The Microbiome Revolution

Hello and welcome to Nutrition Facts – the podcast that brings you the latest in evidence-based nutrition research.  I’m your host, Dr. Michael Greger.

I know that facts have been in the news a lot lately, both real and fake.  The concept of alternative facts is nothing new in the field of nutrition, though, where powerful commercial interests have tried to not only keep people in the dark, but actively try to confuse them.  That’s why I stick to the science:  What’s the best available balance of evidence published in peer-reviewed medical journals right now?    That’s why I wrote my New York Times best-selling book, “How Not to Die”, why I created my nonprofit site NutritionFacts.org and, now, this podcast.

Today we discuss the microbiome revolution.  No, it’s not a political movement or a board game, it’s the under appreciated role our healthy gut bacteria play in nutrition and health.  Here’s the story.

Recently, 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 thanks to two revolutions in biology.  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?  Ah, 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 these symbiotic relationships with microorganisms and, in us, our gut flora can be considered like a forgotten organ.  Health-promoting effects of good bacteria include boosting our immune system, improving digestion and absorption, they make vitamins, inhibit the growth of potential pathogens, and keep 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 it may be the lousy diet in nursing homes that’s causing the 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 on the bacteria in our colon and that diet-driven changes in it occur within days to weeks; change our diet, change our gut flora. 

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 a point 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 complex with bile and feed a 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.

There appear to be just two types of people in the world and, no, I’m not talking about introverts and extraverts, I’m talking about those who have mostly Bacteroides-type bacteria in their gut, and those whose colons are overwhelmingly home to the Prevotella species instead.  Here’s what that means.

The human gut has a diverse collection of microorganisms making up some thousand species, with each individual presenting with their own unique collection.  But it wasn’t known whether this variation is on a continuum or if people cluster into specific classifiable types, until this famous study analyzed the gut flora of people across multiple countries and continents and identified three so-called enterotypes.  

There were people who had lots of Bacteroides in their gut, people who had a predominance of Prevotella species, and people whose stool, instead, grew out a lot of Runinococcus species.  Pretty amazing that with so many hundreds of types of bacteria that people would settle into just one of three categories.  But, they figure our guts are like ecosystems.  Just like there’s lots of different species of animals on the planet, they aren’t randomly distributed.  I mean, you don’t find dolphins in the desert.  In the desert, you find desert species.  In the jungle, you find jungle species, because each ecosystem has different selective pressures, like rainfall or temperature.  Well, this early research suggests there are three types of colon ecosystems.  You can split humanity up into three types:  People whose guts grow out lots of Bacteroides-type bacteria, those whose guts are better homes for Prevotella group bacteria, and those that foster the growth of Ruminococcus.

And if you think it’s amazing they were able to boil it down to fit everyone into just one of three groups, subsequent research on a much larger sample of people was able to fold Ruminococcus into Bacteroides, so now everyone fits into just one of two groups.  So, now we know, when it comes to gut flora, there are just two types of people in the world–those that grow out mostly Bacteroides and those that overwhelmingly are home to Prevotella species.  The question is why?  It didn’t seem to matter where you live, male or female, how old or skinny you are, what matters is what you eat.  

This is what’s called a heat map.  Each column is a different grouping of bacteria and each row is a food component.  Red is like hot, meaning a close correlation between the presence of this particular bacteria and lots of that particular nutrient in the diet.  Blue is like cold, meaning you’re way off, a reverse correlation, meaning lots of that nutrient is correlated with very low levels of that bacteria in our gut.  They looked at over a 100 different food components and a theme started to arise.  This column is Bacteroides and this column is Prevotella.  Note how they’re kind of opposites.  When it comes to things like animal fat, cholesterol, animal protein, Bacteroides is red and Prevotella is blue and when it comes to plant components, like carbohydrates, Prevotella is red and Bacteroides is blue.

Here’s a simplified version, clearly showing the components found more in animal foods, like protein and fat, are associated with the Bacteroides enterotpye and those found almost exclusively in plant foods are associated with Prevotella.  So, no surprise African Americans fell into the Bacteroides enterotype, where most of the native Africans were Prevotella.  The reason this may matter is that Bacteroides species are generally associated with increased risk of colon cancer–our second leading cause of cancer death–yet almost unheard of among native Africans.  The differences in our gut flora may help explain why Americans appear to have more than 50 times the rate of colon cancer.

Inadequate consumption of prebiotics—the fiber and resistant starch concentrated in unprocessed plant foods—can cause a disease-promoting imbalance in our gut microbiome.  Here are the details.

For many years, it was believed that the main function of the large intestine was to just absorb water and dispose of waste but, nowadays, it is clear that the complex microbial ecosystem in our intestines should be considered as a separate organ within the body and that organ runs on a MAC (microbiota-accessible carbohydrates). In other words, primarily fiber.

One reason we can get an increase of nearly two grams of stool for every one gram of fiber is that the fiber fermentation process in our colon promotes bacterial growth.  The bulk of our stool, by weight, is pure bacteria, trillions and trillions of bacteria, and that was on a wimpy, fiber-deficient British diet.  People who take fiber supplements know this:  A few spoonfuls of fiber can lead to a massive bowel movement, because fiber is what our good gut bacteria thrive on.  When we eat a whole plant food, like fruit, we’re telling our gut flora to be fruitful and multiply and, from fiber, our gut flora produce short-chain fatty acids, which are an important energy source for the cells lining our colon.  So, we feed our flora with fiber and then they turn around and feed us right back.  These short-chain fatty acids also function to suppress inflammation and cancer.

That’s why eating fiber may be so good for us.  But when we don’t eat enough whole plant foods, we are, in effect, starving our microbial self.  

On traditional plant-based diets, like Dr. Burkitt described, lots of fiber, lots of short-chain fatty acids, lots of protection from Western diseases, like colon cancer, whereas on like a standard American diet, where we’re eating highly processed food, there’s nothing left over for our gut flora; it’s all absorbed in the small intestine before it ever makes it down to the colon.  Not only may this mean loss of beneficial microbial metabolites, but also a loss in the beneficial microbes themselves.

The biggest issue presented by a Western diet is that not leaving anything for our bacteria to eat results in dysbiosis, an imbalance where bad bacteria can take over and increase our susceptibility to inflammatory diseases or colon cancer, or maybe even metabolic syndrome, or type 2 diabetes, or cardiovascular disease. 

It’s like when astronauts return from space flights, having lost most of their good bacteria because they had no access to real food.  Well, too many of us are leading an astronaut-type lifestyle, not eating fresh fruits and vegetables.  For example, the astronauts lost nearly 100% of their Lactobacillus plantarum, which is one of the good guys, but most Americans don’t have any to begin with, though those that eat more plant-based are, certainly, doing better.

Use it or lose it.  If you feed people resistant starch, a type of fiber found in beans, within days, the bacteria that eat resistant starch shoot up, and then die back off when you stop eating it.  Eating just a half can of chickpeas every day may modulate the intestinal microbial composition to promote intestinal health, by increasing potentially good bacteria and decreasing pathogenic and putrefactive bacteria.  

Unfortunately, most Americans don’t eat beans every day, or whole grains, or enough fruits and vegetables.  So, the gut flora, the gut microbiota, of a seemingly healthy person, may not be the equivalent to a healthy gut flora.  I mean, it’s possible that the Western microbiota is actually dysbiotic in the first place, just because we’re eating such fiber-deficient diets compared to populations that may eat five times more fiber and end up with like 50 times less colon cancer.

To see any graphs, charts, graphics, images, or studies mentioned here, please go to the Nutrition Facts podcast landing page.  There, you’ll find all the detailed information you need plus links to all the sources we cite for each of these topics.

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Thanks for listening to Nutrition Facts.  I’m Dr. Michael Greger.