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Benefits of the Human Microbiome

Updated: Nov 3, 2019

What are microbes, and where in the body are they naturally found?

A microbe is an organism of any type that is so small, it can only be seen with a microscope. On and within the human body, microbes are along the intestinal tract, on the skin, within the sinuses and vagina. As a whole, it is referred to as the microbiome. Its byproducts are also found in the blood stream and organs such as the kidneys (Learn. Genetics, n.d.).

Bacteria within the gut stimulate the immune system that surrounds the intestine. The immune system learns to attack pathogens but leaves alone the beneficial bacteria unless they enter the blood stream. Intestinal, beneficial bacteria can also help decrease inflammation by releasing certain calming compounds. Without an intestinal microbiome, the immune system may not fully develop but more research is needed. Some intestinal microbiome convert carbohydrates, including fiber, into n-butyrate which helps prevent leaky gut and is a good energy source for cells.

Benefits of the human microbiome

Microbes take up space which prevents an outbreak of the unhelpful type of microbes such as viruses or bacterium such a Clostridioides difficile (aka "c. diff"). This concept takes place on the skin, within the sinuses, and the intestine. Some beneficial microbes on the skin convert sebum into moisturizer aiding in keeping skin healthy and smooth to prevent harmful bacterial invasion (i.e. infection) in cracked, dry skin. The human microbiome can also have anti-microbial properties which help defend against other microbes that aren’t welcomed. The microbiome of the vagina creates an acidic environment from the synthesis of lactic acid which helps prevent harmful bacteria and yeast growth which can cause infection.

The gut has a vast network of neurons and the microbiota has an influence on it. For example, some microbiota synthesize serotonin or melatonin which are neurotransmitters neurons utilize. Microbiomes also help to produce ARA and DHA which help promote brain cell division, memory, and learning.

The microbiota can also have an impact on blood pressure. Fiber from complex carbohydrates is metabolized by bacteria which produces formate. This formate travels into the blood stream which effects dietary salt processing within the kidneys. Volume of formate is associated with lower blood pressure (Learn. Genetics, n.d.).

How does the microbiome change throughout the lifespan?

The microbiome starts the day a baby is born. It is influenced by a natural birth and breast feeding and both are protective for beneficial a specific type of intestinal bacteria. When a baby transitions to regular food, the microbiota also changes. Throughout life, the microbiome will continue to change dependent on the types of food that are consumed, the country and environmental cultural influences, and the exposure to antibiotics and/or foods preserved with chemical compounds.

Where do we as humans get our microbiome from? Are we born with it?

Humans get their microbiome from the environment outside of the womb. Thus, infants are not born with their microbiome, but do begin the process of building their microbiome AT birth and through breast feeding. Throughout the lifespan, the microbiome is influenced by dietary intake.

What are 3 nutrition-related diseases that the microbiome can impact? How does the microbiome impact these diseases?

Some auto-immune diseases have been associated with compromised gut microbiota. A healthy microbiota (a diversified microbiome) can help reduce the risk of auto-immune disease by promoting T-cells and making a stronger intestinal mucus barrier (Find My Fitness, 2015).

Heart disease, characterized by chronic inflammation, can be promoted or inhibited depending on the state of the microbiota. For example, if the mucin layer of the intestine becomes compromised and degraded due to a poor quality diet and compromised microbiota. Te immune system detects the microbiota that has been released into the blood stream and attacks it. One function of LDL is to bind to the endotoxins to prevent systemic infection. Fiber in the diet from whole foods can help produce short-chained fatty acids (SCFA) which can help inhibit chronic inflammation. The Western Diet, characterized by low fiber, can cause a shortage of SCFA-producing and inflammation-inhibiting microbiota within the colon (Found My Fitness, 2015).

Metabolic syndrome and insulin resistance is associated with compromised microbiota. This microbiome ecosystem is limited and less diverse compared to an individual without metabolic syndrome. A lean person without metabolic syndrome who has a well-varied diet increases the different types of dietary fiber consumed and the different colonies of gut bacteria which are able to digest these fibers (Find My Fitness, 2015). Obese, metabolic syndrome, and insulin-resistant people tend to have less diverse microbiota in the small intestine (the section of intestine responsible for simple carbohydrate absorption), and this appears to promote insulin-resistance (Vzieze, 2012).

What are some ways the Western diet can affect the intestinal microbiome? What is the significance of short-chain fatty acids?

The diversity of the microbiome is directly related to the types of foods that are consumed. The intestinal bacteria is literally fed by the foods we eat. And some bacteria favor certain kinds of foods. A varied diet with whole foods (foods that contain fiber, complex CHO, lipids, protein) feed a variety of microbiota. Junk foods, processed foods, sugary beverages, diets void of fiber, and high in fat (fried foods) can also influence the types and amounts of microbiota. Simple carbohydrates and lipids, for example, are absorbed in the small intestine and leave the microbiota within the colon devoid of nutrients. This happens when the diet is not diversified with whole foods. Fiber from whole foods can promote gut bacteria to produce SCFA as fiber is fermented within the colon. These benefits of SCFA generation are decrease in inflammation, promotion of T cells, and can help reduce the risk of cancer (Found My Fitness, 2015).


The research article, Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome, is a fascinating read of a research experiment where the microbiome was examined via fecal transplants of lean men and obese men. Here is the summary:

The authors set out to observe the effect on bacteria colony on insulin resistance and obesity in the context of metabolic syndrome. Adult males with metabolic syndrome had small-intestine biopsies, underwent fecal implant of either lean donors (<23 BMI) or reinfusion of own feces. An improvement was found peripheral insulin sensitivity. Feces of the obese/insulin insensitive had lower microbial diversity. Fecal transplant group increased in microbiota diversity including Roseburia intestinalis (butyrate-producer) and oxalobacter formigenes (oxalate-converting). Number of bacteria remained the same in both groups, before and after intervention, it was the diversity of bacteria type that differed. Butyrate microbiota production appears to be associated with and insulin sensitivity.

A consensus regarding specific bacterial species involved and evidence for a causative role for the microbiota in host metabolism is lacking. A compromised or otherwise altered microbiota of both intestines may contribute to obesity and insulin resistance. The authors hypothesized and found rebalancing obesogenic microbiota by small intestinal infusion of gut microbiota may positively affect host energy metabolism and insulin sensitivity in subjects with metabolic syndrome. Specifically, butyrate produced by certain bacteria prevents a translocation of endotoxic compounds linked to insulin resistance to the outside of the gut microbiota and may increase gut microbiota.

The main issue with the findings in relation to the study’s structure and narrative is that The authors do not discuss the diet differences between the donors and the males with metabolic syndrome. Also, this study doesn’t give us long term implications. In conclusion, increased gut microbiota diversity may be associated with reduced insulin resistance. For practice purposes, Intestinal microbiota of a lean donor transplanted in an obese host may be used therapeutically to increase insulin-sensitivity and metabolism of calories (i.e. CHO, lipids). Orally administered butyrate may help glucose metabolism within the small intestine. Diverse microbiotica is associated with improved insulin sensitivity (Vrieze, et al., 2012).


Found My Fitness. (2015, December 02). How The Gut Microbiota Affects Our Health with

Dr. Erica & Dr. Justin Sonnenburg. Retrieved from YouTube.

Learn. Genetics. (n.d.). The Human Microbiome. Retrieved from

Vrieze, A., Van Nood, E., Holleman, F., Salojärvi, J., Kootte, R. S., Bartelsman, J. F. W. M.,

Nieuwdorp, M. (2012). Transfer of intestinal microbiota from lean donors increases

insulin sensitivity in individuals with metabolic syndrome. Gastroenterology, 143(4),



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