The Microbiome as an Ecosystem. What’s in common between wolves and our microbiome?


The microbiome is often described as an ecosystem, but what does that mean really? To understand this, we really have to use a bigger analogy, one that applies to an ecosystem that we can see. A video about the wolves of Yellowstone National Park has been making the rounds on Facebook (, and it does a great job of illustrating how things really work. Most of us are led to believe that biological systems are inherently stable, but that is simply not true-they are truly quite dynamic and always in a state of flux. In the Yellowstone example, the reintroduction of a few wolves after a 70 year absence caused a cascade effect greatly out of perceived proportion to the introduction of a few animals. The wolves chased the elk out of the valleys and river basins, where they had been overgrazing. This resulted in increased grass, shrub and tree growth, which reduced river erosion and altered the whole terrain. The effect was compounded by bears descending to the valleys to eat from the newly grown berries, chasing more elk away. Beavers returned, since they eat the bark of the young trees. Their activities changed the topography even further! Many other species end up returning, bringing stability to the ecosystem. That is a recurrent theme: ecosystem diversity increases function and systemic stability.

When we consider our internal ecosystem, a similar effect happens. When the microbiome is healthy and diverse, its effects can be seen in skin, immune, brain, hormone function along with practically everything else directly or indirectly. The person is healthier, happier and better functioning physically, mentally and emotionally. Isn’t that the goal when we want to become “healthy?”

In contrast is the unhealthy microbiome, often resulting from poor diet or antibiotics in food or as medicine, and function is lost throughout the body. As I’m working on a short book on Lyme disease, I am constantly reminded of this. The tremendous loss of diversity in gut bacteria (one patient’s uBiome results showed her to be in the “0 percentile” compared to other women for gut bacterial diversity) results in immune dysfunction. Examples include a loss of Interleukin-10 production, important because it protects brain cells from bacterial infection as occurs in neuroborreliosis. IL-10 also inhibits inflammatory IL-17 production triggered by the Lyme spirochete, thereby restoring the integrity of the blood-brain barrier and joint capsule membranes, making it harder for the spirochete to evade phagocytic immune cells sent to kill it. Another classic example is microbiome production of alpha-galactosylceramide, which activates invariant Natural Killer T-cells. These iNKT cells are necessary for several of the body’s immune reactions to Borrelia burgdorferi, the Lyme bug. So, through antibiotic treatment to kill Borrelia, the body’s microbiome is decimated-taking with it much of the immune response needed to prevent reinfection or relapse. Why is this important, and what can we do about it? well…stay tuned to find out!








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