What does microbiome mean?

In simplified terms, it means the population of microorganisms that live in a particular environment. Most notably, the collection of microorganisms that live in or on the human body. The human gut microbiome, specifically, refers to the full group of genes of all the microbes in our gut. This includes bacteria, fungi, and viruses.

Bacteria, which comprise the majority of microorganisms in the human gut microbiome, are found in 3 types.

  • commensal (symbiotic)
  • pathogenic
  • opportunistic

A healthy microbiome displays a balance between these, as well as a diverse number of species. Another indication of a healthy microbiome is the correct locations of certain quantities of bacteria. This is 10 m/L in saliva, 10 in the upper small intestine, and 10 in the colon. 

Research and History of the Microbiome

Research shows that human gut microbiome diversity in the western world is declining in comparison with traditional societies in less developed countries. One possible reason is the Biodiversity Hypothesis. This hypothesis holds that contact with the natural environment (soil, water, plants, animals) enriches the human microbiome (gut, skin, GI, airways). In rapidly urbanizing and increasingly populated societies such as the United States, there is a significant loss of biodiversity. Especially when compared to the natural environment in which humans have historically lived.

Why does this matter to the gut?

It matters because a reduction in microbial diversity may correlate directly with a rise in common diseases such as asthma, diabetes, autism, obesity, allergies, inflammatory bowel disease, and some mental health disorders. Further, bacteria from the natural environment can provide us with vitamins, short-chain fatty acids, toxin neutralization, digestion aid, protection from pathogenic bacteria, and more. There is evidence that maintaining a healthy gut ecosystem could aid in avoiding the early onset and development of these diseases.

Achieving a Healthy Microbiome

The ideal goal is to maintain a healthy microbiome. A healthy diet (including the proper balance of fiber, fats, omega-3 fatty acids, meats, fermented foods) and low-stress lifestyle contribute to a healthy microbiome. Various tests are available for testing the microbiome, and if needed, treatment options exist for instance, treatments like antimicrobials, probiotics, prebiotics, and the use of fermented foods.


Berni Canani R, Paparo L, Nocerino R, Di Scala C, Della Gatta G, Maddalena Y, Buono A, Bruno C, Voto L, Ercolini D. Gut Microbiome as Target for Innovative Strategies Against Food Allergy. Front Immunol. 2019 Feb 15;10:191. doi: 10.3389/fimmu.2019.00191. PMID: 30828329; PMCID: PMC6384262.

Haahtela T. A biodiversity hypothesis. Allergy. 2019 Aug;74(8):1445-1456. doi: 10.1111/all.13763. Epub 2019 Apr 4. PMID: 30835837.

join our mailing list