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Understanding Fermentation

Majid Ali, MD.



Majid Ali, M.D.

Our early primordial ancestors were fermenters. Throughout human evolution, some of those fermenting cells thrived in oxygen-poor nitches in the human body, serving many purposes, including food digestion. These were “good fermenters.” Our later human ancestors learned—experientially or intuitively, it seems—learned ferment foods to enhance their value. We can call it “good fermentation.”

Every chronic disease begins with fermentation. This need not raise any eyebrows. Diseases involve inflammation with buildup of acids and alcohols. Fermentation, of course, is conversion of sugars into alcohols and acids. We can call it “bad fermentation.”

Then came the age of fermenting human cells—most notably during the last century—ushered in by the era of antibiotics, sugar abuse, and industrial pollutants. The modern epidemics of inflammatory, immune, and degenerative disorders are rooted in cellular fermentation. In a broader evolutionary context, I recognize these epidemics as evolution-in-reverse. This is “ugly inflammation.”

Laps and Taps: the Good and Bad Guys of the Bowel
LAPs and TAPs are my terms for lactic acid-producing and toxic agents-producing microbes in the bowel. LAPs preserve the normal bowel ecosystem, TAPs disrupt it. 

In my book entitled “The Caanary and Chronic Fatigue” (1994), I discussed many elements that increase oxidative stress on energy and detoxification enzymes. It turns out that almost all these elements also suppress LAPs and — both directly by inhibiting LAPs and indirectly by other mechanisms — promote the growth of TAPs. This subject is of enormous significance in the normal aging process as well as in the accelerated aging process associated with chronic fatigue states. See below

LAPs confer many important host defenses upon the bowel discussed later in this section. TAPs are equally versatile in their functions and produce a very large number of noxious substances in the bowel. Among these are ammonia; phenols; tryptophan metabolites; vaso-constrictive amines such as histamine, tyramine, agmatine and cadaverine; certain steroid metabolites; and many toxins — most notably mycotoxins derived from fungi (yeasts). This area has received rather limited investigative attention, and it is almost certain that future research will uncover a host of as yet undetected bacterial and fungal toxins and metabolic villains. Finally, the bowel flora both produce and potentiate some carcinogenic substances. 

Not unexpectedly, LAPs-TAPs dynamics are profoundly influenced by food choices. American and British individuals show overgrowth of some TAPs such as bacteroides and some types of clostridia as compared with Japanese, Indians and Ugandans (Lancet 1:95-100; 1971). It appears likely that these differences are due to an abundance of fats and beef in the former populations' diet.


Bacteria are living beings capable of executing an enormous number of biochemical reactions. Farmers used bacteria and fungi to turn compost into fertilizer long before biologists understood the metabolism of these single-celled bodies. A partial list of such reactions brought about by the normal bowel flora includes production of ammonia, conversion of amino acids into amines and phenols, inactivation of digestive enzymes such as trypsin and chymotrypsin and other enzymes located on the surface of cells lining the gut, deconjugation of hormones such as estrogen and bile acids, denaturation of bile steroids, breakdown of food flavonoids, hydrogenation of polyunsaturated fatty acids in food, utilization of certain amino acids such as B12, conversion of some compounds into carcinogens, and many other enzymatic reactions.


I list below the three genera of LAPs and several genera of TAPs that most frequently populate the bowel ecosystem. 




Proteus, Pseudomonas, Salmonella, Escherichia


Bacteroides, Clostridium, Peptococci, Peptostreptococcus


Streptococcus, Staphylococcus

About 30 species of LAP microbes have been identified. Some important members of these three groups (L, Lactobacillus; B, Bifidobacterium; S, Streptococcus) include the following:

L. acidophilus
B. bifidum
L. bulgaricus 
B. adolescentis
L. lactis
B. infantis
L. casei
B. breve
L. helveticus  
B. longus 
S. faecium 
S. thermophilous

Most byproducts of modern technology threaten LAP microbes. In addition, alcohol, nicotine, various pharmacologic agents, and highly processed and "preserved" foods have a negative impact on lactic-acid producers.

Normal fecal flora in man includes the following: Bacteroidaceae (Bacteroides and Fusobacteria), Eubacteria, Lactobacilli, Bifidobacteria, Veillonellae, Acidaminococci, Megasphaerae, Peptococcaceae (Ruminococci, Peptococci and Peptostreptococci), Clostridia (C. perfrigens and other species), Enterobacteriaceae, aerobic Lactobacilli, Streptococci, Staphylococci, and yeast and fungi (often used interchangeably).


Dysfunctional Oxygen Signaling

In 1998, I introduced the term dysoxygenosis (dysox, for short) for this disease-causing “ugly fermentation.” This age of respiratory-to-fermentative shift arrived in our times—most notably during the 20th century—was ushered in antibiotics, sugar abuse, and industrial pollutants. The modern epidemics of inflammatory, immune, and degenerative disorders are rooted in cellular fermentation. In a broader evolutionary context, I recognize these epidemics as evolution-in-reverse. In 1998, I introduced the term dysoxygenosis (dysox, for short) for this disease-causing “ugly fermentation. Simply stated, the dysox state is characterized by degradative metabolic shift from high-efficiency human energetics to low-efficiency energetics of yeast and other fermenting microbes. The full text of my original published in The Journal of Integrative Medicine containing numerous photomicrographs and extensive bibliography is available free of cost at www.drali.org (Google ORPEC and Ali for quick search). I devote the 10th, 11th, and 12th volumes of my textbook entitled “The Principles and Practice of Integrative Medicine” to an in-depth treatment of these subjects.

Majid Ali, M.D.'s Seminars
The videos download to your computer.
They are approximately 45 minutes long and are a "seminar" on the subject.

After you order you will receive an email with the download link.

Click on the link, the video downloads - you watch!

$7.50 each

Order SINGLE VIDEOS Yeast and Fermentation problems in the gut
 Fermentation Bundle Set
 Am I Fermenting? Seminar One
 Am I Fermenting? Seminar Two
 Am I Fermenting? Seminar Three
 Anti-Fermentation Diet
 Fermentation - Gut Control
 Fermentation Cellular
 Cellular Fermentation 
Professor Ali defines disease in two ways: (1) disease is a state of separation from one’s nature; and (2) disease is evolution in reverse. In this second of 8 seminars  of “Dr. Ali’s Course on Healing,” he explains what he means by evolution in reverse. 

Fermentation’s Two Faces

Fermentation- Gut - H. Pylori Gastritis
Fermentation- Oral - Mouth Fermentation
In this 40-minute video seminar, Professor Majid Ali, M.D. discusses the causes, clinical features, and consequences of mouth fermentation, including bad breath, canker sores, glossitis (inflammation of tongue), herpes blisters, leukoplakia, and other pre-cancerous lesions. He offers recommendations for natural simple and low-cost remedies for preventing and controlling these disorders.
Fermentation-Small Bowel



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