isolated RS2, they observed first hand that:

  1. It had profound effects that cut through the signal/noise ratio on many gut levels.
  2. Results for the vast majority were positive, over time.

Sorry, I have this quirky fault where I think that giving folks valid generalities, they run with it and create their own specifics. I’m no hand holder. Fucking annoying, time wasting, and manufactures and maintains dependence.

So, some will doubtless stay with the potato starch supplementation forever and call it a day. Optimal? Probably not. But, some folks will always just supplement vitamin D rather than get out in the sun. Optimal? No, but only a stupid fucktarded miscreant would suggest that they ought not then supplement with vitamin D.

Potato starch supplementation in isolation has changed the landscape in many ways. That’s a simple fact. But you watch. There will be many coming on line to tell you it’s not a good idea and that all the foods they used to shun are the way to go—as though they came up with the idea.

Well, biting feeding hands has always been the province of latching-on leeches.

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Richard Nikoley

I started writing Free The Animal in late 2003 as just a little thing to try. 20 years later, turns out I've written over 5,000 posts. I blog what I wish...from diet, health, lifestyle...to philosophy, politics, social antagonism, adventure travel, expat living, location and time independent—while you sleep— income by geoarbitrage, and food pics. I intended to travel the world "homeless," but the Covidiocy Panicdemic squashed that. I became an American expat living in Thailand. I celebrate the audacity and hubris to live by your own exclusive authority and take your own chances. ... I leave the toilet seat up. Read More


  1. pako on October 4, 2014 at 14:37

    Prebiotics and SBO’s have massively reduce my symptoms of chronic cutaneous lupus erythematosus!!! I thank Richard, Tim and Grace for this. I wanted to post on your site first because it all started for me here. My first visit to FTA was last December 2013. I immediately started PS supplementation to my HFLC diet. My methods evolved as new information came available. My current regime is as follows 2 to 3 times a day:

    Prebiotics-BRM raw potato starch, psyllium, inulin/FOS, birch larch, Beta 1,3 Glucans. I premix about a weeks worth and mix 1-3 Tbs a dose.

    Probiotics-Prescript-Assist, AOR probiotic 3, Primal Defense Ultra. 1 capsule each for each dose.

    Diet- Whole foods, high resistant starch and inulin and low gluten. Grass fed and organic. Try to stay away from refined grain and sugar. Moderate alcohol intake. I eat in a very enjoyable way and I find it very unrestrictive. I have cheats of ice cream and such at least one a week.

    Actually last weekend I was ripping it up with some of my old buddies and downed at least eight strong margaritas! Definitely got carried away and paid the price for 2 days but, after that I felt 100%. My ship rights itself now for the first time in a long time!

    This is not to say that I am “cured” yet. I still take 200mg of plaquenil a day. But six months ago I was taking 400mg with poor symptom control. Now i am at near full remission, and only seem to be improving. I’ve done some 24-36 hour water fasts and confident that a couple 48-72 hours one will put this thing to bed.

    One of the biggest sources of misery with lupus is sun sensitivity. Its hard to describe the anxiety and sadness this caused me. I have two young sons and live within walking distance to the beach in California. I used to wear pants, long sleeves, sun hat or hood and sunscreen just to go into the back yard or take out the garbage. I still did outdoor activities but covered up my best and suffered consequential flaring.

    For the last month or so, I’ve been experimenting with sun exposure with excellent result. Started off with short sleeve T shirts, then baseball hat instead of full brim. Labor weekend went shirtless at the beach for an hour or so for the first time in 4 years! I reclaimed my birth right as a furless earth dweller to have sunshine on my skin. Sunburn never felt so good!

    Yes, i am quite far down the road of healing but there was some bumps on the way. I had joint soreness for the first two weeks or so of potato starch. I also had to ease into Prescript Assist very slowly for it initially made my lupus worse. Especially gum bleeding. I still have bizarre reactions to some seemingly useful products like collagen and raw milk/creme for example. More desensitation is needed.

    So once again thank you Richard, Tim and Grace for putting this information where I could find it. I am forever indebted. Now i must go enjoy the sunshine. Richard, I live in Half Moon Bay if you want to me up for a beer sometime!


  2. edster on October 5, 2014 at 00:25

    Did I miss something? What’s happened to your book on the gut Richard, has it been shelved?

  3. Natasha v. Potato on October 5, 2014 at 05:39

    Good morning! Very similiar results here. I arrived on this site fully indoctrinated by LC. Never ate a potato or injested a pinch of starch without suffering a major immune system reaction. I was making a tonne if effort to be healthy and was getting no returns.

    It took six months, but now I can!!. I eat potatoes and starch. Feel good too. Potatoes do something that other things don’t. At the same time I am incorporating more foods, especially prebiotics.

    Interestingly, I also tried raw milk a few weeks ago and irritated my immature-stunted immune system. My plan…have more but slowly. Ironically, the collagen came in the mail yesterday. Thanks for the “heads up” Paul. Being soy baby formula fed 40 years ago was a collosal screw up.

    There is so much to learn of the microbiome. Utterly fascinating. Me too! I have noticed a change in my skin’s reaction to the sun. As a kid, I tanned and enjoyed how good the sun felt on my skin. For the past 10+ years…burn and slather on sunscreen (which I hate). With the changes this year SBO probiotics and prebiotics… I decided to “experiment” and abstain from sunscreen. I DID NOT burn! Spent lots of time outside. West coast. San Diego to Vancouver. Golf. Hiking. NO BURN. I tanned! Skin felt good all summer. One more thing that I believe is regulated from the microbiome.

    I appreciate your honest commentary Richard. I don’t always agree but I am still reading. Keep up the good research.

    • Wilbur on October 5, 2014 at 13:46


      I have seen changes in myself that initially seem unrelated to the microbiome but that later can be connected. My latest is my improved sense of smell, which was just recently connected to overall health. It is with this mindset that I took your suggestion about the gut-sunburn connection seriously. Check this out


      It could be a probiotic effect, or just overall improved gut health.

    • Gemma on October 6, 2014 at 12:02

      @Natasha v. Potato

      Nice observation on the sun and suntanning, me the same.
      The same with sunglasses. Not that I do not need them, I do not want them!

  4. Jennifer on October 5, 2014 at 15:08

    Richard, I just wanna say I really appreciate YOU. Your frankness, your humor, your irreverance, your experiential knowledge. Thank you! Keep it up! You are appreciated, my friend. I’ve learned so much reading your blog and the comments. Just want to post a “shout out” where appreciation is due. Don’t doubt your effectiveness … You’re getting it out there! Thanks again…

    • Richard Nikoley on October 5, 2014 at 15:13

      Thanks Jennifer. And I assume if that changes, you’ll find other avenues. I’ve always looked at this task as a revolving door.

  5. gabkad on October 5, 2014 at 16:23

    Only read the first maybe two paragraphs of Jeff’s description and I’m laughing so hard I needed to take a break. Hi Richard!

    Okay, deep breath. Back to Jeff and the hunter gatherer bumsquirt…..

    • Richard Nikoley on October 5, 2014 at 16:31

      I really loved his write up. How he began it with the deed, segues into the general diet and gut differences, then finishes off with the specific.

    • gabkad on October 5, 2014 at 16:50

      A thorough analysis, I’d say.

      The thing is though, if you don’t feed them, they won’t stay. I think he’ll lose his oxalobacters.

  6. gabkad on October 5, 2014 at 16:48

    ‘biting feeding hands has always been the province of latching-on leeches’


    Too long for a T shirt. Maybe for a nightgown. 🙂

    • Regina on October 5, 2014 at 20:02

      Hah! I liked that too Gadkad.
      I’m with Jennifer. And with Pako in that I just tried things as they came available whilst doing my own due diligence.
      Geez, ‘if you are not the answer to life, the universe and everything, then it’s pitchforks for you’ ?? wtf. This is a rabbit hole folks. And miles to go before we sleep.
      I love the series on animal fiber. I had no clue and it gave me a totally different perspective on how to define fiber. Duh. I was still in diapers thinking fiber was only in whole grains.

      I was already giddy eating PHD and it’s been so enjoyable to add different fibers as I learn about them. Can’t find any fresh jerusalem artichokes this year in Chicago but I found a supplement. Cheap too! 90% inulin.

      LOVED Jeff Leach’s brilliant missive. Now there’s a lad, indeed!

      p.s. I missed the daily fucktard when I saw this:

      to give you a laf.

    • Wilbur on October 6, 2014 at 05:19

      Regina, I find sunchokes regularly at international grocery stores that cater to Koreans. We have several in our area. They keep forever in the fridge. A farmer told me not to worry if they get a little soft – that’s normal. For my gut, sunchokes and inulin supplement are two different things. I can’t be very social after the sunchokes.

    • Regina on October 6, 2014 at 09:17

      Lol Wibur,

      My husband calls them fartchokes. They are the most hilarious of all the foods I’ve tried since exploring this stuff. Yeah, even my fave asian market hasn’t had them this year. And Whole Foods sunchokes taste just bland and watery (not that they have them this year either).

      I can’t tell you how happy I am to learn about all this: fibers (soluble, insoluble, animal fiber) starch, sugars, gut bugs. Yay! My new religion. I’m a born again.

    • Wilbur on October 6, 2014 at 10:30

      I am of the same persuasion – I know exactly what you mean!

      Sorry to hear about the sunchokes. I hear they are really easy to grow, and maybe one day I will try. In fact, I hear they will take over if one is not careful.

      In terms of hilarity, I find dandelion roots and chicory roots to be great substitutes. I grow my own -dandelions are really easy – and I understand that the roots can be eaten all through the winter. I have also found dried dandelion roots online that I have rehydrated while making a cup of tea. I had some dried chicory root, but no amount of soaking or brewing made it chewable. Good luck!

  7. Mart on October 6, 2014 at 09:38

    one particular thing he touched on was chlorinated water helping to kill gut bacteria. Is this true? If I only drink tap water am I killing some of my good bacteria – both pro and pre-biotic?

  8. michael goroncy on October 5, 2014 at 20:57

    On the RS…it’s very rewarding to see articles and blogs talking about it as if it’s ‘always been.’ I don’t care about recognition, but it did take a lot of work getting the word out”.

    The above is a quote from Tim Steele to a ‘hat tip’ I sent him.

    ” blogs talking about it as if it’s ‘always been”
    Bastard! Brilliant, it is what I thought, but couldn’t
    express and he comes along in a flash and nails the scene.
    Tim’s research and Nikoley’s insight/promotion has changed the health for the better of many.

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