Monthly Archives: November 2015

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!







Paleo Diet: Romance vs Reality?

Brown cricket isolated on white

One of the current most popular diets is the Paleo diet. I’ve written in my book, The Symbiont Factor, about how there is fossil evidence supporting the Paleo diet as the way ancient humans ate, and have some additional thoughts on this controversial subject. Like many diets, the Paleo diet has evolved as many individuals and organizations promote their own vision of what a Paleo diet would have been or should be. This is normal, but for someone trying to learn how and why to eat a certain way, it can be bewildering! On one extreme is a Paleo vision that seems really more like an Atkins diet with some vegetables, on the other more like a Vegetarian diet with a little seafood added in. So, with that in mind, why would someone choose a Paleo diet? The basic concept is that our species has spent the majority of its evolutionary trajectory consuming a diet that did not include simple carbohydrates, large percentages of grains or any processed foods. This part of Paleo seems to be univerally agreed on as the building blocks of the diet movement-but what about proteins? I’ve read a great deal about our ancestral origins, and I’m going to run it up the flagpole to see who salutes! I grew up spending much of my childhood in the woods hunting or picking food, fishing or catching things to eat along streams and ponds, and catching blue crabs in the Hudson River (and yes they were yummy). I’ve always followed the licensing and bag limit rules, but since being a child I’ve also somewhat kept tally of those times that I could have taken game if I were starving, yet didn’t because it was out of season in some way. Now I know that many people who follow a Paleo diet likely have an image of ancient hominids that is a bit more romantic or idealized than what I’m about to describe, but hang in there and consider it! First, if we had to survive by hunting and fishing, most of us would starve-some quite quickly. Even if there were no rules, as in ancient paleo societies, hunting and fishing as we think of it today would not work well at all. There is too much energy expenditure involved in an individual capturing an animal for meat. Ancient humans worked around this in a few ways: group cooperative hunts, trapping, and alternative sources of protein. Native Americans, for example, let their children hunt small game while the men either raided other camps and tribes or hunted larger prey in groups. This strategy raised the odds that somebody would catch something! There is evidence that ancient Man had similar divisions of labor, with men hunting game while women and children foraged for other sources of nutrition such as tubers, plants, and…insects. Plains Indians of course had different strategies for hunting Bison, including stalking under cover, chasing on horseback (technically not until they had horses after the Spanish brought horses to the Americas) and driving herds toward pit traps, ambushes or ledges. Fishing is a similar example, with fish being far easier to net or trap than to catch! Fossil remains suggest that any civilizations living near the ocean probably subsisted more on shellfish than anything else for protein. This is evidenced by huge fossilized piles of shells that have been discovered. Having moved to Downeast Maine recently, I can attest to the difference in energy expenditure involved. Any game animals I’ve seen are distant and fleeing, yet I can walk down to the shore and pick a bucket of mussels off the rocks in a few minutes, getting enough to feed several people. Ancient man almost certainly spent much time near or in the water foraging for food. Our bodies come equipped with a functional dive reflex that makes short underwater excursions easier than many would believe! With this in mind, where does it leave ancient people that lived further inland? If you were in the wilderness and had to survive, what would be the easiest and safest source of high-quality protein, fats and nutrients? No, it isn’t that deer that you may or may not ever get…it is insects. They are plentiful and nutritious, and rarely fight back much. I know this sounds “gross” and might not fit what most Paleo afficionados would like to think, but consider it for a moment. Other primates eat insects, survival experts have touted them as a food source, and it doesn’t take nearly as much energy to get enough to sustain life. Some modern businesses have emerged to supply a modern version that is more accessible and perhaps more presentable, in forms such as protein powders or flavored varieties. One of the criticisms of Paleo diets is the need for meat, and the environmental cost/footprint to produce meat. Readers of The Symbiont Factor will also know that commercial meat has a huge number of chemicals included, antibiotics and pesticides, hormones and other goodies, which wreak havoc on our microbiome and our health. Organically raised meat is the way to go, and yet from a global perspective, would it even be possible for many more people to raise and eat organically grown meat? Probably not, as the yield per-acre is lower (don’t get me wrong, that’s a good thing compared to feedlot beef, but not necessarily possible on a global scale). While some of us are still hunters and occassionally can stock the freezer with the original organic, free-range meat, there is still a large part of the population that doesn’t hunt for ethical, geographical or practical reasons. In many families it may have been several generations since anybody hunted! Insects can produce more protein and nutrition with less global impact. I’m not ready to give up completely on meat, but when considering a true Paleo diet, an ento-diet (entomology is the study of insects) is worth study. We’ve been a bit spoiled by sanitized, clean, packaged, pretty foods that don’t resemble their original source in any way-and yet, several times each year there are outbreaks and recalls of such foods due to infectious organisms found in them. Is “sanitary” really an illusion after all? Is it even better for us? Again, in The Symbiont Factor, I reviewed something known as the “Hygiene Theory,” which is the observation that the human being requires a certain degree of bacterial and allergen exposure in order to develop a balanced immune system. When all food is sterile and has no contribution to our inner microbiome, and our children grow up in a sterile, Mr. Clean type of household, the risk of autoimmune diseases is far greater. These can be simple allergies or as severe as ALS, MS, Rheumatoid Arthritis and other modern plagues that are largely the result of our attempts to isolate ourselves from the microbial world. Maybe it is time to consider what we would call “alternative” sources of protein, though they were probably a central source of nutrition for much of mankind’s life. I know, it feels like more of a Paleo thing to eat a Bison steak than chili-lime crickets, but…don’t let it bug you! Paleo article