Cracking the Gut Microbial Code: Are We There Yet?

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“In the future, when you walk into a doctor’s surgery or hospital, you could be asked not just about your allergies and blood group, but also about your gut type.” This is a quote from ScienceDaily (Apr. 21, 2011) referring to a recent article in Nature Magazine. The study, published in Nature, also uncovers microbial genetic markers that are related to traits like age, gender and body-mass index. These bacterial genes could one day be used to help diagnose and predict outcomes for diseases like colorectal cancer, while information about a person’s gut type could help inform treatment.  Researchers found that the combination of microbes in the human intestine isn’t random, and that human gut flora can settle into three different types of communities or ecosystems.

I would call this important work just “a start,” and would like to present some basic molecular biology to indicate the magnitude of the problem of trying to classify bacterial communities.   We now know we have over 1000 species of bacteria in our intestinal tracts, all of whom have their own thousands of genes as well as their own epigenetic codes regulating their genes.

Here’s a primer on the epigenetic code: The epigenetic code (or epigenome) is in part a group of enzymes and methyl groups that attach to, and act on, genes. This ongoing active process allows some genes to be expressed, and other genes to be silenced.

The epigenome responds to most every stimulus coming to the gut bacterial cell’s surface receptors, ranging from food (which can be beneficial or harmful), good or poor hydration, eustress (good stress) or distress; other stimuli include competing or complementary bacteria, viruses and fungi which can team together in biofilms (like a microbial city) in the gut lumen. Other major factors which could affect epigenomic actions are the hormones, growth factors, vitamins, immune factors, and  cytokines which continuously send signals into the bacterial cells to affect epigenetic expression. The resultant expression of genes will then direct the bacterial cells to do what they were meant to do: namely, live in a harmonious symbiotic relationship with us, the host, or remain in a state of alert, which may cause them to stop aiding the host, and become more parasitic in nature.

The above mentioned article did not in their paper find a significant connection between diet and gut bacterial balance.  However, there are many studies that do.  I found one as recently as May 2011.  Here is the summary of the article: “After 4 weeks, weight-loss diets that were high in protein but reduced in total carbohydrates and fiber resulted in a significant decrease in fecal cancer-protective metabolites and increased concentrations of hazardous metabolites. Long-term adherence to such diets may increase risk of colonic disease.”1

The article points out that a low fiber, high protein diet causes biochemical changes to occur on a bacterial level.  First, without adequate amounts of soluble fiber the beneficial gut bacteria cannot produce short chain fatty acids (SCFAs), especially butyrate, which is the choice food of the colonic lining epithelial cells, and a preventer of damaged colonic cells from becoming cancerous.  In addition, the action of the gut bacteria on cooked meat creates increased proportions of branched-chain fatty acids, and concentrations of phenylacetic acid and N-nitroso compounds, which can lead eventually to inflammation and cancer of the colon.

The source of bacterial production of both beneficial SCFAs as well as harmful chemicals comes from epigenetic and genetic changes which lead to the production of these chemicals. I believe we are proving daily that lifestyle changes including: a healthy, 80 percent plant-based diet, good hydration, sleep, exercise, elimination, and stress reduction all help to program our bacterial biomass as much as it does our bodies. Remember there are about 100 trillion bacteria and we have only about 10 trillion cells so we are outnumbered at least 10 to 1 in terms of genes and metabolic activity, so we need to take care of our “guests” as well as ourselves! Just as important as what bacteria are in our guts, is what else passes through and affects our guts. We must be able to step back and look at the entire picture, rather than simplifying it to “three gut types.”

  1. W.R. Russell, et al., “High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health.” Am J Clin Nutr. 2011 May;93(5):1062-72. Epub 2011 Mar 9.