What to Do When Diet and Probiotics Don’t Work

By Samantha Gilbert, FNC, CHNP, CNC     Last updated on February 11th, 2023

What to Do When Diet and Probiotics Don’t Work

Feeling frustrated is understandable when diet and probiotic therapies don’t provide the relief you seek to heal your digestive issues, something I’ve struggled with myself. If you’ve been asking yourself the following questions, please know you are not alone:

  • Why did my probiotics stop working?
  • Can you become resistant to probiotics?
  • Do probiotics lose their effectiveness?
  • Do probiotics stop working after a while?

Dietary changes and probiotic therapies work wonders for restoring gut health, but if you’ve done everything you can including dietary restrictions such as very low carb or low FODMAP, along with pre and probiotic therapies, and are still struggling with digestive problems; a deeper dive into the complexities of why your system may not be functioning properly is key to the healing process.

To learn more about why your diet and probiotics aren’t working, check out my podcast episode 43 below with Steven Wright, Founder of the Healthy Gut Company. You can also find the Eat For Life podcast on Apple Podcasts, Spotify, Google Podcasts, or wherever you listen to podcasts!

Understanding the Principles to Digestion

Each one of us embodies a complex ecosystem of organs and glands that work in unison to protect us and keep things functioning optimally. In our high-tech world, one of the biggest challenges I see is information overload that leads to shiny object syndrome.

Shiny object syndrome occurs when you are bombarded with myriad ads based on your search results to try a new and amazing probiotic or very restrictive diet. Unfortunately, this diverts you away from first looking at why you may be experiencing digestive problems, to begin with.

Your Stomach: The Master Controller

Let’s start with your stomach, one of the most important and overlooked digestive organs. The stomach was designed to be a very acidic environment. Stomach acid secretion is critically important because it is required to not only breakdown the foods you eat, but also so your body can assimilate the nutrients from your food.

If your stomach doesn’t perform its job as it was designed, then essentially every other function in your body is compromised, which is why the stomach is the master controller of your digestion.

The digestive tract is one long tube that runs from the mouth to the anus. Digestion begins in the mouth when food is chewed and mixed with saliva. Saliva contains the enzyme amylase, which starts the digestion of starch in the food. From there, this bolus of chewed food is swallowed down the esophagus and then enters the stomach. In the stomach, it is mixed with gastric juice (hydrochloric acid and pepsin) which starts to digest the protein in your food.

Here’s why hydrochloric acid (HCL) is so important:

  • HCL kills bacteria that enters the GI tract through food and water. When adequate amounts are being produced, HCL keeps the small intestine mostly sterile.
  • HCL’s acidity activates pepsin, a protein-digesting enzyme, which is needed to breakdown the protein molecules in your food.
  • HCL helps activate intrinsic factor through the liberation of vitamin B12 so the body can absorb it. B12 deficiency is a serious condition that can cause brain fog, disorientation, memory loss, fatigue, heart palpitations, pale skin, and tingling in the arms and legs, to name a few.
  • Plays an important role in mineral absorption. Minerals such as zinc, iron, calcium, and magnesium are required for the brain and body to function optimally. Zinc deficiency is by far the most frequently observed chemical imbalance in mental health because zinc is needed to make neurotransmitters. It also helps stimulate the activity of over 300 different enzymes, including digestive enzymes needed to breakdown and assimilate food.
  • HCL is needed to close the lower esophageal sphincter, which keeps the acid from passing back into the esophagus. Contrary to the conventional medicine paradigm, acid reflux (GERD) is actually a result of low stomach acid. Acid suppressing drugs such as H2 blockers (Pepcid) and proton pump inhibitors (PPI’s such as Prilosec) only make the problem worse and are very hard on the liver and kidneys.
  • When HCL levels are low, my clients often have problems digesting protein, struggle with heartburn or acid reflux (GERD), and often have skin issues. An easy at-home test to assess HCL status is to drink a solution of 1⁄4 teaspoon of baking soda in about four ounces of water on an empty stomach. If it takes three to five minutes for you to burp, your HCL levels are low, and if it takes over five minutes for you to burp (or you never burp), your HCL levels are very low.

Enzyme Deficiency and the Small and Large Intestine

Now that we’ve reviewed the role your stomach plays in digestion and assimilation, let’s focus on the importance of enzymes.

Nutrient absorption is directly related to your enzyme function. So, if you’re struggling with bloating, gas, and constipation or diarrhea, then focusing on enzyme dysfunction is the next step.

Pancreatic Enzymes

If HCL is low, decreased pancreatic enzyme output is also commonly seen. Low HCL and low pancreatic enzymes are risk factors for SIBO (small intestinal bacterial overgrowth) as well as SIFO (small intestinal yeast overgrowth) and are very common in autism, ADHD, OCD, and eating disorders. When pancreatic enzyme levels are low, I often hear complaints about trouble digesting food and food sensitivities, as well as high anxiety.

Pancreatic enzymes break down proteins, fats, and carbohydrates into small particles so there isn’t as much remaining for bacteria to feed upon and ferment into gas. Your pancreas should secrete about seven to eight cups of pancreatic juice into the duodenum, every day. This juice contains pancreatic enzymes to help with digestion and assimilation, and also bicarbonate, which neutralizes stomach acid as it enters the small intestine.

If you don’t make enough pancreatic enzymes, or if the pH and transport to the gut are off, then these enzymes might only be functioning at 40% to 50% of their capacity.

The 3 Types of Pancreatic Enzymes

Amylase breaks down carbohydrates into sugars, which makes them more easily absorbed by the body. As I mentioned previously, the amylase enzyme is also found in saliva and digestion actually begins in the mouth, which is why chewing is so important.

Lipase works to break down fat molecules so they can be absorbed and used by the body. It works in conjunction with bile from the liver.

Proteases break down proteins. They support the intestine to keep it free of bacteria, yeasts, parasites, and protozoa.

Brush Border Enzymes

The surface of the small intestine is covered with microvilli, which secretes enzymes called brush border enzymes. These brush border enzymes include disaccharidases, which break down complex sugars into simple sugars (monosaccharides), and peptidases, which break down proteins into single amino acids so they can be absorbed.

Villi are like a shag carpet and often become blunted by too much bacteria in the small intestine. Since the villi are responsible for the absorption of nutrients, we can end up with vitamin and mineral deficiencies. Bacteria prevent the release of disaccharidase enzymes, and keep us from digesting and using the carbohydrates we eat, which allows them to have all those carbohydrates for themselves.

Additionally, lactase – the enzyme required to digest lactose in milk – is also a brush border enzyme. If you find you have an intolerance to lactose, you may have SIBO, something I commonly see in my clients.

Villi also produce the enzyme DAO (diamine oxidase) that is required to degrade histamine in our food, which can lead to histamine intolerance.

When diet doesn’t work and your probiotics stop working after a while, I encourage looking at the underlying mechanisms that may not be functioning properly such as lack of stomach acid secretions and enzyme dysfunction. You can have the best diet in the world but if you’re not breaking down and assimilating your food properly, your body cannot take in the nutrients it needs to thrive.

There are literally thousands of HCL and digestive enzyme products to choose from, but two of my favorites are HoloZyme and HCL Guard from the Healthy Gut Company. If you’re interested in trying them, click here to get $15 off plus free shipping using the coupon code eatforlife15.

Nutrition Counseling To Help You Thrive

To understand why diet and probiotics aren’t working for you, I aim to identify and address the root biochemical causes and imbalances of your symptoms, which includes gut testing and analysis.

I offer a free 1:1 consultation to help you disconnect from the hype and the marketing jargon, and address the true source(s) of your discomfort. It’s time for your healing journey to truly begin.


Champagne E.T. (1989) Low Gastric Hydrochloric Acid Secretion and Mineral Bioavailability. In: Dintzis F.R., Laszlo J.A. (eds) Mineral Absorption in the Monogastric GI Tract. Advances in Experimental Medicine and Biology, vol 249.


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