Tag Archives: probiotics

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 (https://www.youtube.com/watch?v=ysa5OBhXz-Q), 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!







Is Organically Grown, Grass-fed Meat Healthier?

So, you’re walking about in the grocery store, carrying on that inner dialog about what to purchase…when you notice the meat counter. You have a choice now: do you purchase the Angus ground beef, the grass fed beef, or the organically grown grass fed beef? The Angus is less expensive and its high saturated fat content means your grilled burgers will stay moist, but you’ve been wondering if there is any health benefit to the organically raised meat. Sound familiar? Today, I’m going to present a point of view based on the available facts that researchers have shown us, using concepts from my book The Symbiont Factor. And, I’ll try to make it as practical as possible!

A study was just published about the prevalence of the phylum Proteobacteria being a direct indicator of gut and general health. More Proteobacteria is a bad thing, in other words. Why is it bad? This phylum includes the notorious microbial outlaws Helicobacter (ulcers, anyone?), Vibrio, Salmonella, E. coli (all causing gastrointestinal distress) and Yersinia (plague…) How would you know your own levels of Proteobacteria? A simple uBiome test can provide a percentage measurement that correlates with the Shin study mentioned above. How would your Proteobacteria get elevated, you might ask? Well, two major factors that we are aware of: antibiotic exposure and high fat/sugar diet (aka “the Western Diet”, which is the laboratory standard for creating disease).

Going back to your choice of ground meat, some guidelines for a choice are now apparent. Grass-fed beef is much leaner, though this will also require a slightly different cooking method to have it palatable. It tends to have more flavor, which some people call “gamey-ness”, though from my point of view it is how beef should taste as cattle should eat grass and not grain. Wild meat such as venison has even more flavor. When accustomed to it, grain-fed beef is utterly bland. So, the reduction in fat content in the grass-fed beef is less likely to promote an overgrowth of Proteobacteria. Because of the effect of higher fat content, the choice for this reason would be grass-fed. In addition, the fatty acid profile of grass-fed beef promotes less inflammation, as the meat has a higher percentage of Omega-3 and DHA fats.

The second item to consider would be antibiotics. Meat that is not organic has antibiotic residues that, when consumed, exert an antibiotic effect on the human. Antibiotic exposure has been found to promote overgrowth of Proteobacteria, so this is bad! In addition, antibiotic exposure promotes the development of antibiotic resistant species, which is a further health risk. Overgrowth of Proteobacteria causes a suppression of beneficial bacteria as well, creating a disease-prone condition.

At this point the only remaining factor is cost. The healthier product costs more, though now even Hardee’s and Carl’s are advertising a grass-fed organic hamburger-an obvious example of the power that consumers wield. Don’t jump to conclusions, though, as prepared “the fast food way” it will likely still have a high enough fat and calorie content to make it a not-healthy choice. Still, it’s a step in the right direction and will be healthier than the regular burgers they serve!

The easiest way to balance the cost-vs.-health equation is to either buy a sufficiently smaller quantity of the grass-fed meat that your budget is unaffected, or view the extra cost as the cost of health and disease prevention. After all, the doctor bills that occur in later life certainly can outweigh the added cost of the healthier meat choice! The benefits in quality of life, however, are priceless.













Why Diet and Gut Bacterial Symbionts may be the most important thing you learn about Autism Spectrum Disorder

Autism is a neurobehavioral condition that has been dramatically on the rise in the last decade. There are many factors that contribute to its causes, but none so pervasive as gut bacterial imbalance. To see the connections, you first have to realize that our brain development is heavily influenced by the interaction between our gut bacterial symbionts, our immune system, and those little cell organelles that produce energy-known as mitochondria. I explained at length how the gut bacteria influence brain development in The Symbiont Factor; in short there are many pathways for influence including gut bacterial alteration of Brain Derived Neurotrophic Factor or BDNF. This substance is necessary for proper nerve growth and development, and a deficiency or imbalance in gut bacteria results in a reduced level of BDNF. New research has shown another factor in brain development, Short Chain Fatty Acids or SCFA. This substance is produced by bacterial fermentation of carbohydrates (sweets, essentially!)  Eating too many carbohydrates results in increased populations of the gut bacteria that thrive on sugars, including Clostrida, desulfovibrio, and Bacteroides. When these bacteria ferment carbs, they produce high levels of SCFA including propionic acid which is one SCFA. Propionic acid is also a common food preservative in prepared foods, so read your ingredients and eat organic as much as possible. New research has shown that high propionic acid levels interfere with mitochondrial function, reducing the energy available for nerve cell function and producing ASD. It is important to understand that some of the organisms that produce propionic acid are not necessarily pathogens; more like “frenemies” in this case (see Jerry Seinfeld; friend + enemy, and a good laugh too) Establishing and maintaining a microbial balance is really a more accurate way to state the goal. The overuse of vaccines and antibiotics in children, combined with chemicals in packaged food and toxins in farm-raised food are all factors that conspire to imbalance our gut bacteria. It is worth noting that reduced mitochondrial function also results in elevated oxidative stress, which is the neuroinflammatory/degenerative process that drives many diseases from fibromyalgia or chronic fatigue syndrome to Parkinson’s, dementia, and aging in general. Significant variables that we can influence include diet (less sweets, more organic fruits and veggies and organic grassfed meat; organic Paleo diet essentially) and behavior. Pushing ourselves past the point of fatigue, or allowing small children to stay “in overdrive” too long with video games and sweets, causes more bacterial imbalance and neurologic dysfunction. Many supplements, from Curcumin and probiotics with Lactobacillus and Bifido species, to fermented foods and drinks such as GoodBelly and Lifeway Kefir, can help to build and maintain healthy levels of gut bacteria and give our kids the best chance possible of good health and function. The next time a stranger at the bank drive through offers your child “a sucker”, consider the potential effects of regular sugar ingestion on a child’s microbiome and brain function. Really!

For much more about the role of diet and gut symbiont bacteria on brain development, behavior and health, please check out my book The Symbiont Factor: http://tinyurl.com/qyg85t9










11 Easy Steps to Improving your Microbiome and Symbiont-healthy Lifestyle!

So today I thought I would share some simple practical microbiome advice!

Steps to a Healthy Microbiome
1. Start noticing how tense, stressed or up-tight you may have become. Dedicate a few minutes several times a day to taking an emotional census of this, then focus on deep breathing and refocusing your attention on a positive, healthy or loving thought and emotion. Notice how you feel afterward!

2. Be honest with yourself about what you eat or drink. I know many people who eat a great deal of sweets or fast food, making an excuse for each time “it’s a reward for such-and-such” or “it’s just a one-time treat” and my favorites “it’s just a little” and “gotta die from something”. All of these statements are simply our imbalanced gut microbiome craving something and then our mind making excuses for not eating healthier. Be honest with yourself and look at what you’re really eating!

3. Sleep is critical-if you’re not sleeping enough it is very challenging to build a healthy microbiome. We should sleep at least 7 1/2 hours per night and preferably 9 when possible. Notice these are both multiples of 90 minutes, which is the typical length of a sleep cycle that the brain goes through. Waking up halfway through one makes us feel sluggish and irritated-complete your sleep cycles by planning on it!

4. Learn to observe your mood, your bodily functions and their timing in relation to your diet. Did you get sleepy, sluggish and mildly irritated after lunch? You may have eaten something that triggered an inflammatory response in your gut, which then affects the brain. Do you cough or sneeze after eating certain foods? This can also be a clue. If you’re not having a daily bowel movement of normal consistency; not loose and not stone; then your gut bacteria/gut/immune system are imbalanced in function and you have homework to do.

5. Eating organic or wild meat or fish is much better than normal store-bought meat. The antibiotic residues in farmed meat that is not organic are sufficient to seriously imbalance your gut bacteria with long-term consequences. I believe this may be one reason that many people get healthier when they eliminate meat from their diet-no meat is better than unhealthy meat.

6. Eating homegrown or organic vegetables and produce helps also, because if it isn’t it probably has significant RoundUp glyphosate on or in it. These residues are very toxic to beneficial gut bacteria.

7. Limit your use of chemicals such as Roundup. It’s poisoning the planet’s microbiome, and it starts with your microbiome. Pesticides and solvents are also quite harmful so if you must use them, wear protection and use ventilation to avoid inhaling fumes.

8. Read and understand the CDC (Centers for Disease Control) guidelines for medical antibiotic use, and hold your doctor to them. It will help you to understand when you really do need them and when you actually don’t. I haven’t personally taken antibiotics in at least 28 years and intent to extend that as long as possible.

9. Drink filtered water or spring water. Sweet soft drinks are bad for gut bacteria, and so is chlorinated municipal water.

10. Eat or drink some fermented foods such as natural sauerkraut or kombucha tea, yogurt (if not dairy sensitive) or kefir. You can even make your own. Along with taking good probiotics (which should be selected specifically based on your microbiome profile) this can help maintain a good population of healthy gut bugs.

11. Learn more about the microbiome and its tremendous effect on health, both physical and emotional. One great starting point, if I might suggest it, is my book The Symbiont Factor which you can find on eBay. I put a crazy amount of work into making it the best referenced comprehensive scientifically based book on the subject.

I hope these simple suggestions help you to start your own journey toward a healthier and happier Symbiont lifestyle!

New study reveals effect of dietary sugar and fat on gut bacteria, and the effect of altered gut bacteria on memory and cognitive flexibility.

One of the core, pillar concepts of my book The Symbiont Factor is the fact that “our” mind is heavily influenced by the presence and activity of our gut symbiont organisms. Gut bacteria influence different parts of the host/human brain and alter genetic expression and neurotransmitter sensitivity, which alters everything from our stress response to our very personality. In this new research study, researchers demonstrated that changes in gut bacteria resulting from changes in diet result in changes in behavior. Specifically, diets high in sugar and fat resulted in reduced short and long term memory as well as less cognitive flexibility. If you click the link and read the research abstract, you’ll see that the diet used simulates the “Western Diet”. This, folks, is basically the American diet, which has now spread to other parts of the world. In research it is used as the standard diet to produce disease in a laboratory animal! So, what does this have to do with humans, since the study was performed on mice? Well, short and long term memory are daily issues and probably declining across Western society. Don’t think so? Try not using your smart phone to recall phone numbers or addresses but just key them in from memory. Try shopping without any list or remembering the last ten meals you ate. These are not really difficult tasks and yet our modern technology combined with our modern diet/loss of microbiome diversity has resulted in significant reductions in these basic mental functions. What is cognitive flexibility? It is the ability to solve a problem when the rules have changed, or to simply adapt to changes in daily life. When you see a person that gets upset because his/her daily routine gets changed, that is a lack of cognitive flexibility. When you see someone who can no longer figure out how to balance a checkbook because now some of the transactions use debit cards, that is a loss of cognitive flexibility. This research article does a simple, elegant job of pointing out that our diet does in fact alter our microbiome, and that has profound effects on how well our brain operates! The gut microbiome heavily influences the brain, and is in turn heavily influenced by what we eat. Think about that when you see how much sugar today’s children consume…every day that I visit a WalMart I see parents with kids that are unfocused, unruly, and hyperkinetic (all signs of reduced brain frontal lobe function) and then see those parents fill their shopping cart with frozen dinners, cases of sweet soft drinks, and let the kids pick out those fake popsicles that are straight colored sugar water. Think it doesn’t change how a child’s brain and mind develop? The average American is now consuming 152 lbs of sugar per year! that is an average, and includes many like my family who consume far less. So, that is today’s “food for thought”… and also one of the reasons that we should all know more about our gut bacteria. For more information, read my book-The Symbiont Factor-available on Amazon here: http://tinyurl.com/mbb8fvc. If you’d like to know more about your personal microbiome, what organisms are there, good guys and bad guys and what can be done to improve it, contact me. This is one of the services that I now offer!


Top Ten Reasons that the Microbiome Matters:

As I’ve been busily shutting down one clinic to open another, I’ve logged many miles of driving-which has given me time to think about the microbiome as well (really!) Why would the microbiome matter? Here’s my top ten list, as a microbial tribute to David Letterman’s years of late night entertainment:

10. It guides the development of the human brain early in life

9. It influences our moods, desires, behaviors throughout life

8. The microbiome helps develop and guide the immune system

7. Our HPA axis (Hypothalamus, Pituitary, Adrenal) is heavily influenced by the microbiome early in life, which determines our response to stress…

6. The human microbiome can alter the way our brain’s receptors respond to neurotransmitters, changing it significantly.

5. If our microbiome becomes imbalanced (dysbiosis) it can cause inflammation, brain dysfunction, immune dysfunction, changes in appetite, obesity, depression…and many other problems

4. The microbiome is extremely vulnerable to antibiotics from doctors or in (non-organic) meat that we consume. Once species die off and diversity is lost, dysbiosis results

3. Glyphosate, the most commonly used herbicide on the planet, is toxic to gut bacteria (and also mitochondria that supply our cells with energy)

2. Gut bacteria are true symbiont organisms; they aren’t “hitching a ride” but are indeed a part of us that functions more like a vital organ. They are part of why we are alive; death of the microbiome causes disease and aging!

1. The only source of energy that fuels this planet is sunlight, and only plants (true plants, algae, cyanobacteria) can process sunlight into biomass. After that, only bacteria can digest plants to produce energy…so everything from termites to cattle including us can only digest plants because of our gut bacteria. No gut bacteria? very very bad news!

So, get out your copy of my book, The Symbiont Factor, and read up on the microbiome, okay? Oh, you don’t have it yet? Be good to your bugs and buy a copy then!


And the meek shall inherit the Earth…

As a human being living on Planet Earth, I sometimes ponder where my species fits in to the planet’s ecosystem. I know, it’s not really a normal thought, and it might be more entertaining to see what one of the Kardashians wore yesterday (Who? LOL) but as the author of The Symbiont Factor I really do think about such things. You see, from a physics point of view (yes, I was initially an engineering major before biology) this planet really only has one source of incoming energy to keep “the circle of life” going. That incoming source of energy is of course sunlight. Only photosynthetic organisms can convert sunlight into biomass that is usable by other life forms such as humans. Photosynthetic organisms are all some version of a plant, simple or complex. Yes, cyanobacteria and algaes, it could be argued, are not plants-but they have chlorophyll and they photosynthesize, so they could for this purpose be grouped as “plants” in a looser way of thinking.

Here’s where things get interesting, because the only organisms which can digest cellulose are bacteria. The only remaining photosynthetic organisms are cyanobacteria, which are bacteria. It is therefore accurate to say that the processing of all “incoming energy” beyond the plant is dependent on bacteria. Think about it for a moment-termites cannot digest wood fiber, being completely dependent on their microbiome (gut bacteria!) to digest it. The same thing can be said of any other organism on the planet which eats plant material! Cows, horses, rabbits-all depend on a complex gut microbiome to digest plant fiber. We humans also depend on our gut bacteria to digest plant fiber. Nothing can digest plants without the aid of bacteria.

Why is this important? The above discussion should point out that without bacteria there could not be much life beyond the plant world and cyanobacteria. Indeed, some researchers have stated the belief that cyanobacteria may have been the first organisms on the planet, with complex groups evolving into what we see as plants and algaes today. Our present life form would not exist if it were not for our symbiont bacteria. Symbiont organisms, as explained in The Symbiont Factor, have provided us with a fast acting rapid evolution capability that has aided our survival and permitted our continued development. These symbiont organisms guide the development of our brain, endocrine system, and immune system. Without a balanced microbiome we cannot develop normally. Our microbiome greatly enhances our ability to cope with famine, stress, or immune challenges without having to resort to inter-generational evolution. The microbiome has at least 100x the gene count as our human cells and can change the activation of those genes (and our own!) to help us adapt and survive.

When you consider the above discussion and realize that we are routinely destroying our internal microbiome as well as the planet’s microbiome, it should be food for thought that our present level of function at the top of the food chain may be more precarious that we believe. The delicate microbial balance that allows our brain and body to function at a high level is easily disturbed by poor nutrition (think McDonald’s) and high levels of antibiotics from both medicinal use and residues in meats, as well as other factors discussed in my book. Learning the importance of the microbiome is essential to understanding life itself!