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Microbiome, the human ecosystem

By Jesse Davis, DC

Lab250x 250Twenty-five years ago, the role of microorganisms and health was dominated by the question of what pathogen caused a particular disease, and then how to kill it. While that is still the primary paradigm regarding microorganisms and health, there has been a massive growth and interest in another aspect of microbes and health. Specifically,how microbes living in and on our bodies affect us in ways other than infectious diseases. It turns out this is a much bigger area of study than we could have ever anticipated, with the potential to be as important as science surrounding pathogens.

The richest area in terms of total numbers of microbes in the body is the human gut. A review article in the journal Science in a special section appropriately titled “The Inner Tube of Life” had this to say:

“The adult human gastrointestinal (GI) tract contains all three domains of life—bacteria, archaea, and eukarya. Bacteria living in the human gut achieve the highest cell densities recorded for any ecosystem.”

“Our gut microbiota can be pictured as a microbial organ placed within a host organ: It is composed of different cell lineages with a capacity to communicate with one another and the host; it consumes, stores, and redistributes energy; it mediates physiologically important chemical transformations; and it can maintain and repair itself through self-replication. The gut microbiome, which may contain > 100 times the number of genes in our genome, endows us with functional features that we have not had to evolve ourselves.” [1]

Benefits of Gut Microbiome

Strategic Application of Probiotics in Clinical PracticeThere are many potential benefits to a healthy microbiome in people. Microbes in the digestive system, for example, help produce vitamins B12 and K2.[2] Beneficial or commensal (neither harming nor benefiting) organisms can help prevent pathogens prone to causing infection from taking hold. In fact, many microorganisms considered pathogenic are harbored by large numbers of people and are actually only virulent at times.

In addition, a project undertaken by the National Institutes of Health, the Human Microbiome Project (HMP), began publishing data in 2012. They came to several new major conclusions: [3]

Primarily, that “bacterial genomic contribution is critical for human survival. Genes carried by bacteria in the gastrointestinal tract, for example, allow humans to digest foods and absorb nutrients that otherwise would be unavailable.”

“Humans don’t have all the enzymes we need to digest our own diet,” said Lita Proctor, Ph.D., National Human Genome Research Institute’s HMP program manager. “Microbes in the gut break down many of the proteins, lipids and carbohydrates in our diet into nutrients that we can then absorb. Moreover, the microbes produce beneficial compounds… that our genome cannot produce.”

They also believe that the metabolic functions present in the bacteria seemed to matter more than the specific species. In other words, it was what the microbes did, rather than exactly what species they were. “It appears that bacteria can pinch hit for each other,” said Curtis Huttenhower, Ph.D., of the Harvard School of Public Health and lead co-author for one of the HMP papers in Nature. “It matters whether the metabolic function is present, not which microbial species provides it.”

Learn about the role of plant-based fiber and amino acids in supporting cut health.

Obesity and Weight GainScale250x 250

One of the most intriguing There has been growing level of inquiry into how the gut microbiome affects body weight. It has been known for decades that a steady, low-dose of antibiotics given to livestock increases the speed of weight gain.[4] The largest total use of antibiotics is actually in animal feed. Not only is it given to treat infections, but also to prophylactically prevent them. Strangely enough, they have also been routinely given to animals to promote weight gain.

Even more recently, there has been investigation into how the gut microbiome of human and animals affects the development of obesity. A Nature Immunology report in 2012 showed the impact of bacterial strains on mice’s ability to become obese when researchers had tried to genetically predispose them to obesity.[5] And while it is not fully understood, there is growing evidence this relationship exists in humans as well. A study, among several others, in the International Journal of Obesity, found that there was a consistent association between antibiotic use in infants under six months of age and increased body mass at seven years of age.[6]

This exciting and ongoing research will no doubt become a part of patient care. It’s an evolving science that deserves our attention.

Have you considered adding digestive enzymes to your patient’s probiotic protocols? In this research review, Jesse Davis, DC explores the advances in digestive enzyme science, Breaking Down the Basics of Digestive Enzymes.


[1] Bäckhed F, et al. Host-Bacterial Mutualism in the Human Intestine. Science, 2005 Mar 25:307 (5717):1915-1920.;

[2] Conley JM, Stein K. The production of menaquinones (vitamin K2) by intestinal bacteria and their role in maintaining coagulation homeostasis. Prog Food Nutr Sci. 1992 Oct-Dec;16(4):307-343.

[3] NIH Human Microbiome Project defines normal bacterial makeup of the body. Accessed online at

[4] Maxmen A. Antiobiotics Linked to Weight Gain. Scientific American. Reprinted from the magazine Nature. 2012; August 27. Accessed at

[5] Upadhyay V et al. Lymphotoxin regulates comensal responses to enable diet induced obesity. Nature Immunology,2012, Aug.;13:947–953.

[6] Mueller NT et al. Prenatal exposure to antibiotics, cesarean section and risk of childhood obesity. International Journal of Obesity, 2013;37:16–23.

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