The 6 digestive processes - and how they can often go wrong

Feb 23, 2021
how digestion goes wrong

For those of us who don’t suffer from any sort of regular digestive distress, it may feel counter-intuitive to address other health issues by starting with digestion. After all, what does digestion have to do with joint pain, headaches, insomnia, hormonal imbalance, etc?

A whole lot! In the context of the immune system, especially, digestion serves as a major driver of dysfunction. 70% of all immune cells in our bodies are located in the gut, making digestion a fundamental leverage point for regulating immune processes. Often, by resetting, resealing, and repopulating the digestive tract, we can also re-balance and normalize our immune responses – all in one fell swoop.  

Digestion, the act of intaking and converting food into substances that can readily be used by the body for energy and tissue regeneration, is a North to South cascade of processes beginning in the brain and ending in the colon. It can be categorized into six main processes: ingestion, mixing and propulsion, secretion, digestion, absorption, and defecation.

These processes, in turn, take place in five major organ systems: 1) the brain, 2) the mouth, 3) the stomach, 4) the liver/gallbladder/pancreas/small intestine, and 5) the large intestine.

(1) Ingestion

Digestion starts in the brain (1). When food is seen or smelled, the brain immediately begins to signal for increased saliva and stomach acid secretions in preparation for food intake.

After a bite is taken, the mouth (2) engages in chewing and tasting. Chewing mashes and crushes the food, preparing it for efficient chemical breakdown in the stomach, while saliva pre-digests carbohydrates using an enzyme called amylase.

The act of tasting food is not only crucial for deriving pleasure from a meal, it also serves as an important signal to the rest of our digestive tract. For example, eating something sweet will signal to the pancreas that it needs to begin producing insulin hormone, and eating something bitter – a taste often associated with poisonous plants – will signal stomach acid to increase in order to neutralize any threat.

(2) Mixing and propulsion

The mixing process begins in the mouth with chewing, and continues in the stomach with manual mixing and churning. This works to expose the food contents to potent Betaine Hydrochloric acid at every possible angle. Later, in the intestines, continuous contractions called peristalsis ensure the food continues to move steadily along the digestive tract until it’s ready to be eliminated.

(3) Secretion

Once we’ve swallowed, ingested food moves down our esophagus and into the stomach (3). There, acid secretion kicks into high gear, turning the food into a liquid substance called chyme. These secretions continue when the chyme enters the small intestine, where pancreatic enzymes and bile from the liver and gallbladder aid in further breaking down food particles.

(4) Digestion

After the acidic chyme exits the stomach environment and enters the small intestine (4), a hormone called secretin signals the release of an alkalizing agent. This ensures the pH of the chyme is neutralized so that it won’t burn the sensitive intestinal lining.

While nature designed the stomach to withstand its own potent acid, intestinal tissue is geared towards absorption and relies on a lining that is only one-cell-thick to separate the lymph and bloodstream from the chyme. This makes it especially susceptible to irritation.

Once a neutral pH, the chyme is subjected to enzymes from the pancreas (4a), and bile from the liver (4b) and gallbladder (4c). These substances work to break the fats, proteins, and carbohydrates into their most reduced forms: fatty acids, amino acids, and glucose, respectively. They are now ready to be absorbed, transported, and used efficiently by the body.

(5) Absorption

The bulk of absorption happens in the small intestine, where tiny extensions in the intestinal lining called villi and micro-villi work to increase the surface area where nutrients can permeate through the intestinal wall and make their way into the bloodstream. Later in the colon (5), any stray nutrients that haven’t been absorbed are squeezed out, and precious water is recycled.

(6) Defecation

After all of the useful contents of the food have been extracted by the body, waste material forms into feces in the colon. A healthy balance of intestinal flora is crucial for ensuring that the contents of this waste do not become toxic or recirculate. In fact, beneficial microbes will actually work to convert waste material into nutrients such as short chain fatty acids, vitamin K2 and B vitamins. The microflora also play a major role in ensuring that the bowel is evacuated regularly and completely.


Common drivers of digestive dysfunction


Feeling stressed? Better wait to eat dinner. Ever notice that when you feel nervous or agitated your appetite disappears? Think before a big speech when you have butterflies in your tummy. Do you feel like eating? That’s no coincidence.

Digestion occupies approximately 10% of the body’s energy over the course of an average day. An active stressor can put the body in a state known as a sympathetic nervous system response, or “fight or flight” mode. Throughout our evolutionary history this was likely a matter of life and death.

The body was forced to constantly ask: do I want to put my energy into sprinting away from this bear and surviving, or would I rather put my energy into digesting these berries?

In these scenarios it’s no wonder the body makes the executive decision to allocate its energy into dealing with the stressor rather than food

Most of us in modern life are subject to heaps of chronic stress that our ancestors were not, turning the act of daily digestion into a difficult prioritization trick for the brain. This can result in insufficient secretions, slow motility, and incomplete digestion, which, as we’ll discuss below, is the perfect recipe for inflammation and immune dysfunction. In order to optimize the energy your body can devote to this important task we need to be in a relaxed, parasympathetic state before we take our first bite.

Unchewed food

It isn’t uncommon in this day and age to eat the majority of our meals while staring at some kind of screen, while over a kitchen sink, or even while driving in the car. We’ve become increasingly disconnected from our food choices, as well as the physical act of eating itself.

The processed foods ubiquitous in the Standard American Diet (SAD) are low in fiber and require very little chewing, which can lead to a sort of conditioning that causes trouble when we switch to a fiber-rich whole-foods-based diet instead.

Yet, failing to properly chew our food places a greater burden on our digestive secretions to sufficiently break down the food we eat so that it can be absorbed and used by the body. This becomes an even bigger problem in the context of modern life, where most people are already short on these secretions for a myriad of reasons discussed below. Taking the time to mindfully chew our food before we swallow it – especially if we are eating a raw or fibrous vegetable – can mean the difference between proper function and dysfunction.

Too little stomach acid

Stomach acid serves multiple purposes. Did you know stomach acid is part of our immune system? It serves as a natural barrier defense against any foreign invaders that might enter our body through food. Without sufficient supply, our susceptibility to infection markedly increases.

We also depend on stomach acid to break down the food we ingest so that it is in a usable form for our bodies. If there isn’t enough acid, food particles can remain largely intact and cause trouble in the intestines (see below). We can also suffer from nutrient deficiencies as normal acid levels are necessary for most nutrient absorption, especially minerals.

Finally, the specific acidity of the stomach, between a pH of 1.5 – 3, triggers other necessary digestive processes. For example, the lower esophageal sphincter relies on this specific window of acidity to tell it to close, which prevents GERD (acid reflux). When the acid is less strong, at a pH higher than 3, it isn’t strong enough to send the signal but is still acidic enough to cause damage. This results in the esophageal sphincter remaining open and acid creeping up accordingly, causing tissue burns. Counterintuitively, GERD can be understood to actually be an acid shortage rather than an oversupply.

Likewise, the acidic pH of the chyme also works to signal alkalizing agents in the small intestine, which in turn, trigger the release of pancreatic enzymes and bile from the liver and gallbladder. Without enough acid in our chyme, the alkalizing agent never gets signaled to release, resulting in the chyme burning the small intestine and causing problems like duodenal ulcers. The lack of alkalinity then fails to signal the necessary enzymatic and biliary activity.

Proper pH of the stomach is a fundamental pillar of good digestion and a very common deficiency. Culprits for stomach acid suppression include stress, too many sugary foods or starchy carbohydrates, nutrient deficiencies, and, of course, stomach acid suppression drugs such as Prilosec.

Pancreatic enzyme shortage

Our endogenous supply of pancreatic enzymes work to breakdown proteins, carbohydrates, and fats, so we need an ample supply in order to optimize absorption and digestion. Some experts theorize that each of us is born with a finite capacity to produce these enzymes in our lifetime, sort of like the amount of eggs in the ovaries for females. Trouble can arise from SAD diets because we eat so much “dead food” or food devoid of enzyme activity. This places a heavy burden on our pancreas to secrete enough enzymes in order to move this food through our systems. The chronic overburden can result in malfunction, usually manifesting in digestive distress, conditions like metabolic syndromes, or even pancreatic cancer.

Just like dysfunctions for the previous steps, enzyme deficiency can result in food particles being incompletely digested and thus prone to causing damage elsewhere in the body. Supplementing our endogenous enzyme supply with enzyme-rich food sources such as fermented vegetables, can take the pressure off our pancreas and keep things running smoothly.

Biliary stagnancy and congestion

The lifetime of ill-informed dietary advice that embraces a low, no, or poor-quality fat diet has really done a number on our collective bile health. When we don’t consume enough quality fats in the diet our bile can become thick, viscous, and difficult to move.           

As bile is necessary for the absorption and utilization of fats, this stagnation can result in fatty acid deficiency, which contributes to all kinds of common symptoms such as hormonal imbalance, constipation, blood sugar swings and overeating, and skin issues. Conversely, eating plenty of high-quality fat can provide the raw materials for thin, and easy flowing bile. To learn more about how to support bile flow, check out this article.

In the case of those who have had their gallbladders removed, supporting bile health is especially important. While made in the liver, the gallbladder acts as an important storage and back-up housing for bile that can be used at the ready when digesting fat. Those with no gallbladders should introduce extra liver support to ensure it does not experience congestion trying to keep up with production.

Often for those with poor quality bile, or low supplies of bile (no gallbladders), fats don’t get absorbed and emulsified so they move on to the colon instead as waste products. In the colon they sit and become vulnerable to rancidification and inflammation, resulting in toxic byproducts that can cause unpleasant symptoms and conditions such as constipation.

A leaky gut

Our gut lining is only one cell thick – a fact that makes the tissue especially adept at absorbing the maximum amount of nutrients from the food we eat. Yet, because of the fragile nature of the epithelium it is also vulnerable to stressors that can cause abnormalities in its structure. If, say, for any of the myriad of reasons previously listed, a piece of undigested food makes its way past the stomach and into the intestines, that food is poised to do a great deal of damage. The sheer size of it may result in tears in the intestinal wall. Once these tears are present, food can slip out into the blood stream without going through the proper filtering channels that are typically required.

These tightly regulated processes are usually governed and calibrated based on our nutritional needs, allowing our body to pick and choose what it wants carefully and deliberately. This system also prevents any microbial invasions that may have made it past the stomach acid barrier from entering the bloodstream. When the system becomes compromised, our susceptibility to an immune response, either to warranted invaders escaping the digestive tract, or to food particles that are harmless in the proper contexts, is inevitable.

Another cause of increased intestinal permeability is sensitivity to food. Common allergens such as gluten, casein or dairy, soy, nuts, and eggs all contain proteins that are fairly intensive for the body to break down, often resulting in immune reactivity. Gluten, in particular, has been shown to loosen what are known as “tight junctions” – the fasteners that hold the cells of our intestinal lining together. Supporting the potency of our digestive secretions can often prove useful in aiding our systems to more harmlessly shuttle these foods through the body, but people with very compromised guts will often see the greatest benefit from removing them completely while they work on repairing their intestinal lining.

To minimize your chance of developing a leaky gut, it’s crucial to address all of the northward steps that focus on proper food break down and to avoid foods that cause sensitivity or that damage your tight junctions, such as gluten.

Dysbiosis, or a microbial imbalance

Beyond the physical damage that can be affected by undigested food particles, they may also provide an unexpected feast for pathogenic microbes that can colonize the gut lining. These species also tend to compromise absorption by forming defensive biofilms and can cause tight junctions to loosen.

The explosive science on the microbiome indicates that its composition can largely dictate our susceptibility to illness, personality traits, and cognition. In other words, the health of your microbiome can dictate quality of life. When thinking about this idea, it is especially important to embrace a bio-individual approach. Since every person has a completely different composition of microflora, it follows that every person will be sensitive to, and will thrive on different foods.

The following are some common drivers of microbial imbalance:

  • compromised stomach acid secretion - this lowers the acid barrier and allows pathogens to enter and colonize normally sterile parts of the digestive tract

  • bouts of food poisoning that the body never overcomes

  • a round of antibiotics during a crucial development phase

  • favoring low-fiber and sugary starches such as refined grains rather than a whole-foods based diet - these types of sugars selectively feed bacteria and yeast infamous for causing trouble, while simultaneously starving the good guys, who prefer a diverse range of fibers found in whole plant foods

  • thyroid dysfunction

  • over-exposure to chemicals that work as antimicrobials - pesticides and herbicides on food, personal products, cleaning agents, etc.

  • being formula-fed as as baby (as opposed to breastfed)

  • being born via Cesarean section (instead of via the vaginal canal)

  • bathing too often, and having limited exposure to the outdoors or microbes in general

  • social isolation

Often, addressing dysbiosis can be done by tending to the northward steps in digestion. If the problems still persist, a unique protocol may need to be applied, involving a kill phase, a repair phase, and a repopulation phase. Always work with a practitioner before embarking on a protocol like this.

A sluggish colon

There are many potential drivers behind a slow moving colon. Instead of throwing over the counter or natural laxatives at the issue, it’s often useful to look northward. Bile support is commonly indicated. Undigested fats in particular can rancidify and become toxic in the colon, so it’s crucial to shuttle them out of the body efficiently and quickly. Further, bile works as a kind of lubricant for waste products as they pass out of the body. An imbalance can also be a likely culprit, whether that means an overgrowth of pathogens, normal microbes in the wrong places, or a lack of beneficial bacteria.

Probiotics and healthy fats can be a great way to get things moving. Contrary to popular wisdom, fiber can often exacerbate the issue as it works to feed the bugs causing the trouble!