Stomach Acidity, Dietary Intake, and the Microbiome
The Importance of the Gut Microbiome
In recent years, research into the human microbiome has expanded dramatically. The trillions of bacteria, viruses, and fungi that live throughout the body play an important role in health and disease. Alterations in the gut microbiome have been associated with obesity, non-alcoholic fatty liver disease, type 2 diabetes, cardiovascular disease, mood disorders, autoimmune diseases such as rheumatoid arthritis and type 1 diabetes, and many other chronic health conditions.
Researchers have identified numerous factors that influence the microbiome, including age, diet, geographic location, medication use, maternal microbiome, and mode of delivery at birth. Even medications that do not directly target the digestive tract, such as statins and antidepressants, can alter the composition of gut bacteria.
One often overlooked factor is stomach acid. While stomach acid is primarily known for its role in digestion, it also serves as an important regulator of the gut microbiome and a critical defense against infection.
What Animal Diets Teach Us About Stomach Acid
An interesting way to understand the evolutionary role of stomach acid is to examine differences among animal species.
Researchers have found that stomach acidity in animals is closely linked to dietary habits:
Herbivorous animals that rely on fermentation of plant fibers generally have less acidic stomachs.
Scavengers that consume carrion and are regularly exposed to potentially dangerous pathogens tend to have extremely acidic stomachs.
Omnivores, including humans, fall somewhere in between.
A large comparative study found that scavenging birds such as turkey vultures and buzzards had stomach pH values below 2, while herbivorous animals such as sheep, llamas, and sloths often had stomach pH values around 6 or higher.
Humans, as omnivores, typically maintain a stomach pH around 2.5, suggesting that stomach acid serves an important protective function against foodborne pathogens while still allowing a diverse gut ecosystem to thrive.
Why Stomach Acid Is Essential
Hydrochloric acid (HCl) in the stomach is a very strong acid (typically a pH of 1 to 3) and helps break down proteins and prepares food for digestion and absorption further along the gastrointestinal tract. An acidic stomach environment also acts as a natural barrier against potentially harmful bacteria, viruses, and parasites that may enter the body through our food and water supply.
Without adequate stomach acid, digestion becomes less efficient, nutrient absorption may decline, and harmful microorganisms may have a greater opportunity to survive and colonize the digestive tract. An acidic environment is necessary to denature proteins, that is, to allow the protein structure to relax so it can be further degraded by enzymes in subsequent phases of digestion.
Despite the importance of stomach acid, many people are prescribed proton pump inhibitors (PPIs), a class of medications that directly reduce our body’s natural acid secretion. Unfortunately, many individuals end up on these medications for a longer period of time than they are intended to be.
Aging, Low Stomach Acid, and Proton Pump Inhibitors (PPIs)
Stomach acid production typically declines with age. In one study of healthy adults between 80 and 91 years of age, 80% were found to have significantly reduced stomach acid levels, with an average pH of 6.6. Between the years of 1999-2000 to 2017-2018, the use of PPIs in US adults more than doubled from 4.1% to 8.6%, with the majority of these medications being prescribed to adults aged 55 years and older.
When we give an aging population PPIs, we are essentially worsening what already naturally tends to occur with age. And these medications are typically prescribed without even assessing stomach acid levels in the first place, so they may not even be therapeutically indicated.
The impact of PPIs on the gut microbiome is well established. Studies examining individuals who use PPIs have found significant changes in gut microbial composition, including reductions in microbial diversity and increases in bacteria associated with gastrointestinal infections.
Long-term PPI use has also been associated with an increased risk of Clostridioides difficile infection (commonly known as “C-diff”), a potentially serious gastrointestinal illness that can be difficult to treat, and even may be deadly in older adults. Long-term PPI use has also been associated in observational studies with increased risks of gastric cancer, osteoporosis-related adverse events in women and older adults, nutrient deficiencies, and even may increase dementia incidence at younger ages.
The research on the microbiome continues to evolve at a remarkable pace. Advances in microbiome sequencing, computational biology, machine learning, and artificial intelligence are helping researchers better understand how gut microbes influence digestion, metabolism, immune function, and mental health. The more we learn, the more it becomes clear that long-term suppression of stomach acid may have unintended consequences for overall health, not just microbial balance.
The Bottom Line: Stomach Acid Is a Good Thing
As research continues to reveal the complex relationship between digestion and microbial health, one thing has become increasingly clear: stomach acid plays a vital role in maintaining overall digestive wellness. While stomach acid can certainly contribute to symptoms such as heartburn and reflux, stomach acid itself is not the enemy.
At Gorge Naturopathic and Massage, we help individuals identify and address the underlying causes of digestive symptoms through naturopathic medicine, nutrition, lifestyle modification, and abdominal massage therapy. Rather than automatically suppressing stomach acid, treatment focuses on improving digestive function and supporting long-term gastrointestinal health whenever appropriate.
Written by Dr. Carrie Decker, ND
Frequently Asked Questions About Stomach Acid and Digestive Health
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Yes, in some cases. Low stomach acid may slow digestion and cause food to remain in the stomach longer, increasing pressure that can contribute to reflux symptoms. While excess acid can cause heartburn, low stomach acid is another potential contributor that is often overlooked.
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Proton pump inhibitors (PPIs) reduce stomach acid, which helps protect us from harmful microbes. Research shows long-term PPI use can alter the gut microbiome, reduce microbial diversity, and increase the risk of infections such as Clostridioides difficile (C. diff). These findings suggest stomach acid plays an important role in maintaining a healthy microbial balance.
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Common symptoms of low stomach acid include:
Bloating after meals
Excessive burping
Feeling overly full after eating
Indigestion
Nausea
Over time, low stomach acid may also contribute to deficiencies of nutrients such as iron, vitamin B12, calcium, and zinc.
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Abdominal massage may help reduce bloating, improve bowel motility, and support digestive comfort. It can also promote relaxation and activate the body's "rest-and-digest" response, which plays an important role in healthy digestion. For some individuals, abdominal massage can be a helpful addition to dietary and lifestyle approaches for digestive health.