Healthy Stomach Bacteria and the Neuroimmune System – Part 2

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

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healthy stomach bacteria and dysbiosisThere is currently no perfect standard for a healthy stomach bacteria. Due to environmental and genetic considerations, there are considerable differences in people’s “normal” gut flora. Generally, microbes that are healthy and diverse help to promote gut health and to maintain metabolic, structural, and signaling functionality. However, the gut can become imbalanced in a variety of ways; in particular, the term dysbiosis involves a change away from the normal diversity and stability found in the healthy stomach bacteria. This presents with an unstable gut that is unable to function normally and may eventually lead or contribute to neurological, metabolic, or autoimmune disorders. Causes of dysbiosis include environmental toxins, alcohol intake, excess stress, and overgrowth of yeast and bacteria.

For those with Adrenal Fatigue, high stress levels can often lead to dysbiosis. In addition, since your body is in a low energy state, the gut (and other bodily functions) often slows down in an effort to conserve energy. As your gut slows down, food stays in your stomach longer, resulting in reduced assimilation, longer transit times, and increased inflammation, as allergens have more time to seep into the body through the gut. If the food stays in the gut for a prolonged period of time, it can even start to rot in the stomach, releasing toxic compounds into the stomach. This may be another cause for gut dysbiosis.

Leaky Gut and Inflammation

When the mucosal lining of the gut fails in its role as a barrier to protect against potentially damaging molecules that can enter the blood flow, the resulting condition is known as leaky gut. Lipopolysaccharides on the outer membrane of gram-negative bacteria can then be found entering the bloodstream, prompting an inflammatory response. Inflammation influences the brain in several ways and is thought to be a major contributing factor to depression. In fact, selective serotonin reuptake inhibitors (SSRIs)—one of the main classes of drugs used in depression treatment—has been found to reduce inflammation in the brain. This anti-inflammatory effect may be an important part of why the drugs are effective. Thus, it is easy to see how your gut can have a major affect on the neuroaffective circuit and your mood simply through an elevation or reduction of inflammation.

Increased permeability of the intestinal lining can also lead to food allergies, malabsorption, and toxic overload. There is a saying that a leaky gut leads to a leaky brain, as the buildup of toxins can cause changes in mood, depression, fatigue, poor memory, confusion, and anxiety.

Unfortunately, the details of these connections are difficult to study because every individual’s gut microbiome is unique, and the terms healthy and unhealthy are in reference to an individual’s specific state of normality.

Gut Flora and Neurological Disease

healthy stomach bacteria and gut floraDisturbances in the gut — such as an alteration in the composition of healthy stomach bacteria have been linked to neurological disorders such as multiple sclerosis (MS), Parkinson’s disease, and autism spectrum disorders. A Parkinson’s patient’s first symptom is usually constipation; the second is often the loss of taste and smell. These gastrointestinal disturbances are present long before the symptoms of motor neuron dysfunction, such as tremors or a shuffling gait, appear.

Multiple environmental risk factors for neurological conditions have been found to promote an immuno-inflammatory response. In particular, improper folding and aggregation of proteins within the brain is a possible etiology for several neurodegenerative disorders. This could be caused by inflammation in the gut triggering inflammatory effects in the brain that cause misfolding of proteins and degeneration of neural cells.

Gut dysbiosis, healthy stomach bacteria, and inflammation have also been linked to autoimmune disorders. Western nations present with higher rates of multiple sclerosis and also tend to share similar dietary habits. These diets are thought to cause inflammation and disruptions in the optimal functioning of gut microbes. Patients with Parkinson’s disease and MS both have increased numbers of antibodies to a variety of antigens and lipopolysaccharides due to a more permeable intestinal lining. Taken together, the evidence indicates that a dysregulated inflammatory response circuit can be the result of prolonged stress, among other factors.

Alzheimer’s disease and general cognitive decline are marked by changes in the brain, disruptions in immune function, and increasing oxidative stress. These factors are all shaped by diet and gut flora in animal experimental models. One important link involves a neurotrophin, a type of protein that is responsible for the protection and the encouragement of healthy neurons. The production of this neurotrophin is dependent on the gut bacteria, and declines in individuals with Alzheimer’s. Changes to the microbiome occur with age and can be linked to neurodegeneration.

Parkinson’s and Alzheimer’s Diseases

Among the disease states that can be brought on by an imbalance of healthy to unhealthy stomach and gut bacteria are two that seem to be increasing in frequency in our country. Research appears to suggest the huge role of inflammation in both Parkinson’s disease (PD) and Alzheimer’s disease (AD). With inflammation originating in your stomach and gut system with dysbiosis, the connection between bacteria imbalance and these serious illness conditions seems strong.

Some promising research conducted with fecal transplants has suggested improvement in PD symptoms as well as in chronic fatigue conditions. A decade of this type of intervention for patients with Clostridium difficile to alleviate constipation has also led to beneficial changes in patients with PD and chronic fatigue.

other diseases and healthy stomach bacteriaEvidence is surfacing that points to AD as being closely related to a possible Type 3 diabetes condition. A significant increase in the research literature suggests insulin deficiency and insulin resistance, both found in AFS as well, to be present in the neurodegeneration that comes with AD. There appears to be a definite connection between large disturbances in brain insulin and insulin-like growth factor and the progressive abnormalities and lesions seen in AD. This Type 3 diabetic condition posed as a factor in AD appears to be selective for brain involvement only and seems to overlap with both Type 1 diabetes mellitus and Type 2 diabetes.


Currently, one in 68 children born in the U.S. has a condition somewhere along the autism spectrum. This very serious condition affects multiple systems in the body. Prior to the last 10 years, autism spectrum disorder (ASD) was viewed as a neurological disorder primarily. But research now indicates these children suffer from numerous abnormalities in the endocrine, GI, immune, and detox systems among others. The various biological systems involved in ASD have not been clearly delineated. If all of these systems could be shown to be interrelated as in the NEM stress response, new avenues of successful remediation could be initiated.

Interestingly, a few studies have shown oxidative stress to play a role in the pathophysiology of ASD. However, not a lot of scientific attention has been directed at this aspect of the causes ASD. This increased oxidative stress in the brains of ASD children may be connected to chronic inflammation and DNA damage.

A relatively new direction for research into causative factors in ASD shows the use of acetaminophen to possibly be a factor in the development of ASD. Lately, there has been a lot of discussion regarding vaccinations leading to autism symptoms. This trend in thinking started at exactly the same time physicians began giving children acetaminophen rather than aspirin for the fevers associated with vaccinations.

Physicians thought acetaminophen was safer than aspirin for this purpose. But acetaminophen has a high incidence of immune system problems as well as metabolic issues. These metabolic issues include liver failure.

The link between acetaminophen and ASD lies in the fact that acetaminophen also depletes glutathione levels. Especially in children and infants. Glutathione is necessary for your body to have sufficient levels of antioxidants and for good brain function.

Young children can develop toxic overload with depleted glutathione levels. The current thinking among some scientists is the build-up of toxins can trigger changes in the brains of children who are genetically susceptible to autism.

healthy stomach bacteria and autismThis high load of toxins can occur when a person has taken acetaminophen over a period of several days. Like with children who either have or may develop fever associated with vaccinations. Well-meaning pediatricians may recommend parents give their children acetaminophen for several days prior to vaccinations as a preventative against fevers.
Mothers’ stress during pregnancy may also be implicated in development of ASD. The hypothesis is when mothers undergo stress while pregnant their stomach and healthy stomach bacteria changes. Their healthy stomach and gut bacteria are replaced by unhealthy bacteria. The byproducts of unhealthy bacteria have been shown to cause impaired brain development in the fetus. Animal studies have shown offspring to have ASD-like symptoms when their mothers experienced stress during pregnancy. Some researchers hypothesize one pathway from mothers’ stress to their babies’ brains may be through healthy stomach bacteria and the gut microbiome.

Stress during pregnancy leads to changes in the mothers’ vaginal regions. During the passage through the birth canal, their babies gut biome is affected significantly by these changes. These changes then lead to long-term developmental problems.

Researchers also suggest that some types of gut bacteria present in children with ASD produce waste products that appear to affect brain activity.

While many bacteria in the stomach and gut are healthy stomach bacteria, carrying out their processes of digestion, protecting the body against harmful bacteria, and producing vitamins, there are those bacteria that are harmful. If the harmful bacteria are not reduced and controlled, they begin producing metabolites that are detrimental to the gut and the brain.

Previous studies have shown children with ASD to have abnormal colonies of digestive bacteria in their stomachs and gut systems. Studies have also linked these bacteria with the more severe symptoms of ASD.

Other studies suggest microbes in the gut may change levels of neurotransmitter-related metabolites leading to altered brain function. This indicates significant cross-talk between the gut systems of children with ASD and their brains.

Healthy Stomach Bacteria, Gut Flora, and Psychiatric Disorders

The connection between the gut and mental health has garnered increasing attention in recent years. Various psychological disorders, especially depression, may actually be disorders of inflammation, with the gut being a crucial mediator. Several animal studies have demonstrated that transplantation of microbes from anxious or depressed mice to germ-free mice could induce the same behaviors in the previously healthy mice.

Anxiety and depression are also common symptoms of Adrenal Fatigue. It is therefore vital for those suffering from Adrenal Fatigue Syndrome to keep the microbiome healthy. This will help to restore balance to the neuroaffective circuit, calming the body down and enabling a speedier recovery.

Oxidative Stress, Gut Bacteria, and Psychiatric Conditions

One issue that occurs when there is dysbiosis in your stomach and gut is oxidative stress. Oxidative stress occurs when free radicals are released into your system and the system can’t repair the damage they cause or detoxify your body and rid it of these free radicals.

healthy stomach bacteria and stressIn conditions of dysbiosis, your metabolism, hormone, and immune systems are hampered significantly in their efforts to detox your body. Enzymes needed by the liver to carry out the detox process are lowered in dysbiosis.

Research is beginning to show the role played by oxidative stress, inflammation, and lack of immune response in psychiatric conditions. The brain, where psychiatric behaviors begin, is particularly susceptible to oxidative stress. Any causative role of oxidative stress in psychiatric disorders isn’t clear as yet.

One factor that is clearer is that psychiatric disorders, especially depression in its various types, are highly influenced by inflammation. Inflammation is common in AFS and is brought on by an imbalance in healthy stomach bacteria and unhealthy stomach and gut bacteria.

Major depression is one of the more common forms of depression. Research shows the close relationship between increased inflammation and major depression. Possibly this relationship has to do with elevations in proinflammatory cytokines that have been found in patients with major depression. This elevation continues even after the depressive episode has been remediated and may predict future episodes of major depression. Antidepressants will lower levels of proinflammatory cytokines in major depression. Research of this nature helps with understanding of how nonsteroidalantiinflammatory (NSAID) drugs interfere with antidepressants.

These proinflammatory cytokines, which are the type of “messenger” chemicals used by the ENS to communicate via the vagus nerve, also bring on what is called “sickness behavior” as a normal response. This behavior adds to recovery from trauma and infection by conserving energy. It has been connected to depression due to the similarities in symptoms such as anhedonia, anorexia, anxiety, and cognitive symptoms.

The relationship between sickness behavior and depression appears to be one of two sides to the response to proinflammatory cytokines. The sickness behavior side is more positive, leading to recovery of your body from trauma and infection. The depressive side leads to lifelong problems with neuroinflammation and neurodegeneration.
These cytokines appear to start a cascade of reactions resulting in lowered serotonin levels and increased glutamatergic actions that lead to an increase in depressive symptoms.

Research has shown depression to be present when several illnesses brought on by inflammation are present. Inflammatory biomarkers are found whenever a person is experiencing major depressive disorder. Depression risk increases in the presence of immunomodulating agents. Stress activates proinflammatory pathways; antidepressants decrease inflammation. When inflammation is decreased, depression symptoms improve.

Since inflammation is increased with a decrease in healthy stomach bacteria, it is very important for people with depressive disorders, either present or past, to maintain healthy stomach and gut bacteria. Considering the interactive nature of all body systems, improving the neuroaffective system will lead to improvement in other systems.


healthy stomach bacteria and signs of agingEveryone ages. But not everyone ages at the same rate. As people age, they are more likely to develop chronic illnesses of one kind or another. With these conditions, recovery in advanced age takes longer. The higher incidence of these kinds of illnesses and more difficulty in recovering is problematic for older people. And many of the illnesses contracted by older people have in common a high incidence of immune system suppression.

The term immunosenescence has been coined to describe the loss of immune function in these older people. If these elderly have adrenal fatigue, their immune system is already compromised. Aging will increase the loss of immune function in this condition.

The elderly also have increased incidence of Alzheimer’s and Parkinson’s diseases. Studies have shown a clear connection between these two conditions and the stomach and gut system. A commonality between these illnesses and the gut system lies in their contact and susceptibility to environmental issues.

Changes in healthy stomach bacteria of older people also play a role in aging. An animal study using groups of mice in youth, middle age, and old age showed changes in healthy stomach bacteria of the old mice. The old mice had sufficient bacteria in their microbiomes to break down simple sugars, but insufficient bacteria to handle complex sugars, as well as lactate. The importance of this has to do with increased lactose in the stool being connected to development of ulcerative colitis and other inflammatory bowel diseases in elderly people.

The old mice in this study also showed a lack of bacteria that produce vitamins B12 and B7. Lower levels of B7 have been shown to be connected to colon cancer. In addition, the old mice contained bacteria that would break down creatinine. Creatinine builds muscle, so the lack of it would appear to explain at least some of the loss of muscle so common in the elderly.

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