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Modern medicine used to want to eradicate the tiny bugs that live within us. Now we are beginning to understand how important they are in keeping us healthy. That is the role of the microbiome. (NY TIMES magazine, Michael Pollan,  May 19, 2013).

There are 10 bugs for every human cell. More than 99% of our DNA is microbial. This is our second genome.  That is why this is called the microbiome.

The proliferation of the wrong type of bugs in our gut can predispose us to chronic diseases. The use of antibiotics causes a spike in proteobacteria which includes many pathogens such as E. Coli and salmonella.

The resident microbes seem to play a critical role in training and modulating our immune system.

Some researchers feel that the alarming increase in autoimmune diseases is caused by disruption in the relationship between our bodies and our gut flora.

Newborns start off with a sterile gut. The oligosaccharides in mother’s milk nuture Bifidobacterium infantis which makes mother’s milk useable by the newborn. When Bifidobacterium grow, they act to protect us from infection and inflammation.

A probiotic is a population of beneficial microbes introduced into the body to protect us.

Having more diversity of gut flora is better for us. A diverse ecosystem is more resilient. Rural populations have more diversity. American and European guts have high levels of bacteroides and firmicutes and low levels of prevotella. The reason might be the liberal use of antibiotics and lower plant fiber in modern society.

Our gut bacteria play a role in the manufacturing of neurotransmitters including serotonin, enzymes and vitamins (Bs and K) and other essential nutrients including amino acids and short chain fatty acids. This includes a suite of signaling molecules that talk to and influence our immune and metabolic systems.

The gut bacteria regulate our appetite, satiety and digestion with signaling molecules.

Furthermore the gut bacteria are our first line of defence when we confront toxins/infection. Gut bacteria create a new generation every 20 minutes. They can respond quickly to an outside threat. They are very reactive and adaptive. Bacteria can swap genes and pieces of DNA. The microbiota can quickly come up with precisely the right gene needed to fight the threat. This plasticity extends the response of our rigid genome giving us a great resource.

Many processed foods contain emulsifiers which act like detergents. These can damage the gut lining and potentially lead to leakage and inflammation.  The gut lining is large with a surface area which can cover a tennis court.

One of my obese patients had been eating only fast food for about 3 years. I measured his inflammatory index called the CRP. His CRP was very high at 80. Most normal persons have a CRP of 1 or 2.  When he started to eat real food, his CRP fell to about 20.

If the gut wall is damaged, then endotoxins which are the toxic byproducts of certain bacteria can slip into the blood stream causing low grade inflammation.  Metabolic syndrome and chronic diseases  have been linked to it.

One of the keys to health is fermentation in the lower gut or colon. The key to fermentation is to give it lots of plants with different types of fiber including resistant starch found in bananas, oats, beans and soluble fiber in onions and other root vegetables and insoluble fiber in whole grains, bran and avocados.  The by product of fermentation is short chain fatty acids that strengthen the gut wall to prevent inflammation.

Al dente pasta is better than soft pasta. Steel cut oats better than rolled oats. Raw or lightly cooked vegetables are better than over cooked vegetables.

With all this information, we can focus on getting healthy by protecting the diversity of good bacteria in our gut.  And lose some weight in the process.