Gut Bugs: Far More Than Everything You Always Wanted To Know (and then some)

[This series was originally published as A Gut Microbiome, Probiotic, and Prebiotic Resistant Starch Primer. Two other series, Gut Bugs, Probiotics, Prebiotics…And how our microbes make us who we are, and Natural Immunity, Gut Biome, and its Importance in COVID-19 #1 — Introduction have both been incorporated here for a wider, more general resource for all things Gut Bug.]

Take 4 minutes to watch a truly eye-popping video that will make the whole subject and importance of Resistant Starch as simple as possible for you—but not too simple. Then, when you begin going through how to incorporate it into your diet, remember that you need to actually have the bacteria present to get the benefit. Some don’t, often because of antibiotic treatments…so pay close attention also to the information about Soil-Based probiotics, a completely different animal from the stuff in yogurt and kefir.

Now, get yourself on board.

Lots and Lots of Posts; Lots and Lots of Comments

  1. Prepare for the “Resistant Starch” Assimilation; Resistance is Futile (288 comments)
  2. Resistant Starch: 4-Letter Word? Nope. Goal: Create Mashed Potatoes A Diabetic Can Eat Every Day (481 comments)
  3. Resistant Starch: Now We’re Getting Somewhere (105 comments)
  4. Resistant Starch: An Overall Primer, with References (30 comments)
  5. Resistant Starch: Now We’re Getting Somewhere, Part 2 (35 links to research) (175 comments)
  6. The FTA Resistant Starch Trial: N=75 +++ (60 comments)
  7. Beans and the Second Meal Effect: Resistant Starch (49 comments)
  8. Low GI Mashed Potatoes! and the Resistant Starch Content of Foods (47 comments)
  9. How Resistant Starch via Potato Starch and Beans Helped a Type 2 Diabetic (108 comments)
  10. Resistant Starch Content of Foods; Other Anecdote and Miscellania (271 comments)
  11. A Type II Diabetic Rings in About How Resistant Starch and Eating Things Cold Has Regulated His Blood Suger, Even Eating SAD (31 comments)
  12. I’ve Got A [Gut] Feeling, But I’m Not Going to Eat Anything (23 comments)
  13. Success: Pre Diabetic Glucose Regulation With Resistant Starch (Potato Starch) (19 comments)
  14. Resistant Starch Self Experimentation Prelude: Sisson, Konstantin Monastyrsky, and my Commenters (111 comments)
  15. The N=2: Tatertot Tim and Commenter Marie Test Potato Starch on Ketosis Part 1 (36 comments)
  16. Resistant Starch Supplementation Improves Insulin Sensitivity (45 comments)
  17. Paleophil Uses Resistant Starch To Hugely Blunt BG Spikes for His Raw Fermented Honey Habit (67 comments)
  18. A “LADA” Type II Diabetic Finds “Amazing Results” With Resistant Starch (50 comments)
  19. Clearing The Air: My Beef With The So-Called “‘Healthy’ Low Carb Lifestyle” (72 comments)
  20. PhD Physical Chemist Commenter Marie is at it Again! Resistant Starch and Ketosis. Low Carb in Short Pants (49 comments)
  21. Tatertot Tim Experiment: Low Carbers SO IN SHORT PANTS. 140g Starch Carbs in a Single Meal, Blood Glucose “Spikes” to 110 (229 comments)
  22. Commenter Marie, Taking One For Her Dad With Cancer, Part 2 (59 comments)
  23. Tatertot Tim is Far, Far From Your Average Pussyman Metrosexual Hipster Poseur. Photographic Proof (71 comments)
  24. If Raising Your Body Temperature is Important to You… (107 comments)
  25. Government “Shutdown” Juxtaposition (Real Hunter Gatherers: Hadza) (10 comments)
  26. Alright, Now I Have to Work Out a Proper Paleoish Shit on a Shingle (57 comments)
  27. Frenched Pork Chops With Resistant Starch Mashed Potatoes and Gravy (11 comments)
  28. Resistant Starch Ingestion Has No Effect on Ketosis But Blood Glucose Blunting Effects are Highest in A Normal Diet (216 comments)
  29. Mark Sisson Jumps On Board With Resistant Starch (149 comments)
  30. Thinking, Emoting, Reacting and Dreaming With Your Gut Biome (31 comments)
  31. Whole Health Source on Beans, Lentils and the Paleo Diet (14 comments)
  32. Do You Have Real Guts? Will You Do What it Takes?
  33. Chris Kresser and Jeff Leach on Gut Health (3 comments)
  34. Resistant Starch: American Gut Project Real Results And Comparison (Very Big News) (262 comments)
  35. New Free the Animal, Resistant Starch-Based Dietary Guidelines (282 comments)
  36. Just Watch. Bulletproof Exec Dave Asprey is Going to So Biohack Resistant Starch (106 comments)
  37. Shit: That’s One Tough Pill To Swallow (33 comments)
  38. The Most Dramatic Resistant Starch Success Story Yet (101 comments)
  39. Dr. BG Comments in Comments on Resistant Starch vs. FODMAPS (122 comments)
  40. Resistant Starch Fixes The Same Old Low Carb Diet Problems (59 comments)
  41. The Gut-Brain Axis and Narrative Complex Dreaming with Resistant Starch (even X-Rated) (59 comments)
  42. Resistant Starch: Promise for Improving Human Health (12 comments)
  43. My Twitter Dustup Over Resistant Starch with Jimmy Moore (170 comments)
  44. Resistant Starch & Gut Biome: A Family Science Project (12 comments)
  45. “Have we come in from the desert?” – 40-year Low Carber (38 comments)
  46. Everybody: Why Resistant Starch Has to Be Raw & Cold (90 comments)
  47. Why I’m All Over Jimmy Moore’s Ass (122 comments)
  48. Thanks, Jimmy Moore (34 comments)
  49. Diabetics Going Nuts Over Blood Glucose Regulation on Resistant Starch Supplementation (27 comments)
  50. Must Read. Type 1 Diabetic’s Resistant Starch Experiment With Continuous Glucose Monitor Data (60 comments)
  51. A Brief Word on Resistant Starch Critiques (82 comments)
  52. The Importance of Human Breast Milk for Gut Microbiome Development (83 comments)
  53. Link Drops—Mostly About Resistant Starch—and Christmas Greetings (74 comments)
  54. 30 Day Test of Blood Sugar Before & After Resistant Starch (22 comments)
  1. All the posts thus far on RS (90 posts and thousands of comments as of Mar, 2014).
  2. Lots of research here & here.
  3. My latest Resistant Starch-Based Dietary Guidelines (a must read to get an overall sense).
  4. Lots of comments from readers reporting the benefits they’ve seen.
  5. Isolated RS—Like Bob’s Red Mill Potato Starch (NOT to be confused with FLOUR)—has zero carbs if taken raw, because you don’t digest it, your gut bugs do and if they don’t, it passes right through. On average, humans can process about 60g per day. If cooked, it’s about 10g carbs per TBS (per the label) of rapid digesting starch. Don’t cook it unless you intend to, like for thickening a sauce (see here).
  6. Another supplemental source is Plantain Flour.
  7. There is also green Banana Flour, now.
  8. Here’s a long list of foods that contain RS. Some of the highest sources in food is cooked and cooled rice (parboiled is the highest, also lowest GI by far), cooked and cooled beans (prepare by traditional 24hr+ soaking), and cooked and cooled white potatoes. Sweet potatoes have almost no RS. Cooking and cooling forms RS3, a retrograde RS that remains intact when the food is reheated. Fried rice from out of the fridge is ideal for an RS food source.
  9. Per number 2, your BG won’t rise no matter how much isolated RS you consume (such as the potato starch). Moreover, it will significantly blunt spikes from other foods, a “second meal effect” that persists for hours, even into the next day. Regular consumption lowers both fasting BG and blunts spikes from other foods eaten anytime, so dose timing is unimportant if taken regularly. This blunting is most profound on a normal carb intake. In ketosis, there is little blunting (see here).
  10. The benefits most commonly touted are: lowered  fasting BG, BG blunting, better sleep, increased energy, well being and calm, mental clarity, vivid dreams, curing of chronic constipation and infrequency, soft stools, satiation with gentle hunger, and increased body temperature (I think I got them all…let me know if I missed any).
  11. The problems most commonly reported are: flatulence and headache. Most have reported having flatulence, but for most it diminishes over time. It seems most prominent when taken with food and least when taken in water on an empty stomach. Taken with beans can be a hilarious experience if you’re up for it. For some, going periods of 2-3 days now & then without supplementing seems to help get beyond it. Headaches have only been reported by a handful of people. One or two reported intestinal distress, but I chalk that up to oversensitivity to flatulence.
  12. Most of the studies use 30g of potato starch, which is 4 tablespoons. Above 60g will probably pass on through. Many have begun with 1TBS per day, and increased up to 4 each week. However, dose, frequency, how it’s administered (with food, kefir, yogurt—cool or warm—or just water by itself) is something each person has to experiment and figure out for themselves.
  13. In general, even targeting RS foods will probably at best yield 10g of RS daily. Thus, supplementation is a good idea to get into the 20-30g range which, as stated, is what so many studies have used to document many of the benefits we’ve been touting. Paleoman had a far wider variety of high RS foods that just isn’t in our diets commonly (cattail and tree pollen, anyone?).

OK, if I think of anything else or if something gets added in comments that ought be here, then I’ll add as it comes up.

Best wishes. I wouldn’t do this had I not seen hundreds of reports since last April of all of these benefits I outlined in number 7.

Update: Since publishing this a few months back it has become increasingly clear that the reason some people have had less than expected results with resistant starch foods an/or supplementation, or even adverse results, is that they may lack some of the gut bacteria needed and those are really not to be found in dairy based probiotics. Fermented foods may help somewhat, but what we’ve found is the the biggest help comes from soil based probiotics.

Here’s a post about it: Probiotics: The Genetic Component of Obesity. Here’s an update post, April, 2015: Gut Bugs, Probiotics, Prebiotics…And how our microbes make us who we are. See, it always moves forward. Be skeptical of all who don’t.

Here’s the probiotics recommended.

  1. Elixa
  2. Prescript-Assist
  3. AOR Probiotic-3
  4. Primal Defense Ultra
  5. (See this Update post of two additional probiotics I recommend, and why: Gut Bugs, Probiotics, Prebiotics…And how our microbes make us who we are)

I take 1 of each, every day or two, usually with a smoothie:

  • 1 raw egg
  • 1 piece of fresh fruit (apple with skin, banana, handful of frozen berries, orange, etc., or whatever you like)
  • 2 TBS Potato Starch
  • 1 TBS Green Banana Flour
  • 1 TBS Plantain Flour
  • 1/4 tsp Inulin / FructoOligoSaccharides
  • 1 Scoop Amazing Grass High ORAC
  • 4 oz Odwalla-esq fruit/veggie smoothie blend of choice
  • 4 oz Kefir (plain or any flavor of choice)
  • 1 each of the aforementioned SBO probiotics, caps pulled apart and dumped in (or, just pop them; I mix them in because I split this with the wife unit)
  • Handfull of ice cubes
  • Water as needed for desired consistency in a good blender.

This should make 20-24 oz or so, so it’s perfect for 2 people (my wife takes about 10 oz and I take the rest). For in person, I’d just go with 1TBS of the potato starch and one of either the banana or plantain, cut the Odwalla and kefir in half, etc.


You can also read all the subsequent posts about this revolutionary gut-changing, hyper-biotic product, as well as read dozens of customer testimonials in the comment sections.

Coincidentally, I finally watched Rob Knight’s TED talk—that had been in my to-do queue for over two months—on the same day Mark Sisson came out with his reformulated Primal Flora. Mark explains.

The funny thing about science is that it’s a moving target. It’s evolving, and if the science evolves, so too must the supplements based on its findings. To stay abreast of it all, I’m always researching and listening to advisors and other experts to make sure that my formulations are optimal. gut health as a health topic has exploded in recent years, as has the amount of research being done, and what we know about how the foods we eat, behaviors we do, and supplements we take affect our guts has evolved. I recently updated the [easyazon_link identifier=”B007N79QS0″ locale=”US” tag=”fretheani-20″]Primal Flora[/easyazon_link] formulation to reflect the latest developments. It now contains an (almost) entirely new set of probiotic strains. Below I’ll explain what these are, how you can benefit, and share my own experience using the new formulation.

That much is good enough, but it gets better.

…I need to explain a few concepts. You are probably aware that most common probiotics and fermented milk products contain primarily lactobacillus and bifidobacterium species. The reason I elected not to focus on those is because these species are already very prevalent in our guts – there are probably over 20 trillion – so adding even 20 billion more CFU (colony forming unit) is only boosting the population by one one-thousandth. And that’s if they even survive the harsh acidic environment of the stomach (which most probiotics don’t). Instead, what I wanted was a number of well-researched species that I could deliver to the GI tract where they could colonize and do their unique jobs. To do this, most had to be what we call “spore formers” that remain dormant until they reach the appropriate parts of the gut, undamaged by stomach acid. These needed to be the species and strains that were proven effective in years of solid research, in many cases signaling to other bacteria to increase or decrease.

Cool, now we get to wait for the Usual Suspects; the Nattering Nabobs of Negativism to come out of the woodwork over the “dangers” of HSOs (homeostatic soil organisms) or “spore formers.” It’s like they never got the memo that all kids eat dirt if you give them a chance (and this is where you’ll find the bacterial spores in big numbers). …Anyway, I just wish Spiro Agnew hadn’t also coined the trite America, Love It Or Leave It bromide, like he owned the place…

So, now watch the video. It’s a fabulous introduction to the gut biome, absolutely essential in dismissing and then ignoring stupid, presumptuous, pretentious people who have yet to catch on but who will instead act like they always knew, and came up with the idea years ago.

Quick review:

  • There are 300-1,000 different microbial species in the average human gut.
  • In terms of cellular numbers, they can outnumber your 10 trillion human cells by 10 (100 trillion bacteria).
  • In terms of genes, it’s 20,000 of your genes to 2-20 million microbial genes.
  • The microbes between your mouth, skin, vagina, and gut are so vastly different from one-another as to compare a tropical ocean reef with a desert.
  • Cunnilingus takes on new dimensions. It’s probiotic!
  • You are 99.99% genetically identical to every other human on the planet. Whereas, in terms of your gut microbiome genetic sequence, you can be 90% different from the person next to you.
  • Every microorganism in and on your body is a nano-chemical-plant. They’re also warriors and anarchists.

I’ve been using using probiotics for a while now, since I first got the notion that perhaps they were at the root of a lot of problems, including obesity and over-plumpness: Probiotics: The Genetic Component of Obesity. I didn’t know what the magic was, only that I suspected it was there. It goes way back to when I first began using PGP (pretty good paleo), fasting, and heavy lifting to lose an initial 60 pounds: Hunger. That’s from 2009, so perhaps it demonstrates that I was always unsatisfied with “easy” macronutrient solutions (low or high carb; high or low fat; high or low protein, etc.) or “easy” nutritional solutions (high, low, or no grains; high, low, or no starch; high, low, or no animal foods; or high, low, or no vegetable foods).

Remember, this is Free the Animal and from day one, the theme is that we derive our principles by observing wild animals. Biochemistry is cool & all but no amount of understanding or Krebs Cycle remix is going to fix human problems.

Humans need to fix themselves and approaching the wild is an approach that has billions of years worth of earth-laboratory testing behind it. To state it another way: extraordinary claims demand extraordinary evidence.

If I wrote that “Hunger” post today, six years later, it would probably be called “Cravings,” or “Appetite.” I was being amused just this morning over thinking that a sign of a problem is often touted as “are you experiencing a loss of appetite?” You know what? I recall experiencing “loss of appetite” many times as a kid and young adult. My dogs experience “loss of appetite” about 3-4 meals per week. Is that really the key to not getting fat?

What I do think I have come to believe is that the more one eats, the more often, in company with a mentality that always has a hefty appetite, fat is in your future. Whatever the source of your insatiability, it’s not wild animal. It’s not human ancestral. It’s Neolithic. It’s Food Engineering. It’s a shiny new car three times per day. Day in, day out.

You’re welcome to disagree and go buy a keto meter and testing strips.

Here’s my story.

  1. Love hate with various probiotics and various gut foods—from the Mark 1, Mod A potato starch where we started, to my Fart Powder concoction.
  2. I found eventually that the bloated feeling or excessive poop volume most often shows up when I take the probiotics with human food or with the gut food.
  3. Taking whatever probiotics first thing in the morning on an empty stomach, via raw milk, water, OJ, or coconut water most typically (no plan, just what I felt like…even Tea Java) changed everything profoundly for me. Let it settle over at least a couple of hours or, don’t even worry about it. Eat when you have an appetite again.
  4. If you feel hungry, but instead down some probiotics with water, what does it mean when hunger goes away and doesn’t return for hours, sometimes nearly the whole day?

There’s an “intuition” put forth by some stupid people that feeding your gut is per se fattening, because the resident organisms don’t care, just want food, and so are going to motivate you to just eat (brain-gut connection). Well, such thinking does have the virtue of acknowledging CICO and ironically, brain-gut (only works 1-way, though). This is simplistic thinking by egregiously stupid people who’ve no concept of the constituents in the gut, as mentioned way above. Briefly, because too stupid, failing to take an overall big-pic look, fail to recognize the bugs are in perpetual chemical warfare, have an average of a 20-30 minute lifespan to do their thing, give off exotoxins when they die off, can share genes, can give off by-products that feed the gut and give off chemical-hormonal signals your brain understands and acts upon. It can go many ways, not just EAT MOAR! It can make you lose your appetite too.

There are good reasons to assume that sometimes, those brain signals can be a loss of appetite. Gut bugs invented the war of attrition.

So where do we go? What specific gut bugs do you need, in what quantities do you need them—when—and what is the timing, quantity, and formulation of their optimal food?

Let me lay it right out, explicitly:

– You don’t know anything, never will, and everything put forward by other stupid people is completely wrong. I’d be wrong to give you a solution. I care (like Tim Steele). They don’t.

You need to get yourself a shotgun. Saw off about 2 feet. Essentially, rather than trying to figure out what boutique bacterial strain out of potentially a thousand is going to do what you want, and what food is best for them, you shotgun it.

I have recently untaken a little comparison of the probiotics I like. There’s two new ones, the reformulated Primal Flora, already mentioned, and a crazy-super-high dose Elixa, out of the UK. Karl Seddon emailed me some months back.

I’ve been reading your blog a fair amount over the past few weeks. Mainly it’s quite memorable because of your entertaining, less-than-subtle way of wording your views and the (tongue in cheek) confrontational, call-out style of some of your posts. The humour is certainly appreciated over here in the UK, Ha! […]

My name is Karl and I am the creator of a probiotic called Elixa. It’s based on technology I developed over 3 years after graduating from university here in the UK. It’s very different from the standard probiotic supplement (it’s a short-course, it contains 500 Billion CFU per dose, and the encapsulation technology is what I developed after completing my studies in Biomedical Engineering at Oxford in 2011). I got interested in probiotics after my research (on my own IBS condition) lead me to a heap of scientific journal articles about gut microbiota. I realised that this area is not pseudo-science and yet there was still something greatly lacking in the effectiveness of all probiotics that I tried. It was actually fairly obvious where they lacked but the technical solution to that ‘obvious’ problem was very tricky. I still think that a lot of supplement manufacturers simply use the term probiotic based on its popularity/demand rather than their own sincere belief in the effectiveness (or potential effectiveness) of probiotics.

Anyway, after putting 3 years of my life into R&D for this problem, I have recently completed the development phase and begun full-volume production. I think that Elixa will change the pseudo-science reputation of probiotics entirely. Early feedback has been surprisingly awesome. It’s not one of those supplements where people are saying: ‘Er… yeah… I think it does something…’

My customers notice a definitive effect right from day 2/3, onwards (It begins with noticing improvements in their skin). They are in no doubt about it – to the extent that they email me to share their results. This is exactly what I had hoped for – A probiotic that can begin to fulfill what the scientific literature is insinuating (with regards to the huge potential probiotics could play in the future).

So he sent me four 3-day-dose rounds. I took the first over 3 days, the second about a week later; then, upon Karl’s recommendation, did the last 6 doses in a week. This is where it became very obvious to me to take them on an empty stomach, let things settle out, then eat when you’re truly hungry, later. Don’t be surprised if far from going back for 2nds, you very often leave food on the plate.

I dd a comparison of the brands I use.

Screen Shot 2015 04 19 at 7 30 48 AM

Here’s the PDF. Looks like about 50 strains amongst 15 genera. Who the fuck really knows what specifically does exactly what? And that’s The Point. Shotgun. BTW, a lot are spore formers, some aren’t. It’s a mix.

In terms of comparison, I really have to give Sisson props for being completely transparent. The only one that gives the specific strains and the CFU (colony forming units) for each strain (others I had to average, and PA only gives total mg). The others are trying to guard trade secrets, which is fine, but I guess Mark doesn’t feel the need to, because maybe the formulation changes again, over time, as he learns more. That’s the way to truly compete. Salute, Sisson! It isn’t the original Coca Cola recipe.

So, the basic procedure I’ve followed over the last month or so:

  1. Did the Elixa rounds, as described. Because such a massive dose by comparison (like taking a dozen Primal Defense, the nearest in terms of same strains), took them alone and experienced epiphany.
  2. When those ran out, I began with 1-each per day, same way (empty stomach in the morning) of [easyazon_link identifier=”B000GWG8FS” locale=”US” tag=”fretheani-20″]Primal Defense[/easyazon_link], [easyazon_link identifier=”B0082DDQH6″ locale=”US” tag=”fretheani-20″]AOR[/easyazon_link], and [easyazon_link identifier=”B00L82H6HY” locale=”US” tag=”fretheani-20″]Prescript-assist[/easyazon_link]. Same deal. “Loss of appetite.” Only thing, is it would get untoward after 3-5 days (TMI frequency, volume, discomfort, etc.), so I’d back off to zero for 2-3 days.
  3. Then, a few days ago I began doing the same thing with only Mark’s [easyazon_link identifier=”B007N79QS0″ locale=”US” tag=”fretheani-20″]Primal Flora[/easyazon_link]. I’m three days into 3 caps each morning. Very, very gentle. Same appetite.

If you like a good shit, you might want to get Mark’s deal if for nothing else. 🙂

Going forward, after I do Mark’s at 3 per day for 5, 2 per day for 5, then 1 per day for 5, I’m going to do all four (excepting Elixa, which I’ll just do every couple of months exclusively, as that’s the design idea).

I know I have ways to go, but I’m not even using the scale because things just keep going in the right direction quite naturally, i.e., a loss of appetite. I did put up a photo a couple of weeks ago. Updates to follow.

Back about 6 years ago in the midst of the gut biome craze, I had already been in collaboration with Tim Steele on tons of posts on Resistant Starch. Thousands of comments amongst the posts. Tim came up with the idea of further collaborating on a book and he went right to work, doing the drafting. I did the editing.

It eventually died, the reasons for which are not really important anymore.

So, I’ve been sitting on 165,352 words in Google Docs all these years. To give you an idea of what that means as a book:

“…in general, 250-300 words per page. Therefore, a 55,000 word book should be about 200 manuscript pages. A 100,000 word book would be about 400.”

So, somewhere around 600 book pages in draft.

I haven’t thought a lot about it, agonized, or dwelt on it these years. I was always a bit sad it never got out there. On the other hand, all non-fiction books are a year or two out of date on the date of publishing, as that’s the typical ridiculous publishing track. That in itself has disgusted me enough to keep me writing when I want, hit publish. 5,000 blog posts and counting. If my average blog post is 1,000 words, then that’s 5 million words and in book terms at 100,000 per 400-page book, I’ve published 50 books well over 300 pages.

And I never talked to a fucking editor or publisher. I’m both. Plus, I’m the writer. I’m not a best seller, nor have I made a lot of money, though I make a modest stream. What I am is free and unbeholden to write and publish in an instant whatever suits my fancy, knowing it will be read by hundreds; and, on good days, thousands.

I sit pretty as a writer. I wonder how many millionaire writers can say that, accounting for all of it.

So, in the last weeks as I watch the love of Covid-19 begin to crumble, along with its laughable “vaccine” strategy… where, as of today, both Portugal and Sweden have banned travel from Israel—one of the most vaccinated and early adopters of vaccination—now the world’s biggest Covid-19 outbreak by percentage (makes me laugh, I must say)—I thought of this unpublished stuff in my archives.


Because it’s becoming generally acknowledged by all who care about not being intransgent in their fucktardedness that “vaccine” immunity is both short lived and wholly inadequate; that, compared with the 99.85% of people infected and survived, the latter’s immunity is 13-27 times greater, and almost certainly lasts longer by orders of magnitude.

The cliff notes is that our gut biome makes up about 70% of our immune system.

Et voilà !

So, a current reason to put it out there. Covid-19. Of course, not wholly because of that specifically—because that’s just a global masturbation in public—but because general health overshadows. Covid-19 merely affords context, relevance, and prescience because of the global child-like obsession with a favorite cause of death.

So, for members, I shall slog through all 165,352 words once again. Recheck all the references, update them, add new, scour for new knowledge, expunge obvious errors and bad guesses. I figure I can produce a new chapter every 2-4 weeks.

Here is the completely unedited notes, the template, the marching orders for Tim and I.

Table of Contents

(All chapter titles and subtitles within chapters, tentative. Chapters 01-07, and chapter 14, are manuscript draft, everything else is ROUGH DRAFT.)

Chapter 01 – The Whole You (NOW PUBLISHED)

4114 words, 10, sections, 1 sidebar, 9 cites


We wanted the first chapter to be an introduction of sorts, not to the authors, but to the real stars…the gut bugs.  This chapter is intended to be a primer on the microbial life in and on us, some history, and the introduction of a few terms such as ‘Gram negative’ and ‘second-brain.’ 

Chapter 02 – A Curious Collaboration (NOW PUBLISHED)

4775 words, no sidebars or cites

This chapter is an introduction to the goofballs that wrote the book.  I think Richard, Grace, and I all agree it’s not worth the space it will take up in the book.  Maybe use for snippets and dust cover information.  In the entire book, there are very few mentions of any personal triumphs or tragedies, we had initially thought we’d be including more person insights, but we basically wrote ourselves out of the script as we got deeper into the meat of the book.  The real focus is gut bugs and the human host.

Chapter 03 – Your Second Brain (NOW PUBLISHED)

6167 words, 2 sidebars, 27 cites

This is a layman’s look at the gastrointestinal tract and its inhabitants.  No deep concepts or  boring (to some) microbe names or chemical formulas.  If we can get people to read this chapter, they will want to read the entire book.  We originally had loads of pictures in this chapter, but took them out for easier editing…pictures help tell this story, though, so we should consider as many pictures as possible.  People will want to refer back to this chapter as they read the rest of the book.  Here is also where we start using “Science Sidebars” more.  We felt they add value by breaking up the text and giving a bit more insight for the science-minded reader.  You’ll note only 27 cites in the entire chapter…later in the book there are sometimes 27 cites per page!

Chapter 04 – Chemical Warfare (NOW PUBLISHED)

Overview:  3730 words, 3 sidebars, 24 cites

If Grace had been involved when we wrote this, it would have been a gardening chapter!  The war metaphors were a fun way to look at what happens in the gut and pay homage to our (Richard and I) military background.  It’s designed more to get people to consider the enormity of what our gut bugs do for us, what they face in their lifespan that is measured in minutes and hours.  We sometimes refer back to this chapter later on, but we ease up on the war metaphors.  Lots of deeper science and more complex ideas, yet written with a bit of humor and irony.

Chapter 05 – The History or Gut Microbes is the History of Life on Earth

8895 words, 10 sidebars, 101 cites

This chapter is a look at the evolution of microbes and how they shaped all lifeforms.  Great discussions on ‘superorganisms,’ ‘brain-gut connections,’ and human evolution. This chapter doesn’t require that one believe in evolution, but it sets the stage for deeper evolutionary discussions to come.  Here we also introduce the concepts of prebiotics and probiotics, yet use the terms only sparsely.  The concept was to get people to draw their own conclusions about what makes humans so special and how gut bugs play a huge role.

Chapter 06 – Ancient Gut Microbes and Their Food

8354 words, 3 sidebars, 110 cites

Section 1 – Man’s evolution related to starch consumption and microbes

Section 2 – Unique sources of ancient prebiotics (tigernuts, yams/tubers, pollen, cattails)

Section 3 – Ancient sources of probiotics (birth, hunting, socializing, etc..)

Section 4 – The Inuit Diet exposed…not carb free, plenty of gut bugs and gut bug food

This chapter expands on the history lessons in chapter 5 and focuses narrowly on how humans ate to support flourishing gut bug populations. Included are lengthy discussions on human ancestors and their food, some unique food sources, microbes discussed at the phyla and family level, and an introduction to “soil-based organisms.”  Here we also lay out an ancestral reliance on starchy carbs, or in their absence, very potent, non-starch prebiotics from animal and plant sources.  We dismantle the Inuit diet as a zero carb healthy lifestyle and introduce one of our most influential ancestors, P. boisei, AKA Nutcracker Man, and his favorite food, tigernuts.  While this chapter is mainly about prebiotics and probiotics, those words do not appear in this chapter.  

Of special note are the amazing insights provided here by “science editor” Grace, it was she who came up with the concepts of Vit C and Omega 3 from tigernuts fueling the human ‘brain-size’ explosion and physiological changes that have stymied science for centuries.  Much of the information in this chapter has never been tied together in one place, but is found scattered across scientific journals. This new information will raise many eyebrows, but it is fully backed by science.  Grace is also to be commended for digging deep into the greater importance of cooking and ‘cooked and cooled’ starches as a catalyst for enlarging our amazing ‘second-brain.’

Chapter 07 – Our Microbiome Through the Last 12,000 Years

9354 words, 4 sidebars, 104 cites

This chapter picks up where chapter 6 left off…originally envisioned as one or two paragraphs, it morphed into over 20,000 words in three separate chapters!  Here you will be taken on a chronological journey into the decline of the human gut microbiome from the end of the Paleolithic until modern times.  The historical accounts of human diet focus on fermentation, lack of refrigeration, and simple food choices.  The section on ‘modern times’ comprises ¾ of the chapter and focuses on our loss of touch with ancient foods, ancient microbes and the profound effect it has had on the human animal.  Invoked are the writing of Hippocrates, Westin A. Price, Fleming, Blaser and others.  Introduction to the concepts of GMO food, antibiotic abuse, and fecal transplants among others.

Chapter 8 – Bad Gut Bugs – 8716 words

Section 1 discusses various pathogens found in human GIT as a comparison to ‘good’ gut bugs we have been talking about so far (Pathogenic bacteria, viruses, parasites, and yeast).  Also discusses common treatment strategies. (3900 words)

Section 2 discusses the role of the gut microbiome in common diseases, brain disorders, and autoimmune disease. (2900 words)

Section 3 is a light look at what we have started calling the ‘modern, dyspeptic gut.’  A primer on what to expect if you don’t heed the rest of this book. (1800 words)

Conclusion contains some simple ideas to avoid pathogens, gut disease and reverse the modern, dyspeptic gut.

Chapter 9 – Description of the Microbiome – 10,500 words

Section 1 – A fairly in depth discussion on taxonomy and making sense of what’s in our gut and defines what’s in a ‘good’ microbiome. This chapter would probably serve better if it were chapter 3 or 4. (4800 words)

Section 2 –  We called it the “Hitch hiker’s guide to the gut”, discusses the superorganism, acquisition of gut bugs at birth and through life.  Discuss brain-gut connection, immunity, allergies, and other gut bug ‘magic’.. Could easily be standalone chapter. (5600 words)

Conclusion – Great discussion of the worst-case scenario for gut bugs, starving kids in Africa, from director of NIH.

Chapter 10 – Resistant Starch – 10,598 words

This chapter is the most in depth look at RS probably ever conducted.  From the discovery of RS to some practical advice on incorporating into a healthy diet.  I feel this chapter will be worth the price of the book. Loads of interesting sidebars and the full RS contents list from FTA.  

Chapter 11 – Potato Starch – 7800 words

This chapter is a hard look at potato starch and its use as an RS supplement. Since potato starch kind of started the RS craze (rightly or wrongly) it has gotten lots of attention and has raised unbelievable curiosity.  This chapter looks at all of the safety concerns, studies, and adverse effects where appropriate.  Discussed physical science of potato starch granules, manufacturing processes, and DIY potato starch extraction.  Also offers alternatives to potato starch.

Chapter 12 – The Potato Diet – 13,602 words

This chapter is kind of a side-show.  Consider cutting it from the book, or use as a filler if you need an extra 13,600 words—maybe an appendix.  This would probably make a better cheesy e-book, but it does tie in with gut health and resistant starch nicely.  It’s also a great weight-loss hack that people love.  I had a thread on MDA Nutrition forum running for a year with over 1000 comments called Eat MOAR Taters! Huh? and also probably over a dozen follow-on threads with potato hacks from me and others.  Richard also did a huge Potato Hack Expose that was wildly popular.  Jaminet, Guyenet, Peter D, and many others took a look at my potato hack as well.  Grace remained unimpressed, however. 

Chapter 13 – Farting – 5500 words

This is probably my favorite chapter.  Full of fun facts, science, and trivia.  Guaranteed to be a hit!  This chapter is easily cut to make it fit wherever it’s needed.  Could even be separated into sidebars or used as an appendix. 

Chapter 14 – Your Skin and Other Non-Gut Flora – 3830 words (Manuscript Ready)

This chapter was written with major contributions from Dr. Gabriella Kadar, DDS. This is a great chapter that explains all the other trillions of microbes on our skin, eyes, ears, butts, and toes. Lots of fun science, an enjoyable read. Lots of sidebars and a really good conclusion. 

Chapter 15 – No Soap Or Shampoo; Washing With Water Only – 10, 600 words

Again, written with major input from Dr. GabKad, DDS.  Waaaaay more than no ‘poo.  This chapter gives historical and modern methods to practice hygiene without harsh chemicals or sanitizers.  Includes Richard’s personal experience as documented on FTA.  Also a blurb from Mark’s Daily Apple and many sidebars.  Lots of sidebars included at the end that could be used elsewhere.  Cut sidebars to get word count desired.

Chapter 16 – Prebiotics and Fermented Foods – 4495 words

This chapter is a primer on modern concepts of ‘gut bug food’ AKA prebiotics. In it we define terms and fiber types and make a case for real-food alternatives and not just RS or potato starch.  This is the section that ‘takes on’ Konstantin Monastyrsky’s Fiber Menace, though we don’t call him out by name.  You will see why the fiber policies of the ‘80s failed miserably and why prebiotics failed to take off as their discoverers had hoped.  This is also where you will find the Grok-inspired RS Curve.  

There is also a short section on fermented foods.  Here is where we marry the examples of fermented foods from the past with modern day foods, and we break-down the reasons they are so healthy.

Chapter 17 Antibiotics & Probiotics – 11,400 words

Section 1 – Antibiotics (7200 words)

In depth look at antibiotics from their natural occurrence in nature to their discovery by man and the future of antibiotics and antibiotic resistance.  Lots of quotes from Blaser and others.  Lots of things that even Blaser missed in his new book.

Section 2 – Probiotics (4200 words)

Could be a standalone chapter.  Definitions of probiotics, commercial preparations, benefits, and recommendations.  A special cancer section. Lots of good quotes and lists of probiotics.  Lots of good recommendations for serendipitous use of probiotics.

Chapter 18 – 7 Steps to Re-Wild Your Gut (5,000 word or less target)

Working thesis:

7 steps that tie in with book, evolutionary medicine, evolutionary biology and importance of gut microbiome for health and longevity.

Why carnivorous small intestines vulnerable to many assaults and fermentation after antibiotics or gut damage.

Why herbivorous large intestines maintain our health by being the butyrate factory with RS-degrading microbes.

Why SBO probiotics are special and revolutionary by regressing back to our deep and profound evolutionary history with the Earth.

How the neolithic transition disrupted humans particularly in cutting off supply of effective microorganisms from the dirt after foraging activities were replaced by massive grain cultivation

Chart Modern Gut.

Chapter 19 – The Wrap-up… (4,000 words or less target)

General summary and overview. 

Appendix A – RS Research – 15,500 words

This is a ‘filler’ appendix that contains page after page of PubMed abstracts concerning RS and gut bug research.  Can be tailored to how ever long it needs to be or cut completely.  It’s eye-opening to flip through the multitude of studies to convince yourself this isn’t all ‘made-up.’

Should probably be updated if we want to use it…I compiled this in Jan 2014, probably 100 new studies since then! 

Section 1 – Discussion of PubMed and studies

Section 2 – Charts of RS and Gut Bug research since 2004

Section 3 – 20 abstracts of papers from 2013 and 2014 with key words “resistant starch and gut microbiome”

Appendix B – FAQ or Troubleshooting Section (4700 words)

This is the result of thousands of comments on RS and gut bugs.

Section 1 – Potatoes and potato starch

Section 2 – Other RS Sources

Section 3 – Probiotics and Gut bugs

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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, 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

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