As humans we share our lives with 100 trillion organisms. Merely 10% or 10 trillion of the cells in human body are human. For each living cell, there are 10 living bacteria which help us carry out functions we could not execute without their assistance. The dictionary definition of a microbiome is “the microorganisms in a particular environment.” The vast assemblage of microbes or microorganisms that dwell an environment is known as the microbiome. You can decide who owns the body, you or your bacteria.

Our human microbiome is comprised of mutually beneficial bacteria that reside in our skin, our genitals, our eyes, our mouth, and certainly, our intestines. These communities of bacteria from different localities in our body are called the microbiota. There is skin microbiota, vaginal microbiota, oral microbiota, and the gut microbiota or the gut flora.

Scientists are recognizing that the composition and overall health of our microbiome governs whether we will have a healthy body or disease. Over 10,000 different microbial species occupy our microbiome. The bacteria in our gut perform various functions which are critical for our survival to maintain good health and wellbeing. Our gut microbiome is crucial to the breakdown and absorption of nutrients. The gut microbiota play a fundamental role in digesting food as well as extracting the vital nutrients mandatory for bodily functions. We are in a symbiotic relationship with our microbiome, which secretes beneficial juices into our body as a component of its metabolic cycle.

When a baby is born, he or she is sterile and exposed to the microbiome in the mother’s birth canal. The next contact with the microbiome comes from the gut-nurturing potion of the mother’s breast milk. This is mother nature’s method of launching a basis upon which we will develop our microbiome. More exposure to family, diet, and the environment encourages the building of an ecosystem which plays a significant role in the establishment of our health for a lifetime. Every time we come into contact with another human being or a pet, or apply something to our skin, or eat food, we impact the constitution of our microbiome.

An imbalance in our microbiome has been linked to a number of diseases. Even psychological well-being and our immune health depends on microbiome. Harmonizing gut bacteria has become the groundbreaking therapeutic treatment for many chronic diseases. A disturbance of the microbiota-host relationship can drive chronic gut inflammation. According to a recent investigation, bacteria in our colon lining have been correlated with the development of metabolic disease, particularly, type 2 diabetes. Prior studies in mice have suggested that bacteria that are able to invade upon the epithelium might be promoting inflammation that causes metabolic diseases (Chassaing 2017).

As a means to study whether invasion of colonic microbiota on host epithelial cells may associate with elements of metabolic syndrome, confocal microscopy was used to measure the distance of the closest bacteria to the epithelium in left-colon biopsies received from 42 people of an average age of 58.1 years. By and large, 86% of the participating members were overweight, 45% were obese, and a third had diabetes. After standard bowel cleansing, researchers discovered that the remaining bacteria were very nearly detected in outer parts of the mucus layer in healthy subjects without obesity or diabetes, while in obese participants with diabetes, bacteria were found in the dense inner mucus, close to the epithelium. In other words, there was an inverse relationship between bacterial-epithelial distance and markers of metabolic syndrome in all patients, counting BMI, fasting blood glucose levels, and hemoglobin A1c. The bacterial-epithelial distance was almost three times lower in patients with type 2 diabetes, even after disregarding subjects with obesity. The scientists concluded that the microbiota invasion is an element of insulin resistance-associated dysglycemia in humans. This study offers a novel field of research in metabolic function and type 2 diabetes as a method of treating or preventing this condition (Chassaing 2017).

Dietary strategies modulate the gut microbiota. Good bacteria, which live in symbiosis with us, are nourished by fruits, vegetables, grains, and beans. On the contrary, dysbiosis, or the bad bacteria which may contribute to disease, are fed by meat, junk food, fast food, seafood, dairy, and eggs. A typical low fiber diet induces metabolic disease in laboratory animals and decimates the gut microbiota (Tuohy 2014).

We live with trillions of good bacteria that live in symbiosis with us. We help them and they help us. The human intestine is densely populated by trillions of microbial symbionts which aid in nutrient absorption through the fermentation of dietary fiber and protect us from invading pathogens. Dietary fiber induces prebiotic effects that may restore imbalances in the gut microbiota. Research indicates that a month on a strict vegetarian diet results in an increase in the commensal microbes or the good guys and a decrease in the bad bacteria which are called pathobionts or the disease-causing bugs. Scientists measured the stool concentration of lipocalin-2, which is a sensitive biomarker of intestinal inflammation. Within a month of eating healthy, it declined significantly between day 1 and day 28 in all the participants. This suggests that the promotion of microbial homeostasis or a balance by strict vegetarian diet results in reduced intestinal inflammation. This re-balancing may play an important role in the improved metabolic and immunological parameters in patients with metabolic diseases (Kim 2013).

On an animal-based diet, you get a growth of disease-associated species such as Bilophila wadsworthia, linked with inflammatory bowel disease (IBD) and Alistipes putredinis, found in abscesses and appendicitis. Also, an animal-based diet resulted in a decrease in Firmicutes which metabolize dietary plant fibers, reduce inflammation and produce anti-cancer short-chain fatty acids (Tilg 2014). We are what we eat. The antioxidant compounds found in whole grains, legumes, nuts, and seeds are called phytates. There is published literature that shows that the microbiota from the environment of high-phytate content from vegetarians’ intestine is the most effective in degrading phytate, which suggests that microbiota adapt to such an environment and that the diet modulates metabolic activities of intestinal bacteria. The stool samples of adults on a conventional diet or a vegetarian diet were studied. The vegetarians’ microbiota particularly degraded almost 100% phytates (Markiewicz 2013).

Surprisingly, our diet can teach old bacteria in our gut new habits. For instance, there is one type of fiber in nori seaweed that our gut bacteria cannot breakdown. However, the bacteria present in the ocean that eats seaweed has an enzyme to fulfill this task. It was noticed that these bacteria were present in the gut of the Japanese population, but not North American individuals. How could a marine bacteria blossom in a human gut? There was a DNA transfer. The bacteria was acquired by horizontal gene transfer from seaweed-associated bacteria found in sushi. It is almost like a software update. We have the identical hardware, the same gut bacteria, but they just updated their software by consuming new foods. As you know, seaweeds make an important contribution to the daily diet in Japan. Approximately 14.2 grams of seaweed per person per day is ingested in Japan. Nori is the most important nutritional seaweed, traditionally used to prepare sushi in Japanese culture. This suggests that seaweeds with associated marine bacteria may have been the route by which these new enzymes were acquired in the human gut microbes (Hehemann 2010).

Nevertheless, even the hardware can be altered. Certain gut flora can take carnitine from the red meat we eat or the choline found in dairy, seafood, and eggs, and convert it into a toxic compound called trimethylamine N-oxide or TMAO, which can lead to heart attacks, stroke, and death. Individuals adhering to vegan and vegetarian diets have lower fasting TMAO concentrations and produce less TMAO in contrast to omnivores. Compared with vegans and vegetarians, omnivores had elevated plasma TMAO concentrations and significantly higher relative abundance of stool bacteria commonly associated with protein fermentation. Plant based diets have lower concentrations of TMAO, but they also produce less of the toxin even if you were to give them steak (Wong 2014).

Dietary patterns that favorably alter the gut microbiota, especially those that emphasize plant-based foods, may have significant implications to human health, thereby providing novel approaches in the treatment and management of chronic diseases. Specifically, studies in individuals who consume vegetarian and vegan diets have shown a lower risk of cardiovascular events and incidence of diabetes. Plant-based diets high in dietary fiber and fermentable substrate are sources of metabolic fuel that have an impact on modulating the health of the host body (Wong 2014). One kind of bacteria that flourish under a meat-rich diet was correlated with inflammation and intestinal diseases in mice. As a means to determine how diet influences the microbiome, researchers put nine subjects on two extreme diets for five days each: one that included only meat, egg, and cheese, and another that contained only grains, vegetables, and legumes. In the first diet, the participants had eggs and bacon for breakfast. They had ribs and briskets for lunch. The dinner consisted of salami and prosciutto with a wide array of cheeses. The subjects had pork rinds for snacks. After a break, the same volunteers started a fiber-rich diet that was plant-based. The breakfast was granola cereal. For lunch, the participants had jasmine rice, cooked onions, tomatoes, squash, garlic, peas, and lentils. Their dinner looked similar, and they snacked on bananas and mangoes (David 2014).

The microbiomes of the subjects from the study were analyzed before, during, and after each diet. The effects of the meat and cheese were instantaneously evident. Once the subjects had spent about three days on each diet, the bacteria in the gut began to change their behaviors. Specifically, the microbes that love bile or Bilophila dominated the guts of the participants during the animal-based diet. Bile aids the stomach in the digestion of fats. Your body produces more bile when you eat meat and dairy fats. Blossoming of Bilophila caused inflammation and colitis (David 2014).

Our microbiome can even affect our moods. Our gut is an all-encompassing sensory system, signaling system, and immune system. Our gut is like a little brain and has its own intellect. We have a nervous system that is sandwiched between the layers of our gut which has nerve cells ranging from 50 million to 100 million. Recent studies in mouse and rat have shown that the microbes in our gut communicate with the brain and play a significant role in the formation of emotional behaviors of animals. Our body has receptors that respond to signals from the microbes. For instance, some microbes affect the creation of serotonin molecules, which function in appetite regulation, food intake, and sleep. This allows the microbes to impact overall health and wellbeing. Some microbe signals activate the vagus nerve endings in the gut, which act like an information pathway to the brain. Through manipulating the microbes in the guts of mice, scientists have seen various behaviors, which stopped occurring as soon as the vagus nerve was cut. Microbiome may be responsible for our behaviors, cravings and even addictions.

Emotions are reflected at the gut level. As an angry stomach causes contraction, a greater amount of acid is secreted, and blood flow to the stomach increases. Hormones such as adrenaline and norepinephrine are released and begin circulating in our blood. Our heart rate increases and we get sweaty hands. The bacteria in our gut have receptors for these chemicals, and these chemicals change the behaviors of the bacteria. Research shows that behavior of mice can change upon receiving gut microbes from a depressed person. The microbiota in our gut affect the initiation of diseases such as Parkinson’s, Alzheimer’s and autism. The communication between the gut and brain is a two-way street. The brain impacts both the immune and gastrointestinal functions, which can alter the composition of the gut’s microbiome. The gut microbiome shapes the brain at cellular and genetic levels which also has effects on mood, thoughts, and behavior.

In a 2013 study, a small set of women were given fermented milk with probiotics. After drinking this drink twice a day for four weeks, the women had an MRI done while observing photographs of angry or frightened actors. These images normally trigger the part of the brain utilized in processing emotions when alert. The responses of women who drank the fermented milk were less reflexive than the control group. The microbiome in our guts affects how we interact with the universe. Generally speaking, there is a rising understanding that the microbiome or the bacteria that live in our bodies, may play a role in the development of numerous diseases in humans. There may be a cure for type 2 diabetes via unraveling the functions of the microbiome.

We can transform our microbiome through diet. An average person who eats red meat has a disrupted gut microbiome when compared to a vegetarian. Research shows that people who eat red meat generally have a worse microbiome than vegetarians. Long term consumption of red meat causes inflammation in the gut. We can improve our gut microbiome by eating the right foods. We ought to eat a diversity of healthy, non-processed foods, and cut down on sugary foods. We must take a high-quality probiotic which helps maintain our gut’s ecosystem as well as the ecosystem of our respiratory tract and urogenital tract.

What foods can we take to support our microbiome? We can eat prebiotic foods like artichokes, raw dandelion greens, onions, raw garlic, raw leeks, asparagus, chicory, bananas, and beans. We can eat foods rich in probiotics including sugar-free yogurt, kefir (fermented milk drink), lassi (Indian yogurt drink), pickles, cultured veggies, olives, tempeh, miso, natto (fermented soy), and kimchi (spicy Korean condiment). Avoid the consumption of too many artificial sweeteners and alcohol, which have negative effects on the gut microbiota and negatively impact our health. If you want to be disease free, support your microbiome by eating healthy foods.


  • [1] Chassaing, Benoit, Shreya M. Raja, James D. Lewis, Shanthi Srinivasan, and Andrew T. Gewirtz. “Colonic Microbiota Encroachment Correlates With Dysglycemia in Humans.” Cellular and Molecular Gastroenterology and Hepatology (2017): n. pag. Web.
  • [2] David, Lawrence A., Corinne F. Maurice, Rachel N. Carmody, David B. Gootenberg, Julie E. Button, Benjamin E. Wolfe, Alisha V. Ling, A. Sloan Devlin, Yug Varma, Michael A. Fischbach, Sudha B. Biddinger, Rachel J. Dutton, and Peter J. Turnbaugh. “Diet Rapidly and Reproducibly Alters the Human Gut Microbiome.” Nature 505.7484 (2013): 559-63. Web.
  • [3] Drasar, B. S., A. G. Renwick, and R. T. Williams. “The Role of the Gut Flora in the Metabolism of Cyclamate.” Biochemical Journal 129.4 (1972): 881-90. Web.
  • [4] FACLM, Michael Greger M.D. “Microbiome: We Are What They Eat.” N.p., n.d. Web. 13 June 2017.
  • [5] Hehemann, Jan-Hendrik, Gaëlle Correc, Tristan Barbeyron, William Helbert, Mirjam Czjzek, and Gurvan Michel. “Transfer of Carbohydrate-active Enzymes from Marine Bacteria to Japanese Gut Microbiota.” Nature News. Nature Publishing Group, 08 Apr. 2010. Web. 13 June 2017.
  • [6] Kim, Min-Soo, Seong-Soo Hwang, Eun-Jin Park, and Jin-Woo Bae. “Strict Vegetarian Diet Improves the Risk Factors Associated with Metabolic Diseases by Modulating Gut Microbiota and Reducing Intestinal Inflammation.” Environmental Microbiology Reports (2013): n. pag. Web.
  • [7] Markiewicz, L.h., J. Honke, M. Haros, D. Swiatecka, and B. Wroblewska. “Diet Shapes the Ability of Human Intestinal Microbiota to Degrade Phytate- in Vitro studies.” Journal of Applied Microbiology 115.1 (2013): 247-59. Web.
  • [8] Tilg, Herbert, and Alexander R. Moschen. “Microbiota and Diabetes: An Evolving Relationship.” Gut 63.9 (2014): 1513-521. Web.
  • [9] Tuohy, Kieran M., Francesca Fava, and Roberto Viola. “The Way to a Man’s Heart Is through His Gut Microbiota Dietary Pro- and Prebiotics for the Management of Cardiovascular Risk.” Proceedings of the Nutrition Society 73.02 (2014): 172-85. Web.
  • [10] Wong, J. M. “Gut Microbiota and Cardiometabolic Outcomes: Influence of Dietary Patterns and Their Associated Components.” American Journal of Clinical Nutrition 100.Supplement_1 (2014): n. pag. Web.

Have Questions?
We’ll Reply Quickly.

  • Please use this form for general information purposes only. DO NOT send personal health information through this form. Specific patient care must be addressed during your appointment.
  • This field is for validation purposes and should be left unchanged.
Call Us Text Us
Skip to content