What is the Microbiome?
About 100 trillion bacteria live in our gastrointestinal tract. Our own DNA has about 23 thousand genes, but the bacteria that live in us have over 3 million genes. These genes produce thousands of chemicals and many of these are necessary for our health and well being. Below is a diagram from an article in the British Medical Journal. It shows the microbiome in health and disease with some representative inputs and outputs. I will talk about many of these things in more detail later in this post, but this diagram gives a good overview. Red arrows are bad and blue arrows are good. Here is a link to the BMJ article: Role of the gut microbiota in nutrition and health.
A healthy microbiome promotes a healthy gut lining, decreases inflammation, makes us less likely to gain too much fat, improves our lipid levels, improves our mental sharpness, makes us less likely to get diabetes, less likely to have chronic pain and less likely to get certain cancers. These bacteria are definitely our friends!
What constitutes a healthy microbiome?
There is a lot we don’t know yet about how to characterize a healthy microbiome, but we have learned a few things. Diversity of the microbiome is good. The more different kinds of bacteria, the better. We also know that certain types of bacteria promote health. The bacterium F. prausnitzii is present in the gut of all healthy humans and may be a marker for a healthy microbiome. There are too many other bacteria to list individually, but the large classes (called phyla) include Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Each of these phyla contain hundreds of individual species.
What happens when the microbiome is not healthy?
An unhealthy microbiome is called dysbiosis. Dysbiosis is caused by lack of diversity in the microbiome, or the growth of bacterial species that cause harm instead of health. Dysbiosis can be caused by antibiotics, eating too much meat, eating too much fat, eating too much sugar, especially high fructose corn syrup, and not eating enough fiber. An especially severe dysbiosis is caused by PPI medicines, which include things like Prilosec, Nexium and Prevacid. Artificial sweeteners have also been shown to disrupt the microbiome. Emulsifiers, found in many processed foods also cause dysbiosis.
Dysbiosis leads to chronic inflammation and illnesses, including irritable bowel syndrome, chronic constipation, obesity, diabetes, high lipid values and heart disease. Dybiosis is also associated with cognitive decline and there is some evidence that dysbiosis is associated with the development of alzheimer’s disease.
How to maintain or restore a healthy microbiome
Prebiotics
Prebiotics are foods that are incompletely digested in the small bowel and provide food for healthy gut bacteria. Prebiotics are mostly foods with soluble fiber, especially one called inulin. Chicory root has the highest inulin content. It may be a little hard to find but often is added to food supplements. New Orleans style coffee has chicory added and is available in many grocery stores. Other foods that are high in inulin include jerusalem artichokes, dandelion greens (don’t pick them near roads or highways), leeks, onions, garlic, and asparagus. Other foods that promote the growth of good bacteria are bananas, barley, oats, apples and jicama root.
Probiotics
Probiotics are cultures of good gut bacteria that are taken orally. Because stomach acid kills most bacteria, probiotics are enclosed in capsules or micro capsules that resist dissolving in stomach acid and don’t dissolve until they reach the small intestine. It is best to take them on an empty stomach, because then they don’t hang around in the stomach as long. There are several different combinations of bacteria in probiotics. In general, preparations that have multiple types of bacteria are better than single bacterial probiotics. The best thing to do is ask the pharmacist which ones he/she recommends.
It is a good idea to take probiotics after a course of antibiotics. They also can help with irritable bowel syndrome and chronic constipation. They may boost the immune system and decrease the risk of infection.
Probiotics do not permanently colonize the gut. They are only helpful while you are taking them. Prebiotic foods, on the other hand promote long term positive changes in the microbiome.
Bottom Line
The bacteria that live in us, our microbiome, have far ranging effects on our health. The microbiome has effects on the immune system, the central nervous system and the intestinal tract. A healthy microbiome is associated with good health and protection against multiple diseases.
We can maintain a healthy microbiome by eating high fiber, unprocessed foods, particularly those high in inulin and avoiding sugar, high fructose corn syrup, and processed foods. Meat consumption as well as fat consumption should also be limited.
Dysbiosis can be caused by antibiotics, PPI’s, processed food emulsifiers, artificial sweeteners, high sugar and/or fructose intake, and high meat protein intake. Dysbiosis can lead to irritable bowel syndrome, chronic constipation and inflammatory bowel disease. It may also lead to chronic pain, cognitive decline and heart disease.
Dysbiosis improves with probiotics, but they are not a permanent solution. Increasing prebiotic foods helps long term restoration of a healthy microbiome.