Gut Flora Resource Overview
Gut Flora Resource Overview
Inner Circle Topical Program Links
What this page summarizes is now the topic of an entire book: Super
This page may point to updated and/or
more recent resources.
What Have We Inherited (and what have we Lost)?
Probiotics, prebiotics, resistant starch — isn’t this just some fresh fleeting
What we are doing here is attempting to partially mimic 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.
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 Viome results already reveal, a significant swath
of microbiome is stuff that doesn’t even have names yet. We could be looking at crucial
extinctions of unknown unknowns.
Our modern mimic menu, to address this, is partial, because the science about all this
is still quite nascent. We know about as much about it 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 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.
[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.
||By Gene Count
||By Cell Count
You are not 100% you. Depending on how you look at it, up to half,
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, archea and viruses (including bacteriophages).
And then we have:
BMC Biology Direct: Highly
divergent ancient gene families in metagenomic samples are compatible with
additional divisions of life.
The Undoctored / Wheat Belly Program
For your ancestors, 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 many of us. Even for those of
unbroken lineage on ancestral ground, is it even possible to find undisturbed, uncontaminated
foraging acreage, on which we 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 we’d want to take on the pathogen risks.
So instead, we need to apply archaeology, anthropology, science history, modern
scientific, medical and nutritional trial results, and, frankly,
a bit of educated guesswork.
All of this discussion is within the context of the Undoctored or
2014+ Wheat Belly approach to diet. For anyone on a standard diet,
that needs to be corrected first, or this element of the Undoctored
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 top
SEED: Probiotics — the actual gut flora
The program recommends a high potency
(25 billion CFU
multi-species probiotic), started 5 days prior to adding
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:
- mimic ancestral exposure to soil-based microorganisms;
- endeavor to correct modern distortions in your present population
resulting from antagonists in modern diets and personal environments
(see WEED on that);
- actually provide specific strains for their beneficial byproducts in
specific scenarios, or
- attempt to compensate for unavoidable courses of prescription antibiotics.
All but one or two commercial probiotics so far are just bacteria, and those
are probably just the strains with a comfortable evidence base.
Entirely apart from not providing
viruses, protozoans, potentially beneficial parasites, and the unknown unknowns,
it is likely that today’s products are well short of optimal just on bacteria.
So the Undoctored program is aggressively exploring this, for example, the
early 2018 informal testing of Lactobacillus reuteri, and adding
Lactobacillus casei (Shirota) in 2020.
So 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
This all being the case, making your own fermented foods is a growing
topic in the program. Here are some search expression links, on
“ferment” and “recipe”:
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 top
FEED: Prebiotic Fiber
Gut flora have nutrition requirements that can be quite different from what
humans nominally consider food. Many microbes thrive on prebiotic fiber, which usually
needs deliberate attention in diet. Applying that attention has challenges
in today’s markets.
- We don’t just want just the microbes. We also want their metabolites,
and that requires feeding them.
- We 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 we need to encourage other residents and
environmental opportunists by feeding all the beneficials.
Prebiotic fiber, also known as soluble fiber, and which includes
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:
- 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
- Prebiotic fiber
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 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. Prebiotic content
cannot be calculated from the “Fiber” value on the NF panel,
but won’t exceed it. This situation motivated a UIC member to create a guide
- 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.
Present program guidance is to work up gradually to 20 grams of mixed and
varied prebiotic fibers per day. If an adverse reaction is encountered
when doing that, particularly
a prompt reaction, suspect SIBO.
More than 20? Could be. Some members may be getting 50 grams per day
or more. Some studied cultures get as much as 140, but they also have
dramatically different gut flora.⇱ Return to top
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.
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 Undoctored / Wheat Belly 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’s in your municipal water?
What are you doing to eliminate it? 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. More
on water. Commercial ice cubes have been observed that
has even more chloramine added to it.
Most people have figured out that taking an antibiotic is likely to blitz
the gut microbes (and intentionally so in SIBO treatment). Doing a course of 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.
We need to be concerned about the wider concept of anti-microbial.
This includes antibiotics (above), but also anti-virals (yeast, fungus),
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 potential 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.
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 is annoyingly
common in milk and cream. Some candidate prebiotic fibers
have emulsifying properties, and are under continuous review as regard suitability
for use in the program, for example, guar.
- Artificial sweeteners
The natural alternative 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 vast 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
UIC member Video Forum: Megadose
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 top
HEED: Hints of eubiosis
Eubiosis is healthy gut microbiome. No one knows what that is supposed to look
like, much less optimal microbiome. Naturally, there are no tests available
yet that can confirm it, and it’s going to be some time before projects
like Genova GI Effects, Viome, and others yield profiles correlated to
excellent healthspan. So how can we tell if we have a possibly nominal
gut flora, and in particular, how can we tell if a problem like SIBO
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 dietary prebiotic fiber 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
Beyond that, UIC 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 top
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
It’s going to take some time to fix it, and what exactly to
do is very far from obvious. The Undoctored/WB program is
an early adopter of the most promising strategies.⇱ Return to top