The Gut 101: Digestion, Fiber, and the Microbiome

This post will be an attempt to provide some really basic groundwork for building on your knowledge of the microbiome and digestion, in order to further dive into more complex parts of this whole process.

Each of the following sections has had multiple books written on it, so this will by no means be an exhaustive resource, but moreso a starter to the topic.

Future resources will delve into the intricacies of these sections individually.

Digestion from Top to Bottom

Digestion actually begins in the mouth with some enzymes (mostly just amylases and lipases) that begin to break down starches and other forms of simple carbohydrates, as well as some fats, respectively.

Chewing itself is an act of physical or mechanical breaking down of food. The more you chew your food, the more likely you are to be able to easily digest it.

Eating too quickly can result in partially digested food, and delayed hunger and satiety signals (satiety is the feeling of fullness you should get approximately 20-30 minutes after beginning eating).

I generally recommend that my patients try not to eat when rushed. Devote at least 30 minutes to a meal, allowing yourself ample time to chew each bite.

When you eat very quickly, it interferes with normal digestive signalling, which means you may have less stomach acid produced to digest your food, or you may even have delayed feeling of fullness, which means you are more prone to overeating calories in a meal because it takes you a certain amount of time to feel satiated, or full.

The Stomach

The stomach is where the majority of protein begins to break down. The main action happening here is the release of hydrochloric acid, which begins to break the chemical bonds in protein. To a lesser extent, carbohydrates and fats continue to breakdown a little, but not anywhere near as much as protein.

Things that can go wrong with digestion at this point are primarily either:

  • Hypochlorhydria (low stomach acid)
  • Hyperchlorhydria (excess stomach acid)

As much as people take antacids and acid-suppressing medication these days, excess stomach acid is actually not as common as you might think. Usually, the sensation of reflux is not really excess stomach acid, but acid entering the esophagus, which is due to other things.

In some individuals, there is not an obvious acid reflux problem, but excessive burping or belching, even sometimes hiccups, occurs. This is sometimes referred to as silent reflux because the acidic ‘burning’ sensation is absent.

A note on antacid drugs: none of them, literally none of them, were meant to be taken for longer than approximately 4-6 weeks. And in fact, some significant trials and research support that using them longer than that has serious side effects not just on the rest of the GI tract, but on other inflammatory conditions in the body.

Reflux is really a sign that something has impaired the balance of acid and base in the digestive tract, or has put pressure on the stomach (either gas buildup or excess abdominal fat, but can also happen frequently during pregnancy), forcing acid upward into the esophagus and antacids should only be used sparingly, as they mask symptoms, but do not solve the problem in the majority of cases.

Things that have been known to contribute to acid reflux include, but are not limited to:

  • Acidic foods
  • Insufficient bile or weak bile
  • Esophageal sphincter dysfunction
  • Food sensitivities
  • SIBO (small intestinal bacterial overgrowth), especially if high carb meals make this symptom worse
  • Stress
  • Eating too much food volume at one time

It is actually quite common that low stomach acid occurs. The over-use of antacid drugs, coupled with increased prevalence of Helicobacter pylori (an invasive bacteria that lives in the stomach), which can ‘shut off’ stomach acid production, has led to this being a more common occurrence.

Low stomach acid contributes to incomplete protein digestion and impaired nutrient absorption, particularly of amino acids, and some vitamins and minerals (B12, magnesium, iron, copper, zinc, and folic acid).

This can lead to feelings of fatigue, low mood, poor sleep quality, anxiety, anemia, and feeling reduced energy during workouts or other physical activity.

The Gall Bladder

Once food leaves the stomach, it dumps into the upper part of the small intestine, called the duodenum. Here, it is met with a release of bile from the gall bladder. The gall bladder does not produce bile (it’s made in the liver), however, its job is to ‘store’ it and concentrate it.

If you have had your gall bladder removed, you’ve probably been told by your gastroenterologist post-surgery that you don’t need to do anything different long term because the gall bladder doesn’t play a critical role in digestion.


It has been observed by virtually everyone who works with functional digestive disorders (myself included) that gall bladder removal contributes to weak bile that is not fully able to neutralize acidic stomach contents.

This contributes to the contents of the upper small intestine being more acidic than they should, which impairs the release and function of many different digestive hormones, enzymes, and neurotransmitters.

The problem is that the effects of this take years in some cases to accumulate to something clinically significant. Until then, you may just feel uncomfortable, gassy, bloated, and malabsorb nutrients (which you can’t really tell is going on until its been going on for a while).

Even if you DO still have your gall bladder, bile can be weakened for a number of reasons.

Low blood cholesterol levels can actually indicate a bile insufficiency, believe it or not, because cholesterol is a building block for bile.

Why do you need concentrated bile?

  1. Neutralizes stomach acid
  2. Emulsifies dietary fats (to help you digest them)
  3. Binds to toxic byproducts the liver has neutralized and excreted through bile
  4. Aids in absorption of fat soluble vitamins (A, D, E, and K)
  5. Excretes heavy metals the liver has detoxified
  6. Aids in hormone balance by helping absorb fats that are the base for hormones
  7. Prevents build up of acid, which can re-enter the stomach and lead to reflux sensations

You can aid in bile production and quality in the liver by increasing intake of foods high in betaine such as beets, beet greens, and beet juice.

Also, the greater your production of the antioxidant glutathione, the more efficient your liver cells can operate and remove/detoxify everything they are supposed to, which prevents the liver’s production of bile from backing up.

The Small Intestine

The majority of macronutrient digestion happens here. These are your carbohydrates, proteins, and fats. Fiber is largely passed on to the large intestine instead of digested in the small intestine.

Some limited amounts of bacteria reside in the small intestine, but it has far fewer populations of bacteria than the large intestine.

The small intestine’s job is to digest macronutrients and so that they can be absorbed into circulation. Food is chemically broken down through enzymes that are released from the pancreas and dumped into the small intestine.

These enzymes are chemicals that operate at specific pH levels (remember when I said that improper acid/base balance affects digestion further down?).

If the pH of the small intestine is too acidic or too basic, certain enzymes do not work correctly.


There is a delicate balance between the acidic and basic influences of digestion: hydrochloric acid (HCl) and bile.

HCl (a very strong acid) comes from the stomach and enters the upper small intestine (duodenum) where it should be met by bile (a strong base) and neutralized, as the pH goes from very acidic to more basic. It eventually ends up closer to neutral, but still slightly on the basic side.

Digestive enzymes are released by the pancreas and glands in the small intestine called crypts of Lieberkuhn.

Enteroendocrine cells here secrete hormones such as:

  • Gastrin: in the small intestine, it stimulates mucosal growth to protect the intestinal cell layer, and stimulates motility (the muscle contractions that move food and other substances through the GI tract)
  • Cholecystokinin: stimulates the gall bladder to release bile, signals our brain when we’re full, and stimulates motility
  • Secretin: signals the pancreas to release bicarbonate, digestive enzymes, and insulin; shuts off intestinal motility and stops release of stomach acid
  • Somatostatin: stops the release or action of other hormones in the GI tract
  • Motilin: stimulates the stomach to empty its contents into the small intestine and increases motility in the small intestine

There are many other substances that act as either neurotransmitters or hormones in the gut, which we may dive into in other future articles.

Some neurotransmitters act locally in the stomach and intestinal tract to influence digestion and absorption, while others are released in the small intestine and travel to other parts of the body, such as the brain, to influence appetite.

Goblet cells and Brunner’s glands in the intestinal lining secrete mucus, which has two important functions:

  1. Neutralize acid in the duodenum
  2. Create a protective barrier over the intestinal cells along the entire length of the digestive tract

A wave-like contraction of the small intestinal smooth muscles, called peristalsis, moves your partially digested food, fluid, and other contents along the route toward your large intestine, as digestion is taking place.

Vitamins and minerals that are absorbed in the small intestine include:

  • B vitamins
  • Iron
  • Water is also absorbed passively here

The primary possible things that can go wrong with the small intestine include, but are not limited to:

  • SIBO (small intestinal bacterial overgrowth)
  • Impaired motility (things don’t move at an appropriate pace)
  • Insufficient digestive enzyme levels
  • Insufficient bile
  • SIFO (small intestinal fungal overgrowth)

Of all of these, I see a ton of SIBO. The classic hallmark symptoms of SIBO include:

  • Uncomfortable gas or bloating immediately following meals, especially high fiber or high carb meals
  • Distended belly for prolonged periods (1 hour or more) after a meal
  • Acid reflux/GERD
  • Burping
  • Brain fog
  • Fatigue right after meals
  • Chronic diarrhea (in hydrogen-dominant SIBO)
  • Chronic constipation (in methane-dominant SIBO)
  • Alternating constipation followed by diarrhea (mixed-type SIBO)

Some tests exist to determine if SIBO is present. Some of them are not very accurate and often give false negative results, which impedes treatment and resolution of symptoms.

Next most common is impaired bile. Observationally, women are more likely to have impaired bile, and do, in fact, have higher rates of gall bladder removal.

In addition to being female, another really common contributing factor to bile impairment is prolonged or frequent extreme dieting (I see this very frequently in figure and physique competitors) because extreme fluctuations of dietary fat are seen, which affects the amounts and concentrations of bile that can and will be made by the liver.

Often, women who participate in sports or events that require frequent or prolonged low dietary fat intake (eg: show prep diets) have sometimes irreparable alterations to their bile production (as well as significant deleterious effects on their endogenous sex hormone production).

Taking ox bile acid can sometimes remedy some of the symptoms, but does not really solve the problem of weak bile production from the liver. Usually, a gradual increase in dietary fat intake to higher levels resolves some of the underlying dysfunction and restores hormonal influence.

The Large Intestine

Now we get to where all the good stuff happens. The large intestine is where the majority of bacteria reside, which are part of the collective ‘gut microbiome,’ which is composed of not just bacteria, but yeast, and sometimes parasites.

The gut bacteria play a critical role in the breakdown of fiber here, but also in the influence of your immune system, the majority of which resides in the gut. Bacteria influence what messages go to the immune system, which is constantly sampling the contents of the intestinal tract.

If the right bacteria are abundant, the messages are predominantly ‘anti-inflammatory.’ If the wrong bacteria are present, or if you just don’t have enough of the right ones, the messages are either ‘pro-inflammatory,’ or there is no ‘anti-inflammatory’ message being sent.

When we eat a diverse selection and amount of fiber from plant foods, we feed all the right bacteria.

We can also temporarily replace some of the good bacteria we’ve lost (usually because of antibiotic use, or other stressors) by eating fermented foods (more on that later).

Important Keystone Bacteria

Science in the field of microbiome research is barely scratching the surface of what we know about the ecosystem of microscopic lives that inhabit our digestive tract.

What we do know is that in the human gut, there are a number of critical bacteria, some of them are referred to as keystone species, that have a disproportionate influence on our health compared to the size of their populations.

Keystone bacteria include:

  • Clostridia
  • Akkermansia
  • Actinobacteria (phylum)
  • Bacteroidetes (phylum)
  • Firmicutes (phylum)
  • Lactobacillus
  • Bacillus
  • Bifidobacterium
  • Eubacterium
  • Butyrovibrio
  • Ruminococcus
  • Blautia
  • Peptoniphilus
  • Dialister

Loss of or reduction of our keystone bacteria results in massive shifts in things like immune signaling and nutrient digestion/absorption.

Usually these losses occur as a result of taking antibiotics, but can also be caused by other things like acute exposure to industrial chemicals (agriculture, photography, paint, etc), chemotherapy, major emotional or physiological stress, and chronic use of NSAIDs (non-steroidal anti-inflammatory drugs), to name a few.

Using antibiotics just once for something for a short period of time is usually not enough to cause permanent damage to this ecosystem’s balance, but over time, the more we use, plus the more antimicrobial things we come in contact with (eg: hand sanitizer and harsh cleaning solutions), the more we expose the microbiome to things that can permanently change it, or leave it weakened.

By no means does this mean you shouldn’t take antibiotics if you need them to save your life. You just probably don’t need them for every sniffle.

Once this balance shifts, we leave our microbiome wide open for aggressive opportunists and even overt pathogens (think C. diff, E. coli, and Shigella) to establish themselves.

Why this matters is that our critical keystone bacteria have important roles that influence how our immune system reacts (or doesn’t react) to literally everything going on inside the intestinal tract (referred to as the lumen of the intestines).

If our good, helpful keystone bacteria are present, they keep things calm and everyone’s happy. This is due in part to something called ‘competitive inhibition.’

When your intestinal wall is lined with helpful, commensal bacteria that belong there, there’s no room for opportunistic or pathogenic bacteria to flourish.

If we wipe out our helpful bacteria, or if we eat a diet that makes it hard for them to thrive, their populations dwindle and there’s not enough of those anti-inflammatory signals being sent and our immune system is more likely to over-react (higher risk for food sensitivities, autoimmune disease, asthma, and allergies).

And, on top of this, the messages these bacteria send reach far outside of just the intestinal tract.

They are critical for the function of the entire rest of our body (really, they influence everything from inflammation, to hormones, to cognitive function, to mood, to cardiovascular health and diabetes, to our liver, and on and on…).

Nutrient Absorption

But enough about all these bacteria. We also absorb other nutrients here in the large intestine.

We absorb our fat-soluble vitamins in the large intestine (A, D, E, and K) as well as produce some (primarily Vitamin K and biotin). Our gut bacteria do make vitamin B12 in the large intestine, but we do not absorb it, so it is not considered a usable source for human health.

Functional Foods that Improve Digestion (Prebiotics and Probiotics)

A lot of information can be found on the interwebz about probiotics and prebiotics, most of it pushing expensive supplements.

Probiotics and prebiotics are, however, found in foods and don’t have to be purchased in supplement form.

Probiotic Foods

Probiotics are foods with live cultures (bacteria that are usually helpful to the human host). These foods are also referred to as fermented foods and come in a variety of forms, including some fermented drinks.

Common fermented or probiotic foods and drinks include:

  • Sauerkraut
  • Kimchi
  • Yogurt (dairy and non-dairy)
  • Kefir (dairy and non-dairy)
  • Kombucha

Because probiotics are such a hot trend in the food manufacturing and supplement industry right now, you can find a myriad of fermented food sources at most health food stores these days.

Probiotic foods are beneficial to humans because the bacteria in them are complementary and compatible with the bacteria that naturally occur in our digestive tracts.

The bacteria in the fermented foods travel through our digestive tract cross-feeding our own bacteria by producing certain chemicals that our bacteria thrive on. The colonies of our own bacteria grow and we experience a number of health benefits because of this symbiotic relationship.

It is a common misconception that bacteria in fermented foods ‘colonize’ our digestive tract. They actually are transient and usually undetectable in our stool about 7-10 days after consuming the fermented food (or probiotic supplement) they came in.

The main benefit they impart comes from the aforementioned cross-feeding activity.

An example of this is when species of Bifidobacteria consume certain prebiotic fibers (such as fructans and arabinoxylo-oligosaccharides), the byproducts of that fiber fermentation by Bifidobacteria feeds populations of butyrate-producing bacteria like Faecalibacterium, which is a considered a critical keystone species with strong anti-inflammatory effects.

In many cases, probiotic supplements impart little to no benefit to the host simply because they don’t contain strains that individual lacks, their strains are not viable (they’ve perished during storage/transport before purchase), or they are not compatible with the host’s unique gut microbiome composition.

For this reason, many individuals find they may try 10 different probiotic products before finding one that specifically works for them, while a wide variety of fermented foods imparts greater benefit due to the greater diversity of microbes in the fermented food, as well as the closer genetic match of the microbes in fermented food to those found in the human gastrointestinal tract.

Prebiotic Foods

Prebiotic foods do not contain any live bacteria, usually, but do contain different types of fiber that commensal gut bacteria prefer to eat and thrive on.

A prebiotic food is simply a food that contains fermentable carbohydrates that feed populations of good bacteria.

Prebiotic fibers can be broken down into several main categories found in the human diet:

  • Fructans and fructooligosaccharides
  • Galactooligosaccharides
  • Xylooligosaccharides
  • Resistant Starch
  • Pectin

Types of Fiber

Fructooligosaccharides (FOS) are a category of fiber in carbohydrates that either occur naturally in foods or are produced commercially as sweeteners. They are also a type of FODMAP (Fermentable Oligo-, Di-, Monosaccharides And Polyols), which are a class of fibers that can be very difficult for some individuals to digest.

This resource focuses solely on those naturally occurring in food sources, as the commercially produced FOS varieties do not always appear to have the same prebiotic properties.

Food sources high in naturally occurring FOS include, but are not limited to:

  • Chicory root
  • Agave
  • Bananas
  • Inulin (onions, leeks, garlic)
  • Asparagus
  • Wheat
  • Barley
  • Nuts

One important point to note is that, in my findings, individuals who have trouble tolerating FOS fibers often have pathogens or conditional pathogens such as Klebsiella, E. coli, or various aggressive Clostridia species overgrown which ferment the FOS and produce hydrogen gas as a byproduct. This abundance of hydrogen gas creates uncomfortable side effects such as:

  • Excessive gas
  • Extreme bloating
  • Diarrhea
  • Nausea

This is one reason why I discuss with individuals that a low FODMAP diet is simply a bandaid for a deeper problem of bacterial dysbiosis, rather than a lifelong inability to digest FOS fiber (or other types of FODMAP fibers).

If you find that your IBS-like symptoms improve on a low FODMAP diet, its highly likely that you have either or both an overgrowth of an aggressive bacteria that is producing hydrogen when fermenting these fibers and/or SIBO.

Galactooligosaccharides (GOS) are another type of indigestible fiber that our gut bacteria can digest and produce beneficial chemical compounds that stimulate other bacterial colonies, contribute to immune balance, and improve the regularity of bowel movements.

Food sources of GOS include, but are not limited to:

  • Jerusalem artichokes
  • Black beans
  • Kidney beans
  • Lima beans
  • Beet roots
  • Broccoli
  • Chickpeas
  • Lentils

GOS fibers feed Bifidobacteria, also, and are an important factor in how efficiently our bacteria produce certain vitamins for us, as well as how efficiently we absorb nutrients through our gastrointestinal wall.

Xylooligosaccharides (XOS) are another class of prebiotic fibers that primarily feed our Bifidobacterium and Lactobacillus genera of bacteria, which are both considered critical keystone groups that promote immune balance and control inflammation.

XOS sources naturally occurring in foods include, but are not limited to:

  • Milk
  • Honey
  • Vegetables with a high cellulose content
    • Celery
    • Brussels sprouts
    • Cabbage
    • Kale
    • Squash
    • Sprouts
  • Rice bran
  • Soybeans
  • Bamboo shoots

Another type of prebiotic fiber that is closely related to XOS is arabinoxylanoligosaccharide (AXOS) and has similar effects of increasing butyrate production by good bacteria.

Resistant Starch

Resistant starch is found in commonly consumed foods, as well as formed during the preparation of some starches. The main benefits conferred by consuming resistant starch is it is fermented by your gut bacteria and the byproduct is short-chain fatty acids (SCFA), of which the aforementioned butyrate is one.

Resistant starch produces more butyrate than other types of prebiotic fibers.

Butyrate levels in the colon (large intestine) influence everything from how healthy our intestinal cells are, how strong our immune system is in response to invasive pathogens, how our T cells differentiate to squash allergies and autoimmunity, and reducing inflammation in the colon.

Higher levels of butyrate have been shown to reduce colon cancer risk, prevent inflammatory bowel diseases such as Crohn’s and Ulcerative colitis, and increase the functionality of intestinal cells in the colon.

Certain types of bacteria produce butyrate, including those in the Clostridia class such as Faecalibacterium, Butyrovibrio, Eubacterium, and Roseburia. Without enough of these bacteria, we tend to see higher rates of IBS and IBD, as well as higher incidence of autoimmune diseases and allergies.

Naturally occurring sources of resistant starch include, but are not limited to:

  • Banana flour
  • Cooked oats
  • Lentils
  • Green bananas
  • White beans
  • Barley
  • Green peas
  • Whole wheat
  • Nuts

Another way to obtain resistant starch from food is by cooking and cooling some starches (like rice and potatoes). During the cooling process, the chemical structure of the starch/sugar molecules change shape to form starch crystals that are resistant to human digestive enzymes. This allows them to bypass much of the digestive process in the small intestine, entering the large intestine intact, where they are fermented by gut bacteria.


The last common class of prebiotic fiber is pectin. Pectin is commonly found in fruits and vegetables with rinds, or more fibrous structures.

Naturally occurring food sources of pectin include, but are not limited to:

  • Apples
  • Pears
  • Guavas
  • Citrus fruits
  • Plums
  • Gooseberries

A cool feature of pectin is that it binds to cholesterol in the gastrointestinal tract, which may lead to less intestinal absorption of cholesterol or reabsorption of bile acids, which increases the amount of cholesterol the body will use from its own stores (in the liver and blood) to manufacture hormones and cell wall structures.

Pectin also slows the digestion of carbohydrates in the intestines and therefore, is considered a soluble fiber, which provides some beneficial effects on blood sugar regulation if consumed regularly.

Pectin is also fermented by intestinal bacteria to produce short-chain fatty acids, including butyrate.

Emphasizing a Variety of Fibers

Now that we’ve walked (not so) quickly through types of fiber and why each of them has an important place in the human diet as it relates to microbiome diversity and intestinal health, how do you go about creating a pattern of nutritional intake that supports a variety of fiber over time?

Below, I’ve included some suggestions for how a day of meals might be patterned to include most of these types of fiber each day, so that over the course of a week, one might obtain a wider variety of all fiber types.

Obviously, serving sizes will vary by caloric and macronutrient needs, so consult with a professional if you have questions about exactly how much of each of these foods you should be eating in order to meet your nutritional needs.

Pattern 1

Breakfast Egg omelet (with onions, peppers, mushrooms) + berries + oatmeal
Lunch Large leafy green salad (top with choice of protein, chickpeas, veggies, cheese, etc)+ an orange + greek yogurt
Dinner Protein + cooked black beans + asparagus + side salad
Snacks Banana + pistachios

Pattern 2

Breakfast Smoothie: berries, almond/peanut butter, spinach, green banana, protein, flax or chia seeds
Lunch Leftover protein + reheated rice + berries + side salad
Dinner Protein + cooked sweet potato + a cruciferous veggie (broccoli, cauliflower, Brussels sprouts, etc)
Snacks Apple + whole grain crackers + walnuts

Pattern 3

Breakfast Protein + beans + whole grain toast
Lunch Wrap (protein + beans + sprouts + cucumber + onions + tomatoes + dressing) + pear or apple
Dinner Protein + Roasted beets and carrots + kale side salad
Snacks Berries + Flax and pumpkin seed trail mix

Hopefully you survived this extra long post and found it useful!

If you still have burning questions, don’t worry. There will be more posts from me that will help you better understand digestive health (and indirectly, a ton of other health topics, too).


Commenting area

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