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Information about

The Human Microbiome

Your intestinal tract houses 70% of your immune system and is responsible for digestion, assimilation of nutrients, detoxification and waste elimination.  


The "4 R's" of Intestinal Health are:

1. Remove: remove unhealthy foods in your diet and drugs that damage the intestinal tract

2. Replace: take supplemental digestive enzymes or hydrochloric acid if either of these are needed

3. Reinoculate: take probiotics to improve the intestinal milieu of friendly bacteria

4. Repair: take any needed nutritional supplements to improve healing of the intestinal tract.

Human Microbiome Information


  • The bacteria and other microorganisms living mostly in peaceful coexistence inside people are called the “human microbiome”.

  • The types of bacteria, fungi and protozoa present in the microbiome affect how the body functions, or in many cases, how it malfunctions.

  • Diversity of the human microbiome in the gut is crucial to health.

  • Humans are not all human, and in fact, the microbes inside of us, outnumber us! Bacteria inside the body outnumber human cells 10 to 1.

  • The human body is composed of 10 trillion cells.

  • The human microbiome is composed of 100 trillion cells, but only weights about 3 pounds!

  • Intestinal bacteria make up most of the human microbiome.

  • Bacteria and fungi also inhabit the mouth and gums, the nose, the nasal sinuses, the skin, the bladder, and the vagina.


Culture-based techniques previously suggested that about 500 distinct bacterial species colonized the GI tract. Most human studies use fecal analysis as a marker for amounts and varieties of intestinal bacteria living in the colon.


The human microbiome project has used techniques such as 16S rRNA gene sequencing, which suggests that there are about 10,000 species in the intestinal tract.


The  2 predominant phyla make up 90%:

1. Firmicutes, e.g. Clostridium spp.

2. Bacteroidetes, e.g. Bacteroides spp.


with smaller proportions of:

1. Actinobacteria

2. Proteobacteria

3. Verrucomicrobia

4. Cyanobacteria


What are the benefits of having more healthy intestinal bacteria?


  • They prevent harmful bacteria from invading the human body. Friendly germs are an important ally of the human immune system.

  • The friendly germs help our metabolism in many ways.


How do healthy intestinal bacteria help with metabolism?


  • They allow you to eat foods that you would otherwise be unable to eat.

  • They synthesize short chain fatty acids (SCFA) by fermenting dietary fiber.

  • They convert primary bile acids into essential secondary acids.

  • They make vitamins, like vitamin K and biotin.

  • They help with weight management. Obese people have different types of bacteria inside their intestinal tract than normal weight individuals.

  • They break down certain drugs.


Butyrate, a SCFA, keeps colon cells healthy and alive. It also regulates inflammation and helps prevent cancer in the colon. Butyrate is made by friendly bacteria in the colon. While butyrate is the primary energy source for colonic cells, glutamine is the primary source for small intestine cells.


Bile acids modulate cholesterol, glucose, and energy metabolism. Secondary bile acids block the growth of Clostridium difficile.


Think twice before you take antibiotics!


Antibiotics can wreak havoc with your intestinal microbiome and affect your metabolism. After one course of antibiotics, it can take months for the microbiome to recover to pre-antibiotic levels.


Antibiotics can be life-saving. If you have to take antibiotics, be sure to take probiotics while on them and for a few weeks afterwards.


Microbiome-related effects of taking antibiotics


  • Diarrhea

  • Constipation

  • Bloating, gas, and IBS from overgrowth of bacteria in the small intestine.

  • Weight gain. Feeding cows and chickens antibiotics fattens them. The same is true in mice. What about in humans?

  • Auto-immune conditions

  • Decreased numbers and diversity of the human microbiome


Taking antibiotics can cause diarrhea. Taking high doses of broad-spectrum probiotics, helps prevent getting diarrhea.


What are some of the microorganisms associated with antibiotic associated diarrhea?


1. Clostridium difficile is the most common in hospital settings.

2. Other types of Clostridia can also cause diarrhea.

3. Staphylococcus aureus

4. Klebsiella oxytoca

5. Candida

6. Salmonella


The overuse of antibiotics has led to antibiotic resistant bacteria. Methicillin-resistant Staphylococcus aureus (MRSA) is a well-known example. Drug-resistant Clostridium difficile are another. Infection with Clostridium difficlle can cause a life threating infection causing bloody diarrhea.


Infection with Clostridium difficile results from taking antibiotics. Antibiotics skew the normal intestinal bacterial population to favor C. difficile. Certain strains of C. difficile  produce a toxin which causes diarrhea.  C. difficile is resistant to multiple antibiotics, yet taking certain super- antibiotics, like metronidazole (Flagyl) or vancomycin, will sometimes restore normal intestinal function. Other times, super-antibioitic treatment fails, and the treatment of last resort is  “re-populating” the sick colon with feces from a healthy donor.  A fecal transplant, containing  normal, healthy bacteria, is effective more than 90% of the time.  This technique of reintroducing friendly bacteria from a healthy person’s stool has also been called “re-POOP-ulation”. Without it, otherwise perfectly healthy people can die.


Even if diarrhea does not occur, taking antibiotics promotes the overgrowth of potentially unfriendly germs in the the intestines like:

1. mucoid strains of E. coli

2. Klebsiella pneumoniae

3. Pseudomonas aeruginosa

4. Citrobacter



Your doctor can test for the amounts of friendly and unfriendly germs in your intestinal tract by ordering a comprehensive stool test. Labs that do this form of stool testing include Genova Diagnostics and Doctors Data.

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