Tending The Microbiome

You who are reading this are not alone. You may think you are an independent organism with free will, but in fact you are a collection of billions of organisms living together: the ‘human’ element that derived from egg and sperm, and the billions of microbes that live inside and all over you. 

Meet the microbiota.

And the ‘human’ you is badly outnumbered. There are ten times as many organisms in you than there are human cells. More importantly there is a hundred times as much microbial genetic material as there is ‘human’ DNA. That genetic material is the microbiome and it has a lot to say about how the whole project works. In other words, the microbiota aren’t just hanging around doing their own thing. They’re involved.

There are two basic areas in which the microbiota are participating in our physiology. Firstly, they’re involved in the digestion and metabolism of food and drugs. They also play a central role in the regulation and ‘education’ of our immune system. The ramifications of this second function are profound and the subject of an explosion of scientific research. We now have the technology to map the genetic material of the gut flora and have found that the microbiome is associated with conditions as diverse as obesity, mood disorders, autoimmune diseases, heart disease, allergy, autism and irritable bowel syndrome.

In the case of autoimmune disease there are many studies showing that intestinal bacteria are related to inflammatory bowel disease such as ulcerative colitis. Probiotics can be as effective as medication for treatment of IBD, but the microbiome’s effect on the immune system goes far beyond the intestines. In multiple sclerosis, for example there are reduced levels of certain organisms, especially those that digest fiber from our diet to create butyrate. Butyrate promotes regulatory T cells that protect against autoimmunity. It has been shown that the animal form of MS is milder in those subjects whose flora is manipulated by antibiotics. It’s possible that the Swank Diet used is MS is helpful because of its effect on the microbiota.

Obesity is another condition strongly associated with the microbiome. In fact the microbiome correlates with obesity much better than the human genome does. Experiments have shown that ‘transplanting’ flora from obese mice into lean mice causes weight gain and the opposite effect also occurs, even if the ‘donor’ is a lean human. It has even been hypothesized that gastric bypass or other surgical procedures for obesity might work by virtue of the effect on gut flora. Insulin resistance can be improved experimentally with fecal transplant as well.

The gut/brain connection is so pronounced that the GI tract has been called the second brain: The microbiota activate nerve cells in the intestine and produce neuro-active components such as GABA and histamine. Consuming yogurt has been shown by functional MRI to reduce anxiety responses, and bifidobacteria worked better than Lexapro in reducing anxiety behavior in mice. 

It’s obvious that these fellow travelers have an enormous impact on our health and function. Although the time may come when we can use designer probiotics or microbiome manipulation to treat a variety of conditions, we’re presently limited in our tools to cultivate the microbiota. 

It’s becoming clear that diversity of the flora seems to be most desirable. Decreased diversity is associated with insulin resistance, elevated lipids, inflammation, colitis and more severe MS. The Hadza tribes of Tanzania, a classic hunter-gatherer people have much more diversity of their  microbiota and much less autoimmune/inflammatory conditions.

So how do we tap into some of the beneficial effects of a healthy microbiota? We should start before we’re born. Our mothers should avoid antibiotics and employ a diet (described below) to foster healthy gut flora. In addition to its many other benefits, breast feeding has been shown to increase microbiota diversity. Antibiotics should be avoided if at all possible, especially during the first year of life. Studies show that antibiotics given to pre-term babies cause a loss of diversity and white blood cell dysfunction.

Our microbiota reaches maximal diversity by adolescence, so the childhood years are the best time to promote healthy flora. Besides antibiotics in prescriptions, there are also antibiotics in our food supply which should be avoided. The diet should be high in fiber and non-digestible carbohydrates such as cellulose and fiber from fruits, vegetables and wheat bran which are converted to short chain fatty acids that feed our microbiota. Fermented foods such as Kefir, yogurt, kimchi and sauerkraut may also enhance gut flora. Prebiotics found in artichoke, onions, garlic and tomato are foods preferred by the intestinal bacteria. 

The use of commercial probiotics is widespread but the science is still in its infancy. It is generally believed that probiotics are more effective in children. Using probiotics in infants has been shown to reduce the risk of eczema and asthma up to five years later. Probiotic agents have been effective in adults with bowel problems, but these preparations are not well targeted yet. Probiotic preparations may not make big changes in adult microbiota, but they may be beneficial by their effect on cell signaling and gene expression.

What also show promise is the use of fecal transplants. As noted above, there are many studies of health benefits ‘transferred’ to recipients of these transplants. While the medical establishment is evaluating this process an underground do-it-yourself phenomenon has developed. 

One thing seems clear: managing the microbiome will be a big part of the future of medicine. In the meantime it’s good to remember that if you take care of your ‘friends’ they will take care of you.