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We Are More a Product of Our Microbiome and Food than of Our Genes

By Dr. Berkson

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Many diets claim to give you the best results for gut and overall health. But figuring out what’s best to eat for your own life and gut, is not always easy. Until now.

Two different studies out of the University of Sydney and the University of Wisconsin at Madison have found the “ exact best foods” that are “good” or “bad” for your microbiome. Your microbiome is the several pounds of bacteria, fungi and viruses that live inside your gut. They live inside you and in return help protect your health. But only if you feed them appropriately.

The microbiome is turning out to be a major influential player in diverse aspects of health, from gut health, to lung health, to mood, cognition, autoimmune diseases, heart health, and even winning or losing the battle of obesity.

Now hot off the press, the microbiome is also turning out to be the middleman between your food choices and how your genes turn on and off to try to keep you well.

The food-microbiome link. Australian researchers are showing what you eat shapes your microbiome, or another way to say it, your food eco-system. Healthy menu choices (which we will discuss in a moment) encourage, while unhealthy dietary choices discourage, “cooperation” between yourself, your gut bacteria (your microbiome), and of all things, your genes.

When you eat in a way that doesn’t inspire cooperation, your gut bug bacteria can then go rogue. They can send out unhealthy signals. Mayhem, even genetic misfortune, can follow.

Carbs vs. Protein

These Australian researchers served 25 different diets composed of various amounts of protein, carbohydrates, and fat to 858 mice. These diets mimicked the ways that diverse human cultures consume foods. They then observed how each diet affected the health of the microbiomes.

A healthy microbiome is diverse. It has a large number of microbes and these vast numbers of bacteria, fungi and viruses, send healthy dialogues to the gut as well as to far reaching tissues. An unhealthy microbiome is monotone. It lacks diversity. It sends out less healthy signals. So these scientists looked to see which foods made more diverse and healthier signaling microbiomes.

Of all the foods served, two-microbiome response patterns emerged revealed the two most powerful dietary factors.

• A diet higher in simple carbs created less diverse and less healthy microbiome terrains.
• A diet higher in protein (which supplies nitrogen) in comparison to the amount of simple carbs, created more diverse and healthier microbiome terrains.

The scientists found that by varying the amount of protein or sugars in food, they could increase or decrease the amount and diversity of gut microbes. It happened due to the presence of nitrogen.

Nitrogen drives your microbiome. Carbohydrates contain no nitrogen. Proteins do. The researchers found that the protein to carbohydrate ratio vigorously affected bacterial community response to the animal’s diet.

The more carbs consumed, the less diverse the microbiome. The less the nitrogen could healthfully influence it. This means the more breads, cakes, cookies, sugar, candy bars, and sugary sodas you consume, the less diverse and the less healthy your microbiome, no matter how much protein you eat. With excess sugars, the microbiome becomes less cooperative and less health promoting.

The healthier proteins you eat, along with less refined sugars, the more diverse your microbiome. This then sends healthier messages to your immune system, your brain, and to your genes.

Food is Powerful

Your microbial ecosystem inside your intestinal terrain is fundamentally shaped by what you put into your mouth.

A healthier microbiome has a craving for nitrogen. This comes from protein-based foods, like seeds, nuts, eggs, fish, beans, and meat (in the Wisconsin research, less meat was better than too much meat). Nitrogen feeds healthier gut bacteria more than simple carbohydrate type foods do.

When we have a healthy ratio of protein (was well as plant food and fiber) in ratio to carbs, our microbiome does amazing things. One of them is to turn our genes on and off in protective ways.

Microbiome and Epigenome

The University of Wisconsin at Madison wanted to see how diet affects the far-reaching influence of the microbiome, especially its influence on our genes. Genes are the basic signals of life. They are the library of information you inherited from your mom and dad. And that your parents inherited from their moms and dads.

The mice in this study were given two diets. One was a healthy plant-based diet and the other was a typical Westernized diet high in carbs and simple sugars and also high in unhealthy fats.

The Wisconsin scientists also tested how these two types of diets affected the microbiome and its influence on our genes. The healthy plant diet created beautifully complex microbiomes that favored healthy communication with the mice’s immune systems, and also with genes all throughout their bodies. Fiber and plant material helped the microbiome make short-chain fatty acids that sent healthy messages to the rodent gut walls, and also sent healthy messages to genes in tissues far and wide.

In contrast, the microbiota of the animals that were fed a typical Westernized junk food diet had less diverse microbiomes. These microbes sent unhealthy signals to local gut cells and to genes throughout the body. Why would this be? The template for a healthy human microbiome was set in the distant past, when food from plants made up a larger portion of the diet. And there was not as much meat or any processed foods. Or the meat that was available was much leaner and not as high in saturated fat or toxic chemicals.

Your gut longs for healthy proteins from plants, such as seeds, nuts, and legumes. Or from milks made from these seeds and nuts. Or from fish and eggs. But only so much from meat. Certainly your gut does not long for sugar, pretzels, popcorn, or croissants. Or meat filled with antibiotics, hormones, chemicals and fear. Many animals are so mistreated from commercial processes of raising and slaughtering meat; one has to wonder what effect that also has on the microbiome.

The Wisconsin research highlighted that the gut microbiome sends signals to genes. And that what you eat affects whether these are good or bad signals. But it was exciting to understand that the microbiome is the go between from your plate to your genes. This means that your gut health is a mediator of your genetic expression. You are not just a victim of your genes, good or bad. How you eat affects your microbiome, which then can create what is called epigenetic change to make your genes work more FOR you rather than AGAINST you.


Surrounding your genes are hovering proteins. For example, some are called histones. These encircle your DNA. They have strong influence. They can actually morph how your DNA signals. This is called epigenetics. When not your genes, but proteins surrounding your genes, affect the way your genes turn on and off.

Your epigenome is a vast number of chemicals that can influence, for good or bad, your genes ability to signal your cells to tell them what to do to keep you well. With this new understanding, we see that gut bugs co-create your epigenome. In this way, gut bugs co-create your genetic expression. And they do this for good or for bad, depending on how you eat, for good or for bad.

Your microbiome, based on what you choose to eat, releases chemical information that travels from your gut throughout your body, regulating genes, turning their switches off or on, making genes active or inactive.

• Diet drives gut bugs.
• Gut bugs drive genetic expression.
• That’s why food is your best medicine.
• Or if you make bad food choices, it becomes your worst.

Your microbiome lives out loud. It talks or “dialogues” to cells in your colon, cells in your liver, in fatty tissue far removed from the gut (like your brain), in the skin that surrounds all cells (cell membranes), and also with your very amazing genes.

All these conversations are based on what you choose to eat. You make about 200 food decisions a day. These all affect your gut bugs that then affect your gene expression. This “screams” at you to make smarter choices at each “fork in your food road”. Your genes and health will be glad you did.


Andrew J. Holmes, Yi Vee Chew, Feyza Colakoglu, John B. Cliff, Eline Klaassens, Mark N. Read, Samantha M. Solon-Biet, Aisling C. McMahon, Victoria C. Cogger, Kari Ruohonen, David Raubenheimer, David G. Le Couteur, Stephen J. Simpson. Diet-Microbiome Interactions in Health Are Controlled by Intestinal Nitrogen Source Constraints. Cell Metabolism, 2016.

Kimberly A. Krautkramer et al. Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues. Molecular Cell, November 2016.

Dr. Devaki Lindsey Berkson MA, DC, DACBN, CNS, ACN
“Complexity is my specialty”

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