Far Reaching Affects of the Gut Microbiome

The Far Reaching Affects of the Gut Microbiome

By Moira Fitzpatrick, PhD, ND

March 2018

The gut microbiome is the gut flora, the bacteria of the gut that contains about 4 million microbial genes. Humans have approximately 26,000 genes. There is a strong relationship between each of us and our gut. Perhaps we need to attend to this relationship. Each of us is host to bacteria in our gut and it is our job to feed these bacteria. In return the bacteria support our immune system and the breakdown of indigestible carbohydrates to create short chain fatty acids. Colonization of the gut begins at birth and develops as the individual grows. It is affected predominantly by diet, where you live, genetics, age and sex.


The intestines contain both pathogenic and symbiotic bacteria. There are many influences on the gut bacteria with diet exerting maximum influence. Recent research demonstrates that changes in certain members of the microbiota are associated with diseases and pathologies such as diabetes, liver, inflammatory bowel disease, autism spectrum disorder, obesity and neurodegenerative diseases. (1)


What is dysbiosis? It is the overgrowth of commensal bacteria and opportunistic bacteria. The result of dysbiosis predisposes us to infection, inflammation, nutrient depletion, especially B12, iron and fat- soluble vitamins.


What causes dysbiosis?

1)     Antibiotic use

2)     Stress

3)     High carbohydrate diets

4)     Gut inflammation often secondary to food sensitivities

5)     Toxic exposures

6)     Lack of physical activity


What are the roles of our gut bacteria?

1)     Stimulate the development of a competent mucosal immune system

2)     Maintain the integrity of the epithelium or lining of the gut

3)     Healthy intestinal bacteria metabolize fiber and produce short chain fatty acids (SCFA), which are essential for colonic health and to regulate the intestinal immune system

Ex. Butyrate is a SCFA that fuels the colon cells.

4)     Intestinal commensals also produce neuroactive molecules and neurotransmitters that affect the function of the enteric nervous system. Animal studies on germ free mice have shown a decrease in enteric neurons, which is associated with decreased gut motility.


There is significant cross talk amongst the gut, the nervous system and the immune system. This is exemplified by the growing research on the “gut-brain axis”. The “microbiota-gut-brain axis” is an extension of the gut-brain axis. This means there is bidirectional communication between our microbes and the brain. The intestinal microbiota can stimulate the production of neurotransmitters. Animal studies show changes in serotonin and glutamate signaling, plus expression of brain-derived neurotrophic factor (BDNF) when there is a depletion in gut microbes. Serotonin in the gut affects motility, pain perception and the tone of the vessels. Serotonin in the gut is regulated by serotonin-selective reuptake transporter, which is expressed by the intestinal epithelium. Short chain fatty acids are involved the activation of the processes that affect the transporter. There is a relationship between inflammation and different bacterial groups in the microbiome. Links between the gut microbiota and brain function have been identified in MS, Autism Spectrum disorders and ADHD. There is suggestion that decreased levels of bacteria that produce butyrate are a factor in ALS. Individuals with Parkinson’s disease show higher gut permeability (leaky gut) and decreased short chain fatty acids. Patients with Parkinson’s disease have increased constipation which is associated with changes in the microbiome. (1)


While there is need for more research, perhaps the gut, our unique microbiota holds the key to health.


Is there a relationship between leaky gut and a leaky blood brain barrier (BBB), hence neurological and psychological diseases? What is the role of dysbiosis and the microbiome?


There is increasing evidence that the gut microbiota affect the integrity of the blood brain barrier. Specifically, the short chain fatty acids (SCFA) are key players in the gut brain axis. SCFAs are produced when the gut bacteria are involved in the fermentation of fibers or complex carbohydrates. There are three types of SCFAs including acetate, propionate and butyrate. These SCFAs are involved in gut motility, enhance satiety, influence water and salt uptake and provide energy for colon cells through butyrate. Butyrate has gotten most of the attention in research. Butyrate has anti-tumor properties. It activates the vagus nerve and hypothalamus and indirectly affects appetite and eating behavior. Butyrate also increases insulin sensitivity. Intestinal propionate has been associated with decreased stress behaviors and reward pathway activity in both mice and humans. Propionate has a protective effect on the BBB by mitigating inflammatory and oxidative stimuli.


It may be that gut dysbiosis and the resultant changes in metabolite levels affect the blood brain barrier. Variation in blood barrier function is increasingly recognized to impact cognitive processes. Defects in blood brain barrier have been linked to impaired memory and linguistic function. Antibiotic induced intestinal dysbiosis has also been associated with cognitive deficits and decreased gut derived microbial metabolites. There are 200 distinct microbial metabolites that have been associated with healthy individuals. Is there a link between gut dysbiosis, blood brain barrier and cognitive defects? What we do know is that patients with early Parkinson’s and Alzheimer’s disease have reduced levels of Bacteroides species in their feces, which are important producer’s of SCFAs. Does this decline lead to a decrease in circulating propionate and hence vulnerability of the BBB?


Evidence points to short chain fatty acids being the key to a balanced microbiome and health? SCFAs control inflammation, regulate immune function, reduce excessive free radicals and mitochondrial dysfunction.


How do I increase short chain fatty acids?

1)     Eat a wide diversity of vegetables, including sprouts.

2)     Eat fermented foods such as kefir, homemade yogurt, kombucha, cultured coconut water, sauerkraut and sour dill pickles.

3)     Take good quality prebiotics and probiotics


We often have individuals do the GI Effects, a comprehensive 3-day stool test. This test provides a report on the following:

1)     Functioning of the GI system

2)     Identifies the amount of short chain fatty acids, including levels of butyrate and proprionate

3)     Identifies inflammation

4)     Shows levels of pancreatic enzymes

5)     Provides a description of each individual’s microbiome. We can see the ratio of firmicutes to Bacteroidetes phylum of bacteria. These bacteria compose 90% of the bacterial population in the colon.

This test plus food sensitivity and your subjective report of your digestion provides the guide to healing.


We can eliminate inflammation by supporting you in changing your diet, supplement the microbiome with pre-biotics and probiotics and alter the groups of bacteria in your microbiota. The stability of the microbiota depends on the food you eat.


Changes in the microbiome can modulate homeostasis, improve functioning and prevent disease, and can alter immune responses and modulate the severity of disease.


The prevention of disease begins in the gut.


(1)  Marietta, Eric, et al. Microbiome, Immunomodulation, and the Neuronal System. Neurotherapeutics (2018) 15:23-30.

(2)  Hoyles, Lesley et.al. Propionate affects the blood-brain barrier. July, 2017

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Gut & Brain Health

Gut and Brain Health
Intestinal Microbiome – “Forgotten Organ”
by Moira Fitzpatrick, PhD, ND, FICPP, CHT

April 2017

Digestion is the foundation of health. There is a significant connection between the brain and the gut which is regulated by the microbiota. The gut microbiota contains bacteria, fungus, parasites and viruses. There are more than 100 trillion bacteria that live in the gastrointestinal tract. The genome size of the microbiota exceeds the size of the human genome by 100 times. Thus, the microbiota can stimulate the brain. The brain also affects the microbiota. The gut is initially colonized at birth when the fetus moves through mom’s vagina. The mode of delivery, type of feeding (breast or formula), the mother’s diet, the environment and the use of antibiotics affect the microbiota of the neonate and its maturation. The microbiota is established by the first three years of life. There is a symbiotic relationship between each of us and the microorganisms within us. It is noteworthy that gut microbiota, neurodevelopment and emotional development all co-occur during this three-year period and to a less extent during adolescence.

What affects the microbiota? Even short exposure to stress can affect the microbiota by altering the proportions of the bacterial families. Experimental alteration of the microbiota influences anxiety and the Hypothalamic-Pituitary-Adrenal axis, which affects our stress hormones, sleep, inflammation and leaky gut. Increased stress suppresses the thyroid. Increased cortisol decreases reproductive hormones. Long term stress affects the hippocampus, the center of memory. There is a strong interconnection of the endocrine, nervous and immune systems that begin in the gut.

Medications affect the bacteria in the gut. Opioids are linked to constipation. NSAIDs affect the immune system in the gut. Proton pump inhibitors can trigger bacterial overgrowth in the upper GI tract. Broad spectrum antibiotics cause a disturbance in the microbial gut community and reduce the diversity of the gut microbiota.

Environmental toxins affect the microbiota. For example, Polycyclic Aromatic Hydrocarbons (PAH) are catalyzed by the microbiotia to estrogen. PAH’s are a risk factor for prostate cancer. We need to avoid charcoal grilled and smoked meats to avoid PAH’s.

What can we do to protect ourselves from toxins? Maintain a strong gut and brain barrier. Decrease stress, insure that the liver is functioning well, maintain homeostasis in the microbiota.

What about mood and the gut? Ninety five percent of serotonin is produced in the gut mucosa by the enterochromaffin cells and enteric nervous system neurons. Peripherally serotonin is involved in regulating GI secretions, gut motility and pain perception. Serotonin in the brain helps to regulate mood. What if a dysfunctional communication between the gut and brain is related to mood disorders?

A dysfunctional gut-brain axis can contribute to leaky gut. This means that the tight junctions in the intestines become enlarged and undigested proteins, toxins and bacteria leak through. The immune system becomes activated as these particles are foreign and an inflammatory process begins.

What lifestyle factors contribute to leaky gut? Let’s start with food sensitivities, processed foods, alcohol, stress, lack of sleep and exposure to environmental toxins.

Are you ready to learn more about the gut-brain axis affects your health?

Dr. Fitzpatrick: “Healthy Gut, Healthy Brain”
April 4th at 6:30 PM Pacific Pearl La Jolla – studio 6933 La Jolla Blvd. Back entrance.
Free. Limited seating, must RSVP: 858-459-6919

Discover the joy of eating nutritious foods and supporting your unique body, the temple of your inner essence.

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