Fatigue, Depression, & Protein Digestion: Connecting the Dots

written by Dr. Jamie Chan-Ortega, Ph.D. 9/26/20

TIRED. IRRITABLE. ANXIOUS, DEPRESSED. Chances are, one or more of these terms describes you or someone you know. It’s the epidemic of fatigue and mood disorders that’s been plaguing us Americans long before the coronavirus pandemic reared its ugly head, but that’s certainly seemed to intensify this year. Stress is at an all-time high for many people, and with increased stress comes poorer food choices, a decline in mood, and gut problems.

There are a multitude of reasons and causes for fatigue and depression. Some common causes are:

  • Childhood trauma
  • Sudden loss
  • Chronic stress
  • Strained relationships / social conflicts
  • Sleep disorders
  • Insufficient body movement
  • Nutrient deficiencies
  • Diet high in sugars and refined carbs
  • Hidden gut infections
  • Accumulation of toxins
  • The inflammation caused by all of the above

Typically, fatigue and depression are multifactorial in genesis, meaning there’s usually more than just one thing that’s causing you to feel tired and down. You may be working from home now and stuck on your screen more than ever before; you’re juggling your own work with your children’s schoolwork; you’re taking care of a relative, eating more drive-through and take-out, and you’ve stopped working out since the gyms closed due to the pandemic. All of these factors absolutely bear addressing. But for this article I want to focus on just one simple yet surprisingly common factor in the development of fatigue and mood disorders: protein digestion.

What protein does to the body?

We all know protein, right? It’s one of three macronutrients (the other two are carbohydrates and fats) and is most known for building muscle, maintaining healthy hair and nails, and healing tissues from injury. But proteins do so much more. Proteins make up the enzymes that jump-start millions of chemical reactions in our bodies, and are an integral part of the hemoglobin that carries oxygen in our blood. Most Americans consume more than adequate amounts of protein, so meeting one’s daily protein requirements is seldom an issue. The issue is if we’re breaking it down and absorbing it.


From the moment we begin to anticipate a meal, our stomach starts secreting hydrochloric acid in preparation for the food that’s about to come down our mouths and into our stomachs. Just seeing food and certainly chewing food stimulates our vagus nerve to send a message (via the neurotransmitter acetylcholine) to the parietal cells in our stomach to produce acid. This is called the cephalic phase of digestion.

Seeing/eating food → activates the vagus nerve → releases acetylcholine → sends a message to stomach to produce acid → acid fills the stomach

The truth of biology is that stomach acid is normal, necessary, and good. But stomach acid has gotten a bad rep, and I think a lot of it has to do with marketing campaigns promoting OTC and prescription antacids. We’ve been influenced to think that stomach acid is bad. But in scientific fact, stomach acid is a critical part of normal digestion. Acid is supposed to be released in the stomach when we eat for 4 super important reasons.

What are the four functions of stomach acid?

  1. Stomach acid kills harmful bacteria and viruses that enter our bodies via the foods we eat
  2. Stomach acid breaks down proteins into their absorb-able and usable form: amino acids
  3. Stomach acid shifts the pH of the stomach, which then triggers the release of digestive enzymes and bile to break down carbohydrates and fats
  4. Stomach acid cleaves vitamin B12 from proteins, readying it for absorption

How do you know if you lack stomach acid?

If we don’t have sufficient stomach acid, the above mentioned functions become impaired.

  • Our bodies can fail to neutralize harmful microbes entering the stomach, allowing them to infiltrate and infect our gut.
  • Insufficient stomach acid impairs the release of digestive enzymes and bile, resulting in poor digestion. 
  • Without enough stomach acid, the B12 bound to proteins in our food won’t get separated and made available for absorption and utilization by our cells. This can result in impaired energy production and fatigue. Since B12 is necessary for transporting oxygen through our bloodstream, insufficient B12 can result in fatigue and anemia. B12 is also necessary for a healthy nervous system, so without enough of it we can get muscle weakness, tingling and numbness, and difficulty walking and moving.
  • Lastly, if we don’t have enough stomach acid, we can’t fully break down proteins into amino acids. If a protein isn’t broken down fully, it’s called a partially digested protein. Partially digested proteins act as antigens that can trigger your immune system to attack and create inflammation (which in itself can trigger fatigue and depression). If the protein is fully digested, however, your body’s immune system will not be primed for attack, because a protein that is fully digested breaks down into amino acids, and amino acids do not trigger the immune system to attack. Your body will begin to use those amino acids to build muscle, hair, nails, enzymes, and most relevantly, neurotransmitters. Yes, your neurotransmitters are made up of amino acids. Think of the most commonly known neurotransmitters: serotonin and dopamine. They powerfully influence your mood, happiness, energy, appetite, sleep, motivation, and focus – and they’re made from the amino acids tryptophan and phenylalanine, respectively.

NUTSHELL VERSION: If you’re not breaking down your proteins into amino acids, you won’t be able to create sufficient neurotransmitters to balance your mood and energy, and you may trigger inflammation with these partially digested proteins, which will further drain your energy and throw off your mood and mental health. You also won’t digest and absorb B12.


This is a very common scenario and one that is handled quite erroneously by the medical community. The burning pain in your stomach and throat is in all likelihood NOT due to too much stomach acid production, but actually, not enough stomach acid and digestive enzymes. Without adequate amounts of stomach acid and digestive enzymes, food isn’t broken down and digested properly. These poorly digested foods begin to ferment, which results in gas. Gas pressure and stomach distention can push the stomach contents into the esophagus, resulting in the heartburn and esophageal erosion associated with GERD and indigestion. So the real cause of the burning pain is not excess stomach acid, but poor food choices and not enough digestive acid and enzymes to digest the foods, so the foods end up being fermented by bacteria in our gut.

What are the ways to increase stomach acid to digest proteins adequately? 

  1. Eat slowly and mindfully. When you eat calmly and with mindfulness (as opposed to eating while on your computer, phone, or doing work) you stimulate your friendly vagus nerve to send the message to your gut to produce acid, release digestive enzymes, and move the food along your digestive tract smoothly. If you eat when you’re stressed or distracted, your vagus nerve shuts down and so does your digestion.
  2. Get tested for hidden infections in your gut, particularly infections caused by helicobacter pylori. H. pylori is a common bacteria that infects your stomach, inflames your stomach lining, and neutralizes/weakens stomach acid. The ideal lab test you’d want to do is the GI-MAP test. It will detect if you have a gut infection like h. pylori, and it’ll also reveal if you have inflammation or leaky gut.
  3. Take Digestive Enzymes with Hydrochloric Acid (HCl). The digestive enzymes formulation I offer contains dozens of enzymes to break down starches, carbs, sugars, and fats, along with hydrochloric acid to fully break down your proteins into those amino acids your brain and body need to make neurotransmitters that control your mood and energy. It will also help you to digest vitamin B12. It’s one of the easiest things you can do to immediately begin improving your gut health, energy, and mood. You can purchase these digestive enzymes on my website or in-store at Oasis Healing Arts. Use promo code DIGEST10 to get 10% off through 10/5/20.
  4. Consider getting off of antacids like PPI’s (proton-pump inhibitors). These block your natural production of stomach acid and impair digestion. Get your diet right and work with your healthcare provider to wisely wean off your antacids.

Surely stress and psycho-social issues contribute to the development of fatigue and depression. But many times these are complex issues that can prove challenging to address, much less resolve. So it’s empowering to focus on the areas of our lives that are much more readily under our control, and those areas are diet and digestion.

  • You are in control over what foods you put into your mouth.
  • You are in control of how slowly and mindfully you eat.
  • You are in control over the supplements you purchase.

And you actually have power and control over the antacids you take – you could greatly minimize or eliminate antacids from your life if you optimized your diet.

So if you’re chronically tired and you struggle with low mood or outright depression, start here, with your protein digestion. It’s simple enough to tackle, and easy enough to correct. And always remember that what you eat, how you’re digesting, and how you’re feeling are intricately connected.

Where can I find the best functional medicine doctors near me in Whittier?

You’re feeling tired, irritable, and imbalanced but not sure what to do about it? Would you like expert medical advice to figure out the cause of your symptoms and start feeling your best? Our friendly and expert team will design a treatment plan unique to your condition and contributing factors.

No matter if you’re located in Whittier or elsewhere in the area, now is the time to take control of your health and schedule a video or in-person Functional Medicine consultation with Dr. Jamie to address your digestive health and get personalized medical guidance. Book online or give us a call at 562-789-1588!