As our Microbiome digests the dietary fiber and other material that cannot be digested in our stomach and small intestine it produces a variety of by-products. The most important of these are short-chain fatty acids, complex carbohydrates and lysine. The short-chain fatty acids that are produced migrate through the mucous membrane that lines the gut wall and become the base materials for a variety of compounds that affect the function of every organ in our bodies, including the brain. These short chain fatty acids have also been shown to interact with the T cells that are the “soldiers” of our immune system. In ways that are not yet fully understood, this interaction seems to inform the immune system about which gut products are harmful and which are benign.
A healthy microbiome is a necessary ally in keeping our bodies and minds healthy and functioning properly. However, an unhealthy microbiome can be the source of serious health problems. Just what problems develop and how they affect us depends on how and why the microbiome is stressed.
The most common and widespread problem involves malnourished gut bacteria due to the general drift of western diets to refined and manufactured foods. These foods typically contain far more sugars, simple carbohydrates and complex fats than traditional foods. They also provide us with very little of the dietary fiber that nourish our gut bacteria. Too little fiber results in a stressed microbiome that produces fewer short chain fatty acids than we need to maintain good health and it also results in harmful changes in the make-up of our microbiome. The number of “good” bacteria that specialize in breaking different complex fibers drops sharply and are replaced by “bad” bacteria that produce toxic by-products and/or feed on the carbohydrates in the lining of our gut wall. Also, the reduced production of short chain fatty acids deprives our bodies and immune system of critical compounds and enzymes that contribute to the functioning and modulation of every organ in our body. Depending on how seriously our microbiome is stressed by our low fiber diet the health impacts can range from discomfort to death.
Our dietary assault on our microbiome has been seriously compounded by our over use of broad spectrum antibiotics. While these drugs can can offer life saving relief when a harmful bacteria has gained the upper hand, they have become the drug of choice for even inconvenient ailments and are routinely prescribed even for viral ailments just to assure that no bacteria can complicate the situation. There is now a fairly widespread recognition that the over use of antibiotics has spawned a new generation of “super bugs” that have evolved a resistance to most antibiotics. The less well recognized result of the over use of antibiotics is the serious depletion of gut bacteria. Broad spectrum antibiotics are just what their name says – they are designed to kill all microbes. A five day course of antibiotics can kill as much as ⅓ of our gut microbes and may completely wipe out species that are critical to our ability to digest certain types of dietary fiber. The disruption caused by antibiotics – particularly extended or repeated treatments – can lead to a condition called dysbiosis where the “good” bacteria that prefer to feed on dietary fiber and normally dominate the microbiome are overwhelmed by “bad” bacteria that feed on the carbohydrates in the gut wall. Dysbiosis can happen to anyone that goes through repeated or extended treatment with antibiotics but those of us that already have microbiomes stressed by inadequate fiber in our diets are particularly at risk.
While the primary cause of Dysbiosis is the repeated or extended use of antibiotics, it can also result from an attack of a hostile bacteria in a microbiome that is too weak to fight it off. However it occurs, dysbiosis leads to lots of problems. The attack on the gut lining generally leads to a variety on issues related to the inflammation of the gut wall. As the gut wall thins a condition called “Leaky Gut” begins to allow bacteria and toxins to move from the gut and into the blood stream where they are recognized by the immune system as hostile agents and attacked. Because short chain fatty acids and other helpful compounds are caught in this contaminated flow they can also be tagged as hostile agents and attacked. The result is a heightened state of inflammation in the body and the all too frequent episodes of “auto-immune” diseases where our immune system pursues desirable compounds into healthy organs and tries to destroy them.
The bottom line is that we need to both feed and protect our microbiome. I believe that the best first step is to make sure that our daily diet includes 25-35 grams of dietary fiber. That means eating plenty of vegetables, whole grains, nuts and legumes. Bran cereals and muffins in the morning and psyllium can be helpful supplements if you are having trouble hitting the target every day with whole foods alone. The second step is to avoid antibiotics unless they are absolutely necessary to deal with a serious health problem. In today’s world that means asking your doctor to confirm the urgency and efficacy of a course of antibiotics with a culture before you start killing helpful gut bacteria. It also means avoiding meat, fish and poultry that have been raised on antibiotics. We know that these protein sources carry their residual antibiotic load into our systems where they damage our microbiome and encourage the development of antibiotic resistant bacteria.