Normal Gut Flora: The Inside Story

Most microbes in the intestinal tract have only a brief existence in our bodies.  They are ingested or “born” at their beginning and then pass right on through and are “eliminated” with fecal material.  Some microorganisms, however, take up a more permanent residence.  Why doesn’t normal flora multiply out of control and take over the body?  What holds them in check?  How do we protect ourselves from these bacteria?  What about pathogenic organisms?

We have our immune system; we have the enzymes, acids and bile salts that are added into the gastrointestinal tract along with its continuously secreted mucosal lining.  And we have the metabolic activities of bacteria.  There is actually a “check and balance” system in place. 

Besides this long tube that begins at the mouth and ends at the anus, there are organs involved in your digestive tract.  These organs include the liver, pancreas, and gall bladder.

Bacteria in the Mouth and Stomach
The first line of defense is the saliva secreted by salivary glands into the mouth.  Saliva suppresses bacterial over growth by first of all removing it from the mouth, and sending it into the acidic environment of the stomach.  It is constantly cleansing particles from the teeth and gums and cleansing the mouth.  In addition, it contains enzymes and antibodies that directly destroy bacteria.  In the stomach, bacteria that have made it into the system with our food and beverages encounter hydrochloric acid.  As a result of the acidity, the bacterial count falls to almost undetectable levels after a meal.  New born infants and the elderly have less HCL that is normal, and people who are not healthy may find the same thing.  Low stomach acid levels allow pathogens to survive.  The HCL also aids in digestion by breaking down complex sugars and the change in pH activated protein enzymes for protein digestion.  Low HCL levels open the body up for an increase in pathogens and a decrease in the nutrients being digested and assimilated by the body.

There are glands in the stomach that secrete mucus to line the stomach wall and protect it from the harsh stomach acids and digestive enzymes.  In addition, this mucus protects the gastrointestinal tract from abrasion as the food passes through.  It is also a barrier, to prevent harmful bacteria from attaching to the intestinal wall.  People with inflammatory bowel diseases do not have the same healthy mucus that is found in a healthy gut. (Quigley and Kelly 1995)  It is believed that disease-causing bacteria disrupt the protective mucus layer by degrading it penetrating through it and causing ulcers and inflammation. When the mucosal lining is broken down inflammation of the lining of the gut, absorption of toxic and carcinogenic compounds occurs and overgrowth and attachment of harmful bacteria to the intestinal wall occurs.  I have found, however, that people taking Caucasus Kefir Capsules, who have this problem, recover.  It seems the good flora takes over and the pathogenic bacterial populations diminish.  This allows the lining of the stomach to heal.  I have also noticed that when there is pain, and the mucosal lining is not protecting the body from harmful microorganisms, that the kefir capsules along with aloe vera juice, (even if it is from Sam’s!) can do wonders.  Aloe vera, Slippery Elm bark, ground flax seeds, and pectin are all high in soluble fiber and mucilaginous.  They help to heal damaged, bleeding membranes lining the intestinal tract and can be very instrumental in the healing process.

Bacteria in the Small Intestine
The bacteria that survive the high acid content of the stomach will then pass on into the small intestine.  First in line is the small intestine.  Its first sections is called the duodenum.  It is here that most people develop ulcers.  It is here that the pancreas and liver dump their digestive enzymes, bicarbonate and bile salts, respectively. The digestive enzymes, from the pancreas protect us from harmful bacteria such as E. coli, Klebsiella pneumoniae and Shigella (Rubenstein et al., 1985 Sarker and Gyr 1992) by digesting the cells walls of these bacteria.  The bile salts coming from the liver are acidic.  They are made in the liver, stored in the gall bladder and released.  Primarily, bile salts are used for fat digestion and transportation.  Yet, bile acids are potent as antimicrobial agents, so much so that they are currently being evaluated for use as antibiotics (Li et al., 1999; Guan et al., 2000)  When bile salts are altered within the duodenum this has been shown to lead to an overgrowth of some bacterial species. (Kocoshis et al., 1987) In addition, a substance called lysozyme is secreted by cells that line the digestive tract.  Lysozyme is a potent enzyme that attacks bacterial cell walls and is believed to be another primary control preventing bacterial overgrowth in the upper GI tract.  Unlike the stomach, in the small intestine (because of the bicarbonate secreted from the pancreas), the environment is more of a neutral pH.  This does allow for the growth of intestinal flora. So as food travels through the small intestine it gradually becomes more and more “populated.” (Linskins et al 2001) The body’s defense against these organisms is the secreted enzymes and bile sales, the mucus secreted by the cells lining of the GI tract, and in addition peristalsis helps to keep the bacteria from adhering to the epithelial cells of the small intestines (Kirjavainen, 1999).  Constipation, drugs that slow peristalsis, or other problems increase the tendency for the gut to become colonized by harmful bacteria.

The predominant organisms in the small intestine are largely lactobacilli, streptococci, staphylococci and yeasts, although some coliforms and anaerobes are present in low concentrations.  What is definitely missing, however, are the gram negative organisms such as Bacteroides and E. coli.  These organisms are in very high numbers in the last section of the small intestine, however. (Gorbach et al. 1967a; Gorbach et al. 1967b; Gorbach et al 1967c) Bifidobacteria, Fusobacteria and Clostridia are also present in the last section of the small intestine (the ileum).  It is here the organisms greatly rise in number and the gram negative organisms begin to out-number gram-positives (Linskins et al., 2001). 

The bacterial that are able to survive the above environment.  They need to be able to adhere to the lining of the intestinal wall.  This means they must contain adhering proteins, have their own means of locomotion and are able to multiply rapidly enough to overcome the forward peristaltic movements.  Bacteria that fail to meet the criteria for attachment, motility and propagation will pass on into the fecal matter and into the large intestine.

Bacteria in the Large Intestine
Eventually the small intestine connects to the large intestine.  It is here that most normal flora lives and there is a very high bacterial count.  Separating the small intestine from the large intestine is the ileocecal valve.    This valve prevents the backflow of  microorganisms from the colon into the small intestine.  In the large intestine there is over 350 different species of bacteria numbering  from the billions to the trillions in every gram of dry feces.  Over 99% of these organisms die in the presence of oxygen.  This class of bacteria are called obligate anaerobes.  Bacterial growth here is largely dependent upon availability of nutrients.

Even though there is extensive digestion and absorption that occurs in the small intestine, many nutrients still pass into the colon not yet completely digested.  Interestingly, the very nutrients that stimulate some bacterial species simultaneously suppress the activities of other bacteria.  It appears that the important factors governing bacterial composition within the large intestine are the amount of food eaten and the types of nutrients available to them. 

Energy from Bacteria?
The bacteria in our intestines obtain their energy by breaking down carbohydrates and proteins – a process called fermentation. The major result of this fermentation process is short chain fatty acids (containing 2,3 or 4 carbon atoms). (Legakis et al., 1982)  In return for the food we supply the bacteria through our diet, they supply us with necessary vitamins and energy and protect us from disease-causing invaders.  The short chain fatty acids produced by our gut flora are tremendous sources of energy. (Roediger 1980)  This energy is used by the bacteria for growth as well we use it too.  The cells that line the intestinal tract get up to 70% of their energy from bacterial fermentation products. (Cummings1995) The liver, muscles and all the cells of the body greatly benefit from these short chain fatty acids. It is estimated that up to 10% of the body’s total daily energy requirements come from these fatty acids. (Roediger, 1980)

Nutrients from Bacteria?
Bacterial flora in the colon are involved in synthesizing hormone and vitamin precursors.  One example is vitamin B12.  This vitamin is not found in any plant source.  Instead, it is produced almost entirely by gut bacteria.  Vitamin B12 is essentially for red blood cell function and is also required for nerve activities.  Deficiencies are not uncommon and they lead to disease such as anemia and painful nerve disorders.

The Colon, Cancer and Microorganisms
Of all the SCFA’s producted by intestinal flora, butyric acid sees to be the most important as numerous studies have show its affect on the growth and heath of intestinal epithelial cells.(These are the cells that line the intestinal tract.) In contrast, butyric acid inhibits the growth of cancerous tumors. (Siavoshian, 2000)  There is a direct relationship between the amount of butyric acid produced in the gut and colon/rectal cancer.  It has also been demonstrated that some bacteria in the colon actually neutralize dietary carcinogens such as nitrosamines, which are produced when high protein diets are eaten (Kailaspathy and Chin, 2000)

SCFA’s have been shown by much research to inhibit the growth of disease-causing bacteria like salmonella (Durant, 2000, Rabbani et al. 1999).  Short chain fatty acids lower the pH of the large intestine this greatly helps to hold bacterial growth in the intestine by pathogens.   In addition, SCFAs have many similar anti-microbial properties to those of medium chain fatty acids found in oils such as coconut oil.  Normal gastrointestinal flora compete with other bacteria for nutrients and for binding sites on the intestinal wall. (Kailasapathy and Chin 2000)  It is speculated that normal gut flora serve as a final defense against invading disease-causing organisms.

In addition to the short chain fatty acids produced by friendly flora “the good guys”, other antimicrobial substances such as peroxides and bacteriocins are produced.  Bacteriodes organisms in the colon actually produce toxins that selectively destroy the disease-causing Clostridium difficile.  Many people suffering from life-threatening, chronic, persistent Clostridium difficle-associated diarrhea have been cured when bacteroides species were replaced in their colons (Borody 2000)

SCFAs speed the rate of peristalsis which indirectly removes invading microorganisms and accelerates their movement through the digestive tract (Kailasapathy and Chin, 2000)  When “probiotic” foods such as plantains and pectin are added to the diet is has been shown that the resulting increased growth of good flora, then in turn changes the environment in the intestines (Increase in SCFAs) and pathogens are reduced while diarrhea and inflammation is greatly improved. (Rabbani et al., 2001)

Nutrients that Promote Healthy Flora
There are many nutrients studied in human milk that play a protective role in the guts of infants.  The roles of lactoferrin (an other glycoproteins), oligosaccharides and iron in altering the microflora have been well studied.  There has been a fair amount of research recently with oligosaccharides.  This substance is also present in breast milk and concentrations of oligosaccharides in the feces and urine of breast-fed infants are much higher than those found in formula-fed babies..  They are complex sugars that appear to act as scavengers, collecting, removing and neutralizing disease-causing bacteria and their toxins.  These oligosaccharides in this way promote the clearance of pathogenic organisms.  In addition, these substances selectively stimulate the growth of “healthy” gut bacteria and have been given the name “prebiotics”

In general, the bacteria living in the large intestine are living under starvation conditions.  Most of the sugars and carbohydrates have been digested and assimilated into the blood stream.   Therefore,  by the time the “remaining” food reached the large intestine there is little “energy” foods available.  By adding probiotic foods to our diets we can dramatically increase healthy gut flora.  This type of food does not get totally digested and the intestinal flora use it for energy.  Most bacteria including bifidobacteria, lactobacilli, ruminococci, eubacteria, clostridia and Bacteroides prefer to use carbohydrates as their preferred energy sources.  They are well-adapted to breakdown complex sugars and synthesize many glycosidase enzymes.

Proteins are found abundantly throughout the entire digestive tract.  The breakdown of proteins occurs by digestive enzymes secreted into the digestive tract, and by bacteria-secreted digestive enzymes.  Bacteria are very important in their assistance in digesting proteins.  When undigested proteins show up in a live blood analysis, this is a strong sign that the person has gut flora issues.  Not all flora can breakdown proteins (some can only breakdown carbohydrates).

The important knowledge to gain from all this is:

1. Stomach acids reduce the number of live bacteria in the intestinal tract.
2. Digestive enzymes not only break down food, but also prevent bacterial overgrowth.
3. Bile salts, additionally, helps to provide a line of defense against bacterial overgrowth in the small intestine.
4. The fermentation of our food by friendly flora creates B vitamins and other nutrients that we need are difficult obtain from our food.
5. The fermentation of our food by friendly flora creates short chain fatty acids which our bodies use for energy, inhibits the growth of pathogenic bacteria, aids in the health of the  cells lining the intestinal tract.
6. Peristalsis, the constant movement through the digestive tract helps to prevents bacteria from adhering to the epithelial cells of the small intestine
7. A lack of digestive enzymes combined with abnormal gut flora is directly related to gut inflammation, allergies, asthma, eczema etc.

Meet the Family that should be living inside us:

Gram negative bacillus (rods) obligate anaerobes (can not survive in the presence of oxygen):
The major organisms in this category are in the bacteroides genus.  These are the bacteria who make bacteroicins or toxins to inhibit the growth of other bacterial species.  Fusobacterium also fit into this category and are commonly found in the colon.  These organisms are the ones that produce butyric acid a major short chain fatty acid that we use for energy and have many other benefits.

Also in this category are bacteria such as Eubacterium, Lactobacillus and Bifidobacterium.  These three species are capable of digesting a wide variety of substances such as cellulose, mucin, polysaccharides (complex carbohydrates) and proteins.  Like Fusobacterium, the major metabolic product from Eubacterium is butyric acid while lactic acid is the most abundant byproduct of lactobacilli and bifidobacteria is lactic acid.  These species also produce peroxides and bacteriocins.  The over-all effect of these products is an acid environment with antimicrobial activity which inhibits the growth of pathogenic bacteria.  In addition, these bacteria compete with pathogens for attachment sites on the walls lining the intestinal tract. This is called competitive exclusion.

Most people firmly believe these organisms are essential for good intestinal health.  Lactobacillus and Bifidobacterium species are used in most studies that have been done with probiotics and disease.  These are an important category of normal flora.

Gram positive cocci
Peptostreptococci and enterococci are members of this family.  They reside in the large intestine and account for approximately 10 billion organisms per gram of fecal material.  All these strains found in the intestines are resistant to acidic environment and they actually produce acetic acid as a major metabolic byproduct (Onderdonk, 2000). 

Spore-forming Gram Positive Bacillus (Rods):
Clostridium species are found in the intestinal tract, but their number are usually under 100 million organisms per gram of fecal matter.  These bacteria are harmless, yet they are capable of producing toxins that can damage the intestinal tract.  Clostridium difficile is the most important disease-causing anaerobic microorganism acquired in hospital settings. (Onderdonk, 1000/ Kelly et al., 1994)  These organisms rarely cause problems unless changes occur in the gastrointestinal environment as happens with antibiotic therapy.  Clostridium difficile is suppressed by good bacteria, but when these organisms are killed off it has the chance to proliferate and produce toxins that cause abdominal cramps, bloody and mucus-filled diarrhea, fever, weight loss, yellow plaques on the intestinal wall, etc.  Failure to obtain prompt treatment when Clostridium difficile overgrowth can lead to a very toxic intestinal tract and even death.

Coliforms:
Enterobacteriaceae bacteria are probably the most widely studies group in the large intestine.  This group includes Escherichia coli (E. coli).  These bacteria are closely monitored by water treatment facilities, and swimming beaches.  Normally, these bacteria only cause disease when they get outside the intestinal tract.  Examples of infections caused by enterobacteriacea include those of the abdominal cavity that occur follow injury to the intestinal tract, pelvic inflammatory infections, urinary tract infections, or ingections in newborn infants.  In recent years, the spread of disease-causing E. coli of the 0157:H7 genus has caused considerable concern to the general public.  It is this genus that has caused several deaths due to contaminated food stuffs in restaurants during the past decade.  However, under normal circumstances, within the confines of the intestinal tract, the total number of enterobacteriacea are kept under control by butyric acid produced by other microbial species.  Fortunately, these organisms typically do not migrate, but tend to remain relatively localized in thed digestive tract (Onderdonk, 2000).

More information on Digestive Track follow the links below:

Prebiotics
Chicory Root
Reading the Signs: The First Sign
The Next Signs
Colic in Babies
Sauerkraut