The beginning of all life on earth was the development of microorganisms. All of the processes of life which every living cell depends on to this day were originated by bacteria and other microbes. For the first two billion years of life on earth, all life was microbial. All cells began as single cells and all life forms are meticulously organized and highly sophisticated organizations of microbial life. They invented all of life's essential, miniaturized chemical systems including fermentation, photosynthesis, oxygen breathing, DNA repair systems, cellular movement and the removal of nitrogen gas from the air. Because bacteria can routinely and rapidly transfer bits of genetic material to each other, they are capable of adapting at the genetic level very quickly. They do not need to wait for genetic mutation and reproduction in order to adapt to environmental change. Genetic recombination is a natural process of bacteria. An even faster form of change available to microbes is symbiotic alliance, the merging of organisms into new collectives.
We carry the descendants of the first bacteria from the oceans that learned to use oxygen in each of our cells now as our mitochondria. Long ago the mitochondria took up residence in other microorganisms providing their specialized ability to utilize oxygen for energy production in exchange for food and shelter and they are now present in nearly every cell on earth. But they retain their bacterial habit of multiplying by simple division, at their own times using their own DNA. This was a symbiotic alliance that became permanent. This process of symbiosis occurs throughout all life on earth. Our cells maintain an environment that is carbon and hydrogen rich, like that of the earth when life began. They live in a medium of water and salts like the composition of the early seas. We co-exist with present day microbes and harbor remnants of others in our cells.
Without nitrogen-fixing bacteria, many soils would be sterile and unable to support plant life. Neither cows or termites can digest cellulose without the microbes in their guts. Ten percent of our own dry body weight consists of bacteria, many of which we can't live without. Photosynthesis originally began in cyanobacteria not plants. The green plastids such as chloroplasts were most likely originally eaten but resisted digestion by some of their hosts. Their resemblance to cyanobacteria to the present is even more obvious than the bacterial nature of mitochondria. The chloroplasts have their own DNA and RNA, their ribosomes are bacterial and they have their own membrane within the cell. They divide directly in two within the cell and their DNA, RNA and protein strongly resemble those of cyanobacteria. The plastids are now dependent on their hosts but still make some of their own proteins. Plant photosynthesis is the basis of all larger forms of life on earth. Bacterial symbiosis continues within and upon us.
We each have about one billion living bacteria per gram of large bowel content. This is greater than the number of people who have ever lived. This amounts to about 3 to 4.5 pounds of bacteria in the gut. Along with sheer numbers is the great variety of species present which are somewhere between 400 to 500 different types of bacteria. Nearly all of these bacteria are anaerobic which means they cannot use oxygen in their energy metabolism. For millions of years, all life on earth consisted of anaerobic bacteria and other micro-organisms. We carry that heritage with us to this day. When considering just the known metabolic capabilities of E. coli alone, it is obvious that the metabolic functions of the gastrointestinal flora are immense and are even greater than the functions of the liver. Without the constant assistance we receive from our beneficial flora, we could not live.
In many ways, the flora can be considered as a separate metabolic organ of the body. There is much evidence that what is considered normal gut structure and function is, in fact, the combination of a complex set of interactions between the host and the microbes that colonize the gut. This includes intestinal peristalsis, absorption, and the composition of the intestinal cells and their growth and health. About 60% of our immune system's receptor cells are in the large intestine. 15% are in the lower part of the small intestine. This means that 75% of the body's immune system happens in the gut and is dependent on a healthy bowel flora.
The entire digestive tract is coated with a bacterial layer on the surface of the intestinal walls. This provides a natural barrier to invading organisms, undigested food, toxins and parasites. The beneficial flora such as Lactobacteria, Bifidobacteria, Propionobacteria, and certain strains of E. coli, Peptostreptococci, and Enterococci, produce antibiotic, anti-fungal, and anti-viral substances that can dissolve the membranes of viruses and bacteria. E. coli is able to use oxygen and helps to clear any oxygen that may be present to create the oxygen-free environment the beneficial flora require. E. coli is only normal in the colon and lower parts of the intestine. E. coli found anywhere else in the body is a sign of gut dysbiosis.
The flora are also essential in triggering the production of a wide range of immune cells and factors in the body including neutrophils, macrophages, immuno-globulins, interferons, interleukin-1 and tumor necrosis factor. Bifobacteria are the most active in synthesizing nutrients. About 30 different species have been identified and they are most numerous in the colon, vagina and genital areas. Protozoa, yeasts, and other fungi occur only in very low numbers in the healthy human gut. A disturbed flora both lowers immunity and weakens the barrier functions of the intestinal wall allowing a wide range of organisms and toxins to enter the blood.
The beneficial flora should make up 85% of the intestinal bacteria. About 100 different kinds have been identified so far. They are primarily lactic acid producing bacteria and when they are dominant in the gut, they reduce the pH near the gut wall to 4.0-5.0. This acid environment is a strong deterrent to the growth of pathogenic bacteria and yeasts which prefer a more alkaline environment. They are also able to neutralize a wide range of toxins both those produced by bacteria and yeasts, and those that are ingested with food and drink. They can chelate heavy metals and other poisons. A healthy gut level of the probiotics is 100 billion to 1,000 billion per milliliter of digestive tract. In many Americans today, the count is as low as 5 per milliliter. Pathogenic bacteria can include bacteroids, peptococci, staphylococci, streptococci, clostridia, yeasts, proteus, clebsielli, and many, many others.
The specific composition of the gut flora is unknown. There are at least 17 families of bacteria with 50 different genera. Within this are hundreds of species and subspecies. Somewhere between 400-500 is the estimated amount in a single person. The major problems with identification of the flora are the complexity of the internal ecosystem and the inaccessibility of many parts of that ecosystem in a healthy person. Getting samples from anywhere but the mouth and anus is difficult. There are variations in the content of microbes even in different parts of the stool specimens taken. All other sampling requires invasive methods which may subject the sample to contamination. About 60% of the species are not able to be cultured in the laboratory even with excellent equipment and methods. This may be due to unknown nutritional requirements on the part of the organism, or because they must grow with other microbes that provide essential substances for them. This means they have not been studied in any detail. Methods using the identification of bacterial DNA are beginning to overcome this problem but much study remains to be done.
In a sterile gut such as is used in certain experiments, the intestinal walls degenerate due to the decline in cell production. The production of new cells slows down. Less cells are produced and their development is disturbed which can lead to cancer. The intestinal villi degenerate and can no longer break down and absorb food properly resulting in mal-absorption, nutritional deficiencies and food intolerance. In addition to protecting and nourishing the intestinal wall itself, the beneficial flora take an active part in digestion and absorption. The flora help digest proteins, ferment carbohydrates, and break down fats and fiber. Bacterial by-products are important in absorbing minerals, vitamins and many other nutrients through the gut wall. In addition, the flora produces many vitamins including vitamin K, pantothenic acid, B1, B2, niacin, B6, and B12. This keeps the body's supply of these nutrients steady. Normal digestion and absorption of food is probably impossible without normal flora. Certain foods cannot be digested at all without it such as fiber and lactose.
Fiber is an important food for the beneficial flora. They feed on it providing nutrition for the gut wall, and the body. The fiber is primarily broken down into short-chain fatty acids (acetic, propionic and butyric acid) and carbon dioxide. In omnivores such as humans these acids are produced throughout the large intestine. These fatty acids supply 50-75% of the energy requirements of the cells of the large intestine, but only about 5% of the overall energy required by the body. In ruminant animals such as cows and horses it may supply 35 – 75% of the energy for the animal.
The short chain fatty acids are converted to acetyl coenzyme A and other forms of coenzyme A either in the gut lining or the liver. Coenzyme A is then converted to energy in the mitochondria or used to make fatty acids in the cells. The bacterial action on dietary fiber allows the fiber to absorb toxins, recycle bile acids and cholesterol, and take part in electrolyte and water metabolism. The beneficial flora work on the fiber and if they are not present, it will be taken over by the pathogenic bacteria which produce toxins that cause illness and inflammation. This is what is happening when a low fiber diet is recommended for intestinal problems. Without the beneficial flora, fiber can become a source of disease.
Another problem which can be worsened by gut dysbiosis (imbalanced gut flora) is anemia. When the beneficial flora are weak or absent and the pathogenic bacteria such as actinomyces, mycobacterium, E. coli, corynebacterium and many others are dominant, they consume any free iron available from the food being eaten. Supplementing iron in the absence of beneficial flora actually makes these pathogenic bacteria stronger and can result in many gastrointestinal side effects from the iron supplementation. An abnormal flora results in many nutritional deficiencies and promotes widespread degeneration.
The iron-binding protein transferrin is also the major aluminum-binding protein in the blood plasma, and through its binding to transferrin, aluminum can enter the brain. Iron absorption is controlled by the status of the body iron stores. The lower the body iron stores, the larger the percentage of ingested iron that will be retained in the body. The same absorptive mechanisms that increase iron uptake are involved in the uptake of lead and cadmium. This is why an iron deficiency will worsen lead poisoning. When the available iron is low, transferrin easily carries molecules of aluminum into the cells along with whatever iron there is. Aluminum is closest in size to iron and magnesium and will compete with them in the body. An iron deficiency increases the absorption of toxic metals into the body where they will cause a wide range of toxic effects by interfering with the functions of the proper nutrients and promoting free radical damage. Abnormal flora strongly promotes this imbalance.
Iron is required for the production of the heme proteins including hemoglobin – the red blood cells, and myoglobin. Iron is also essential for the production of another type of heme protein, the cytochrome proteins. The cytochromes of the mitochondria are used in the respiratory chain for energy production. The cytochromes of the endoplasmic reticulum include the Cytochrome P450 enzymes.
Cytochrome P450 is a group of Phase I detoxification enzymes which are essential to the first step in the detoxification process which converts toxins to a water soluble form that can be excreted. This includes drugs, pesticides, carcinogens, alcohol, and non-nutritive compounds found in plants. A reduction in the Cytochrome P450 enzymes can cause multiple chemical sensitivity because even small amounts of toxins can result in damage throughout the body. Iron deficiency will reduce energy production, and oxygen uptake, impair detoxification and increase the absorption and retention of aluminum, lead and cadmium. This can all be caused or worsened by a pathogenic flora which consumes the iron available from food.
The toxicity of aluminum usually results from inhibition of magnesium dependent enzymes as it can readily replace magnesium in biological systems because of its much higher affinity for the substrates involved. Even tiny amounts of aluminum can compete with much larger quantities of magnesium. But the enzyme action of aluminum is much slower than magnesium reducing enzyme functions. Nearly all enzymes that require ATP use it in the form of Mg-ATP complex.
Interference with these enzyme pathways affects the neuromuscular functions, and the glycolytic pathway which produces energy from sugar. Magnesium is also required for the synthesis of DNA, RNA, protein, fats and carbohydrates. It plays a structural role in cell membranes, ribosomes and chromatin. It is essential for energy production in the mitochondria. Aluminum is a very common metal in the environment and is widely used as a food additive, antacid, in deodorants, and in packaging and cookware. Disturbed bowel flora can greatly increase the absorption and toxicity of aluminum.
Low hydrochloric acid production has many negative effects on the body including an increased risk of pneumonia and other infections such as salmonella and osteoporosis. Hydrochloric acid kills most of the pathogens present in the food being eaten including parasites. Low hydrochloric acid leads to poor absorption of many nutrients. Many minerals such as calcium and iron, amino acids and numerous vitamins depend on HCl for absorption. Low levels can also reduce liver and pancreas enzyme production and function.
Stress, over eating, drinking cold drinks with meals, eating too much protein at once, poor chewing, low zinc and iodine, chlorinated water and other factors will lead to low HCl. Depleted beneficial flora, and low hydrochloric acid will usually result in reduced digestive enzyme production and will result in creating an overly alkaline intestine which favors pathogenic bacteria and yeast. Various forms of metal toxicity can also interfere with the production of hydrochloric acid.
Hydrochloric acid production requires the presence of sodium and potassium chloride which are converted in the stomach to hydrochloric acid. Copper toxicity is an important cause of reduced HCl. This is because copper imbalance causes slow oxidation due to copper's ability to raise calcium levels in the tissues. As the metabolism slows down, the sodium and potassium levels in the tissues decline and hypo-acidity occurs.
Slow oxidizers usually have an overly alkaline intestinal tract and are very prone to yeast infections. Copper toxicity is often due to zinc deficiencies and the accumulation of toxic metals that will replace zinc such as mercury and cadmium. Slow oxidizers retain metals very easily due to the sluggish metabolism that makes it harder to excrete them. Prolonged adrenal stress is a cause of zinc loss as is over-eating sugar and using stimulants. As zinc declines, copper rises. Metal toxicity can be both a cause and an effect of adrenal stress.
Copper toxicity is a condition where there are high levels of copper building up in the body tissues, but the copper is in an unbound state and is bio-unavailable to the body. This causes simultaneous toxicity and deficiency. Copper is essential for the control of all types of fungi and yeasts throughout the body. Copper toxicity also impairs thyroid function which makes the body more vulnerable to yeast.
When a high intake of sugar or alcohol is present, zinc is rapidly lost, promoting a copper rise. In addition, yeasts and pathogenic bacteria thrive on sugars of all kinds. If the gut flora is very disturbed, any type of carbohydrate foods could promote the growth of yeast and pathogenic bacteria. When dysbiosis is present, sugar and alcohol must be completely eliminated from the diet, at least for a while.
The effect of heavy metals on bacteria is quite variable. For many the effects are the same as they are for cells in the body such as blocking uptake of needed nutrients, substituting for them in the cell metabolism, creating more free radicals, inactivating enzyme functions and so forth. Some bacteria have developed the ability to block heavy metal absorption, rapidly excrete heavy metal or bind the metals in the cell in ways that deactivate their toxic effects. Due to the lack of full knowledge of the bowel contents and of the exact effects of metal on the millions of bacteria, it is hard to say what effect ingestion of heavy metal has on the flora in any specific way.
The toxicity of metals in the gut are strongly moderated by the presence of metallothionein. Metallothionein is involved in many functions of the body, including immunity, brain and gastrointestinal tract maturation, and the regulation of metals. Metallothionein is essential for maintenance of the proper ratio of copper to zinc. So much so, that a zinc/copper imbalance is the main indicator for a metallothionein malfunction. The malfunction could be due to a genetic weakness but may also be primarily induced by nutritional deficiencies and imbalances. The primary nutrient needed in the formation of metallothionein is zinc.
Therefore, metals that compete with zinc such as mercury and cadmium could eventually disturb metallothionein function. Metallothionein is crucial to the body in regulating and coping with toxic metals. It envelopes metals such as mercury, lead and cadmium, binding with them and carrying them out of the body. Mercury or lead in the gut require metallothionein in order to disable the toxic substance. When mercury is ingested in any form, it produces destructive changes in the mucous membrane linings of the gastro-intestinal tract. It enters blood circulation, travels to the tissues, and then damages literally every cell with which it comes into contact. Mercury is commonly used as an antibacterial preservative so it is likely that it would also kill at least some of the flora. Ideally, ingested mercury is bound to metallothionein and transported out of the body through the bile and through the kidneys.
Without the metallothionein, the toxic metals are most likely to interact with chemicals called sulfhydral groups. A combination of sulphur and hydrogen, these groups have tremendous power to bind to mercury, lead, and cadmium but especially mercury. Among the sulfhydral groups in the intestines are the enzymes that break down casein and gluten. Toxic metals and low zinc interfere with the enzyme functions giving rise to gluten intolerance to grains such as wheat, rye, barley and oats, and to dairy intolerance.
The use of probiotics is an ancient practice thousands of years old. All over the world people have used lactic acid producing bacteria to ferment milk, fruit and vegetables, beans, fish meat and cereal. Fermented foods taste better, are easier to digest and keep longer. Sauerkraut, sourdough breads, salami, olives, yogurt, kefir, cheeses, soy sauce, miso and fermented grains are still eaten all over the world. Lactobacilli are a large family of bacteria that are essential inhabitants of the gut, mucous membranes throughout the body, and are present in large numbers in human breast milk.
Drugs of all kinds, chlorine, sugar, alcohol, heavy metals, toxic chemicals, nutritional and immune deficiencies all deplete the beneficial flora and favor pathogenic organisms therefore we must constantly promote the health of the flora. Probiotic supplements, probiotic foods, pre-biotics which feed the flora such as fiber and inulin and avoidance of toxins of all kinds must be a lifetime process to restore and keep the tremendous health benefits of a healthy flora.
Dysbiosis can require an aggressive program of no sugar, and low carbohydrate intake combined with increasing levels of beneficial flora as tolerated along with various herbs and other substances that kill yeasts and pathogenic bacteria. I have found garlic supplements of all kinds to be very important in this process. Although eating garlic is always a good idea, supplements are required when fighting infections and over-growths of pathogens.
The most effective herbal treatment I have ever found is Health Concerns Phellostatin. This product must be used very cautiously at first as it is very effective and can cause discomfort due to the toxic effects of die-off pathogens in the gut. It is best to establish a high dose of probiotics and garlic and get the diet right before attempting to use Phellostatin. But it will not only kill pathogens, it will help the body heal from the damage that has occurred.
The well known and commonly available Chinese herbal formula called Yin Chiao, or Yin Qiao is very helpful in relieving detox and die-off symptoms as well as general discomfort ranging from sore throats, insect bites, ear aches, and non-chronic headaches to poison oak and neuralgia, especially trigeminal neuralgia. It is especially helpful in candida detoxification and can be used quite freely to control the flu-like symptoms typical of candida die off.
It can be taken every hour at first until symptoms begin to subside. Then take it whenever the symptoms re-occur. Taken right away and frequently during the onset of a cold, it can stop it or make it much milder if the flu is not very strong. If it comes on anyway, Yin Chiao is very helpful with the symptoms and reduces fever. The main contraindication is loose bowels although only a few have this problem and it is usually temporary. For some, it is just too laxative at high doses. After a while, as the pathogens clear the system, the die-off and detox symptoms will become mild or non-existent as there will not be as much in the system dying off all at once. The liver will be able to handle the toxins released and no particular symptoms will occur.