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The Lower Esophageal Sphincter and Its Connection To Heartburn, Acid Reflux and GERD

When discussing the discomforts of heartburn, acid reflux, and GERD (Gastroesophageal Reflux Disease), many overlook a key player: the Lower Esophageal Sphincter (LES). This critical muscular valve serves as the barrier between the esophagus and the stomach, ensuring the proper flow of food and preventing the backflow of stomach acids. Understanding the LES and its overlooked causes can shed light on why you might be experiencing acid reflux more frequently and how best to manage these often distressing symptoms. In today’s article, I will explain the connection between the Lower Esophageal Sphincter and Heartburn as well as review the most common problems that affect the lower esophageal sphincter. Lastly, I will review some important tips and why prokinetics are so beneficial for those suffering with a dysfunctional LES and heartburn.

The Many Causes of Acid Reflux, Heartburn and GERD

Acid Reflux Disease

More than 15 million Americans suffer from acid reflux disease, also known as gastroesophageal reflux disease or GERD, in which the acid from the stomach flows up into the esophagus, causing discomfort, inflammation, and sometimes scarring. GERD is a digestive disorder that is diagnosed when the burning happens frequently or even continuously. The reverse flow of acid into the esophagus takes place when there is pressure on the lower esophageal sphincter (the valve between the esophagus and the stomach) and the stomach itself.

Instead of food being pushed down from the esophagus into the stomach and staying there as it should, the food and acid reverse their flow and push back up.

If you’re already taking medication whether it’s a proton pump inhibitor like omeprazole (Prilosec) or Nexium, or you are taking antihistamines H2 blockers like Tagamet, Pepcid AC, or the “new” Zantac 360, I’m going to share with you the often overlooked root causes of these conditions and hopefully with this information calming down your digestive symptoms so that you can decrease your dependency on these acid-blocking medications.

Proton Pump inhibitors and H2 Blockers

I’m often asked by people who have GERD, and acid reflux why histamine blockers or PPIs aren’t the answer for acid GERD and acid reflux. So, here’s the thing. PPI can cause headache, rash, dizziness, nausea, abdominal pain, flatulence, and constipation, and if you take this Long-term, it can lead to chronic kidney disease, bone fractures, dementia, pneumonia, vitamin B12 deficiency, amino acid deficiencies, and infectious diarrhea.

But the 2nd reason and MORE important reason is that these medications don’t address the root cause of your acid reflux and GERD.  If you ignore the Root cause, this only snowballs into health problems that can be much worse.

When you take medication to block acid production, it’s not a real solution long term. Over time these medications worsen your nutritional status, worsen your digestion, and worsen your motility disorder. When your digestion is healthy, your stomach produces hydrochloric acid (HCl) to acidify the stomach. This is very important because Pepsin which is the enzyme that breaks down protein in amino acids only works in a highly acidic environment, so when HCl production is low or the PH of the stomach becomes more alkaline, your Pepsin doesn’t get activated and then you have problems digesting protein.

If this happens often enough, your stomach attempts to release even more HCL (which is also called an acid rebound). This can also happen when you take an antacid like TUMS, which neutralizes the acid.

Unfortunately, using acid-inhibiting medications such as PPIs or Histamine (2)-2-receptor blockers like (Pepcid AC, Zantac, and Tagamet) these medications can cause a state of hypochlorhydria, or chronic low acid, perpetuating the cycle of indigestion, poor protein digestion without providing relief for the underlying cause of your symptoms. Instead of masking your symptoms with H2 histamine blockers and Proton pump inhibitors, it makes more sense to investigate what’s causing your GERD and acid reflux, and thats what we are going to do!

LES and heartburn

Lower Esophageal Sphincter (LES) and Acid Reflux

The Lower Esophageal Sphincter (LES) plays a crucial role in digestive health, often taken for granted until it malfunctions. Positioned between the esophagus and the stomach, the LES is a muscular ring that opens to allow food and liquid into the stomach and closes to prevent harmful backflow.

When you swallow, the LES opens to let food pass into the stomach. After food enters, it should (emphasis on “Should”) close tightly to prevent stomach acids and food from creeping back up into the esophagus. This backflow, if it occurs, leads to symptoms commonly known as heartburn, acid reflux, or gastroesophageal reflux disease (GERD).

One of the LES’s primary functions is to keep stomach acids in their place. When the LES closes properly, it prevents the highly acidic contents of the stomach from flowing back into the esophagus.

Effective closing and opening of the LES ensure food moves smoothly down the esophagus and into the stomach without interruption. This efficient movement is essential for proper digestion and the overall health of the digestive system. Chronic malfunctioning of the LES can lead to GERD, a condition characterized by persistent acid reflux. This not only causes discomfort but also increases the risk of more severe esophageal diseases, such as Barrett’s esophagus or esophageal cancer. If this sounds interesting to you, let’s review some common causes of GERD and acid reflux that most likely, your GI doctor or your GP didn’t check for. it is widely accepted that problems with the LES will lead to Heartburn, acid reflux, and GERD.

overlooked causes of acid reflux, heartburn and GERD

#1 Atrophic Gastritis-

Atrophic gastritis is a chronic condition characterized by the thinning and loss of the gastric mucosa, the inner lining of the stomach. This thinning is due to the destruction of the stomach’s glandular cells, which play a key role in producing stomach acid and digestive enzymes. Over time, atrophic gastritis can lead to significant hypochlorhydria (low stomach acid) or achlorhydria (complete absence of stomach acid). This condition is also associated with a risk of developing gastric cancer and malabsorption issues, particularly of nutrients like Vitamin B12, Folic acid, iron, and calcium.(*)

In the early stages of atrophic gastritis, the body often attempts to compensate for the low stomach acid production by stimulating the remaining gastric gland cells to produce more acid. This compensatory mechanism can lead to an overproduction of acid at certain times, contributing to GERD and acid reflux.

There are two main types of Atrophic Gastritis. Autoimmune gastritis is a chronic inflammatory disease with the destruction of parietal cells of the corpus and fundus of the stomach. The known consequence is vitamin B12 deficiency and, consequently, pernicious anemia. Individuals with autoimmune atrophic gastritis often have other autoimmune disorders, such as Hashimoto’s thyroiditis or Type 1 diabetes.(*)

Atrophic gastritis can also be caused by Helicobacter pylori (H. pylori). Long-term H. pylori infection causes chronic inflammation, leading to atrophy of the stomach lining.

Atrophic gastritis is a significant condition that can lead to serious health issues if left untreated. It can be either autoimmune or due to chronic H. pylori infection. Early diagnosis and a comprehensive treatment approach can help manage symptoms, correct nutrient deficiencies, and reduce the risk of complications like gastric cancer and severe forms of anemia.

Causes of GERD acid reflux and heartburn

#2 Hiatal Hernia.

Another common problem for people suffering from heartburn, Acid reflux, and GERD is Hital Hernia. A Hital Hernia occurs when the upper part of the stomach pushes through the diaphragm into the chest cavity. This can be another cause for those suffering from acid reflux, heartburn, and GERD.  The diaphragm is a large muscle that helps with breathing and separates the abdominal cavity from the chest cavity. Under normal circumstances, the esophagus passes through the diaphragm through an opening called the hiatus to connect to the stomach. When a hiatal hernia is present, part of the stomach squeezes through this opening. When it comes to hiatal hernias there are two main types.

1. Sliding Hiatal Hernia: This is the more common type where the stomach and the section of the esophagus that joins the stomach slide up into the chest through the hiatus.

2. Paraesophageal Hiatal Hernia: Less common, this type occurs when part of the stomach pushes through the hiatus and lies next to the esophagus. While it is not always symptomatic, it can be more severe than the sliding type and may cause more complications.

A hiatal hernia can exacerbate acid reflux and GERD in several ways. The first is by weakening of the Lower Esophageal Sphincter (LES)

Remember the LES is a valve at the junction of the esophagus and stomach that prevents stomach contents from flowing back into the esophagus. When a hiatal hernia is present, the stomach’s misplaced position can compromise the LES’s functionality. As a result, the barrier that prevents acid reflux weakens, allowing stomach acid to flow back into the esophagus more easily.

Another way a hiatal hernia can exacerbate or cause acid reflux is by increasing Intra-Abdominal Pressure. An increase in the pressure within the abdomen, particularly if the herniated section is large forces stomach contents, including acid, back up through the LES into the esophagus.

Activities that increase intra-abdominal pressure like coughing, straining, or heavy lifting can exacerbate this problem. Finally, a hiatal hernia can alter acid clearance. Think of it like this.  When you swallow, this helps clear acid from the esophagus back into the stomach. A hiatal hernia can interfere with this process by disrupting normal esophageal peristalsis—the wavelike muscle contractions that move food down the esophagus. As a result, acid clearance is slower, increasing the duration and intensity of acid exposure to the esophageal lining. Depending on the extent of the hiatal hernia, this sometimes requires surgery.

#3 Being Overweight/Obesity.

Obesity and being overweight puts you at significant risk for acid reflux and GERD. Not only will extra weight increases the pressure on the LES so that it stays partially open and allows stomach acid to reflux into the esophagus.(*) it increases your risk of developing a hiatal hernia which I talked about above.  This anatomical shift can unbalance the esophagus-stomach angle, impair LES function, and exacerbate acid reflux.

There is another reason you should focus on weight loss if you suffer from acid reflux or GERD and it has to do with visceral fat. Fat tissue, especially visceral fat located around internal organs, releases pro-inflammatory cytokines and other compounds like leptin and adiponectin. These chemicals can disrupt gastrointestinal function, slow down gastric emptying, and aggravate acid reflux symptoms.(*)

#4 Loss of muscle tone in the LES.

Remember the LES is a muscular flap (sphincter) and so the tone of that muscle determines whether that flap (sphincter) stays open or closed. The lower esophageal sphincter (LES) is partly under the control of the Vagus Nerve and partly under the control of the sympathetic (splanchnic) nerves.  The Vagus nerve is intricately involved in almost every part of the digestive process, from moving food through the digestive tract and signaling fullness to regulating inflammation. Its extensive influence makes proper vagus nerve function crucial for maintaining overall digestive health and the muscular tone of the LES.  Performing Vagus Nerve Exercises are helpful for people suffering from acid reflux, heartburn, and GERD.

#5 Prescription Medications 

Anticholinergic agents- Anticholinergics are a class of drugs that block the action of acetylcholine, a neurotransmitter in the parasympathetic nervous system (PNS). Earlier I said the digestion process is under the control of the parasympathetic nerve system. These medications can affect peristalsis which is the muscular waves of digestion that propel food and waste down and out. Instead of food and waste going down and out, here again, it refluxes upwards into the esophagus. These drugs work by binding to the acetylcholine receptors and preventing acetylcholine from exerting its effects. Here’s how anticholinergics affect the parasympathetic nervous system:

Saliva: Decreased saliva production, leading to dry mouth (xerostomia).

Gastric Juices: Reduced gastric secretion, which can affect digestion.

Mucus: Decreased mucus production in the respiratory and gastrointestinal tracts.

Motility/Digestive Tract: These drugs can slow down digestive tract motility, leading to constipation.

Bladder: Reduced bladder muscle contractions, leading to urinary retention. Medications used to treat chronic pain like Codeine and other opiates slow down the action of smooth muscle tissue and affect LES tone.

Another medication known to cause acid reflux and GERD is your Tricyclic antidepressants.  Remember that motility and digestion are under the control of neurotransmitters. Many of these neurotransmitters in the gut work on and in the brain as well as muscular contractions of the gut. Serotonin increases motility. Serotonin influences the tone of the LES, the muscle that prevents stomach contents from flowing back into the esophagus. Excessive serotonin can cause relaxation of the LES, thereby allowing acid and food to reflux into the esophagus.

Other medications include antibiotics, birth control pills (*), and medications women are put on for osteoporosis (bisphosphonates).(*)

Thyroid disease and acid reflux GERD and Heartburn

#6 Thyroid Disease including Hashimoto’s disease.

Thyroid Disease including Hashimoto’s disease is another overlooked root cause of GERD and acid reflux. Thyroid disease affects every aspect of digestion and motility and stomach acid is no different. Hypothyroidism contributes to hypochlorhydria, a condition in which the stomach acid is too low. For someone with acid reflux or chronic indigestion, this may sound like a good thing but in fact, low stomach acid often causes heartburn, indigestion, or GERD. Hashimoto’s disease is an autoimmune disease of the thyroid gland. It’s common when a person has Hashimoto’s to also have Autoimmune Atrophic Gastritis and other autoimmune motility diseases like Celiac disease and a Leaky Gut.

Here is an article I wrote on some Tips to Improve Heartburn and Acid reflux When You Have Thyroid disease or Hashimotos.

#7 Bacterial Overgrowth.

SIBO is a condition where there is an overgrowth of bacteria in the small intestines. This is often an overlooked cause in patients with acid reflux and GERD.  Multiple studies show that SIBO (bacterial overgrowth) and GERD are connected and each can be a cause of the other. Remember what I said earlier about Stomach acid?

Stomach acid also plays a role in keeping bacterial populations within the stomach and small intestines in check. If there is insufficient stomach acidity, the small intestine loses its acid-base ratio. This allows bacteria to colonize the small intestines and when this happens you can develop bloating, gas, and acid reflux along with diarrhea or constipation.

You can learn more about the connection between SIBO and Heartburn/GERD in an article that I wrote here.

Hypochlorhydria and acid reflux heartburn

#8 Hypochlorhydria

Hypochlorhydria is a deficiency of stomach acid. If you don’t have enough stomach acid, you can’t digest food properly or absorb its nutrients. This leads to indigestion, heartburn/GERD malnutrition, and sometimes bacterial overgrowth. Remember heartburn and GERD are conditions often caused by low stomach acid production or when the PH of the stomach changes to become slightly more alkaline. The majority of the time it’s NOT too much acid as the problem, it’s insufficient acid production.

Gluten Dairy and acid reflux

#9 Gluten Sensitivity, Dairy Food Allergies

If you suffer from gas, bloating, or acid reflux after meals, you may be dealing with a possible allergy or a possible food sensitivity. There’s more to acid reflux than the so-called spicy foods causing acid reflux. If you have food allergies or food sensitivities, stomach acid may not be able to break down the proteins, carbohydrates, and sugars.

Gluten sensitivity and dairy allergy are increasingly recognized as significant contributors to gastrointestinal distress, including heartburn and gastroesophageal reflux disease (GERD). These conditions, while distinct, share common pathways in exacerbating symptoms of acid reflux. (*)

Gluten sensitivity, also known as non-celiac gluten sensitivity (NCGS), refers to a condition in which individuals experience adverse reactions to gluten — a protein found in wheat, barley, and rye. 

Both gluten sensitivity and dairy allergy can trigger inflammatory responses in the body. Inflammation in the gut lining can compromise the integrity of the lower esophageal sphincter (LES), a muscle that acts as a valve between the esophagus and stomach. When the LES doesn’t function properly, stomach acids can reflux into the esophagus, causing heartburn.

Individuals with gluten sensitivity or dairy allergy often experience bloating, gas, and abdominal pain. This excess gas pressure can increase intra-abdominal pressure, pushing stomach contents, including acid, through the LES and into the esophagus. This recurrent acid exposure can lead to chronic GERD and heartburn.

Symptoms to Watch For When it Comes To Gluten Sensitivity:

– Bloating and gas

– Diarrhea or constipation

– Fatigue

– Headaches

– Joint pain

Acid Reflux/GERD

Symptoms to Watch For When it Comes To Dairy Allergy:

– Abdominal pain and cramping

– Nausea and vomiting

– Skin reactions (hives, eczema)

– Wheezing or difficulty breathing


– Burning sensation in chest/throat

– Regurgitation of food or sour liquid

– Difficulty swallowing

– Chronic cough or hoarseness

#10 Alcohol and Tobacco.

Smoking can decrease the pressure in the Lower esophageal sphincter. Alcohol delays gastric emptying which means food sits in your stomach rather than being digested. Alcohol and tobacco also lower the pressure in the lower esophageal sphincter. The lower esophageal sphincter is like a trap door between the esophagus and the stomach. If it doesn’t seal shut and stay closed, bacteria, food, and acid can regurgitate and reflux back up into the esophagus.

I gave about 8 reasons in my last video on Digestion and Motility why alcohol needs to be avoided when you have digestion and motility issues). Alcohol affects the central nervous system, which in turn can lessen the tone of the LES, making reflux more likely. Alcohol slows gastric emptying, meaning that food and acidic content stay in the stomach longer. This prolonged retention increases pressure within the stomach, causing acid to be pushed back into the esophagus.

Stress and acid reflux

#11 Stress.

Can stress cause acid reflux, heartburn, and GERD? let’s dig a bit deeper here. When you’re stressed, your body produces more of the stress hormones adrenaline and cortisol. High levels of these stress hormones shut down motility and shut down digestion. When you shut down digestion, food does not get enzymatically broken down. This leads to acid reflux and GERD.

Stress also thins out your gut barrier and promotes intestinal hyperpermeability, better known as a leaky gut. People with leaky gut are more prone to allergies, food sensitivities, inflammation, and motility disorders. Elevated cortisol, inflammation, and a leaky gut or acid reflux predispose you to every motility digestive disorder you can think of. Stress hormones are a vital part of life, but when they become dysregulated, just about every organ in the body is negatively affected especially our digestion.

Prokinetics for Acid Reflux and GERD

Prokinetics are a class of medications or natural herbs used to enhance gastrointestinal motility. Prokinetics are particularly beneficial for individuals suffering from gastroesophageal reflux disease (GERD) and acid reflux. Here are several reasons why prokinetics are important in managing these conditions:

One of the primary effects of prokinetic agents is their ability to expedite gastric emptying. Slow gastric emptying can contribute to GERD because food and stomach acid sit in the stomach for longer periods, increasing the likelihood of reflux. By speeding up the passage of food, prokinetics reduce the volume and pressure in the stomach, which can minimize the backflow of stomach contents into the esophagus. I should also mention that not only will food sit in the stomach for longer periods, but so can bacteria! This can allow bacterial overgrowth to develop in the upper part of the small intestines- which is often missed on a lactulose breath test.

Prokinetics can help improve the Lower Esophageal Sphincter (LES) Tone as well as increase esophageal peristalsis, the wave-like muscle contractions that move food through the esophagus. Enhanced peristalsis means that any acid that does make its way into the esophagus is more quickly cleared, reducing exposure time and damage to the esophageal lining.

If you are interested in learning more about natural prokinetic options when you have Acid reflux, heartburn, GERD, or Small Intestinal Bacterial Overgrowth, and why I recommend them, you can read this article on “Natural Prokinetics





SIBO- Everything You Wanted To Know About Small Intestinal Bacterial Overgrowth 1



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