The microbiome

What is the microbiome?
At a microscopic level the microbiome inside our bodies, consists of trillions of microorganisms (also called microbiota or microbes) of thousands of different species. These include not only bacteria but fungi, and parasites. In a healthy person, these coexist peacefully, with the largest numbers found in the small and large intestines but also throughout the body. The microbiome is even labeled a supporting organ because it plays so many key roles in promoting the smooth daily operations of the human body.

A person is first exposed to microorganisms as an infant, during delivery in the birth canal and through the mother’s breast milk. Exactly which microorganisms the infant is exposed to depends solely on the species found in the mother. Later on, environmental exposures and diet can change one’s microbiome to be either beneficial to health or place one at greater risk for disease.
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The microbiome consists of microbes that are symbiotic (where both the human body and microbiota benefit). In a healthy body symbiotic microbiota exist without problems. But if there is a disturbance in that balance—brought on by environmental toxins, drugs, poisons, chemicals, certain diets, or the prolonged use of antibiotics or other bacteria-destroying medications—dysbiosis occurs, stopping these normal interactions. As a result, the body may become more susceptible to dis-ease.

How microbiota benefit the body
Sugars like table sugar and lactose (milk sugar) are quickly absorbed in the upper part of the small intestine, but more complex carbohydrates like starches and fibers are not as easily digested and may travel lower to the large intestine. There, the microbiota help to break down these compounds with their digestive enzymes. The fermentation of indigestible fibres causes the production of short chain fatty acids (SCFA) that can be used by the body as a nutrient source but also play an important role in muscle function and possibly the prevention of chronic diseases, including certain cancers and bowel disorders. Clinical studies have shown that SCFA may be useful in the treatment of ulcerative colitis, Crohn’s disease, and antibiotic-associated diarrhea.

The microbiota of a healthy person will also provide protection from organisms that enter the body such as through drinking or eating contaminated water or food.
Large families of bacteria found in the human gut include Prevotella, Ruminococcus, Bacteroides, and Firmicutes. In the colon, a low oxygen environment, you will find the anaerobic bacteria Peptostreptococcus, Bifidobacterium, Lactobacillus, and Clostridium. These microbes are believed to prevent the overgrowth of harmful bacteria by competing for nutrients and attachment sites to the mucus membranes of the gut, a major site of immune activity and production of antimicrobial proteins. 

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The role of probiotics
If microbiota are so vital to our health, how can we ensure that we have enough or the right types? You may be familiar with probiotics or perhaps already using them. 
A diet rich in fermented foods enhances the diversity of gut microbes and decreases molecular signs of inflammation, according to researchers at the Stanford School of Medicine.

In a clinical trial, 36 healthy adults were randomly assigned to a 10-week diet that included either fermented or high-fiber foods. The two diets resulted in different effects on the gut microbiome.
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Eating foods such as yogurt, kefir, fermented cottage cheese, kimchi and other fermented vegetables, vegetable brine drinks, and kombucha tea led to an increase in overall microbial diversity, with stronger effects from larger servings. “This is a stunning finding,” said Justin Sonnenburg, PhD, an associate professor of microbiology and immunology. “It provides one of the first examples of how a simple change in diet can reproducibly remodel the microbiota across a cohort of healthy adults.”

The microbiome is a living dynamic environment where the relative abundance of species may fluctuate daily, weekly, and monthly depending on diet, medication, exercise, and a host of other environmental exposures.