The Human Microbiome: The Beneficial Bacteria Within

Time magazine, Scientific American, and National Geographic have all recently published articles describing exciting new research on the human microbiome, the trillions of bacteria and other microbes that call our bodies home. There are over 1,000 species that make up the human microbiome and all together, they weigh in at about three pounds. Science is showing that these beneficial bacteria play a critical role in the healthy functioning of the body. However, studies also show how easy it is for helpful bacteria to get caught in the crossfire between antibiotics and their intended targets. The wide spread use of antibiotics and other aspects of modern life have significantly altered the human microbiome. There is now strong evidence that the inadvertent destruction of beneficial microbes in the human bacterial ecology is likely a contributing factor in the increase in obesity and immune related diseases in Western society.

The complex ecosystem of the microbiome contains trillions of bacteria and other microorganisms that inhabit our skin, genital areas, mouth and especially intestines. These good bacteria in our intestines help us digest our food, particularly our fiber. They help us absorb nutrients like vitamin B12 and biotin. Bacteria throughout the body are part of the defensive team against harmful bacterial overgrowth like staph infections, meningitis, traveller’s diarrhea and more. Good bacteria help the immune system to mature and to maintain a balance between pro and anti-inflammatory immune responses. Therefore, they help prevent allergies and auto-immune responses, where the immune system attacks our own tissues. Good bacteria even help moisturize our skin.

Interesting research shows that even bacteria we associate with disease may be of benefit. Helicobacter pylori is a bacteria that lives in the stomach and is associated with peptic ulcers. Antibiotics that target H pylori reduce ulcers, but are associated with weight gain. It turns out that H pylori is considered part of the normal bacterial lining of the stomach and it helps to regulate ghrelin, a hormone that stimulates appetite. People who take antibiotics for H pylori have higher levels ghrelin, and therefore are predisposed to eating more and subsequently gaining weight. Years ago, 60% of the population carried H pylori. Now only 6% of children have it due to the widespread use of antibiotics for common infections. Could this factor play a role in the epidemic of obesity in our society?

Modern medical practices have radically changed the microbial make up of our bodies and are affecting our health in ways we are just beginning to understand. The overuse of indiscriminate antibiotics is one culprit, as is the increase in c-section deliveries. For thousands of years babies have benefited from receiving their first dose of essential bacteria from vaginal deliveries. The natural birth process gives infants lactobacillales, the bacteria needed to digest milk. C-section babies lack these essential bacteria in their microbiome, and this contributes to allergies and digestive problems.

The increasing rates of allergies, asthma and autoimmunne disease appears to be linked to the changes in our modern microbiome. While genetics play a role in the inheritance of a hyper-active immune system, there is evidence that parents may pass on their altered microbiome as well. (There is an interesting article being presented at a gastroenterology conference I will be attending this spring on the connection between Crohn’s patients and the altered microbiome of their relatives.)

What can an individual do to maintain or enhance their microbiome to ensure optimal health? First, one can take general steps to improve their health and therefore reduce the need for antibiotics. Naturopathic physicians help guide and coach their patients on lifestyle practices that lead to optimal health and on natural medicines to enhance immune function.

Second, when possible avoid the use of antibiotics for infections. In my pharmacology training at UBC, our instructors emphasized that science shows many people overestimate the power of antibiotics to help common infections. For instance, taking antibiotics for strep throat and ear infections reduces the time spent in pain by only a few hours versus placebo while causing significant diarrhea for some people due to the effect of stripping the intestinal microbiome. Naturopathic physicians can prescribe antibiotics but prefer to bolster the body’s own infection fighting mechanisms with natural medicines. Ultimately, having a strong immune system and aggressive early intervention for colds and flus help prevent viral infections from setting the stage for bacterial infections like sinusitis and ear infections.
Third, many of us already have both deficient levels of good bacteria and an overgrowth of harmful organisms that have already taken hold. Antibiotics and other medications can not only strip the good bacteria, but allow for naturally occurring internal yeasts such as Candida albicans to proliferate to unhealthy levels. There are ways to re-establish the healthy microbiome in the body. Naturopathic physicians have been addressing this issue head on for decades and have successful protocols for enhancing their patients’ microbiome. Taking good quality probiotics supplements while reducing the overgrowth of opportunistic harmful bacteria and intestinal yeasts through supervised programs is very beneficial to overall health, energy and immunity.

I am very excited that science now has the tools to explore and understand the human microbiome. In my naturopathic medical practice, I have worked with thousands of patients to improve their internal bacterial environment and have seen the profound impact that doing so has on their health. I look forward to having new tools and protocols to more specifically address chronic autoimmune and digestive issues in the future.


Scientific American, June 2012, The Ultimate Social Network

National Geographic, January 2013, The Secret World of Microbes

Science and Society Journal, Who are we? Indigenous microbes and the ecology of human diseases

Curr. Issues Intest. Microbiol. (2003) 4: 1-8, Studies on Colonization Resistance of the Human Gut Microbiota to Candida albicans and the Effects of Tetracycline and Labtobacillus

Recommended Posts