Healthy Stomach Bacteria and the Neuroimmune System – Part 3

By: Michael Lam, MD, MPH; Justin Lam, ABAAHP, FMNM

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Promoting Healthy Gut Flora: Strategies

healthy stomach bacteria and microbiomeEvidence continues to grow regarding the beneficial effects of healthy stomach bacteria. And it has become very clear how unhealthy bacteria in this part of your body has a tremendous impact on your overall health.

That makes it imperative for you to put into your life those food products and other strategies for building or repairing your stomach and gut bacteria. Taking charge of your diet and lifestyle choices will enable you to improve your health status considerably. Your stomach and gut bacteria are significantly influenced by the foods you eat and the choices you make about how you live your life.

In those with psychiatric or neurological conditions, it is difficult to determine which came first, the disorder or the unhealthy gut. Dysbiosis of the gut could account for both, but so could stress. It is also important to consider the environmental risk factors—such as an unhealthy diet and lifestyle—that may upset healthy stomach bacteria, gut flora, and the brain. Promote healthy stomach bacteria with a microbiome diet.

It is clear that neurological/neurodegenerative and psychiatric disorders share similar causes and symptomatology, as well as a common underlying pathophysiology of an unhealthy gut that influences numerous intersecting pathways on the microbiome-gut-brain axis. However, it is difficult to determine the function of these individual systems separately. The entire microbiome-gut-brain axis is therefore still poorly understood. For brain conditions, the gut could prove to be the missing piece of the puzzle, providing new understanding of the etiology in ways that might support the introduction of new public health and clinical interventions.

The composition of the gut microbiome is quite resilient and adaptable. The key factors that are essential to its stability and diversity are all components of lifestyle. Several strategies for healthy stomach bacteria, and in turn brain health, are given below.

Agricultural Chemicals

Some of the foods and other substances you ingest that have the most significant negative impact on your healthy stomach bacteria include the following:

Refined sugars – especially high fructose corn syrup.

These simple sugars tend to raise blood sugar levels significantly, pushing your pancreas to release more insulin to control them. In people with AFS, insulin levels are already unbalanced and depleted; insulin resistance is a major issue with this condition. Consuming these refined sugars (and there is a tendency to crave sugars with AFS) will only lead to more significant problems. Sugars fuel pathogenic yeasts and fungi in your gut.

Note: You must be certain to wash vegetables and fruits very well to remove as much of the residue from these chemicals as possible.


healthy stomach bacteria and antibioticsIngesting these medications may help in some cases of infections, but the use of antibiotics seems to be reaching epic proportions. They are exactly what their name implies: killers of bacteria. All bacteria. There is no antibiotic that can differentiate beneficial bacteria from harmful ones. Overuse of antibiotics simply kills off the healthy stomach bacteria. When you have AFS, you already have problems with your gut flora. Don’t add to them by taking an overabundance of antibiotics.

Non-steroidal anti-inflammatory drugs (NSAIDS)

These medications damage cell membranes and inhibit energy production by mitochondria.


Make changes in your lifestyle to reduce or eliminate as much stress as possible. Already, you understand the impact stress has on your life, often leading to adrenal failure and its detrimental symptoms. Stress also impacts the healthy stomach bacteria that keep you working at your best.

Knowing the types of foods to avoid is the first step toward healthy stomach bacteria again. Stay away from processed foods, farm-raised animal products that contain antibiotics and growth hormones, sugars, and gluten products.

Microbiome Diet

Diet plays an important part in determining the amount of each type of bacteria and the phylogenetic diversity of gut flora. A healthy diet of vegetables, fruits, and a variety of whole grains, will help the population of Bacteroidetes. Bacteroidetes are particularly useful in the production of short chain fatty acids (SCFAs), which assist in the regulation of gut inflammation. Large amounts of SCFAs tend to decrease intestinal pH and prevent growth of some pathogenic bacteria such as E.coli and Enterobacteriaceae. SCFAs also help curb appetite; they attach to the receptors in the gut and regulate the hormones for appetite control. Thus, the microbiome and its production of SCFAs may play important roles in dietary intake, rate of fat deposition, utilization of fat, insulin resistance, and diabetic inflammation. Vegan and vegetarian diets also increase phylogenetic diversity of the gut flora compared to diets that include meat.

Body weight in mice can be affected by the transplantation of microbes in the cecum (the beginning of the large intestine). In one study, genetically obese mice had significantly less Bacteroidetes and more Firmicutes relative to their lean counterparts; but in another, when the gut microbes of a lean mouse that had undergone gastric bypass surgery were transferred to germ-free mice, those mice experienced weight and fat loss. These studies showed that dietary patterns that favorably alter the gut microbiome—specifically those that emphasize plant-based foods—might have significant benefits to human health and confer greater resilience and adaptability to change.

There are three food components that are largely thought to promote gut health:

Probiotics, living microorganisms that can be found in consumer goods such as yogurt and kimchi,

healthy stomach bacteria and whole grainsNon-digestible carbohydrates, such as fiber commonly found in vegetables, whole grains, and fruits,

Secondary plant metabolites, especially flavonoids found in red wine and brightly colored fruits.

Individuals who adopt what’s known as the Standard American Diet (SAD) experience fewer benefits of plant foods, while simultaneously provoking disruptions of other metabolic functions by eating large quantities of processed sugar and fat. These two aspects of the SAD both contribute to the development of gut inflammation and dysbiosis.

Prebiotics, Probiotics, and Fermented Foods

Prebiotics fibers that are not digestible by your gut enzymes. They are usually fermented in the GI tract by bacteria and selectively stimulate certain intestinal flora and metabolic activities. Probiotics are foods that contain helpful microbes that are able to survive stomach acid and bile; they enter the intestines and adhere to the lining, growing and establishing temporary residence in the intestines.

There is evidence to suggest that prebiotic and probiotic supplements and fermented foods are beneficial for the gut. The digestion of fermented fibers has natural anti-inflammatory effects. Fermentation of food makes it more digestible, turning polyphenols into an active state. It also produces more vitamins, enzymes, and amino acids while breaking down phytates, tannins, and oxalic acid. An additional benefit of fermented food is, of course, the lengthened shelf life.

Probiotics and Behavior/Central Neurotransmitters

Since 90% of neurotransmitters are made in the gut, it makes sense that gastrointestinal conditions can influence mood and behavior. Irritable Bowel Syndrome (IBS) is found in 10-20% of adults in the US, and they have much higher rates of anxiety and depression than the background population. Studies have shown that probiotics are beneficial in the treatment of both the GI symptoms and anxiety and depression, in those affected. There is mounting clinical evidence for probiotics reducing stress and anxiety responses, as well as for improving the general mood of IBS patients who suffer from chronic fatigue. Studies have assessed the effect of a mixture of Bifidobacterium longum and Lactobacillus helveticus on human subjects and rats showing that anxiety was reduced . Although the mechanism of action is still to be determined, some probiotics seem to lower inflammation, decrease stress from oxidation, and improve general nutrition.

Specific probiotic strains can assist in the modulation of various facets of the microbiome-gut-brain axis. However, it is important to note that these effects vary from organism to organism and individual to individual. Nevertheless, the data strongly suggests that probiotic strains have great potential to bolster the gut flora and thus regulate behavior and the brain.

What to Add to Your Diet to Gain Healthy Stomach Bacteria?

Probiotics and prebiotics are a good first choice. Significant research shows adding these supplemental foods to your diet increases the good bacteria you need. Do what your mother always told you:

healthy stomach bacteria diet update

Eat your vegetables!

Especially green vegetables. These foods break down in your system, giving your healthy stomach bacteria the nutrients they need to thrive. So eat your carrots, broccoli, spinach, onions, and peas, among others.

Add fruits – whole fruits – and not just juice

Grapes contain resveratrol and flavonoids that will feed not only your gut but also your brain. Apples, blackberries, blueberries, and cherries are also good for you.

Wild caught fish and cage-free eggs

They are beneficial and higher in Omega 3 fatty acids than farm-raised fish or chicken. And you don’t have to worry about added antibiotics or other substances that you don’t want in your body.

Add supplements

Co-enzyme Q10, selenium, antioxidants like vitamins C, D, and E and Omega 3 fish oil are good for your stomach and gut system. Dietary supplementation of this kind will enable your stomach and gut bacteria to grow.

There are other enzymes that can be added as supplements or through foods you eat. These enzymes all have significant beneficial effects on healthy stomach and gut bacteria and in digesting foods.


Probiotics are especially important for rebuilding healthy stomach bacteria. Foods that are probiotic in nature build up your healthy stomach bacteria in your gut microbiome. These fermented foods increase the nutrient and phytochemical value of the foods. Consuming probiotic foods will improve your brain health. Probiotics that contain 20-50 billion live organisms per dose and have combinations of Lactobacillus and Bifidobacteria are best.

These foods should be taken with meals once or twice a day. At this time, the field of study of probiotics is in its infancy, but more and more studies are being conducted on a regular basis. From this will come more science-based probiotics available for consumer use. Gas and bloating may be the common side effects of probiotics. Uncommon side effects include overstimulation of the immune system.

Digestion begins when food enters your mouth. Salivary amylase begins breaking down larger polysaccharides into smaller disaccharide molecules like maltose and dextrin. Farther into your gut, pancreatic amylase further breaks these starches into monosaccharides like glucose. It’s also involved in anti-inflammatory reactions. If you’re low in amylase, you have an increased risk for abscesses since amylase also digests dead white blood cells or pus. One form of this enzyme, beta-amylase is contained in some plant seeds, bacteria, and yeasts. Amylase is the enzyme that furnishes energy for the body to use. If you have low levels of amylase, both diabetes and metabolic syndrome are possible. Side effects may include abdominal cramps, diarrhea, and nausea. Severe abdominal cramps or painful urination are uncommon and may need attention from your healthcare provider.


healthy stomach bacteria and lipase aids in digesting and absorbing fatReleased mostly by the pancreas, lipase aids in digesting and absorbing fats. With low levels of lipase, there may be associated high levels of cholesterol and fat in the blood. Sufficient levels of lipase enable your body to absorb vitamins and minerals appropriately. If you have gallbladder issues, a supplement with lipase may help. High doses of lipase supplement may lead to nausea and stomach upset. Some digestive enzymes can destroy lipase.

Fats must have extra digestion before being absorbed because their end products are carried through the body in a water medium in which fats are not soluble. Lipase is one of those enzymes that aids in this process. Mild side effects such as nausea, cramping, and diarrhea may occur. If you’re pregnant or breastfeeding, it’s best to avoid lipase.


Lactase is an enzyme that aids in digesting lactose. Many people have too little lactase and thus can’t digest lactose. This may lead to a lack of calcium if people can’t digest dairy products. Stomach cramps, diarrhea, and gas may also result from lactose intolerance. Milk is a good source of nutrients for people.

Being able to digest and utilize this source of nutrition is very important. This enzyme is produced by fungi and bacteria. Lactase reactions take place along the tissue walls of the small intestine. Lactase is most prevalent during infancy when milk is the main nutrient. After weaning, lactase becomes less available until in adulthood, some people have so little they become lactose intolerant. There are very few side effects of lactase. Rarely, severe allergic reactions may occur. If this happens, consult your physician immediately.


The major function of this digestive enzyme is to break down proteins. In this digestive process, amino acids needed by the body are released as protease breaks the peptide bonds in proteins. Protease has benefits in immune regulation and inflammation. A lack of protease possibly leads to calcium deficient conditions because protein bound calcium requires protein to be carried around the body in the blood.

One source of glucose for the body is the conversion of protein. With a lack of protease, there is an increased risk of hypoglycemia. Protease is also an aid to breaking down toxins in the blood, thereby aiding the immune system. Possible side effects of protease include diarrhea, constipation, headache, dizziness, nausea, and vomiting. If any of these become severe, your healthcare professional should be consulted immediately.


Pepsin requires a strongly acidic environment in which to break down protein into peptides. It’s produced in the stomach lining. It’s one of three enzymes that break down protein, the other two being chymotrypsin and trypsin. In the stomach, it breaks down protein into polypeptides. It works to sever links between some types of amino acids and helps break protein into amino acids and peptides which can then be absorbed by the intestinal lining. Pepsin also stimulates the liver to produce bile that helps the body get rid of toxins and plays a role in the production of antibodies and collagen.


healthy stomach bacteria and papayaPapain is a digestive enzyme extracted from papaya fruit and involved in breaking down tough to digest proteins. It breaks down larger protein molecules into smaller molecules or amino acids. It does this by cutting the bonds on the interior protein chains in a process called endopeptidase or by cutting bonds on the ends of protein chains (exopeptidase). By doing either of these processes, papain increases the absorption of the nutrients in proteins. Additionally, papain works as an antioxidant, supports the immune system and healthy stomach bacteria.

It may have use as an alternative to other chemicals in increasing the survival of probiotic bacteria in yogurt. There is little research into the long-term effects of papain. Some irritation of the stomach and throat have been reported. Pregnant and breastfeeding women should avoid papain.


A mixture of enzymes, bromelain is found in pineapples. It may have some effect on inflammation from infections. It’s a protein digesting enzyme with many other possible health benefits. It enables the body to absorb nutrients, especially from protein, more effectively and is exceptionally effective at healing gastrointestinal ailments. It has also been shown to have some benefit in treating sinus infections and various joint pains.

Eating the core, not just the fruit, of pineapples will supply this enzyme. It’s best to let the pineapple ripen a little more than typical so the core is softer. If taken to improve digestion, bromelain is best taken with meals. Due to its anti-clotting properties, consult your healthcare professional before taking a supplement if you’re on blood-thinning medications.


A flavonoid antioxidant, quercetin is found in foods like leafy greens, tomatoes, and broccoli. It fights free radical damage, aging, and inflammation. It has strong effects on immunity and inflammation and is one of the most diffused nature-derived flavonols. It lessens the effects of oxidative stress on the body, thus decreasing the effects of this stress on the aging process. As an anti-inflammatory, it has a beneficial effect on chronic fatigue. It also supports heart health through its anti-inflammatory properties.

Adding apples, peppers, and cherries to your diet will increase the amount of quercetin in your system. In reasonable levels, there appear to be no side effects of quercetin. In very high levels, there may be headaches and tingling of the extremities. It may interact with antibiotics, chemotherapy, and blood thinners. For this reason, and if you’re pregnant or breastfeeding, consult your healthcare professional before taking supplements.

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healthy stomach bacteria