A total of one hundred trillion bacteria live together in our digestive system, in either symbiotic or antagonistic relationships. That’s ten times more intestinal bacteria than cells in our body. Their total weight is about four pounds—the size of the liver. They have many functions and act like a symbiotic organ to protect our health.

Eighty percent of the dry weight of our stool is composed of gut bacteria, and half of that is still alive. Gut flora accounts for half of the volume of the contents of the large intestine. We have four hundred to five hundred types of bacteria in our digestive systems, each of which has many types of strains.

This variety may seem overwhelming, but twenty types make up three-quarters of the total. The most common are bacteroides, bifidobacteria, eubacterium, fusobacteria, lactobacillus, peptococcaceae, ruminococcus, and streptococcus. Most of these bacteria are anaerobic, meaning they do not need oxygen to thrive; some are aerobic and do need oxygen for survival.

A third group produces lactic acid and can be either aerobic or anaerobic. Lactic acid–producing bacteria help acidify the intestinal tract and protect us from overgrowth of harmful bacteria. Billions of bacteria inhabit our mouths. While the stomach has few because of its high acid content that prohibits their growth, the small intestine has many billions of bacteria.

The overwhelming majority of intestinal flora reside in the colon—trillions and trillions. Each day, we produce several ounces of these microbes and eliminate several ounces in stool. These bacteria manufacture substances that raise or lower our risk of disease and cancer, the effect of drugs, immune competence, nutritional status, and rate of aging.

Some of these bacteria cause acute or chronic illness. Other bacteria cause illness in people who are genetically susceptible but no problems in other people. Another group of bacteria offers us protective and nutritive properties. These friendly bacteria are called intestinal flora, probiotics, or eubiotics.

The last two terms mean “healthful to life.” The term probiotics is commonly used to refer to supplemental use of these bacteria in powder or capsule form. It was coined in 1965 by researchers Lilly and Stillwell to mean organisms that promote life of microorganisms, in opposition to antibiotics, which kill microorganisms.

The two most important groups of flora are the lactobacilli, found mainly in the small intestine, and bifidobacteria, found primarily in the colon. These bacteria live symbiotically within us in a mutually beneficial relationship that has evolved to enhance our health and theirs.

The bacteria within us live at about 98.6° Fahrenheit and thrive on the constant nourishment we provide in a warm, dark, moist environment. We allow them to inhabit us because they give us valuable preventive and therapeutic benefits. Where did these trillions of bacteria come from?

Up until birth, we receive predigested food from our mothers and are born with a sterile digestive tract. The trip down the birth canal initiates us into the world of microbes that thrive everywhere. Babies are exposed to bacteria in breast milk and formula and when sucking on nipples, fingers, and toes.

With every breath and touch, bacteria enter the body to colonize on the skin and mucous membranes. In no time, every conceivable space in the colon is occupied by microbes. Within the first few days of life, colonization of E. coli and streptococcus occurs.

Within a week of birth, bifidobacteria, bacteroides, and clostridium are established in bottle-fed babies. Breast-fed infants have increased numbers of lactobacillus and bifidobacteria species. The microbes set up homogeneous neighborhoods that push out competing microbes trying to break into their territories.

This normally happens in a predictable way, and once established, the colonies flourish. When babies are unable to properly colonize friendly flora, they become irritable and colicky and have gas pains and eczema in their diaper area. Babies who don’t develop the right balance of beneficial bacteria are more susceptible to allergy, asthma, and eczema.

After weaning, the specific types and strains of dominant flora change from Bifidobacteria infantis in infants to other strains of bifidobacteria in children and adults. The colonization patterns we set up in infancy continue to prevail throughout our entire lifetime. Successful colonization of the gut-associated lymphatic tissue (GALT) is necessary for the development and maintenance of the immune system.

Lack of gut bacterial stimulation has resulted in a decreased amount of mucosal surface area, altered mucosal enzymes, defects in intestinal barrier function, reduction in inflammatory responses, defective secretory IgA (sIgA) protection of the mucosal membranes, and poor oral tolerance to protein antigens.

Intestinal flora play an important role in our ability to fight infectious disease, providing a front line in our immune defense. As noted in a 1988 report by the U.S. surgeon general, “Normal microbial flora provide a passive mechanism to prevent infection.”

Friendly flora also manufacture many vitamins including the Bcomplex vitamins biotin, thiamine (B1), riboflavin (B2), niacin (B3), pantothenic acid (B5), pyridoxine (B6), cobalamine (B12), and folic acid, and vitamin K. Lactobacillus acidophilus and bifidobacteria increase the absorption of minerals that require acid for absorption, such as calcium, copper, iron, magnesium, and manganese.

Farm animals are routinely given supplemental flora, which enhance absorption of both vitamins and minerals. Friendly flora help increase our resistance to food poisoning. In 1993, the Centers for Disease Control reported twenty to forty million cases of food poisoning, although the FDA estimates the true total to be eighty million.

Many cases go unreported because the symptoms closely resemble the flu. Some food-borne infections lead to chronic illness, causing heart and valve problems, immune system disorders, joint disease, and possibly even cancer. Use of supplemental acidophilus and bifidus can help prevent food poisoning by making the intestinal tract inhospitable to the invading microbes.

It is a common misconception that friendly flora kill invading microbes. They actually change the environment by “competitive exclusion”—they secrete large amounts of acids (acetic, formic, and lactic acids) that make the area unsuitable for pathogens.

Not All Intestinal Bacteria Are Friendly

Friendly bacteria comprise only a small percentage of our total bacteria. You could call the rest the OK, the bad, and the ugly. Most intestinal residents are “commensal” bacteria: they have neither good nor bad effects on how we feel. Other intestinal bacteria are pathogens causing acute illness (salmonella causes food poisoning) or chronic illness (Helicobacter pylori causes ulcers).

Disease-causing microbes produce bothersome gas and toxic secretions that irritate the intestinal lining and get absorbed into the bloodstream, making us sick. Some bacteria are extremely virulent and cause sudden and violent illness. Our body reacts to a strong bacteria such as salmonella with diarrhea, fever, loss of appetite, and vomiting.

The body screams, “Get this stuff out of me!” So, it attempts to rapidly flush or starve it out. Most disease-causing microbes thrive at human body temperature, while fever kills them by overheating them. Bacteria that cause chronic illness are generally weak organisms of low virulence.

They are often found in small quantities in all of us and have been assumed to be harmless. But when large colonies are given the opportunity to thrive, they can and do cause illness. This type of illness is called intestinal dysbiosis.