What is the human microbiome?

The human microbiome is the diverse ecological community of microorganisms that inhabit every surface of our bodies; our skin, our mouths, noses and gastrointestinal tract (gut). Micro comes from the Greek (mikrós) meaning (extremely) small. Biome meaning the plant and animal community within a habitat; often referred to as an ecosystem.

The microorganisms that live happily with our own cells, cooperating with our immune system to ward off infection and helping our gut to break down nutrients, are called commensal microorganisms or good bacteria. Those that infect, or cause illness are called, pathogenic microorganisms or bad bacteria. At any given time, our bodies contain a complex balance of commensal and pathogenic microbes. This melting pot of microorganisms outnumbers our own cells ten to one!

Gut Microbiota: The community of microbes that lives in an individuals gastrointestinal tract.

Each portion of the microbiome can be affected by the various ways we treat our bodies. Lotions, creams and soaps can change the microbiome of our skin, toothpaste and mouthwash change the microbes in our mouths, and the food that we eat can change the balance in our gut, (The portion of the microbiome that you can affect significantly with nutrition is that of the mouth and the digestive tract, which is called the gut microbiota). Because of the important role the commensal bacteria play in our immune system and nutrient absorption, maintaining the correct balance between the "good" bacteria and the "bad" bacteria is necessary for optimal health. Things like medications, diet, diseases, and your environment can upset this delicate balance.

The Importance of a healthy balanced gut microbiota; The hygiene hypothesis

During the second half of the 20th century, developed western nations have successfully controlled infectious diseases by improving sanitation, using antibiotics and developing vaccines. At the same time, a rise in new diseases such as allergies, autoimmune diseases, and inflammatory bowel disease have been observed in children and adults alike (1). It is hypothesized that improvements in hygiene together with decreased microbial exposure in childhood are responsible for this increase in new diseases (2). Indeed, a slew of new research is showing that imbalances in the gut microbiota are associated with such diseases.

Diet affects the composition of the gut microbiome

The complexity and diversity of the gut microbiota is different in every individual, although there appears to be a core set of microorganism species. The gut microbiota is established early in life and influenced initially by genetics, birth route and geography. There is a significant difference, for instance, in the composition of the gut microbiota between infants born through the birth canal versus caesarian section. By early adulthood the complexity and diversity of the gut microbiome is fully established.

One of the most important environmental factors that influences microbial diversity is diet.

Development of the gut microbiome.
Development of the gut microbiome.


Prebiotic: Food ingredient that supports the growth and expression of a beneficial biological property of one or more resident gut organisms.

Prebiotics are defined as fiber components that pass through the upper part of the gastrointestinal tract undigested and stimulate the growth and/or activity of good bacteria that colonize the large intestine (3). Thus, fiber is arguably the most important factor in maintaining a healthy balanced gut microbiota.

Dietary fibers are complex carbohydrates consisting of both soluble and insoluble parts.

Insoluble fiber (that which will not dissolve well in water) is resistant to digestion; you’ve probably heard Grandma call it roughage. Insoluble fiber has many benefits; amongst other things it helps keep you regular, prevents constipation and may reduce the risk of diverticular disease (4).

Soluble fiber (which will partially dissolve in water) is found in varying quantities in plant foods. Importantly, soluble fibers can be broken down by certain species of bacteria in the gut to produce physiologically active byproducts. Short chain fatty acids are the most abundant metabolites produced by the fermentation of soluble fiber and studies have shown that short chain fatty acids are associated with a number of the health benefits linked to fiber.

Current guidelines from the Institute of Medicine (5) recommend 14 g of total fiber per 1000 Kcal consumed daily in order to maintain a healthy balanced diet. This equates to 25 g of fiber per day for women and 38g per day for men. However, fiber is often lacking in the average American diet, with the average adult only consuming 15 g per day.

The specific amount of prebiotics in fiber is difficult to define. There are a number of prebiotic supplements available. Ingredients currently classified as prebiotics include galacto-oligosaccharides, fructo-oligosaccharides (FOSs) (6), inulin, and lactulose.


Probiotic: A live microorganism that when ingested provides benefit to the host, either directly through interactions with the host cells or indirectly through effects on other members of the microbiota.

Within your gastrointestinal tract lies a complex ecosystem containing over 400 bacterial species. Small populations can be found in your stomach and small intestines, but the majority of these bacteria are found in your colon. These intestinal microbiobes aid in digestion, synthesize vitamins and nutrients, metabolize some medications, support the development and functioning of the gut, and enhance the immune system.

The health benefits of probiotics have been recognized for some time, and a large body of scientific research (including clinical trials) has confirmed the benefits of probiotics in supporting a healthy digestive tract and a healthy immune system.

The Food and Agriculture Association (FAO) of the United Nations defines probiotics as “live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.” Probiotics therefore contain ‘good’ live bacteria and/or yeast that help restore the balance to the gut microbiota. Adequate amounts means at least one billion live cells per serving which is measured in ‘colony forming units’

Strains associated with a favorable gut environment include:

Bifidobacterium (adolescentis, animalis, bifidum, breve and longum) and Lactobacillus (acidophilus, casei, fermentum, gasseri, johnsonii, paracasei, plantarum, rhamnosus and salivarius).

Diet Affects the Microbiome.
Diet Affects the Microbiome.


Postbiotics: Gut microbial products derived from food that affect a range of host processes.

Dietary fiber can be digested and subsequently fermented in the colon by gut microbes into a number of products. One set of predominant products produced by the gut microbiota are the short chain fatty acids (SCFAs) acetate, butyrate and propionate. We refer to these products as ‘postbiotics’.

Scientific research has focused mainly on butyrate, which is an important energy source for the cells lining the gut. The production of SCFAs is determined by factors including the numbers and types of bacteria present in the gut microbiota and the fiber source (3,7). The main microbial species producing butyrate are clostridia, eubacteria and roseburia (8). Researchers have found the number and variety of butyrate producing bacteria to be significantly reduced in people with a variety of gut disorders (9,10).

The effects of SCFAs permeate beyond the gastrointestinal tract . Propionate and acetate are carried in the bloodstream to a variety of different organs where they are used for important metabolic processes (11,12).

Short chain fatty acids are one of the most important products of the gut microbiota. They affect a range of host processes including; energy utilization, communications between the host and the microbiome, and control of acid levels in the colon. These effects have consequences on the composition of the gut microbiota and general colon health.

*These statements have not been evaluated by the FDA. Information is provided for educational purposes only.


  1. Blaser, M. J. Who are we? Indigenous microbes and the ecology of human diseases. EMBO Rep.7, 956–960 (2006).
  2. Strachan, D. P. Hay fever, hygiene, and household size. BMJ299, 1259–1260 (1989).
  3. Roberfroid, M. Prebiotics: the concept revisited. J. Nutr.137, 830S–7S (2007).
  4. Strate, L. L. Lifestyle factors and the course of diverticular disease. Dig Dis30, 35–45 (2012).
  5. Trumbo, P., Schlicker, S., Yates, A. A., Poos, M.Food and Nutrition Board of the Institute of Medicine, The National Academies. Dietary reference intakes for energy, carbohydrate, fiber, fat, fatty acids, cholesterol, protein and amino acids. J Am Diet Assoc102, 1621–1630 (2002).
  6. Mariat, D. et al. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. BMC Microbiol.9, 123 (2009).
  7. Cook, S. I. & Sellin, J. H. Review article: short chain fatty acids in health and disease. Alimentary Pharmacology & Therapeutics12, 499–507 (1998).
  8. Nicholson, J. K. et al. Host-gut microbiota metabolic interactions. Science336, 1262–1267 (2012).
  9. Frank, D. N. et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. U.S.A.104, 13780–13785 (2007).
  10. Wang, T. et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J6, 320–329 (2012).
  11. Wong, J. M. W., de Souza, R., Kendall, C. W. C., Emam, A. & Jenkins, D. J. A. Colonic health: fermentation and short chain fatty acids. J. Clin. Gastroenterol.40, 235–243 (2006).
  12. Samuel, B. S. et al. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. Proceedings of the National Academy of Sciences105, 16767–16772 (2008).