Gut Health and Your Microbiome


More than ever before, health aficionados are focusing on the impact our gut bacteria has on our overall health. There is more evidence coming to light that our microbiomes, or the universe of good and bad bacteria that live inside our bodies, have a huge roll to play in our immune health, digestive health and even some chronic diseases.

The world is full of microorganisms and so are our bodies—bacteria can be found in the skin, mouth, nose, orifices and the gut. Friendly bacteria are vital for proper development of our immune systems, for protecting us against microorganisms that can cause disease, for detoxification, and for the digestion and absorption of food and nutrients.

The bacteria that live in our guts get the most attention in relation to these functions, in part because there are cells in the digestive tract linked to the immune system. There is also growing evidence linking the state of our gut bacteria to chronic illnesses such as colitis, inflammatory bowel disease, autoimmune diseases, inflammatory conditions and even obesity.

Digestion is a simple, yet complex, process. The food we eat gets chewed in the mouth, goes to the stomach where it is ground up, starting the digestive process. The food then goes into the small intestine where it is digested by digestive juices and enzymes from the liver and pancreas. The vitamins, minerals, carbohydrates, protein and fat are absorbed into the blood stream from the small intestine. What is left is fiber and this goes into the large intestine. The fiber is then broken down by friendly bacteria using a process called fermentation.

The ideal situation is to have a favorable balance of healthy bacteria (probiotics) and the fuels that feed them (prebiotics). This balance can get skewed when foods or substances enter the microbiome and kill off good bacteria. This can be caused by disease, yeast, or parasites. It can also be caused by eating foods that are highly processed and full of chemicals and hormones, taking antibiotics, or even habitually using antibacterial soaps. The good news is that the health industry is bursting with products that attempt to restore that balance, from supplements to probiotic-laden foods.



According to the Human Microbiome Project by the National Institutes of Health, there are about 50 billion bacteria that inhabit our bodies. 50 billion. Some are healthy and some are not. The “friendly bacteria” or “good bacteria” help your gut digest food and synthesize vitamins and essential fatty acids. Probiotics that you ingest are live microorganisms (in most cases, bacteria) that are similar to beneficial microorganisms found in the human gut. Probiotics are available mainly in the form of supplements and foods.

Some of the “friendly” bacteria that are being added to our food supply or that are made into supplements include Bifidiobacterium animlis, L. acidophilus, Bifidus, L. Casei Immunitas, Saccharyomyces boulardii. Foods that may contain live probiotics include yogurt, cottage cheese, buttermilk, kefir, soy sauce, miso, tempeh and sauerkraut, and kimchi.

Although the research tying probiotics directly to certain health conditions is still young, some of the examined benefits include:

  • Synthesizing vitamins (particularly the B vitamins)
  • Improving immunity
  • Decreasing allergies
  • Speeding recovery of vaginosis
  • Decreasing risk of developing dental caries
  • Help with lactose intolerance
  • Decreasing risk of colon cancer
  • Decreasing cholesterol
  • Recovery from antibiotic-associated diarrhea
  • Decreasing problems associated with inflammatory bowel disease, ulcerative colitis and irritable bowel syndrome
  • Recovery from helicobacter pylori infections (associated with ulcers)

The benefits of one strain of probiotics may not necessarily apply to others, or even for different preparations of the same species or strain. Scientists are attempting to find which probiotics and which combinations of strains work for which conditions.


Probiotics are not the same as prebiotics—indigestible food ingredients that selectively stimulate the growth and or activity of beneficial microorganisms (probiotics) already in your colon. So the two form a symbiotic relationship, and it is often recommended that they are ingested together if taken as supplements. Prebiotics come from food fiber. Too little fiber could starve the good and necessary bacteria. When we starve our bacteria, they get nutrition from our intestinal lining. Yuck!

Some of the common health benefits associated with prebiotics include decreased cholesterol and triglyceride levels, reduced risk of colon cancer, and relief of constipation. Prebiotics also decrease the pH of the colon and thereby increase mineral absorption and possibly even reduce the survival of some harmful bacteria.

So what can you do to improve your immune system and gut microbiome? Simply eat a healthy diverse diet with lots of fruits and vegetables and fermented products. In order to have adequate dietary fiber, limit processed, low fiber foods. Consider taking a probiotic and prebiotic supplement for specific conditions or after a course of antibiotics, in consultation with a health professional.

Want to know more about how specific prebiotics or probiotics could help you? Email Lea at and see your question answered on our site.

*Resistant starches come from cooked and cooled starches, partially-milled whole grains. Read more here.

DSC01005Lea Basch is a registered dietitian and has been in the nutrition industry for over 30 years, most of which she spent at Longmont United Hospital in Boulder, Colorado, where she was one of the founders of the facility’s nutrition program. Longmont’s Planetree philosophy of caring for the body, mind and spirit of patients is very much in line with Lea’s interest in both traditional and alternative therapies for treating chronic illnesses. Gluten-intolerant herself, Lea now focuses much of her time on the latest research and issues relating to gluten-free diets and other food intolerances. She is a diabetes educator and is a Registered Dietitian with the American Dietetic Association. Lea’s lifelong passion has been combining the science of nutrition with the heart that it takes to change lifelong habits.

Lea received her BS and MS in Nutrition and Dietetics at Florida International University and BA in Education at University of Florida. Ask Lea your nutrition questions at

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