Ancient Microbiome & Recreating Past Health

All throughout our human history, accompanying us has been an ecosystem of bacterial life both outside and within. Deeply seeded, there lies a network of digestive tract, home to another worldly biome influencing nutrient absorption, neurotransmitter creation, and protection from infection. This hive like organism has been influencing both our subjective and objective health, all in optimal concert when aligned with their cultured ancestral past. What we know, is this organism is multiple in species, and highly influenced by our environment and diet. As we separate and further plasticize our environment, stepping away from organic to artificial and engineered, we are by self experiment beginning to understand just how critical this system is via the proof of disfunction. This change of environment and linkages to health is certainly manifesting in the degradation of longevity via obesity, diabetes, heart disease, depression, anxiety, and overall disbiosis of health. Our gut microbiome is evolving further and further away from the populations of careful curation; artifacts of many past healthful generations, and this may indeed by the lost link we must recover to remember our health.

WHAT HAPPENS WHEN OUR INTERNAL GUT BACTERIA BECOMES “DOMESTICATED”

When we create conditions that are far removed from the our ancient roots (via diet & pollution exposure) we inadvertently facilitate an environment inviting species of the colon to migrate northward, infesting the upper GI tract (species of lower & upper are different for digestive stage purpose). When over colonized and out of place microbes migrate to the upper GI tract, a perfect storm brews. From outcompeting upper tract species (often conditions are catalyzed when upper GI species are weakened by antibiotics, chemicals, & poor nutrition) to potentially degrading mucosal membranes creating gut permeability. Compound this with normal turn over cycles (bacterial cell death), invading cell wall contents are liberated within an environment where the LPS (lipopolysaccharides) from cell walls pass through to the blood up to 10x normal rates. Here elevated LPS travels to the liver where eventually made systemic in circulation affecting organs and causing inflammation called endotoxemia. This pathology sets the base for many symptoms whereby we treat with modern pharmacopeia and often times ineffectively (treating symptoms not causes). The increased leakiness of the gut also allows formerly benign but larger food pieces into circulation potentiating immune response and contributing to the host of issues.

SYMPTOMS OF SIBO & SIFO:

Food allergies, obesity, diverticular disease, colitis, compulsive behaviors, IBS, anxiety, depression, diabetes, heart and auto immune issues etc. Many of the chronic first world health issues could in fact be a systemic manifestation of a dis-regulation of our digestive tract bacterial colonies. This especially appears a valid explanation as advances in pharmacological treatment often prove ineffective in complete symptom resolve…perhaps this is more evidence that despite modern medicine and technology, increasing rates of impaired health and longevity continues to increase. Symptoms sometimes being managed, but causes remaining intact.

An interesting example is found in depression research where the linkages between this disorder appears concomitant with inflammation. In studies where subjects are injected with LPS (lipopolysaccharides) endotoxin, symptoms of depression rapidly onset: evidenced by impaired cognitive function, dark moods, anxiety, and motivation decrement. Further strengthening the idea that depression could be a result of systemic inflammation, similar to conditions experienced in small intestinal bacterial & fungal overgrowth (SIBO & SIFO). This could also explain the ineffectiveness of anti-depression medications as these do not act on lessening inflammation.

SIBO & SIFO: Small Intestinal Bacterial Overgrowth / Fungal Overgrowth: result in increased gut permeability -> endotoxemia -> inflammation -> auto immune response.

CAUSES OF THE GUT MICROBIOTA SHIFT

As we seek out to ways to recreate conditions of optimal ancestral health, the microbiome is a critical area of adjustment. From examinations of ancient fossils records, it is confirmed that the microbiome of ancient hunters and gatherers differs much from modern humans of today. Interestingly, there is evidence of lacking variability across different global regions of modern hunter gather communities; which means that independent of temperature, native food sources, and diet, there is consistency in gut flora speciation from those living a lifestyle more aligned with generations of before. Evaluations of current hunter and gather tribes in modernity also reveals a much more diverse community of microbes when compared to urban sprawl humans.

Shifts in composition of the gut microbiota evolved in step with ancient humans adoption of agriculture and the subsequent changes in diet. Implications of this new way of life resulted in lesser diversity in fruits and vegetables and a greater reliance on starchy crops. Degradations to the gut community balance also continue to punctuate epochs as our technology and profit margins of big pharma, food, and government evaporate the environment. Antibiotics, C-Section births, preservatives, refrigeration, emulsifiers, artificial sweeteners, GMO foods, pesticides, and overall lessening of nutrient diversity have adjusted and eliminated the bacterial strains that we carried for thousands of years, and most significantly changed in less than 100. This acute change can be viewed as an extinction level event whereby other species have taken dominance and resulting in the peril of our health. The below protocols and interesting above history provided by Dr. William Davis through his book Super Gut can potenitally guide a path to resolving the overpopulation of upper GI tract by colon based microbes (SIBO & SIFO) and how to re-seed with ancient and better suited microbes that once flourished in past hunter & gatherer epochs.

RESOLVING SIBO & SIFO:

Step 1: Prepare the soil & adjust diet

• Avoidance: excessive sugars, synthetic sweeteners, emulsifying agents (I.E. carrageenan, dextran sulfate, propylene glycol), alcohol, NSAIDs, & acid supressing drugs .
• Choose Organic: these items are less likely to contain pesticides, GMOs and in the case of meats, no antibiotics.
• Filter Drinking water (triple osmosis filtration): removes disrupting chlorines, fluorides, and anti corrosives.
• Avoid Or Minimize Wheat & Grains: Gliadin protein in found wheat & grains increase intestinal permeability.
• Strengthen the intestinal barrier: supplement with curcumin 300-600mg 2X per day, or use clove green tea (increases cross linkages and mucus and stimulate akkermansia microbes that increase mucus production). Can also use berberine as substitute.
• Disrupt biofilms: NAC (N-acetyl cysteine) 600-1200mg 2X per day. Cycle this supplement.
• Prebiotic fibers to disrupt sporulation from runaway fungus: 800g per day is a good target and stimulates health in lower GI tract colonies.
• Essential Oils: concentrated chemicals from plants that are fat soluble and can also disrupt the cell walls of fungi. Most effective are peppermint oil, cinnamon oil, clove oil, and oregano oil. 1-2 drops in tablespoon of oil.

Step 2: Re-seed with keystone microbe species that collaborate maximally.

• Start with multi-species probiotics from below and or make your own supercharged at home yogurt. (see recipe at bottom that I’ve used directly from “Super Gut”.
• Begin introducing fermented foods such as sauerkraut, kimchi, kefir etc.Keystone Species

1. Bifidobacterium infantis: species that is no longer being passed to newborn babies via the mother. When restored to mother and passed on to babies, this microbe reduces bowel movements, less colic, skin allergies, better quality sleep, less asthma, type 1 diabetes, and overall autoimmune issues. Ferment 100F X 36-40 hours.
2. Lactobacillus reuteri: smoother skin, fewer wrinkles (increased dermal collagen), accelerated healing, oxytocin boost (increases empathy and feelings of connection), and increased strength (when combined with b. coagulans). Also provides protection against SIBO & SIFO. Ferment 100F X 36 hours.
3. Lactobacillus gasseri: reduction in waist size / visceral fat, IBS, levels of oxalate and protection against SIBO & SIFO (due to augmented bacteriocin producing properties). Ferment 109F X 36 hours.
4. Lactobacillus casei shirota: increases immunity, mental clarity, quality of sleep. Ferment not listed
5. Lactobacillus rhamnosus: recovery from diarrhea and anti fungal properties. Ferment not listed.
6. Lactobacillus plantarum: reduces bloating, abdominal discomfort, IBS, and exerts antibacterial and mucus stimulating effects. Ferment not listed.
7. Faecalibacterium prausnitzii: anti inflammation properties, moderate immune cells and produces butyrate which is fuel for gut lining cells. Ferment not listed.
8. Bifidobacterium longum & helveticus: reduces anxiety and increases mood. Ferment 100F X 36-40 hours.
9. Akkermansia muciniphila: prevents inflammation, strengthens gut lining by pruning actions of mucus. Preliminary studies suggest this microbe may help manage glucose levels / increases insulin sensitivity. Harder to inoculate, but can create better environment for this species by eating copious healthy fats and polyphenols. Ferment not listed.
10. Bacillus coagulans: reduction in inflammation, arthritis, pain, IBS, increased muscle recovery post exercise, and notably tasty strain. Ferment 115F – 122F X 36 hours.

Step 3: Tend your Garden

• Microbes can form a consortium where the whole of their combined efforts are more than the sum of their individual contributions. “Plant” a wide variety of species from foods containing cultures.
• Fuel with prebiotic fruits and vegetables. These fibers, flavonoids, and polyphenols fuel bacteria maintaining colonies, preventing the overgrowth of lower GI tract
• Fatty acids & olive oil. Can disable the LPS (by-products of misplaced strains), repair disrupted intestinal barrier, and contain the ability to shape the microbiome.
• Maintain adequate levels of vitamin D. Deficiency of this nutrient is associated with the weakening of the intestinal mucus barrier.

Super Gut’s High Potency Probiotic Yogurt

1. Mix together these 3 items:
   • (2) tablespoons of kefir (I use Lifeway from Trader Joe’s as it contains R. Reuteri and many other keystone species recommended above).
   • (2) tablespoons of prebiotic fiber (I use Acacia fiber from Whole Foods).
   • (2) tablespoons of organic half and half.
2. Mix above slurry with remaining 1 quart of organic half and half in mason jars.
3. Place mason jars (lids lightly placed on top) into fermenting device (I use a InstaPot) and cook at 106F X 36 hours.

Davis, W. 2022. Super Gut. Hachette Book Group.