The Hidden Consequences of Low Stomach Acid: How It Disrupts Digestion, Nutrient Absorption, and Overall Health

After publishing yesterday's article, a few people reached out asking for more details on how low stomach acid actually works. I assume they are looking for the biochemistry behind it, but in layman's terms. Since biochemistry is my forte, I decided to write this follow-up article, diving deeper into the mechanisms of stomach acid and its impact on health.

While I have covered this topic extensively in my published book, The Hidden Dangers of Low Stomach Acid available on Amazon and my digital book on the website, I believe a more accessible breakdown will help clarify its importance. 

Introduction

Many people assume that acid reflux, bloating, and indigestion stem from excessive stomach acid, but in reality, the opposite is true—insufficient stomach acid (hypochlorhydria) is a major underlying factor. Low stomach acid disrupts digestion from the start, creating a cascade of dysfunction that affects nutrient absorption, gut health, and systemic conditions like autoimmune disorders, chronic fatigue, and skin problems.

This article discusses the physiological consequences of low stomach acid, its role in chronic health issues, and why addressing it will usually lead to significant symptom relief.

Physiological Cascade of Low Stomach Acid

1. Impaired Protein Digestion

Stomach acid is essential for activating pepsin, the enzyme that breaks down large proteins into smaller protein fragments called peptides. These peptides then move into the small intestine, where enzymes trypsin and chymotrypsin further break them down into even smaller peptides. Finally, brush-border enzymes called peptidases complete the breakdown of peptides into individual amino acids, which can then be absorbed into the bloodstream.

Without sufficient stomach acid

Pepsin remains inactive, preventing proper protein breakdown. Undigested protein ferments and putrefies in the stomach, producing excess gas and increasing intra-abdominal pressure. This pressure usually leads to reflux and discomfort.

Bloating, fullness, and reflux often occur after eating, symptoms that are frequently mistaken for excess stomach acid rather than insufficient acid. This misinterpretation can lead to the unnecessary use of acid-suppressing medications, further worsening digestion.

Amino acid absorption is reduced, impacting critical functions such as muscle repair, neurotransmitter production, and immune system regulation. Over time, this deficiency can contribute to fatigue, mood imbalances, and increased susceptibility to infections.

2. Delayed Gastric Emptying & Reflux (GERD-like Symptoms)

Low acid prevents the lower esophageal sphincter (LES) from closing properly. As undigested food ferments and produces gas, stomach contents are forced into the esophagus, mimicking acid reflux symptoms. This often leads to misdiagnosis and unnecessary acid-suppressing medications, which further worsen the problem.

3. Small Intestinal Bacterial Overgrowth (SIBO)

Stomach acid is a natural disinfectant, killing ingested bacteria and preventing their overgrowth in the small intestine. Without enough acid, bacteria migrate downward from the stomach into the small intestine, leading to small intestinal bacterial overgrowth (SIBO) and fermentation of undigested carbohydrates, leading to bloating, gas, and diarrhea/constipation).

4. Poor Nutrient Absorption

Low stomach acid leads to deficiencies in essential nutrients:

• Iron: Fatigue, hair loss, anemia.
  
• Vitamin B12: Neuropathy, brain fog, mood disorders.
  
• Calcium & Magnesium: Osteoporosis risk, muscle cramps.
  
• Zinc: Weak immunity, poor wound healing, and hair thinning.
  

5. Gallbladder & Pancreatic Dysfunction

Stomach acid triggers the release of cholecystokinin (CCK), a hormone that stimulates bile flow from the gallbladder and enzyme secretion from the pancreas. Stomach acid also triggers the release of secretin, a hormone that stimulates bile production in the liver, and the release of alkaline bicarbonates from the pancreas.

Low stomach acid means weaker bile production and release, leading to poor fat digestion, gallbladder stagnation, and an increased risk of gallstones. Pancreatic enzyme secretion is also reduced, impairing carbohydrates and further protein breakdown, contributing to food intolerances and gut inflammation.

6. Increased Risk of Gut Inflammation & Leaky Gut

Undigested food particles and bacterial overgrowth irritate the gut lining, increasing intestinal permeability (leaky gut). This activates the immune system, triggering food sensitivities, autoimmune issues, and chronic inflammation.

Conditions Linked to Low Stomach Acid

Autoimmune Disorders

Examples: Hashimoto's, Rheumatoid Arthritis, Lupus

• Poor protein digestion leads to a leaky gut, triggering immune hyperactivity.
  
• Low stomach acid worsens inflammation and autoimmunity.

Observed Improvement:

•  Reduced antibody levels (e.g., anti-TPO in Hashimoto's).
•  Decreased joint pain and fatigue.

Anxiety & Depression

Symptoms: Panic attacks, brain fog, low mood

• Stomach acid is essential for amino acids needed to produce serotonin, dopamine, and GABA (key mood-regulating neurotransmitters).
  
• Low iron absorption further contributes to fatigue and depression.
  
• Gut dysbiosis caused by low stomach acid exacerbates brain inflammation.

Observed Improvement:

•  Enhanced mood, reduced anxiety, and better sleep.
•  Improved focus and motivation.

Skin Conditions

Examples: Acne, Rosacea, Eczema, Psoriasis

• A leaky gut from low stomach acid allows toxins into circulation, triggering skin inflammation.
  
• Nutrient deficiencies (zinc, B12) impair skin healing.
  

Observed Improvement:

•  Reduced acne, rosacea, and eczema flares.
•  Healthier, more radiant skin.

Chronic Fatigue Syndrome & Fibromyalgia

Symptoms: Low energy, muscle pain, unrefreshing sleep

• Low B12, magnesium, and iron absorption lead to mitochondrial dysfunction.
  
• Bacterial overgrowth (D-lactic acid, H2S) worsens fatigue and brain fog.
  
• Histamine buildup from gut dysfunction increases inflammation.
  

Observed Improvement:

• Increased energy, reduced muscle pain, and brain fog.
• Better sleep and recovery.

Hormonal Imbalances & PCOS

Symptoms: Irregular cycles, estrogen dominance, low testosterone

• Poor nutrient absorption reduces testosterone and worsens PCOS symptoms.
  
• Slow liver detoxification increases estrogen dominance, leading to PMS and weight gain.
  

Observed Improvement:

•  More balanced hormones, improved fertility, and better muscle mass.

Chronic UTIs & Bladder Issues

Examples: Recurrent UTIs, interstitial cystitis (IC)

• Bacterial overgrowth from SIBO increases the risk of urinary infections.
  
• Histamine intolerance worsens bladder irritation.
  

Observed Improvement:

• Fewer UTI episodes and IC flare-ups.
• Improved immune response.

Misinterpreted Symptoms & PPI Use

Many people who suffer from bloating, acid reflux, and indigestion often assume they have excess stomach acid when, in fact, their symptoms are a result of insufficient acid. Even though stomach acid is already low, some can still be in the stomach. When this acid refluxes into the esophagus (which has no protective lining), it causes burning and discomfort. PPIs and antacids neutralize or suppress acid, temporarily reducing the burning sensation and providing symptom relief—but not fixing the underlying issue (low stomach acid).

PPIs and antacids may provide temporary relief but exacerbate the root cause by further suppressing acid production, leading to:

•  Increased bacterial overgrowth (SIBO, H. pylori).
•  More bloating, indigestion, and nutrient deficiencies.
•  Chronic inflammation and systemic health decline.

Conclusion: It All Comes Back to the Gut

The body thrives on proper digestion, nutrient absorption, and microbial balance—all of which depend on healthy stomach acid levels. Addressing low stomach acid can help resolve GERD, SIBO, and bloating while improving systemic conditions like autoimmune disorders, fatigue, skin issues, and hormonal imbalances.

By optimizing stomach acid, we lay the foundation for better digestive health, immunity, and overall well-being.