Digestion and it’s Impact on Lyme: Part 1

This is a blog about Lyme Disease, so why do I stress so much importance on digestion? Gut symptoms are common in people with Lyme Disease. In fact, gut issues are common in people with all sorts of illnesses. When we look at the body as an interconnected world, we can understand why.

Here are just a few ways the digestive system affects other bodily systems:

  • The intestinal lining has a layer of immune cells, which keeps foreign pathogens (ingested along with food) out of our bloodstreams.
  • Digestive enzymes and stomach acids defend against pathogens.
  • Digestive enzymes break down foods.
  • The digestive system absorbs nutrients from broken down foods needed for hormone synthesis, neurotransmitter synthesis, for growth, repair and maintenance of organs.

This article will give you an introductory understanding of the digestive system, its components and how it works.

Digestion Metabolism Lyme Disease

Defining Digestion

The digestive system breaks foods down into smaller parts – molecules – so that these smaller parts can be absorbed into the bloodstream and metabolised by our cells. Put in other words, our digestive systems “eat” our foods, breaking them down into molecules, so that our cells can “eat” those molecules. Whatever is not broken down, becomes waste.

The digestive tract, or the gastrointestinal tract, begins with the mouth, continues to the pharynx, esophagus, stomach, small intestine, and large intestine, and ends with the anus (teehee). There are some “accessory” structures along the way: the teeth, tongue, salivary glands, liver, gallbladder and pancreas all have their roles in digestion.

Long Story Short

In the body, food is digested first, then absorbed into circulation, and then metabolised by cells. Then, the end game of cellular metabolism is the production of energy. Point by point:

  1. Food is digested.
  2. The digested version of food is absorbed into circulation.
  3. It’s metabolized by cells.
  4. Cells are fed and therefore acquire energy.


It’s slightly more complicated than that, so let’s get into more details. You don’t have to memorize any of this, but it’s worth understanding for as long as your memory permits.

It all starts with eating. The food we chow down needs to be broken down by various enzymes. This processes is called mechanical digestion, which involves chewing with your teeth and churning foods with your stomach.

Your food makes contact with the enzyme amylase in your mouth first. Besides amylase, your saliva also contains water and mucus. Amylase metabolizes complex carbs, or polysaccharides, so starchy foods already start breaking down into smaller molecules before swallowing your grub.

Your tongue forces your food into your pharynx – the passageway that connects your mouth to your esophagus. Then involuntary movements begin. From beginning to end, muscle contractions move the food-guck along through the digestive tract. These muscle contractions are known as peristalsis.

Food goes down the esophageal tube into the stomach, which has room to hold 1.5 to 4 liters of your favorite foods and beverages.

Once the food reaches the stomach, it needs to be broken down. How is this achieved? Gastric juices are secreted through tiny holes in the mucosa called gastric pits. Three types of cells make these juices: mucous cells, parietal cells, and chief cells. Typically 2 to 3 liters of gastric juices are produced per day. The mucous cells create – you guessed it – mucus, which protects the stomach lining. The parietal cells produce hydrochloric acid, which kills bacteria and increases stomach acidity required for enzymes to metabolize food. Parietal cells also release something that helps with B₁₂ absorption. Chief cells secrete something that later becomes pepsin (an enzyme that breaks down proteins).

Now that your foods are really mushed up in there, your body starts pinpointing carbohydrates, proteins and fats. These are broken down from complex molecules into simple molecules with the aid of water in a process called hydrolysis, as well as digestive enzymes. Chief cells create an active form of pepsin, which breaks proteins down into smaller units called peptides.

Another cell lives in the gastric glands: the endocrine cell. Interesting hey? When we think “endocrine” we think “thyroid.” But endocrine cells play a role in digestion, as well. Endocrine cells secrete the hormone gastrin into the bloodstream, which triggers the above mentioned cells (mucous cells, parietal cells, and chief cells) to produce their juicy secretions in the first place. Here is yet another way we see the interconnection between bodily systems and yet another reason why allopathic medicine is neglectful of the whole bodily picture. But I diverge.

Once these gastric juices turn your food into an even mushier product, now called chyme, a valve at the bottom of the stomach called the pyloric sphincter opens. Chyme enters the duodenum before entering the small intestine. In the U-shaped duodenum, intestinal hormones are released that signal the stomach to stop gastric secretions. After all, once the food has left the stomach, there is no more need for all that acidic enzyme action.

The chyme makes its way into the small intestine at a rate dependent on the health of the small intestine and on the content of the chyme. For example, liquids digest very quickly, carbs digest fairly quickly, proteins take a little longer and fats can take up to 6 hours to digest. Within four hours, generally speaking, all of the food will most likely be in the small intestine in its chymey state. The slower the stomach empties, the less nutrients get absorbed. Conversely, if the stomach empties too quickly, the acidic chyme can damage the mucus membrane of the intestinal lining.
It is important to note that all along the way, the brain is greatly involved in the stop and start actions of the digestive system. The brain, as well as your hormones, are involved in gastric secretions and in regulating stomach emptying.

Back to the duodenum for a moment: another feature is that it receives pancreatic enzymes and bile before finally emptying into the small intestine. Pancreatic amylase breaks complex carbohydrates down into disaccharides (double sugars). Trypsin, another pancreatic enzyme, breaks proteins down into amino acids, or peptides. And pancreatic lipase breaks down fats. The pancreas also contains bicarbonate ions, which neutralize acidity.

The end products of complex carbohydrate digestion are always monosaccharides – single sugars. Amylase breaks down carbs. Pepsin and trypsin break down proteins into amino acids – or peptides. Fats break down into monoglycerides and fatty acids. Fat molecules like to clump together, which makes it harder for enzymes to break them down completely. Hence, fats are emulsified in bile, which simply means that they disperse more there. It isn’t until pancreatic lipase acts on fat globules in the small intestine that fats really begin to break down.

The Small Intestine

Microvilli are hair-like fingers in the small intestines that grab and absorb nutrients. They also have other functions: they secrete yet more enzymes, including: peptidase, which breaks down remaining proteins into peptides; carb munching enzymes like maltase, sucrase and lactase; and lipase to break down fats.

Intestinal cells also secrete cholecystokinin, which signals the gallbladder to release bile, a fluid produced in the liver and stored in the gallbladder. Bile helps emulsify fats, neutralize acid, and eliminate damaged red blood cells and cholesterol. Through the digestive process, the liver assists with maintaining blood glucose levels by converting excess glucose into its storage form, glycogen. It breaks glycogen back down into glucose when the body needs an energy kick.

Sometimes the liver convert’s excess glucose and peptides into fats, and sometimes it converts fatty acids and peptides into glycogen; the conversion paths depend on the ratios of macronutrients you are putting into your body and the ratios that your body actually needs. The liver also has a role in protein metabolism: it converts amino acids into other amino acids, as needed, and it converts a toxic by-product of protein called ammonia into urea, which can be excreted in the bile.

The Large Intestine

There are many structures in the large intestine, but to keep it simple, the biggest feature is the colon, and the end feature is your butthole.

The large intestine is like a barren land; there are no villi and the walls of the colon are smooth. By the time the chyme reaches the large intestine, chemical digestion is complete. The only thing the large intestine actually secretes is mucus from its goblet cells. The mucus prevents tears and gives the colon a slightly alkaline pH. The main purpose of the large intestine is not to absorb nutrients, but to first absorb fluid and electrolytes, and then to eliminate the remaining waste.

Whatever is leftover – indigestible fibers, for example, need to be eliminated and there is one way out in a process fancily called defecation. As the rectum fills with waste, the defecation reflex is triggered and it’s time for a bathroom break.


Typically, ten liters of food and fluids are ingested every day. Nine of these liters get absorbed during digestion in the small intestine. In the end, all that we get rid of after the digestive process is roughly a liter of water, some undigested food and some bacteria, along with toxic by-products received from the bile.

The molecules that were previously broken down from carbohydrates, fats and proteins into simple molecules are absorbed mainly through the intestinal linings microvilli. Glucose (previously converted from carbohydrates) and amino acids (previously converted from proteins) are absorbed right into the blood capillaries and transported to the liver in the hepatic portal vein. Fatty acids, monoglycerides and fat-soluble vitamins are absorbed into lymph capillaries, circulating the lymph first before entering the blood stream.

Cellular metabolism takes over from here. Read more about that here.


This descriptive chapter on the digestive system may have seemed long to you, but that’s only a brief overview. There are many more features I overlooked so as to not overwhelm you even more. But at least now, if you hadn’t already, you have a basic understanding of your digestive system and how it interconnects with your brain, hormones, liver, hematological system and more. Re-read it a few times to understand which hormones play which roles. Perhaps there are a few things that stuck out to you that you can take a note of, and investigate with bloodwork at your next doctor’s visit.

Why It Matters

The digestive system is not an entity separate from other units of the body. It’s a hub where neurotransmitters, bacteria and immune cells hang out and interact. It’s a manufacturing plant that breaks food down into resources that can be shipped off to the other “islands” in the body. It’s so much more important to your health than I can express in words – and that includes your recovery from chronic infections.

Digestion and It's Impact on Lyme Part Two

In Part 2, I’ll go over 4 reasons why digestive health impacts Lyme recovery – digestion results in the break down of foreign invaders, it’s responsible for the elimination of toxins, it hosts about half of our immune cells in the intestinal lining, and it hosts ecosystems of “make-or-break” bacteria – all of which are hella important to fighting Lyme Disease.

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