Three Reasons Why Your Brain Needs Stomach Acid

Laura Duffy
Feed Your Brain
Published in
8 min readFeb 24, 2021


Stomach acid is essential and is involved in mood, learning, and neurological disorders.

Photo by Pierre Acobas on Unsplash

A growing body of research is shedding light on the intimate connection between your gut and brain. While most of the studies focus on the billions of microbes inhabiting your intestines, research is beginning to reveal that this “gut-brain axis” includes multiple factors, such as how well you are able to digest your food. This process relies on something that acid-blocking medications have falsely demonized — stomach acid.

All too often, stomach acid is viewed as irrelevant. Suppressing it before it can cause problems like heartburn has become commonplace. In 2014, the U.S. Food and Drug Administration approved powerful, acid-blocking medications for over-the-counter use, adding to the arsenal of relief for any self-diagnosed indigestion. Since then, acid-blocking medications have exploded in popularity. They are given to babies and adults alike, often on a long-term basis. Approximately 60% of therapy initiated in a hospital setting is considered “inappropriate.”

While this was once considered perfectly safe, side effects that have emerged over the past decade suggest that acid-blocking medications may not be as harmless as once thought.

The Risks of Suppressing Stomach Acid

In 2012, the FDA published a warning that acid-blocking medications, like Proton Pump Inhibitors (PPIs), increase the risk of Clostridium Difficile, a bacterium that can cause a dangerous infection in the GI tract. Recent research has also shown that long-term use of acid-blocking medications may increase the risk of complications elsewhere in the body, like the bones and kidneys. Pneumonia, bone fractures, and chronic kidney disease are more common in people taking acid-blocking medications long-term. A large 2020 study published in the International Journal of Environmental Research and Public Health even showed that adults taking acid-blocking medication had a significantly higher risk of developing dementia. This study showed a clear association between the dose and duration of both PPI medications and H2 blockers (another type of acid suppressant) — the risk for dementia increased in tandem with the amount of acid-blocking medication prescribed during the 5-year study period.

As you ponder how medications that block the production of acid in the stomach could possibly affect the brain, let’s take a step back and review how stomach acid fits into the process of digestion.

Stomach Acid 101

Digestion largely begins in the stomach, where hydrochloric acid (HCl) is released in response to eating. Once food reaches the stomach, muscles in the stomach wall churn and mix that food to ensure that it is bathed in acid. HCl begins to break proteins, which are made up of amino acids, into smaller fragments called peptides. Vitamin B12 is separated from its protein carrier, and minerals like calcium, magnesium, and iron are converted to a form that can be absorbed when they reach the intestines.

After food passes into the intestines its acidity is neutralized, and enzymes complete the process of digestion. Peptides, the fragments of partially digested protein, are further cleaved into individual amino acids before being absorbed through the intestinal wall. Minerals like calcium, magnesium, and iron are absorbed and vitamin B12 is bound to intrinsic factor so it can be absorbed in the latter part of the small intestine. Without stomach acid and intrinsic factor, vitamin B12 passes through the intestines and out of the body.

By understanding the process of digestion, you can see how skipping the entire first step in the stomach could be problematic. Without sufficient acid, proteins do not get “predigested”, so they pass into the intestines in fragments larger than the intestinal enzymes were designed to handle. As a result, proteins are not digested effectively, nor their amino acid components absorbed. Vitamin B12 and mineral absorption also suffer, which explains why research has shown that long-term PPI users have lower B12 and magnesium levels and are more likely to suffer from bone fractures.

These nutrients affect more than the strength of your bones. Your brain needs these nutrients, too.

Why is stomach acid essential for your brain?

Much of your mood, memory, and ability to focus are governed by neurotransmitters, chemicals that transmit signals in the brain. Antidepressant medications called SSRIs (selective serotonin reuptake inhibitors) and SNRIs (serotonin and norepinephrine reuptake inhibitors) work by keeping more of these neurotransmitters in the brain. Therefore, more serotonin is available to create feelings of happiness and contentment. Other neurotransmitters like dopamine, epinephrine, and norepinephrine are responsible for feelings of energy, reward, and motivation. GABA creates a feeling of focused relaxation, while acetylcholine has been linked to learning and memory. All of these neurotransmitters must be in balance for you to feel happy, content, and focused.

Where do these neurotransmitters come from, you ask? Neurotransmitters are made from amino acids, the building blocks of protein, with the help of vitamins and minerals in food. This brings us to the first reason that stomach acid is essential for brain function.

Reason #1: Stomach Acid is Essential for Digesting the Nutrients needed to Make Neurotransmitters

Without HCl, proteins are not adequately digested and absorbed. This can result in a compromised ability to make neurotransmitters. Furthermore, turning amino acids into neurotransmitters requires a number of vitamins and minerals. Many of these cannot be extracted from food without stomach acid.

The vitamin that is the most compromised by a lack of HCl is vitamin B12. It is used to make almost every neurotransmitter noted above, along with myelin and oligodendrocytes, which insulate and facilitate connections between neurons. The nervous system cannot function without vitamin B12, which explains why so many symptoms of B12 deficiency are neurological and include dementia, memory loss, difficulty concentrating, mood changes, difficulty walking, and numbness and tingling in the extremities.

Several minerals are also needed to turn amino acids into neurotransmitters, but two minerals, in particular, are poorly absorbed without adequate stomach acid: magnesium and iron.

Magnesium is an essential mineral used in over 300 metabolic reactions throughout the body, including many relating to mental health. It regulates several neurotransmitters, including serotonin, the “happy” neurotransmitter, and GABA, the “relaxing” neurotransmitter. Scientists are now starting to view magnesium as being so crucial for the brain that in the journal Nutrients, researchers from the Department of Psychology, Behavior, Cognition, and Neuroscience at American University in Washington, DC stated the following:

“Magnesium is a mineral of intense interest for the potential prevention and treatment of neurological disorders…There is strong data to suggest a role for magnesium in migraine and depression, and emerging data to suggest a protective effect of magnesium for chronic pain, anxiety, and stroke” (source).

Given the importance of magnesium, it is alarming that patients taking acid-blocking medications for several years have been reported to have lower magnesium levels and even severe magnesium deficiency.

Another mineral that is poorly absorbed without stomach acid is iron. The creation of red blood cells that deliver oxygen all around the body is dependent on iron. The brain is particularly susceptible to a drop in oxygen levels, making iron critical for mental health and cognitive function. Indeed, research shows that people with iron deficiency anemia are more likely to suffer from psychiatric disorders.

However, the role of iron in mental health goes beyond oxygen transportation.

The Linus Pauling Institute at Oregon State University explains that iron is needed for the creation of multiple neurotransmitters and for oligodendrocytes, the cells that insulate and protect neurons in the brain. Without enough iron during development in the womb and during childhood, children have a higher risk of impaired cognitive development and learning disorders. This makes the rapid increase in the number of pregnant women and babies taking acid-blocking medications over the past 20 years especially alarming. Between 1999 and 2004, prescriptions of PPI medications for U.S. infants less than 6 months old increased more than 7-fold.

Your brain requires an adequate supply of these micronutrients to function optimally. With studies showing that long-term users of acid-blocking medications have lower levels of B12, iron, and magnesium, it’s no wonder that the rate of mood, learning, and neurological disorders have skyrocketed in tandem with the rise in acid-blocking medications.

Reason #2: A Lack of Stomach Acid Makes Your Microbiota Miserable

Impaired absorption of amino acids, vitamins, and minerals can make it difficult for the body to get what it needs to make sufficient neurotransmitters. But the consequences of insufficient HCl do not end there.

In addition to predigesting proteins and aiding in vitamin B12 and mineral absorption, stomach acid also helps regulate the bacteria that reside in the gut, collectively called the microbiota. Bacteria in your food that might otherwise make you sick are killed when they reach the powerful acid in your stomach. Ironically, while stomach acid kills some bacteria, it also creates an ideal environment for others.

Research published in the World Journal of Gastroenterology in 2019 revealed that acid-suppressing medications cause an overall shift in the population of bacteria inhabiting the gut.

“Chronic treatment with PPIs strongly impacts small intestine microbiota and, in particular, causes small intestinal bacterial overgrowth (SIBO), likely due to the loss of the gastric acid defensive barrier.” (source)

SIBO is found in almost half of all patients diagnosed with IBS and it can cause a wide array of digestive symptoms. SIBO can also cause malabsorption and nutrient deficiencies, which can further deplete the body’s resources to make neurotransmitters. On top of that, the bacteria that overgrow in SIBO produce inflammatory compounds that promote systemic inflammation. Scientists believe that these inflammatory compounds explain why dysbiosis is associated with depression and autism.

Reason #3: The Inflammatory Cascade that leads to Leaky Gut and Leaky Brain

The inflammatory compounds produced by a gut inflicted with SIBO cause inflammation of the cells making up the intestinal wall. When these cells become inflamed, they are no longer able to maintain a barrier that keeps large particles in the intestines while allowing small particles, like nutrients, to pass through into the bloodstream. This syndrome is called leaky gut, or intestinal hyperpermeability. Like dysbiosis, it has been linked to an increased risk of mood and psychiatric disorders.

Research comparing depressed and suicidal patients with healthy controls found that markers of leaky gut correlated with higher measures of inflammation — as both increased, so too did the risk of suicidal behavior and severe depression. Other brain disorders share this correlation. Research has repeatedly shown that patients with autism are more likely to have leaky gut, and the correlation is also being made with Alzheimer’s disease.

A leading theory explaining the connection between leaky gut and disorders of the brain revolves around the barrier protecting the brain called the blood brain barrier (BBB). This barrier is remarkably similar to the intestinal wall. It is composed of a single layer of cells, connected by tight junctions. According to research published in the journal Nutrients,what had been able to make the intestinal barrier more leaky can also have the same effect on the BBB.” In essence, the same inflammation that can lead to a leaky gut can also lead to a leaky brain.

Thus, the name “gut-brain axis” encapsulates this connection between stomach acid, dysbiosis, inflammation, leaky gut, and psychiatric disorders. Stomach acid is not the enemy — it is produced by our body for a reason and is essential for digestive and mental health. In fact, having low stomach acid is often the point of origin in the gut-brain axis for the cascade of digestive, mood, and neurological disorders that are becoming so common.

Viewed as a whole, this research shows just how important stomach acid is for your mental health. It is essential for the proper digestion of proteins, minerals, and vitamin B12, so they can be used to make neurotransmitters. Stomach acid is crucial for keeping the probiotics in your gut happy, allowing you to absorb nutrients effectively, produce neurotransmitters and subdue inflammation so it does not become systemic and lead to a leaky gut or leaky brain.

Our bodies are made up of a symphony of systems, working together to create harmony. If one system is out of balance, other systems will be affected. Stomach acid is just one element that needs to be considered in the overall picture of mental health.



Laura Duffy
Feed Your Brain

Graduate student. Food blogger. Nutritionist. Busy mom. Spreading hope by sharing all I’ve learned throughout my lifelong journey with depression & anxiety.