How Eating a High Fiber Diet Keeps the Gut Microbiota Happy and Healthy

Feed Your Gut Bacteria or They Will Feed on YOU!

In this article I discuss:

  • How gut health impacts our overall health

  • How gut bacteria plays a role in inflammation and disease

  • How diversity is the key to a healthy gut

  • How fiber and probiotics play a role in gut health

  • How antibiotics affect our gut biome

  • How birth and childhood experiences affect our gut biome

Let’s begin with the idea that your gut is a rainforest.  A rainforest is full of variety, variability, and species population numbers beyond our comprehension.  The rainforest is one of the most diverse and stable ecosystems we know of and houses species we haven’t even discovered yet.  That is exactly how our gut is when it comes to the bacteria living in it.

As Dr. Justin Sonnenburg, Ph.D, an associate professor of microbiology and immunology at Stanford and Dr. Erica Sonnenburg, Ph.D, a senior scientist in the Sonnenburg Labs, discuss with the host of FoundMyFitness, Rhonda Patrick, Ph.D in the  Youtube video ‘How The Gut Microbiota Affects Our Health with Dr. Erica & Dr. Justin Sonnenburg”, there are 10 times more bacterial cells associated with our bodies than human cells and 100 times more bacterial genes associated with our collective genome than human genes.  Meaning? Yep, you guessed it.  We are more microbial than human!  Therefore, this complex and dynamic ecosystem of bacteria that makes up so much of us is connected to every aspect of our biology.    

As we take a dive into the biome of our guts, we see that the gut microbiota is a population of beneficial and symbiotic bacteria, as well as pathogenic microorganisms that literally share our body space.  It is not only a community, it is a microbial organ that is extraordinarily important and is connected to almost every piece and part of our health.  This organ holds the key to the health of our immune systems, metabolism, and, due to the brain-gut axis, can dictate our moods and behavior.

To explain the gut-brain axis (GBA), this is the communication between the gut and the brain.  This communication goes both ways and links the lower gut with the emotional and cognitive centers of the brain through messages sent chemically.  

So, that’s a pretty big deal, which I will explain.

These interactions affect our mental capabilities, our ability to manage and cope with pain, and determine if we will be afflicted with anxiety, depression, and neurodegenerative diseases.    

So where exactly is this rainforest of bacteria harboring in our body?  

Well, most of the bacteria associated with our gut live in the distal part of our large intestine, which means they hang out in the colon.  The interesting thing here is that the gastrointestinal (GI) tract also has the most amounts of immune cells.  

Why is that important?  

Just as the gut microbes interact with the brain in the GBA, the gut bacteria also interacts, a lot, with the immune cells.  Before studying the gut biome we believed that gut bacteria and immune cells didn’t get along, which is pretty easy to see why.  

The job of immune cells is to keep us from getting sick by ridding our bodies of foreign invaders, like bacteria.  

However, when it comes to these little living beings of our guts, the immune cells talk to them all day long.  This constant interaction regulates how our immune system functions.  Since immune cells leave the gut and go all through the body, they naturally affect the whole body’s immune function, including respiratory function, vaccine response, and autoimmune disease manifestation.

That’s not all…

Over the past decade we have learned a great deal more about the gut microbial community of our colon.  In learning the importance and function of the gut biome we have learned that our diet has a huge impact on it. What we choose to eat directly influences this microbial community which in turn has a huge impact on our biology.  

Let me repeat that as it is important.

What we choose to eat directly influences this microbial community which in turn has a huge impact on our biology.  

To put it even more plainly, we have the ability to control our physical health, mental well-being, and even some gene expression through diet, by way of these gut bacteria.  Therefore, we need to feed them, and feed them the right stuff.

How can you actually use this important fact?

Dietary fibers, which are complex carbohydrates, are the essential food for feeding the gut microbiota. Our bodies do not digest complex carbs well, which is a good thing, because it means that this fiber makes it to the colon to feed our gut bacteria.  When the fiber reaches the bacteria, they metabolize it and change it into Short-Chain Fatty Acids (SCFAs) such as butyric acid, propionic acid, acetic acid, and lactic acid. SCFAs are also called Volatile Fatty Acids (VFA) and are produced when dietary fiber is fermented in the colon and primarily absorbed through the portal vein (the vein that goes from the GI tract to the liver) during fat digestion.  

Related: 12 Foods to give up now if you want to stay healthy and strong

And here is your gross out fun fact for the day: these SCFAs are actually the bacterial wastes (aka microbe poop) that we absorb.  

Nice thought huh?

Well to help you deal with that thought here is another.  

We need those SCFAs because they provide signals to regulate our immune function, whether it is to heighten or suppress it.  

For a quick trip down the proverbial rabbit hole, here is some information on our immune system response.  

A component of the immune system is that it suppresses the responses of other cells.  With SCFA signaling we can increase the number of T-regulatory cells (T-cells or Tregs).  The T-cells can suppress cell response.  By doing this it creates a built-in self-check to prevent excessive reactions.  Without this self-check, our bodies would go haywire and continually attack itself.  

Inflammation anyone?  

Yes, inflammation is often the effect of when our bodies are not functioning properly, but why is this important?  

Operating your body in a high inflammatory state can lead to the development of chronic diseases, such as asthma, heart disease, cancer, metabolic syndrome, allergies, and autoimmune disorders.  Plus inflammation drives aging, and I don’t mean the accumulation of wisdom, in fact, it can bring about cognitive decline.

This is especially worrisome in our westernized culture. We often live stressful lives with little physical activity and a diet full of the wrong kind of fats, processed simple carbohydrates and simple sugars.  

Why does it matter that we live and eat this way?  

With western diets loaded with simple carbohydrates, such as highly refined grains and processed/packaged foods, we begin a detrimental process that is harmful to our much-needed gut biome.  Simple sugars are absorbed in the upper GI, so therefore the bacteria, which live all the way down in our colon, are simply starving.  

Without the aforementioned intake and fermentation of dietary fibers, we cannot feed our gut bacteria.

So to sum that part up: No dietary fiber = No SCFAs = inflammation = chronic disease.  

Got it?


Related: Eating high fiber foods can help you stay fit

Ok, so here is the really cool part.  Feel free to wow your friends with this one at your next party.  When gut bacteria are starving, they become aggressive and look for an alternate food source besides the dietary complex carbohydrates (fiber) they should be getting fed, but aren’t.  So with zero fiber coming in, the gut bacteria begin to rely on the mucus layer that lines our large intestines as a food source.  They do this because the mucus has carbs (aka energy) in it.  The mucin in the mucus is largely a glycoprotein (basically a protein with carbs attached).  The mucin is secreted by the epithelial cells that line the gut, producing a barrier that prevents infection by microorganisms living in the gut.  

Related Post: Probiotics and your gut health. The numerous benefits of good bacteria

So as this barrier breaks down, the immune system begins to get out of balance and inflammation begins.  

Are we seeing a pattern here?

Another way the immune function can be detrimental, via inflammation, is by the production of cholesterol.  When immune cells kill bacteria they release lipopolysaccharides (basically a fat with carbs attached).  These are found in the outer membrane of gram-negative bacteria, such as salmonella and E. coli., and will cause a sequence of immune responses in animals.  The lipopolysaccharides are also known as endotoxins.  When endotoxins are released, our bodies produce more cholesterol (specifically Very Low Density Lipoproteins -VLDL) as an adaptive response.  They do this because cholesterol has binding sites, called LDL receptors that bind these endotoxins to protect the body so you don’t go into sepsis.

This is good.  

However, when you are more inflamed you make more cholesterol and this leads to things like heart disease.  

Obviously not good.    

Now there is some predisposition to get chronic disease based on what is called single nucleotide polymorphism (SNP).  SNP is a variation in a single nucleotide that may occur at some specific point in the genome, where each variation is present to some appreciable degree within a population (e.g. >1%). The basic idea here is that because of SNPs, our genes are different from person to person and that can open us up, or help us ward off, certain diseases.  However, even with our different mix of genes, food still plays a critical role.

The typical western diet is really poor in nutrition and fiber.

Our westernized diets, as mentioned before, are full of things that don’t make it to our gut bacteria, plus it lacks dietary fibers.  

To put that into perspective…

the typical American eats about 10-15 grams of fiber per day.  

However, we should actually be eating 30-35 grams of fiber per day.

So you need to at least DOUBLE your fiber intake.

Just for comparison, when studied, it was noted that Tanzanian hunter-gatherers, and most likely our ancestors, consumed somewhere between 100-150 grams of fiber each day.  

So obviously we need to increase the amount of fiber we take in.  But that’s not the whole story.  Remember that analogy about the rainforest in the very first paragraph, well that comes into play here.  

Not only do we need to eat a whole lot of fiber, but we need to eat a wide variety of complex carbohydrates.  If we only eat 1 – 2 types of fiber, we lack variety in food sources our bacteria need.  If we limit our variety of fiber, then only 1-2 bacteria species would survive and thrive.  Therefore, we would not have the large, diverse, all-encompassing, multi-faceted, rainforest ecosystem we need for optimal health.  This is important because with diversity comes stability, and with stability comes the ability to withstand impactful events.  

Quite the circle we are creating.

So what type of complex carbohydrates should we be eating?  

Well, glad you asked.  

Here is a quick list of what your gut biome would like to see on the menu.

  • Cellulose: found in cereals, legumes, fruits, and vegetables – all plants

  • Lignin: found in flax, stones/seeds of fruits, vegetables, and cereals

  • Inulin: found in a variety of plants

  • Pectin: found in fruit skins (mainly apples and quinces) and vegetables

  • Hexosan: found in wheat and barley

  • Pentosan: found in rye and oats


To get all these into your diet the best approach is to eat foods in season.  Avoiding packaged foods, even if they have claims of high fiber, is also a good idea.  The fiber in these processed products is not the same diverse fiber you will find in whole foods.  Plus, there is a possibility that artificial sweeteners in many of those packaged foods impact insulin resistance and the emulsifiers used have the potential to break down our mucus layer, which as you know affects the gut bacteria.

So we have talked about some things that are helpful to the gut bacteria, but what about those things that can harm your gut microbe population?  

Well, one thing that can throw our gut biomes out of whack, are antibiotics.  

But there’s a catch.

While antibiotics are needed to treat serious illness, they can wreak havoc on our guts.  These antibiotics can kill the bacteria in our guts.  Even though we can work to help our guts rebound from this, they rarely return to their original state.  

However, if you must take antibiotics you can mitigate the consequences.  

For one, eat your fiber, you know this.  Also consume probiotics such yogurts and other fermented foods.  These probiotics do not take up permanent residency in your gut, but as they pass through they can help.  There is thought out there that they act as a placeholder and prevent harmful bacteria from overpopulating your gut.  However, this mechanism is not fully understood.  You can also take probiotics in supplement form.  A word of caution though, as with any supplement, they are not FDA regulated, and may not live up to their claims and/or may be contaminated.  Be sure to look for the USP symbol and buy trusted brands.  

Related: The many health benefits of Apple Cider Vinegar

Being around the family pet is another way you can add bacterial species back into your biome.  So go ahead, go give Rover and Fluffy some love.

As you are probably guessing by now, the gut biome is pretty complex.  So complex that it actually begins at birth.  While the baby lives in a fairly sterile environment while in utero, once the baby is born the population of the gut with bacteria begins.  

The type of gut biome the baby will have is dependent on several variables.  These variables include how the baby is born, vaginally or by C-section.  Also, whether the baby is breastfed or formula fed impacts the species of bacteria in the gut.  

Babies born vaginally will take on a more diverse population of bacteria, often from the mother.  A C-section baby has less diversity and the gut is populated with bacteria that are more often found on the skin.  These bacteria may or may not come from the mother.  In fact, they could even come from the doctor, nurses, etc.  

A baby who is breastfed will also have a more diverse and robust population of gut bacteria.  There is actually a something called Human Milk Oligosaccharides (HMOS) in breast milk.  HMOs are a family of unique oligosaccharides (carbohydrates) in human breast milk that are indigestible by infants and thought to have evolved to serve as selective probiotics for certain beneficial bacteria which co-evolved with the unique ability to more efficiently utilize those carbohydrates as a substrate.  So breast milk not only has food for the baby, but also the gut bacteria!  And so far, the HMOs have not been replicated in formula.

So while we are learning about the gut biome, in what seems like leaps and bounds, we still have a long ways to go.  Gut bacteria are vast and diverse population that we are still trying to get a grasp on.  To make things even more complicated, these bacteria are busy producing a variety of chemicals, not just SCFAs, that we have not yet identified either.  So knowing the full impact of the gut biome on our biology is wide open universe we have just begun to explore.   

Related: Eating Healthy even at old Age – Women Healthy Diet Plans

Final takeaway

You need to eat and the right foods so your gut bacteria don’t starve. This means eat a wide variety of whole foods in the forms of vegetables, fruits, and sprouted legumes to get at least 30 grams of fiber each day. Also, keep the probiotics in your system by eating fermented foods or reputable supplements, especially if you have been on antibiotics. Remember, starving gut bacteria will find a way to eat, one way or another. They will eat the food you give them, or they will eat you. So a happy gut biome equals a healthy you!
You need to eat so your gut bacteria won’t starve

  • Choose whole foods high in fiber like soaked and roasted nuts, green leafy vegetables, fruits, seeds, and sprouted legumes.

  • Eat enough fiber – 30-35 grams of fiber per day.

  • Take in probiotics after a dose of antibiotics.

  • Vary your fiber to create diversity in gut bacteria and that creates an overall healthier you



Why Athletes Need Magnesium to Maximize Performance

Are you feeling exhausted, or getting unusual muscle cramps during workouts?

You might be deficient in magnesium.

Magnesium is an essential mineral that 75% of the U.S. population is deficient in. “Studies have shown that only about 25% of U.S. adults are at or above the recommended daily amount of 310 to 320 milligrams for women and 400 to 420 for men,” says Dr. Danine Fruge, Associate Medical Director at the Pritikin Longevity Center in Miami, Florida.1

One of the benefits of magnesium is the ability to help produce more mitochondria during exercise.

There are two ways to become a high performing athlete.

  1. Increasing the total number of mitochondria
  2. Increasing the efficiencies of the mitochondria

To increase exercise performance, you must increase the ability of your cells to consume more oxygen known as ‘oxidative capacity’. This is the ability to breakdown oxygen in your muscle cells via the mitochondria which ultimately produces adenosine triphosphate or more commonly known as ATP. ATP is the biochemical way to store and use energy in your muscles. To be an efficient athlete you must produce more ATP than you are consuming. If you don’t, you will get muscle fatigue, feel tired and even get muscle cramps.

Dr. Rhonda Patrick talks about Maximizing Your Mitochondria with Magnesium

Studies have shown that high-intensity interval training (HIIT) can increase the development of new mitochondria. This is done by cloning the cells via enzymes that require magnesium as a cofactor. So if your magnesium levels are low, you will have a hard time cloning new mitochondria cells. Not making new mitochondria cells will lower your exercise performance. Having low levels of magnesium will reduce your ability in making new mitochondria cells and thus your ability to maximize exercise performance diminishes. So you want to make sure your levels of magnesium are within the recommended level of 310 mg for women, and 420 mg for men.

The best way in getting more magnesium is by eating dark leafy greens like kale, spinach, collard greens. Nuts like sesame seeds, almonds, walnuts, and cashews are also excellent sources.


  1. CNN, Magnesium, an invisible deficiency that could be harming your health