Microbiome: The Inside Story

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The microbiome revolution in medicine is beginning to uncover the underappreciated role our healthy gut bacteria play in nutrition and health.

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Recently, thanks to two revolutions in biology, it has become apparent that our DNA does not tell the whole story of our individuality, and other factors, environmental factors, play an important role in human health and disease.  First, there was epigenetics, where diet and lifestyle changes have been shown to turn genes on and off. And the second, our unfolding understanding of our microbiome, how changes in our gut flora appear to impact greatly on human biology.

Until relatively recently, the colon was viewed as a retention tank for waste, and water absorption was its big biological function. The problem was it was hard to get in there, and we weren’t able to grow most of the bugs in a lab. As many as 99% of all microbes fail to grow under standard laboratory conditions, and so, how do you study something you can’t study? But, now we have fancy genetic techniques.

It took 13 years to sequence the DNA of the first bacteria ever. These days, the same feat might only take two hours. And, what we learned is that we can each be thought of as a superorganism, a kind of human-microbe hybrid. We have trillions of bacteria living inside us. One commentator went as far as to say, we are all bacteria, a provocative way of acknowledging that there are more bacterial cells and genes in our own body than there are human cells and genes, and most of those bacteria live in our gut.

All animals and plants appear to establish symbiotic relationships with microorganisms, and, in us, our gut flora can be considered like a forgotten organ. Health-promoting effects of our good bacteria include boosting our immune system, improving digestion and absorption, making vitamins, inhibiting the growth of potential pathogens, and keeping us from feeling bloated, but should bad bacteria take roost, they can produce carcinogens, putrefy protein in our gut, produce toxins, mess up our bowel function, and cause infections.

Researchers are still in the process of figuring out which bacteria are which. There are more than a thousand different types of bacteria that take up residence in the human colon. Just to give you a sense of the complexity, let me show you a diagram from a typical study of gut flora. This happens to be the largest such study done on the elderly, showing the frailest older folks tend to harbor similar bugs, suggesting further that it may be the lousy diet in nursing homes that’s causing this shift, which may play a role in ill health as we grow older, as you can clearly see in figure 4. I mean, duh. Thankfully, not all microbiome diagrams are that complex.

Based on studying what comes out of twins, those that eat different habitual diets, and stools from around the world, it has become evident that diet has a dominant role in the bacteria in our colon and that diet-driven changes can occur within days to weeks.

The hope of impacting health through diet may be one of the oldest concepts in medicine; however, only in recent years has our understanding of human physiology grown to the point where we can begin to understand how individual dietary components affect specific illnesses through our gut bacteria. Milk fat on that piece of pizza, for example, may compete with bile and feed bacteria that produce the rotten egg gas hydrogen sulfide, and has experimentally been associated with colitis (inflammatory bowel disease). Fiber, on the other hand, feeds our good bacteria and decreases inflammation in the colon. Choline, found in eggs, seafood, and poultry, as well carnitine, in red meat, can be turned into trimethylamine oxide and contribute to heart disease and perhaps fatty liver disease, and excess iron may muck with our good bacteria and contribute to inflammation as well.

The good news is that specific dietary interventions offer exciting potential for nontoxic, physiologic ways to alter gut microbiology and metabolism to benefit the natural course of many intestinal and systemic disorders.

To see any graphs, charts, graphics, images, and quotes to which Dr. Greger may be referring, watch the above video. This is just an approximation of the audio contributed by Katie Schloer.

Please consider volunteering to help out on the site.

Recently, thanks to two revolutions in biology, it has become apparent that our DNA does not tell the whole story of our individuality, and other factors, environmental factors, play an important role in human health and disease.  First, there was epigenetics, where diet and lifestyle changes have been shown to turn genes on and off. And the second, our unfolding understanding of our microbiome, how changes in our gut flora appear to impact greatly on human biology.

Until relatively recently, the colon was viewed as a retention tank for waste, and water absorption was its big biological function. The problem was it was hard to get in there, and we weren’t able to grow most of the bugs in a lab. As many as 99% of all microbes fail to grow under standard laboratory conditions, and so, how do you study something you can’t study? But, now we have fancy genetic techniques.

It took 13 years to sequence the DNA of the first bacteria ever. These days, the same feat might only take two hours. And, what we learned is that we can each be thought of as a superorganism, a kind of human-microbe hybrid. We have trillions of bacteria living inside us. One commentator went as far as to say, we are all bacteria, a provocative way of acknowledging that there are more bacterial cells and genes in our own body than there are human cells and genes, and most of those bacteria live in our gut.

All animals and plants appear to establish symbiotic relationships with microorganisms, and, in us, our gut flora can be considered like a forgotten organ. Health-promoting effects of our good bacteria include boosting our immune system, improving digestion and absorption, making vitamins, inhibiting the growth of potential pathogens, and keeping us from feeling bloated, but should bad bacteria take roost, they can produce carcinogens, putrefy protein in our gut, produce toxins, mess up our bowel function, and cause infections.

Researchers are still in the process of figuring out which bacteria are which. There are more than a thousand different types of bacteria that take up residence in the human colon. Just to give you a sense of the complexity, let me show you a diagram from a typical study of gut flora. This happens to be the largest such study done on the elderly, showing the frailest older folks tend to harbor similar bugs, suggesting further that it may be the lousy diet in nursing homes that’s causing this shift, which may play a role in ill health as we grow older, as you can clearly see in figure 4. I mean, duh. Thankfully, not all microbiome diagrams are that complex.

Based on studying what comes out of twins, those that eat different habitual diets, and stools from around the world, it has become evident that diet has a dominant role in the bacteria in our colon and that diet-driven changes can occur within days to weeks.

The hope of impacting health through diet may be one of the oldest concepts in medicine; however, only in recent years has our understanding of human physiology grown to the point where we can begin to understand how individual dietary components affect specific illnesses through our gut bacteria. Milk fat on that piece of pizza, for example, may compete with bile and feed bacteria that produce the rotten egg gas hydrogen sulfide, and has experimentally been associated with colitis (inflammatory bowel disease). Fiber, on the other hand, feeds our good bacteria and decreases inflammation in the colon. Choline, found in eggs, seafood, and poultry, as well carnitine, in red meat, can be turned into trimethylamine oxide and contribute to heart disease and perhaps fatty liver disease, and excess iron may muck with our good bacteria and contribute to inflammation as well.

The good news is that specific dietary interventions offer exciting potential for nontoxic, physiologic ways to alter gut microbiology and metabolism to benefit the natural course of many intestinal and systemic disorders.

To see any graphs, charts, graphics, images, and quotes to which Dr. Greger may be referring, watch the above video. This is just an approximation of the audio contributed by Katie Schloer.

Please consider volunteering to help out on the site.

Doctor's Note

This is the first of a long series of in-depth videos on the microbiome, though I have touched on friendly flora before:

How does the body maintain the right balance of bacteria? Check out the following video— Prebiotics: Tending Our Inner Garden—you’ll be amazed (I know I was!)

I regularly add new videos on this topic. See them all on the microbiome topic page.

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