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Dear Dietitian – what is the microbiome?

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PICT Leanne McCrate Dear Dietitian
Leanne McCrate, RD, LD, CNSC

Dear Readers,

When I told friends and family that I would be writing about the microbiome this week, there were some raised eyebrows.  My friend Ken said, “Of course, the microbiome. What is that?”  

The microbiome, sometimes referred to as microbiota, is the collection of microorganisms (think tiny bugs) living in certain areas of the human body.  It is made up of bacteria, viruses, fungi, and parasites.  While most of the microbiota reside in the intestines, they are also found on the skin, in the vagina, nasal passages, and in the mouth. We are first introduced to the microbiome in the birth canal and through human breast milk.

The term microbiome was coined by Joshua Lederberg in the 1990s. However, a much earlier discovery that microorganisms live in the human body dates back to the 1880s when Austrian pediatrician Theodor Escherich discovered a certain bacterium in the intestines of both healthy children and those who suffered from a diarrheal illness ( This bacterium was named for him, and most of us have heard of E. Coli, or Escherichia Coli. 

The purpose of the microbiome is to help control digestion, stimulate the immune system and protect us from disease. Perhaps the study of the human microbiome brings more questions than answers at this point, as it is a very new area.  Questions like, “Can the microbiome be used to prevent cancer? Can it be manipulated to help prevent obesity?”  “Does it help prevent diabetes?” Scientists are working diligently to find answers to these questions.

One practical application of the microbiome involves Clostridium difficile (C. diff), which is an opportunistic bacterium that resides in our intestines. When the immune system is severely weakened, C. diff flourishes and causes a diarrheal illness, which can be serious and, in some cases, life-threatening.  To treat this condition, fecal material is taken from healthy individuals and transplanted into the colon of those suffering from recurrent C. diff colitis. These transplants have produced positive results. 

There are ways to increase your microbiome.  Simply eat more fiber, including fruits, vegetables, beans, and whole grains, like wheat, oats, and barley. These foods are sometimes called prebiotics because they feed the good microbiota in your gut. In addition, fiber cannot be broken down by the human body.  It is metabolized by enzymes and microbiota in the colon.  Short-chain fatty acids are produced in this process, which lowers the pH of the colon.  Harmful microorganisms cannot live in an acidic environment, so the end result is a healthier gut. Does a heathier gut bring about a healthier body?  Again, more questions than answers.


Dear Dietitian

Leanne McCrate, RD, LD, CNSC, aka Dear Dietitian, is an award-winning dietitian based in Missouri. Her mission is to educate the public on sound, scientifically-based nutrition.  Do you have a nutrition question? Email her today at