Not unlike the original sourdough starter, or sponge, as it’s called; which if nurtured properly can keep forever while small portions are harvested and used to “infect” your next batch of sourdough baguettes. They have that uniquely yeasty-sour flavor made famous during the Gold Rush era in what is now called the Bay Area or just The City. I’ve heard that some sourdough sponges hail from the late 19th century. Any pastry chef and baker will tell you how important it is to have the exact proportion and type of yeast and other organisms in that sponge since all subsequent flutes will have the characteristics of that particular sponge. It therefore is critical that the inoculum not become contaminated and contain nothing but the organisms you have selected. Otherwise it’s a disaster for your patrons who have become accustomed to the unique flavor.

Not unlike a mixer full of virgin bread dough, before being born a neonate’s gut is totally sterile just like your boring, tasteless, dough-ball before being inoculated with the sponge. The baby’s innards are populated at the time of birth when passing through the vagina providing the proper beneficial starter colonies.

A woman’s vaginal flora is made from her bowel flora which came from her mother and to a lesser extent her husband. So whatever type or composition mom has in her GI tract, good or pathogenic, the baby inherits it. The baby also gets a complement from the fathers groin flora determined by his bowel flora which came from his mom and so on. Genital and rectal flora share many of the same bugs. The father’s flora will continuously inoculate the mother’s flora as frequently as mom and dad hook up so to speak.

We talk about how finely tuned our genes are to a world of pure air, water, sunlight, grass-fed organic game and a variety of gathered wild foodstuffs. So too have our gastrointestinal systems been fine-tuned and dependent on this inoculum right back to the scat of the very first Eve who provided us with these beneficial organisms. To say that we are super-tuned to this fragile, bacterial economy is an understatement. What we gain from this symbiosis is nothing short of life itself: a sturdy immune system, a sound mind and strong body. In particular, these lil buggers can ferment indigestible carbohydrates to provide additional energy, make various vitamins, break down toxins we might ingest, and limit the growth of pathogenic bacteria by out-competing them.

Although there are literally millions of different bacteria in the environment, only about 500 species actually reside in our gut. If we did a head count we would be at it for centuries since researchers theorize we have 100 trillion bacteria in our GI tract. These gut bacteria can be divided into three distinct bacterial ecosystems.[1]

Just like there are four unique blood groups that can classify every human, we also have three distinct bacterial systems. Once one of these systems becomes established in the gut, it begins to alter the gut environment that only certain species of other bacteria can follow and safely begin their symbiotic relationship with us. Some experts contend that once this formulation is established within the newborn baby it cannot fundamentally be changed although through diet differing species may predominate especially with the SAD diet resulting in a form of dysbiosis.

Let’s back up a tad so we are all on the same page. First of all what is the gut? It’s a term that basically describes the tube running from mouth to anus. It’s the transit and digestive pipe that runs for dozens of feet throughout your chest, belly and pelvis. Seen a different way it starts at the dinner table and ends in Aunt Gertrude’s rose garden. In our discussion of dysbiosis we refer to the regions that are normally populated by a microfloral universe, the large intestine mainly and the small intestine under unnatural conditions. Indeed some insist that we are simply dumb, hairy, lazarettos of gristle housing our bacterial “organ” not unlike Dawkins’ lumbering DNA carrying robots.


Because the gut is in constant contact with the outside world through the process of eating and drinking,

nature has provided the gut with a formidable barrier to pathogens (disease-causing unfriendly microbes) by providing it with intestinal micro flora, the mucosal lining (lumen) and the immune system (up to 85% of the immune system is found in the gut). Its health therefore plays a huge part in the health of every other aspect of the human organism.

Our digestive tract works hard to suppress the growth of harmful gut microbes with the help of stomach acid, mucous, bile, digestive enzymes, antibodies and friendly bacteria. Meanwhile our gut flora provides a barrier from our polluted world, the chemicals in our food and drink and the polluted air we breathe. It coats the entire surface of the gut protecting us from invaders and toxins and produces substances that have an anti-bacterial, antiviral and antifungal action. Thus it can protect us from infections, carcinogenic and toxic substances by engulfing and excreting them. Cancer is far less likely to occur in a healthy digestive system

The gastrointestinal tract (GIT) is one of the largest interfaces between the outside world and the human internal environment. From mouth to anus, it forms a nine-meter long tube, constituting the body’s second largest surface area and estimated to cover approximately 250-400 m2. Over a normal lifetime, approximately 60 tons of food will pass through the GIT…Food is obviously extremely important for well-being, but its passage through the GIT can also constitute a threat to health. While the GIT functions to digest and absorb nutrients, food also provides exposure to dietary antigens, viable microorganisms, and bacterial products. The intestinal mucosa plays a dual role in both excluding these macromolecules and microbes from the systemic circulation and absorbing crucial nutrients…

As mentioned above, the mucosa is exposed to bacterial products – endotoxins,.. hydrogen sulphide,.. phenols, ammonia, and indoles… –that can have detrimental effects on both mucosal and host health… The presence of many of these toxic metabolites is directly dependent on the type of fermentation that occurs in the bowel. In turn, this fermentation is dependent on the type of bacteria present in the bowel, as well as the substrates available for fermentation. Diets high in protein…and sulfate (derived primarily from food additives)… have been shown to contribute greatly to the production of these potentially toxic products. The production and absorption of toxic metabolites is referred to as bowel toxemia..[2]


The microflora of the gastrointestinal tract represents an ecosystem of the highest complexity…The microflora is believed to be composed of over 50 genera of bacteria…accounting for over 500 different species…The adult human GIT is estimated to contain 10ˣ [where x is 14; the number ten taken to the 14th power i.e., ten with 14 zeros after it-in other words a very big number] viable microorganisms, which is 10 times the number of eukaryotic cells found within the human body… Some researchers have called this microbial population the “microbe” organ – an organ similar in size to the liver (1-1.5 kg in weight)…Indeed, this microbe organ is now recognized as rivaling the liver in the number of biochemical transformations and reactions in which it participates… The microflora plays many critical roles in the body; thus, there are many areas of host health that can be compromised when the microflora is drastically altered. The GIT microflora is involved in stimulation of the immune system, synthesis of vitamins (B group and K), enhancement of GIT motility and function, digestion and nutrient absorption, inhibition of pathogens (colonization resistance), metabolism of plant compounds/ drugs, and production of short-chain fatty acids (SCFAs) and polyamines[3]….[Emphasis mine]


Let’s then cover some basics on this fascinating organ. The following tidbits come from a very informative slide show created by Dr Leo Galland for the Foundation for Integrative Medicine:[4]

1.      The gut is a neuroendocrine organ. Every neurotransmitter found in the brain is also found here.

2.      The gut has a brain of its own, an intact and independent nervous system.

3.      The gut is the largest organ of immune function in the body; 70% of our lymphocytes live here.

4.      The normal intestinal microflora constitutes a huge chemical factory that alters our food and our GI secretions presenting our immune systems with a massive inoculation of foreign antigens on a daily basis.

5.      Gut bacteria allow us to use food up to 30 percent more efficiently than we could without them. (This is about the same as boosting the gas mileage in your care from 20 miles per gallon to 26 miles per gallon.)[5]

6.      Some of the normal functions of the gut include:

Synthesize vitamins

Synthesize short chain fatty acids

Metabolize xenobiotics/toxins

Prevent colonization by pathogens

Stimulate normal immune system maturation

Convert dietary flavonoids to active aglycones

7.      Plays a vital role in detoxification of various chemicals

8.      The GI microflora stimulates and or increases the number of several classes of immune cells.

9.      Numerous toxic metabolites are routinely formed in the gut such as ammonia from urea (meat digestion); amines, nitrosamines from nitrites and nitrates and naturally occurring nitrates found in foods.

10.  Sex hormones are metabolized in the gut.

11.  Dysbiosis associated diseases include:

Cancer: colon/breast

Inflammatory bowel disease

Irritable bowel syndrome

Chronic fatigue syndrome

Rheumatoid arthritis and Spondyloarthropathies

Acne, Psoriasis and Eczema

Food allergy/intolerance

Malabsorption syndromes

[1] ( Original: Arumugam M, Raes J, Pelletier E, et al. “Enterotypes of the human gut microbiome.” Nature DOI: 10.1038/nature09944 (2011)


[3] Jason A. Hawrelak, BNat (Hons), PhD Candidate and Stephen P. Myers, PhD, B Med, ND The Causes of Intestinal Dysbiosis: A Review.

[5] Robillard Ph.D., Norman (2012-04-12). Fast Tract Digestion Heartburn (Kindle Locations 6533-6535). Self Health Publishing. Kindle Edition.

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Category: Dysbiosis

About the Author ()

Dr. Christopher Rasmussen (aka Reality Renegade) is the author of his upcoming book, "InflaNATION: Industrial Diners & A Doc In The Box." By deliberately avoiding harmful industrial foods and the Commercial Sick Care System with its Pills and Procedures paradigm, Dr Rasmussen cured himself of a deadly disease-which became the reason for writing this book. In the book, he provides the facts you must know and the solutions to regain your health, maintain wellness, and outlive your parents' generation in an extraordinarily toxic world.

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