Getting To Know The Microbiome

Posted By Dr. Jeannie Thomason on Feb 20, 2015 |

By Jennifer Lee, A.C.A.N. graduate and Certified Carnivore Nutrition Health Coach

A microbiome can be described as the unique community of microorganisms that inhabit a living organism. These microorganisms are found living on the skin and genitals, as well as in the mouth and gut. It’s estimated that the amount of bacteria typically outnumber the hosts cells by as much as 10 times.

Aside from contributing to the synthesis of vitamins, amino acids and fatty acids, scientists have discovered that the microbiome also has an influence on the immune system, genetic expression, brain development, mental health, memory, body weight and development of disease.

Several factors are shown to change the composition of the microbiome such as diet, exercise, stress, toxins and most importantly, antibiotic use. Besides taking antibiotics for medical reasons, there are more antibacterial substances present today than ever before. They’re in the soaps we use, the meat we eat, and the water we drink. One human study demonstrated that a short course of the antibiotic ciprofloxacin reduced the diversity of the intestinal microbiota, with significant effects on approximately one-third of the bacterial species. This study also found that while much of the diversity eventually recovered, there were still several species that failed to recover after six months, suggesting that even a short course of antibiotics may cause permanent changes to the community of bacteria in the gut.

Human studies show that changes in diet can alter the microbiome almost immediately (from hours to days). There can be an 80 to 90 percent difference in the variety and abundance of intestinal bacteria in any two people. People eating non-western diets have a much greater diversity of microbes within their gut. Interestingly, researchers found that ancient human gut bacteria is more similar to what is found in the guts of non-human primates, such as chimpanzees. In comparison, the intestinal contents of modern humans appear more depleted in diversity.

Animal studies have shown that mammals belonging to the same mammalian order or sharing the same type of diet have a similar gut microbial community. (See image below)

Sophisticated analysis of the fecal microorganisms of 12 healthy pet cats and dogs revealed that the most common type of bacteria was Firmicutes, followed by Bacteriodes in dogs and Actinobacteria in cats.

There was no mention of any individual information such as diet, age or health of any animals that were sampled. It would be interesting to see the results of a broad sampling of numerous species taking into account any diet differences. Overall it is an interesting field of study.


To learn more about the latest human microbiome research or to have your microbiome or your pet’s microbiome analyzed visit

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