Gut Flora Resource Overview

SEED   Frequently      FEED      Daily Constantly      WEED      Opportunistically   HEED

Edition: 2024-09-08 cultures,fermented,flora,gut,live,MACs,microbiome,prebiotics,probiotics
Note: Although this article is public, not all links within it are.

⟲ Context

What this page was originally created to summarize, for Wheat Belly, Undoctored and Infinite Health (the “program”) became an entire book in 2022: Super Gut (SG)

This page still has the same approach, so is useful to members without the SG book. The page now points to new and updated resources since the SG book.

The end⭳notes of this page also record changes to the SG strategies, targets and recipes subsequent to the book’s publication.

⟲ Contents

⟲ Inner Circle Topical Program Links

⟲ What’s Been Inherited (and what’s been lost)?

Probiotics, prebiotics, resistant starch (the MACs)—isn’t this just some fresh fleeting food fad?
  No.
What this is about is attempting to partially mimic the beneficial aspects of an ancestral intestinal adaptation, one which has been derailed by modern food-like substances, pervasive anti-microbials and adverse personal environments. This dysbiosis appears to be a major contributor to the pantheon of rising, chronic, non-infectious, non-injury, largely optional ailments (and not a few actual infections: e.g. SIBO, Candida albicans, Clostridium difficile). Implications for behavioral disturbances must be pondered.

Putting this train wreck back on the rails needs to be a priority, just in consideration of the ASD trend alone. Some of that effort will, bluntly, be guesswork. As stool sequencing results already reveal, a significant swath of microbiome is stuff that doesn’t even have names yet. There could be crucial extinctions of unknown⇩unknowns.

The modern mimic menu, to address this, is partial, because the science about all this is still quite nascent. About as much is known today about probiotics as was known about overt microbial pathogens a century ago.

The ancestral case takes note that until quite recently, human hygiene was rather casual (if not entirely absent). Food intake included a high microbial load, probably included more partially-processed starchy vegetables, esp. root crops, wild game offal, and lacked multiple modern gut antagonists: it had more microbes, more microbe substrate, and only natural antibiotics.⇱ Return to Contents

⟲ The Problem

[Too] often seen on the blogs and the forum:
◊ I get lots of “fiber”. Doesn’t that cover it?
◊ I take probiotics regularly. So I’m good, right?
◊ I eat yogurt from time to time. So, under control, eh?

In a word, no. Those steps don’t cover it. As the lead artwork for this page suggests, there are four distinct aspects to this topic, which all must be attended to, and with different levels of stewardship.⇱ Return to Contents

⟲ The Biological Context

You are not 100% you. Depending on how you look at it, up to half, ⎆possibly more of you, is non-human living matter: the microbiome(s). The human body has ⎆multiple microbiomes, but the focus of this article is the intestinal one, the ⎆gut flora.

Gut microbes maintain gut barrier function, contribute to food digestion (producing important nutrients as byproducts), and regulate immune function. They influence mood and behavior.

The spectrum of microbes in the human gut is already known to include bacteria, eukaryotic parasites, fungi (e.g. yeasts), protozoans, archaea and viruses (including bacteriophages). And there’s: BMC Biology Direct: Highly divergent ancient gene families in metagenomic samples are compatible with additional divisions of life.⇱ Return to Contents

⟲ The Program Approach

For your ancestors, and extant hunter-gatherers today, none of this required any specific attention. It was just an inherent adaptation to daily life-support activities. For moderns, deliberate action is required, along with staying aware of new developments.

The ancestral experience is now inaccessible to most. Even for those of unbroken lineage on ancestral ground, is it even possible to find undisturbed, uncontaminated foraging acreage, on which you could resume a diet of frequent, casually-cleaned root crops? Or perhaps wild game, consumed snout to tail, including offal? And even those gambits assume you’d want to take on the ancestral and modern pathogen risks.

So instead, it’s necessary to apply archaeology, anthropology, science history, modern scientific, medical and nutritional trial results, and, frankly, a bit of educated guesswork.

Note:
All of this discussion is within the context of the program (2014+ Wheat Belly, Undoctored, Infinite Health, Super Gut) approach to diet. For anyone on a standard diet, that needs to be corrected first, or this element of the program approach is not likely to have a level of benefit commensurate with the effort. For legacy members of the Cureality and Track Your Plaque programs, the gut flora topic came in during 2014, and might have escaped your notice.⇱ Return to Contents

⟲ SEED: Probiotics—the actual gut flora

The program recommends a high potency (25 billion CFU multi-species probiotic), started 5 days prior to adding MAC to the diet. Program reference material has specific product suggestions. Routine inclusion of fermented foods is also gaining prominence. “Seed” may need to become more frequent. Some interesting microbial species may not colonize well, and may need frequent topping-off.

A course of probiotics can have any of several objectives:

1. mimic ancestral exposure to environmental microorganisms;
2. endeavor to correct modern distortions in your present population resulting from antagonists in modern diets and personal environments (see WEED on that);
3. actually provide specific strains for their beneficial byproducts in specific scenarios, or
4. attempt to compensate for unavoidable courses of prescription⇩antibiotics (more below).

Most commercial probiotics so far are just bacteria. A few have yeasts. All are are probably just the strains with a comfortable evidence base. Entirely apart from not providing viruses, protozoans, potentially beneficial parasites, not to mention the unknown unknowns, it is likely that today’s products are well short of optimal just on bacteria. So the program is aggressively exploring this, for example, the early 2018 informal testing of Lactobacillus reuteri, adding Lactobacillus casei (Shirota) in 2020, and many more since.

Another source of probiotic cultures is fermented foods that deliver live cultures. At retail, this requires some effort, because few fermented foods still have living microbes in them at point of sale. Live culture foods often require refrigeration, and have a much shorter shelf life than those subjected to various preservative techniques.

Of those products that do have live cultures, the CFU counts (colony forming units) may be uselessly low. With retail yogurts in particular, in addition to low CFUs, far too many are low-fat, high-sugar junk foods that raise blood sugar and could easily promote growth of adverse gut microbes.

This all being the case, making your own fermented foods is a growing topic in the program. Both the Site🥄Kitchen and the Blog🥄Recipes have sections devoted to it.

By the way, if your fermentation attempts fail using your tap⚠water, drinking that water likely has the same result for the desired fermentation in your gut.

So far, no upper limit has appeared for ingested gut microbes (probiotics), and this may well need some attention.⇱ Return to Contents

⟲ FEED: Microbiota-Accessible Carbohydrates (MAC)

Note: MAC is the emergent umbrella term for prebiotic fibers, soluble fibers, and resistant starches.

Gut flora have nutrition requirements that can be quite different from what humans nominally consider food. Many microbes thrive on MAC, which usually needs deliberate attention in diet. Applying that attention has challenges in today’s markets.

• You don’t just want just the microbes. You also want their metabolites, and that requires feeding them.
   
• You want trillions of these microbes, and probiotics only provide billions, perhaps only millions in fermented foods. Feeding them grows populations.
   
• Even if doing daily probiotics, whether as probiotic capsules or as live-culture fermented foods, these do not represent the entire spectrum of desired commensal life forms. So you need to encourage other residents and environmental opportunists by feeding all the beneficials.

MAC is a carbohydrate, but essentially never listed separately on food packages. All carbohydrates are saccharides (sugars), but their molecular forms vary greatly in effect. From a digestive (but not chemistry) point of view, carbohydrates can broadly be broken into three categories:

1. Net carbs (digestible fiber)
   These are the digestible carbs, either inherently simple sugars, or saccharide polymers that are easily cleaved by human enzymes to simple sugars (such as grain amylopectin, cleaved by amylase). These foods become (principally) blood glucose and blood fructose promptly (usually before reaching the colon). FDA-style Nutrition Facts panels do not state net carbs, but it can be calculated trivially:
     Net_carbs = Total_carbs minus (total)Fiber
2. MACs
   These are saccharide polymers not easily cleaved by human enzymes, but which are digestible by gut flora, producing more gut flora, and various byproducts, chiefly SCFAs (short chain fatty acids). NF panels never state MAC (prebiotic) content (and the FDA has no standards for it, if the brand desires to). Most nutritional apps are useless on this as well, often failing to differentiate raw/unripe vs. cooked/ripe whole foods. MAC content cannot be calculated from the “Fiber” value on the NF panel, but won’t exceed it. Here are some site resources listing MAC sources:
   Members: 🗏Advanced Topic: Regularly Consuming Prebiotic Fibers
   Public: 🗏Prebiotic Fiber Sources
   Members: 🗏Simple Prebiotic and Net Carb Chart
3. Insoluble fiber
   Also known as roughage, these polymers (cellulose is an example) pass through intact. Program guidance is that we need some amount of this, but not a lot. Due to unlimited amounts of non-starchy vegetables in the diet, most people usually get ample. Deliberate supplementation is often a mistake. It makes more sense to address any underlying dysbiosis than to try to compensate for consequences by throwing this kind of fiber at it. Where constipation is the concern, there are numerous site resources for it, such as:
   🖵New Insights Into Constipation (members), and
   🖵🗐Special Protocols: Constipation (members)

Present program guidance is to work up gradually to 20 grams¹ of mixed and varied MAC per day. If an adverse reaction is encountered when doing that, 🖵🗏particularly a prompt reaction, suspect SIBO.

⟲ WEED: Cultivation disruptors and frank dysbiosis

There are two separate sub-topics here:
🦝 modern gut antagonists (what Dr. Davis terms 🅑raccoons), and:
🔥 dysbiosis conditions that don’t respond to program guidance on cultivation of gut flora.

Gut antagonists

You can do a course of probiotic, then implement daily prebiotic fiber, and be wasting your time, if the ecosystem, or even physiology, is being clobbered by toxins and stealth antibiotics. Our ancestors, again, other than avoiding poisonous plants, didn’t need to worry very much about this; you do.

The program diet already accounts for the important physiological toxins that open the tight junctions of the gut, or cause direct gut wall damage, allowing random food-borne elements into the bloodstream, provoking inflammation and needless allergic reactions. Eliminating the grains that precipitate zonulin, and lectins like WGA (including rice) are major elements here.

As Dr. Davis’s raccoons article points out, several other modern food, food-like and non-food hazards need to be watched for, and eliminated if possible. I’ll add some remarks to his from that article:

• Water treatment
  What hazards lurk in your municipal water? What are you doing to eliminate them? You might consider stopping consumption of establishment-prepared beverages (except where RO filtering is in use, such as Starbucks), due to chloramine being pervasive and persistent in muni water. Commercial ice cubes have been observed with even more chloramine added.
• Prescription(℞)/OTC/second-hand antibiotics
  Most people have figured out that taking an antibiotic is likely to blitz the gut microbes (and intentionally so in treatment of resistant SIBO). Doing a course of time-separated probiotics in concert with that may prove useful. But most people are unaware of all the other sources of antibiotics (triclosan in toothpaste might be an egregious example). You may have given some thought to antibiotics in CAFO animal products, but that might actually be a smaller hazard than undeclared antibiotic properties of various medications you might be using. The term antibiotic strictly means anti-bacterial. You need to be concerned about the wider concept of anti-microbial. For an unavoidable course of anti-biotics, a fermented food based on S. boulardii CNCM I-745 is suggested; see 🅑My recent antibiotic experience
• Anti-microbials
  This includes antibiotics (above), but also anti-virals, anti-fungals (yeasts), and anti-parasitics. Preservatives fall into this category, and are yet-another reason why processed food-like substances need to be avoided. Field, storage and transport pesticides are a problem on vegetables that are not organic (and maybe even some that are, as an organic-approved pesticide is still an anti-microbial). Wash your food. Even something as simple as pre-shredded cheese is a frequent hazard, as an anti-fungal like natamycin will often be seen in the Ingredients list (not to mention grain-based flow agents). If you can’t find a shredded cheese that’s just cheese, shred your own.
• Emulsifiers
  These are another reason to avoid processed food-like substances, until you know how to recognize benign ingredients. Program advice is to avoid all added emulsifiers, whether synthetic or natural. Carrageenan and polysorbates are annoyingly common in milk and cream. Some candidate MACs have emulsifying properties, and are under continuous review as regard suitability for use in the program, for example, guar.
• Artificial sweeteners
  The natural non-nutritive 🖵🗏sweeteners endorsed in the program have no known adverse effects on gut flora. The same cannot be said for the artificial sweeteners pervasive in the majority of retail sugar-free products. That the synthetic sweeteners commonly fail to deliver on their weight loss promises appears to largely be due to disruption of gut flora.
• Megadose iodine
  🖵🗏 Megadose Iodine? (members)
  So don’t do that (except as an intentional antibiotic in a specific therapy, if a protocol emerges). Attend to  Iodine intake, but within program targets.

Actual weeds (undesired species or strains)

Despite doing all of the foregoing, it is still possible (and too commonly so) to discover that what’s been present all along is some sort of persistent overgrowth, most frequently SIBO, but Candida, C. diff and H. pylori need to remain on the radar until ruled out.

The program has a specific protocol for 🅟SIBO, and still evolving. If cultivating gut flora doesn’t result in a clear trend toward eubiosis (below), further investigation may be required.⇱ Return to Contents

⟲ HEED: Hints of eubiosis

Eubiosis is healthy gut microbiome. No one knows yet what that is supposed to look like, much less optimal microbiome. Naturally, there are no tests available yet that can unambiguously confirm it, and it’s going to be some time before testing services yield profiles correlated to agreeable health-span. So how can you tell if you have a possibly nominal gut flora, and in particular, how can you tell if a problem like SIBO is resolved?

Easy-to-observe near-term presentation indicators include:

• no general intestinal distress
• no constipation
• no diarrhea
• smooth and regular outcomes
• no free oil residues
• no excess or foul-smelling flatulence
• no adverse reaction to mixed and varied MAC in the 20-gram range

And then, over time, expect:

• periodic occult stool test is negative
• food sensitivities go away
• skin issues clear up
• autoimmune labs improve
• weight loss plateau un-stalls
• gradual improvements are seen in secondary markers, like BG, BP, and inflammation
• some aches and pains, e.g. migraines, might recede noticeably
• you return to your optimal self

Budget and interest permitting, or in tougher cases, consider one of the stool sequencing services.
🅐Advanced Topic: 🗏Bowel Flora Testing - A Practical Guide (members) but have realistic expectations:
🧵Review and Comparison of Four, PCR-based Stool (public)

Beyond that, IC members may want to follow the discussion on this🧵thread, in which several common markers were proposed, plus one emergent lab test (Dunworthy). A home H₂ and CH₄ breath test (the AIRE2 device) is also now available. Its use is discussed in the SIBO Protocol.⇱ Return to Contents

In Conclusion

A crucial problem moderns settler populations face is the development of antibiotics, food preservatives, water treatment and field pesticides. Over the last century, human guts may have been blasted by an ever-changing, ever-growing assault from the food system, routine prescription and OTC meds, gratuitous antiseptics, and a near complete lack of routine exposure to environmental microorganisms to top off with, and a diet deficient in microbial substrate. The resulting dysbiosis further compounds over human generations (due to deficient maternal transfer, and may be a major factor in the pandemic ASD trend). It’s going to take some time to fix it, and what exactly to do is not obvious. The Infinite Health program is an early adopter of the most promising strategies.⇱ Return to Contents

⟲ End Notes:
The following Super Gut topics have been revised since the publication of the book. Page numbers are for the U.S. print edition.

111. AIRE2 device capabilities:
     As of the latest⇧update to this page, the AIRE2 device still tests only for H₂ (hydrogen) and CH₄ (methane). The H₂S capability expected in 2022 has yet to be released.
189. Iodine (intake):
     The upper bound of 500µg/day has been reduced. See the  Iodine QR for the current recommendation.
235. LACTOBACILLUS CASEI SHIROTA YOGURT (recipe):
     Editions of the book using the original U.S. customary units are correct, but export edition publishers evidently misread
     1 2-ounce bottle Yakult as
     12-ounce… and metric converted it to
     350 mL Yakult. It should have been:
     60 mL Yakult
240. SUPER GUT SIBO YOGURT (recipe):
     The Bacillus coagulans (GBI-30,6086) can optionally be omitted from the yogurt blend, and replaced with a second fermented food made with Bacillus subtilis DE111. See 🅑Make your own Bacillus subtilis probiotic. B. subtilis likely reproduces too rapidly to use directly in the yogurt blend.
309. SUPER GUT SIBO PROTOCOL:
     Choices #1 (herbal antibiotics) and #2 (yogurt blend) are now swapped, with the yogurt blend now being the first thing to try. The yogurt was found to be at least as effective as the herbals, and at lower cost and with fewer potential unpleasant effects.

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