The Zimmerman File: Your Inner Ecosystem – Part One

posted in: Digestive Health | 0

By Marcia Zimmerman, CN, June 2013. Scientists have discovered that microorganisms in the human digestive tract are involved in inflammatory bowel disease, irritable bowel syndrome, gut derived infections and possibly many other ailments.

Microbes in the body mean only one thing to most people. They can make you very sick. But researchers have recently begun to unravel the many beneficial roles microbes play in fostering health. These are the so-called “friendly” microbes that exist in a symbiotic relationship with humans.

To better understand this relationship, the National Institutes of Health (NIH) has established the Human Microbiome Project (HMP). Its mission is to characterize the entire human microbiota and analyze its role in health and disease. Advances in DNA sequencing technology, as established through the human genome project, allow analyses of genetic material derived from complete human microbial communities.

Biologists have made good progress in characterizing the most prevalent species of microbes in the body and have begun to identify the specific effects of these tiny residents. (1) This is no small task because the microbial genes in the human digestive system alone – 3.3 million genes (from more than 1,000 species) – outnumber by 150 times the 20,000 to 25,000 genes in the human genome. (2)  Many of the microbes cannot be cultivated outside their native habitat and this has stymied scientists trying to speciate them.

Researchers have found they can bypass this problem by extracting DNA and RNA from the microbes and then associate a certain genetic blueprint with a specific function. Amazingly, this scientific advancement was only discovered in the 1990s. Today it is a fertile area of research and has even given birth to a new scientific discipline.

Metagenomics is a new term that combines the power of genomics, bioinformatics, and biology, to provide new access to the microbial world. It is a hot topic among scientists throughout the world. It is considered breakthrough and is the topic of presentations at scientific symposia. It is even beginning to appear in media reports. While most of us think of the microbiome in reference to the intestinal tract, scientists are busy discovering the microbiome composition of other body areas as well. (3)

The Human Microbiome

The microbiome is home to 100 trillion microbes and they outnumber human cells by a factor of 10 to 1. All humans have a microbiome from very early in life, even though they do not start out with one. Newborns pick up microbes as they pass through the birth canal and add new species from association with family, clothing, bedding and even pets. Yet no two people share the same microbial makeup – even identical twins. (4)

Some of these microbes possess genes that encode for beneficial compounds that the body on its own cannot make. The intestinal microbiota regulates host genes that control metabolic processes through nutrient absorption, mucosal barrier function, enzymatic functions, angiogenesis, and others. (5)

Other microbes seem to train the body not to overreact to outside threats.(6)

Estimates of the weight of the microbiome vary from only a few ounces to as much as 2 kg. (5.3 pounds). The microbiome is an interface between food and the human body, and thus plays a major role in health and disease. The microbiome is also the second largest pool of neural cells, the brain being first, and is intimately involved with immune system function.  (7)

We think of the microbiome only as an organ within the digestive system. However, the NIH Human Microbiome Project is studying microbes in the upper respiratory tract (sinuses, nasal pharynx), oral cavity, skin, and urogenital areas, as well as the entire gastrointestinal tract. Each area of the body harbors its own microbial colony populated with unique species. The microbes are dependent upon the environment provided by their host. In turn, the health of their host is determined by the health of the microbial colony. It is a true symbiotic relationship. You do for me and I do for you. Our lives depend upon it. So delicate is the balance between the host and its microbiome that the composition of the microbiome can change dramatically in just 24 hours, depending on what the host eats or drinks! (8)

The Microbiome and Disease

Scientists have discovered that the microbiome is involved in a number of clinical problems including inflammatory bowel disease, irritable bowel syndrome, colorectal cancer, gut-derived infections, and even frailty in the elderly. Additionally, there are proposed links between the microbiota and appetite control, energy balance, obesity, diabetes, immune function, allergies, behavioral problems, cardiovascular disease, and some cancers. Therefore, it becomes increasingly important to understand the effect of nutrition on microbial populations in the microbiome. (9)

Next month’s Zimmerman File Your Inner Ecosystem – Part Two, will examine the impact of nutrition on the intestinal microbiome. Part three will focus on dietary supplements that benefit the microbiome.

Posted May 15, 2013. r/ar


  1. The NIH Common Fund; Human Microbiome Project, 2013.
  2. Ackerman, J.; “The Ultimate Social Network” Scientific American June 2012 vol. 306, no. 12:37-43.
  3. Turnbaugh, P.J.; Gordon, J.I.; “The Core Gut Microbiome, Energy Balance and Obesity” J Physiol2009;587:4153-4158.
  4. Turnbaugh, P.J.; “A Core Gut Microbiome in Obest and Lean Twins” Nature 2009;457:480-484.
  5. Tilg, H.; “Obesithy, Metabolic Syndrome, and Microbiota Multiple Interactions” J Clin Gastroenterol. 2010;44:S16-S18.
  6. Bested, A.C. et al.; “Intestinal Microbiota, Probiotics and Mental Health” Gut Pathol 2013;doi:10.1186/1757-4749-5-4.
  7. Flint, H.J.; “The Impact of Nutrition on the Human Microbiome” Nutrition Reviews 2012;70(suppl.1):S10-S13.
  8. Ibid.
  9. Wang, Z.K.; Yang, Y.S. “Upper Gastrointestinal Microbiota and Digestive Diseases” World J Gastroenterol2013;19:1541-1550.