Microbiome Glossary – Learning About Gut Health


Did you know that your body is a host to trillions of one-celled microbes that outnumber your own cells by about 10 to 1? These microbes or microbiota include bacteria, protozoa, fungi, yeast and others. They are found in your digestive tract, on your skin, groin, and in your respiratory tract. The microbiome refers to the self-contained mictobiota and the genes of these microbes that inhabit our body and interact with each other.

Research on the microbiome continues and one researcher, Rob Knight, PhD, author of Follow Your Gut, co-founder of American Gut, and UC San Diego Professor, has stated The Earth Microbiome Project is the largest crowd-funded research project in the world. Rob explains that we now have the computing power to understand the microbiome and to use the information for research. The National Institute of Health (NIH) has a special site dedicated to its study.

The microbiome may influence many aspects of our health including: our immune system, moods, sleep, weight, the amount of inflammation in our bodies, food allergies, and certain autoimmune disorders. While the research is very new and emerging, it is fun to learn more and to see one more reason why a low-fat, plant-based diet is even more beneficial than just being heart-healthy and lowering our risk for chronic diseases like type-2 diabetes, certain cancers, and Alzheimers Disease. Healthy people have the most stable and diverse microbiomes.

Rob Knight, PhD, cautions, the research is too new to make any changes to a microbiome and that a whole year of eating is what can influence it. In his book, Follow Your Gut, he states that eating a more vegetarian diet is beneficial but it will only slowly change the microbiome while switching to a meat and cheese based diet will drastically change it  to a less healthful state. He also goes on to state that the vast amount of supplements on the market called probiotics have not been proven for efficacy or even verified for their contents.

Many of the terms sound a little similar so we have prepared a glossary to help you understand this emerging and exciting research.

Microbiota - the collective plural term of the single-celled microbes that inhabit the human body and perform many beneficial and important tasks like helping us digest our food. Most of these are beneficial but some, like the ones that cause illness, are not. The microbes outnumber the body's cells by 10 to 1 in over 10,000 species and they weight 3 pounds in the adult body (NIH).

Microbiome - the mictobiota and the genes of the microbiota found in one person are called the microbiome and these outnumber the human genome. Unlike DNA, the microbiome can be changed and influenced by what you eat as well as how much you sleep and exercise and by the environment around you. Scientists also call this your tree of life. Your DNA contains about 20,000 genes whereas your total microbiome can contain 150 times this amount. Most of these are found in your gut.

Biome - self contained eco-system

Gut - refers to your entire digestive tract and it starts with your mouth and ends with your anus.

Pathogens - organisms that can make you sick, with salmonella being one example because it can cause infections and food poisoning.

American Gut - crowd funded study by Rob Knight, PhD, and other researchers at UC San Diego that everyone can participate in and get live-time results of their microbiome. See http://americangut.org/how-it-works/ for more information. The fee is $99 at present and is available to anyone who wants to participate by registering and completing a 7 day food log.

Influencers of the microbiome:

Prebiotics: a nondigestible food ingredient that promotes the growth of beneficial microorganisms in the intestines. This non-digestible ingredient is plant fiber that occurs naturally in foods such as fruits, vegetables, whole grains, and legumes. Fiber is also valuable for its aid in digestion and keeping cholesterol lower as part of a heart healthful diet and for helping people with type 2 diabetes to regulate their blood sugar. You need about 25 to 35 grams of fiber per day and you might only be getting half of that amount if you have a standard Western or American diet that is high in animal products, sugar, and fat.

Probiotics - live, good, bacteria and the products that contain them; researchers do not know if they can influence the microbiome yet according to the American Gut website. Dr James Kenney says we should think of these like tourists - they visit an area but do not change it. Dr. Knight, in his book, Follow Your Gut, says there is nothing wrong with eating a little yogurt but none has been tested in quality studies to see if it has long-term effects on the microbiome.

Alcohol - reduces the numbers and diversity of the microbiome.

Fat - saturated fat, excessive fat, sugar, and meat also tend to lower the diversity and quantity of the microbiome. Researchers made a study of a high, fat, low-carb diet on their own microbiomes and found they were "starving their guts."

Antibiotics - reduce the diversity of the microbiome; consult a doctor before making any medication decisions because some antibiotics are life saving and the microbiome can return to normal after medication.

Exercise and sleep help you promote a diverse and healthful microbiome (Rob Knight, Follow Your Gut)

Fats and sugars, along with meat, refined oils, and animal products also reduce the diversity of the microbiome.

Bottom line: The only sure way to improve and maintain the diversity and health of your microbiome is to increase the amount of plant fiber that you consume from foods like fruits, vegetables, whole grains, legumes, nuts, and seeds, while lowering the amount of added sugar, saturated fat, and alcohol that you consume. You should also increase your physical activity and exercise and get enough sleep. Even though this research is emerging and researchers do not want people to make health decisions based on it, the results so far give everyone one more reason to eat a heart-healthful, high-fiber, plant-based diet and to exercise every day. There is growing evidence that altering the gut microbiota can cure C. difficile infections. It will be fun to watch the research and see if this is the case for the risk of other diseases as well.

For more research:


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