Decode Your Digestion: Unleashing the Full Potential of Your Diet

Embarking on a nutritious diet is a commendable stride towards a healthier life. However, have you paused to consider the efficacy of your digestion in harnessing the full benefits of your diet? The essence of digestion goes beyond mere food breakdown—it’s a sophisticated process that significantly impacts your health and nutritional uptake.

This article unravels the fascinating journey of food within your body, shedding light on how each digestive phase contributes to your overall health. Moreover, it reveals actionable insights to revamp your digestion, ensuring you reap the maximum rewards from your nutritious meals.

Your pathway to a more energetic and healthier life is a read away—dive in to unlock the treasure trove of dietary potential awaiting you!

The Process of Digestion: A Bit of Physiology

To identify why your digestion may be less than optimal, it’s crucial to understand how it works.  Let’s jump in!

It might surprise you that digestion begins at the sight of food.  Our salivary glands produce saliva when we see, smell, taste, or even think about food.  Saliva is a mixture of water and enzymes that break down your food as soon as it hits your mouth.  

Chewing is the first step of mechanical digestion.  It then mixes with your saliva, which begins the process of chemical digestion.

Lingual lipase and salivary amylase are the primary enzymes released in the mouth.  Salivary amylase begins the breakdown of starches as you chew, and lingual lipase breaks down fats.  However, lingual lipase is most active in the stomach.

Once you’re done chewing, your food and saliva mixture makes its way down the tube we know as your oesophagus through the valve between your stomach and your oesophagus, known as your pyloric sphincter, and into your stomach.  This is where the real fun begins.   

Hydrochloric acid, or ‘stomach acid’, mucus, lysozyme, and more enzymes are released in the stomach.  The acid begins the breakdown of protein into amino acids, the enzymes continue the digestion of fat, the mucus shields your GI system from harmful elements and traps bacteria, and all other substances serve as natural antimicrobials for any germs or pathogens that may have made it into your system from food or water. 

Your stomach acid starts the digestion of protein and serves as a catalyst like the first domino to release other digestive juices.  Additionally, adequate stomach acid signals to your oesophageal sphincter—the ‘safety door’ between your stomach and oesophagus—that it’s time to close so digestion can ensue.

Healthy stomach acid levels are somewhere between a pH of 1.5 to 3.0.  If the pH is not low enough (remember, the lower the pH, the more acidic something is), then:

  • protein digestion doesn’t occur,
  • stomach acid’s antimicrobial effects are not the same,
  • your ‘trap door’ oesophageal sphincter does not shut (hello, acid reflux!), and
  • successive digestive substances like bicarbonate, bile, and pancreatic enzymes are not released.

A lot can go wrong if this step isn’t functioning correctly!

Once food mixes with stomach acid, it is squeezed and squished to continue mechanical digestion.  Eventually, it makes a semi-digested ball of food called chyme, which makes its way into the small intestine.  While most people think the stomach is the main site of digestion, it is actually the small intestine. 

The small intestine is divided into the duodenum, jejunum, and ileum.  While it is called the ‘small’ intestine, it is actually the longest of the two.  All sections consist of many layers, but the most important for the sake of this article is the epithelium, which lines the inside of the tube we call the digestive tract.  This is where the absorption happens.  

In the epithelium, many circular folds and finger-like projections increase the small intestine’s surface area.  These are known as villi.  You can liken this to a bunched-up cloth, whose purpose is to compound absorption.

Lining these villi are your enterocytes, the absorptive cells that take in all your nutrients.  These enterocytes are lined up side-by-side in a layer that’s only one cell thick.  They are held together by ‘tight gap junctions’, which ensure food doesn’t leak into your bloodstream on the other side.

To compound absorption even further, each enterocyte has its own hair-like projections, conveniently called microvilli. 

This has been coined the ‘brush border’, and it is estimated that it increases the surface area up to 600 times more than if it were smooth!  So, as you can see, the surface of the small intestine is very purposeful, especially when it comes to digestion.

The presence of chyme in the small intestine stimulates the liver, gallbladder, and pancreas and triggers several substances that release bicarbonate (HCO3), pancreatic enzymes, and bile.  In summary:

  • Bicarbonate (HCO3) neutralises stomach acid;
  • Pancreatic enzymes break chyme into smaller components that can be absorbed by the small intestine, like individual amino acids, fatty acids, and simple sugars; and
  • Bile is a substance that emulsifies fatty acids, meaning it helps make fats more absorbable.

As these substances mix with chyme and move throughout the small intestine, they continue digestion and nutrient uptake.  So, different areas of the small intestine are responsible for taking up different nutrients, which is pretty neat.

After chyme reaches the end of the small intestine, it passes through the ileocecal valve into the large intestine.  The large intestine is the major site of mineral and water uptake and has the highest bacterial concentration.  These guys are responsible for fermenting the fibre in your food and making short-chain fatty acids and even some nutrients like B12 and K2.

Once food has sat in the large intestine, fermented, and been squeezed of all the water and minerals left, it passes out the chute. 

Voila!  This is the whole digestive process, in a nutshell. 

What Happens When Things Don’t Go as Planned

Now that you’re familiar with the process of digestion, we can talk a little bit about where digestion can go wrong.

Digestion is a north-to-south process, like an assembly line.  Every action down the line relies on the upstream processes working correctly.  So, if one of the initial reactions is off, successive processes will likely not work as well as we want them to.

This can have adverse outcomes, including:

  • Reduced nutrient absorption,
  • Bacterial overgrowth,
  • Constipation, and
  • Increased wastes.

Where Can Digestion Go Wrong?

So, where can digestion go wrong? 

One of the first steps of digestion happens to be one of the most common processes that are interrupted. 

The part of your brain that regulates involuntary processes like heart rate, respiration, digestion, and blood pressure (i.e., your autonomic nervous system) is broken down into two categories that balance one another:

  • the parasympathetic nervous system (i.e., PNS or rest-and-digest) and
  • the sympathetic nervous system (i.e., SNS or fight-or-flight).

Someone is in a parasympathetic state when they are rested, relaxed, and their bodies feel safe.  Someone is in a sympathetic state when their body perceives danger in stress.  But unfortunately, our bodies today are stuck in perpetual states of fight-or-flight.

To release digestive juices like salivary enzymes and stomach acid, heal, and regenerate, someone must be in a relaxed, parasympathetic state.  Being stressed can inhibit digestion as the body doesn’t release digestive juices, meaning the body can’t break down, emulsify, or absorb foods well. 

So, eating on the run in between stressful meetings, around big exams, or after a heated argument might result in poor digestion.  Have you ever felt bloated when you eat when you’re stressed?

Moving down the line, the next interruption we might see with digestion is if we don’t adequately chew our food.  You can think of it as trying to shove a ton of food scraps down a sink without a garbage disposal unit; the blades help predigest them so they can move through the pipes.  Chewing is the first step of mechanical digestion, so foregoing it and scarfing your food leaves your digestive system at a disadvantage.

Additionally, diluting saliva and stomach acid from drinking too much water with meals or too many other fluids can also impair digestion.  Drinking and eating certain substances and foods have also been shown to affect salivary enzyme production.

The Role of Nutrients in Digestion

Our main mission is to get enough of all the nutrients into our body!  But nutrients also play a critical role in digestion. 

We require nutrients to synthesise digestive juices and catalysts to the digestive process like saliva, stomach acid, pancreatic enzymes, bile, and mucous.  Hence, if we’re not eating a nutrient-dense diet, we’re likely not getting the raw ingredients we need to synthesise these components that enable us to absorb our nutrients.

Zinc is one of the most critical nutrients for stomach acid production.  Hence, if we’re not getting enough zinc or taking medications that deplete zinc, we can expect to see our stomach acidity suffer.  In addition, certain medications, alcohol, and tobacco also deplete stomach acid. 

As we mentioned, stomach acid is one of the first digestive substances to be released and functions as an antimicrobial.  Hence, low stomach acid can result not only in poorly digested protein but also can result in bacterial overgrowth and poor bile and pancreatic enzyme release.

Aside from stomach acid, bile and pancreatic enzymes are also critical for food digestion.  But they also depend on the body producing adequate stomach acid!


Bile is critical for emulsification, or the process in which fats are made into a substance that can be easily taken up by the cells of the small intestine.  It also serves as an antimicrobial.  Inadequate fat intake, microbial infection, conditions related to a metabolic disorder like non-alcoholic fatty liver disease (NAFLD), and nutrient deficiency can impair bile flow and production.  Additionally, relying upon processed foods has links to conditions resulting in gallstones, which form from poor bile flow.

Much like bile, the release of pancreatic enzymes depends upon adequate stomach acidity.  These substances continue the breakdown of food into pieces that are small enough to be absorbed by your enterocytes.  They also serve as antimicrobials.  Inadequate pancreatic enzymes can contribute to malabsorption and poor digestion over time.

If stomach acid is not adequate, bile and pancreatic enzymes are not released.

Leaky Gut

Many nutrient-poor foods, like processed foods high in starches, sugars, and seed oils, are known to be hard to digest.  When food is maldigested, it can make its way into the small intestine and onto those hair-like structures known as microvilli. 

Over time, this becomes irritating to this surface, and it becomes inflamed.  That inflammation is known to begin to break down and penetrate those tight gap junctions in between the cells that line your intestines.  As a result, poorly digested food can make its way through those gaps, resulting in intestinal permeability, or ‘leaky gut’.

Once food makes its way through these gaps, it ends up in your bloodstream, where your immune system is ready to protect the body from other foreign invaders.  These food particles can activate your immune system, leaving you with food intolerances, sensitivities, and even allergies over time.

Interestingly, this occurrence has been tied to chronic conditions like autoimmunity; poorly digested foods engage your immune system, which makes your body prone to mistaking various organ systems for food proteins.

Processed Foods

Because processed foods are so high in sugars and starches—what bacteria love to feed on—eating a lot of them or using them as a dietary staple can allow chronic bacterial and fungal infections to take root in the GI tract.  Like the processed foods that feed them, these infections can break down the tight gap junctions in between your enterocytes.  This is known as dysbiosis.

Sitting in between your small and large intestines is your ileocecal valve.  Like all the other valves—muscles, nerves, and other tissues—in your body, they do their jobs because of minerals.  Hence, inadequate water or mineral intake can cause this valve to work improperly.


Your small and large intestines are intricately balanced environments unique to you.  However, because they rely on the microbes that populate them, activity in the small intestines is largely disturbed with prolonged antibiotic use.

Not only do these drugs kill the bacteria that produce nutrients and short-chain fatty acids and break down food, but they also can throw off the equilibrium between healthy and pathogenic strains of bacteria that reside in your gut.


Lastly, chronic constipation can impair the digestive process, as this is how wastes are removed from the body.  If someone is not going to the bathroom regularly, this waste sits in the colon, where toxin reabsorption and bacterial overgrowth can occur.

Other Things That Can Inhibit Digestion

While we’ve talked about some steps in digestion that may go awry, some behaviours and substances we (might) use every day can contribute to its malfunction.  So, we’ve included why and how below.


Whether they be prescribed or recreational, the use of certain drugs can definitely block up your digestion. 

  1. The overuse of antibiotics is notorious for contributing to bacterial overgrowth.  While this might seem contradictory, killing off the healthy bacteria in your gut provides an opportunity for pathogenic strains to take over.  
  2. The use of Proton Pump Inhibitors (PPIs) can also impede digestion.  Because they block acid, they often impair digestion in the upper GI and every other successive reaction that depends on the release of stomach acid.  While these acid-blocking medications are often prescribed for heartburn and acid reflux, these conditions have actually been linked to low stomach acid!
  3. Over-the-counter anti-inflammatories like naproxen, ibuprofen, and acetaminophen are known for their harmful effects on gut health.  These medications work by inhibiting substances that produce mucus in your GI tract, which helps to lubricate it and keep it safe from damage.  Thus, some of them contain stomach bleeding warnings and have been linked to intestinal permeability (i.e., leaky gut).  Others are somewhat hard on the liver, too.
  4. While the use of high-strength pain medications is sometimes inevitable, long-term use of prescriptions like hydrocodone, morphine, and other similar opioids can retard the movement of your GI system (ever had to take MiraLAX when you were on them?).  This keeps you constipated, which can contribute to toxin reabsorption and bacterial overgrowth.

Environmental Pollutants. 

While it can be easy to steer clear of pills and prescriptions, avoiding environmental pollutants may not be so easy.  Chlorine in water may be one of the biggest threats to the gut microbiome, as chlorine’s disinfectant properties make it a potent antibiotic!  Aside from chlorine, bacteria and viruses can lurk within your tap water, which undoubtedly can affect your gut long term.  There are also tons of substances in our air, food, water, and even skin products that can influence the health of our microbiome.  


Alcohol might sound like a no-brainer, but we wanted to include it and explain why it might be rough on your GI tract.  The mucous cells of the stomach are responsible for protecting the delicate cells lining the GI tract, like the stretched sheet over your mattress.  Without it, the lining of your stomach and intestines is a bit bare. 

Alcohol is known to damage these mucous cells and breach the mucosa, which can interfere with GI function.  Alcohol is also inflaming, which can bring on conditions like gastritis on its own.  While we can go on and on about the detriments of alcohol, one last thing to note is that we must use the nutrients we need for digestion to metabolise them.  So, a lot can suffer here!


Smoking has a couple of downsides, but several of them come back to its effects on digestion.  Studies have shown smoking increases someone’s risk for Inflammatory Bowel Diseases (IBD) like Crohn’s and Ulcerative Colitis.  Smoking is also linked to heartburn, peptic ulcers, and gastroesophageal reflux (GERD).  It’s also been shown to decrease gastric acid and mucosal secretion.   

A Nutrient-Poor, Inflammatory Diet

Because nutrients catalyse digestive processes, eating a nutrient-poor diet will likely impair your ability to break down food.  Additionally, processed foods—especially those from hard-to-digest industrialised grains—are tough to break down and often pass through the digestive system in a poorly digested state. 

Not only can this give bacteria a medium to fester on, but it can also cause inflammation in your GI tract.  Over time, maldigested food can contribute to breaks in those tight gap junctions between cells and damage the microvilli atop cells that help facilitate absorption.  This is precisely how food sensitivities develop!

Nutrient Deficiencies

As we mentioned in our last point, the vitamins, minerals, fatty acids, and amino in your diet help catalyse every bodily reaction.  Hence, not eating enough of these nutrients can inhibit digestion because we require them to move the muscles of the bowels, synthesise digestive juices and hormones, and regulate processes.


Have you ever felt queasy and experienced indigestion before or after something stressful, like a big game, workout, meeting, or presentation?  When stressed, our bodies enter a sympathetic state or a ‘fight-or-flight’ state.  If you remember from earlier, this means digestive processes are halted as your body perceives it’s trying to survive. 

Instead of producing saliva, stomach acid, bile, pancreatic enzymes, or moving matter through your intestines, your body is trying to get away from that lion it thinks it’s trying to outrun or it’s trying to climb over that cliff edge it thinks you just fell over.

Poor sleep

How do you feel when you don’t get enough sleep? 

Studies have shown links between poor and irregular sleep habits to just about anything, whether it be hormone imbalance, diabetes, autoimmunity, neurodegenerative conditions, and even cancer. 

Our sleep sets our body’s internal clock or circadian rhythm.  So, poor sleep can throw off the hormones regulating digestion, stress levels (see above), and poop schedule.

What Does Digestion Have to Do with Nutritional Optimisation?

Flowers are pretty until you take their roots and water supply away.

Your iPhone is handy, too, until it goes without a charge for a day (or less).

While you might wonder why we decided to pivot and go into detail about digestion, it’s because nutrient density isn’t as powerful if this critical process isn’t working correctly.

We need digestion to work well to absorb what we eat.  Otherwise, those nutrients go in through you and make their way right on out.

We also need nutrients to make digestion work, as we need the raw ingredients to drive digestive reactions (amongst other things).

Digestion and Satiety

Through our satiety analysis, we have compiled and analysed data showing the relationship between nutrient density and how many calories you eat. 

Most—if not all—essential nutrients show an inverse relationship between calorie intake and the amount of a nutrient you consume.  Increasing your nutrient density means you get to consume more nutrients while consuming fewer calories. 

Per our multivariate analysis, some of the most satiating nutrients that provide the greatest long-term satiety effect are protein, calcium, potassium, sodium, fibre, riboflavin, pantothenic acid, and selenium.  Thus, if we aren’t consuming enough of these nutrients, we’re more likely to keep eating as our appetites send us in search of what we need.

While it’s easy to quantify and visualise the relationship between the quantity of each nutrient we are eating and the amount of calories we’re consuming, it becomes a bit harder to do the same because it’s difficult to quantify the amount of nutrients we are absorbing. 

However, from our multivariate analysis of the relationship between nutrient density and satiety, we could infer that the more nutrients we absorb, the more likely we are to feel satiated, eat less, and stop eating before we overconsume energy beyond what we truly need.  Thus, improving our digestion would likely improve the satiety factor of our nutrient-dense food, too!

Aside from this concept, it’s important to highlight those imbalances within the gastrointestinal system, like bacterial overgrowth, can lower satiety.  Have you ever felt insatiable cravings for sugar and starch no matter what you do? 

While a few things can contribute to these cravings, it’s important to note that bacteria, yeasts, and even parasites feed off of sugars found in a lot of processed foods.  But those microbes have to eat, too!  

A healthy microbiome contains a complex array of many bacteria.  But ultra-processed foods tend to feed some while others whither, leading to an overgrowth of ‘bad’ bacteria. 

The bottom line is that optimising your digestion will not only improve your ability to absorb your food which will give your cravings a run for their money, but it will also quell the critters that could be inexplicably revving your appetite. 

Digestive Health and Autoimmunity

The presence of autoimmune diseases, or diseases that result from the body attacking its own tissues, is steadily on the rise.  This includes, but isn’t limited to:

  • Rheumatoid arthritis (RA),
  • Multiple Sclerosis (MS),
  • Systemic Lupus Erythematosus (SLE),
  • Hashimoto’s,
  • Grave’s disease,
  • Ehler’s Danlos,
  • Sjogren’s disease,
  • Crohn’s disease,
  • Ulcerative colitis,
  • Type-1 Diabetes (T1D), and
  • Scleroderma.

So, what’s making these once-rare conditions now so prevalent?

Around 60% of your immune system sits on the other side of your gut.  Because this is the main tube, or what you could think of as the ‘main highway’, from outside the body, your defences aren’t far behind.

If you recall, your gut is lined with cells one layer thick, known as enterocytes.  These enterocytes are essentially ‘glued’ together with tight gap junctions, which keep the contents of your gut from ‘slipping between the cracks’ of your gut cells.

Now, when you’re eating a ton of hard-to-digest processed foods, have a lot of bacterial overgrowth, are drinking alcohol, or have any gut inflammation, these tight gap junctions aren’t very tight anymore.  As a result, food that isn’t fully digested starts to slip through the cracks into your bloodstream.

As a result, immune cells patrolling your circulation on the other side recognise it, signalling to other cells there’s an invader.  Now, some of these proteins in your food can mirror various parts of your body; this is known as molecular mimicry.  Subsequently, your body might start to attack an organ system, which could segue into an autoimmune condition.

Interestingly, some of the most common allergens—gluten, corn, and soy—contain proteins that are known to mimic the thyroid gland.  Hence, the removal of some foods can help to bring down inflammation and minimise the activation of the immune system in the body. 

Chinese medicine refers to the gut as the second brain, and it’s no wonder why!  Once this important tube goes awry, other tissues and organs that depend upon it can fail.

Digestion and Metabolic Syndrome

Metabolic syndrome and conditions stemming from it often result from a conglomerate of things gone wrong.  One of those things seems to be poor gut health and an unhealthy microbiome.

It’s not surprising that constantly feeding on ultra-processed food creates an overgrowth of some bacteria and excessive growth in the human host. 

Many studies have shown links between poor gut health and metabolic syndrome.  While this might be somewhat of a ‘chicken or egg’ thing (i.e., is it the metabolic syndrome causing an unhealthy gut and poor digestion, or is an unhealthy gut and poor digestion causing metabolic syndrome), there are some good indications the latter may be at play.

Various strains of microbes in the gut are known to contribute to metabolic syndrome; many are known to fester in high-sugar and high-starch environments, which are both characteristics of a highly processed diet.

On the other side of the chicken-or-egg equation, metabolic syndrome is associated with conditions affecting many digestive organs, like acid reflux—which may make someone choose to go on PPIs—Non-Alcoholic Fatty Liver Disease (NAFLD), gallbladder disease, irritable bowel syndrome (IBS), diverticulosis, diverticulitis and pancreatitis.

Using your newfound knowledge of digestion, you probably know that impediments in any organ system can negatively affect digestive function.  For example, food is not digested if stomach acid, bile, or pancreatic enzymes are not released.  If their gut is inflamed, nutrients aren’t absorbed.  And if someone is constipated, there are ill effects related to autotoxicity.

Whether or not metabolic disorders directly cause the conditions listed above is a little hard to say.  Instead, most research shows they likely stem from similar root causes as metabolic diseases: energy toxicity, nutrient deficiency, and eating inflaming, ultra-processed foods.


  • Getting plenty of nutrients from your food is only part of the story.  You also need to absorb them effectively for them to be used by your body.
  • Your digestive tract is fascinating and complex, and many things can go wrong if we don’t look after it. 
  • Fortunately, consuming a nutrient-dense diet with fewer processed foods will give you a better chance of having healthy digestion, ensuring all the valuable nutrients in your food make it into your body to be used. 


6 thoughts on “Decode Your Digestion: Unleashing the Full Potential of Your Diet”

  1. Much gratitude for your efforts Marty. To you and your family’s health in 2023.

    I don’t know much about the vagus nerve – does this impact upon digestion also?

    • Thanks Helen. If you’ve got your stress in check, you’ll be doing what you can to manage the vagus nerve.

  2. What a great read. So much ‘food for thought’. This really helps explain the downward spiral that happens when we don’t prioritize nutritious food. Although I think it is intuitive that eating heavily processed foods isn’t good for us, it is nice to understand the ‘why’s’ behind it as I think that will help us make better choices (at least I hope it will help me).

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