Tag Archives: vegetarian

SIBO, Small Intestinal Bacterial Overgrowth

small intestine

What happens if your microbiome becomes too excessive and colonizes parts of the body where it really shouldn’t set up camp? SIBO, or Small Intestinal Bacterial Overgrowth, is an example of just that! Since this comes up very frequently in discussions with patients, it’s time to share some information about it. This problem is much more common than most would realize, and like many such things can be looked at as a “spectrum” from mild to severe/debilitating. If you feel worse after eating, and feel like taking probiotics makes things worse instead of better, these are some of the symptoms of low stomach acidity.

In the normally functioning digestive tract, the stomach is (relatively) sterile, having a very low pH due to the production of HCl, hydrochloric acid along with enzymes. This means that the stomach is a filter of sorts, killing most bacteria and viruses that might be present on food or beverage you consume. This understanding is validated by the observation that an animal’s stomach acidity is directly related to its place in the food chain. Animals that are pure carrion eaters or predators have the most acidic stomach secretions, while those that eat plants have the least. This serves two purposes: the first is to disinfect food that may even be actively decomposing, while the second is to break the peptide bonds that hold amino acids together to build proteins in meat. Since the stomach is so acidic in meat-eaters, they can eat roadkill and not become ill. A healthy human’s stomach acid inhibits bacterial growth in the stomach and the first part of the small intestine, before it is neutralized by bile secretions. This limits the amount of bacteria that can exist in those areas. This is part of our evolutionary heritage that allowed early Humans to survive on anything from seafood to insects, hunted or trapped meat animals, or stealing the prey of other predators.

Modern lifestyles conspire to reduce this needed acidity. Lack of sleep, too much stimulation, poor breathing dynamics all cause an autonomic imbalance that promotes everything from high blood pressure to poor digestion from low stomach acid. If stomach acid stays abnormally low for too long though, some organisms such as Helicobacter pylori can colonize and take over. This organism will then inhibit stomach acid production, wrecking your health in the process. So, without high stomach acid levels the predator (or human) would get infections and become ill; he also wouldn’t be able to digest the meat he consumes. Humans do not produce quite the stomach acid levels of a cat or dog, but are much closer to that level than a goat or cow.

The first question that brings up is the old debate about whether we are evolved to be vegetarians or meat-eaters. The facts here point squarely toward our physiology being optimized for some of each; definitely a meat-eater but capable of digesting plants too.

It is important to note that in this way, our individual “optimum diet” may be tied to our gastric acid status. If you have low stomach acidity, you’re not likely to digest meat very well, and may find yourself gravitating toward a vegetarian diet. If this choice is made due to low stomach acidity, it’s really running from the problem and still leaving the door open to a dysfunctional disease state. On the other hand, if you’d really like to do well on a Paleo type diet, you should also make sure your autonomics are balanced enough that you can produce adequate stomach acid to break down meat.

The second question is about what would happen if our stomach were not acidic? The obvious answer is bacterial colonization of the stomach and small intestine, with overgrowth compared to the normal condition. This results in a variety of symptoms, from heartburn (think summer roadkill in your stomach…ick) to bloating, allergic sensitization, indigestion, etc. It most definitely results in disruption of the entire microbiome downstream from the stomach also, with many consequences!

Now it gets interesting: What do most people do when presented with those symptoms? Take antacids! I have seen many patients who have been prescribed PPI (protein pump inhibitor; acid-blocking) medications, despite having never undergone any tests to confirm their symptoms indicated excess stomach acid. Stomach acidity declines with age, which is probably because of autonomic imbalance. Our fight-or-flight system (sympathetic system) becomes the dominant system when we’re under stress, fatigued, or if our brain is slowing down. Sound familiar? The parasympathetic system is stimulated by relaxation, deep breathing, less stress, slow relaxed eating, better sleep. Are you getting these things in your life?

To really build a balanced and high-functioning microbiome, it is necessary to start with balanced stomach function, then work downstream from there. Better liver function, small intestine function, large intestine function. One of the reasons many people cannot balance their large intestinal microbiome is that they haven’t managed their stress, breathing, sleep, and eating habits and therefore still have low stomach acid and SIBO to one degree or another.

Lifestyle habits that can help re-balance your autonomic function include deep breathing, yoga, meditation, taking time for yourself to do those things you love, scheduling and planning sleep more effectively, and taking the time to relax and breathe when you eat. There are also very specific functional neurology rehab activities that can aid in this goal. It is also possible to take a supplement that includes HCl and enzymes, to help kill off excess bacteria/H. pylori and begin to heal from SIBO.

So, be nice to your stomach, and your symbionts will thank you!



The Symbiont Factor: http://www.amazon.com/Symbiont-Factor-Bacteria-Microbiome-Redefines-ebook/dp/B00LV6H1UY/ref=tmm_kin_title_0?_encoding=UTF8&qid=1455197979&sr=8-1











Australopithecus sediba, our vegetarian past? What does it take to grow a brain?

Very detailed and scientifically correct human skullcutaway, with all brain details, mid-sagittal side view, on white background. Anatomy image.

I’m watching a PBS special about some new fossils of our ancestors, specifically Australopithecus sediba, discovered in a cave in South Africa. I noted that the reconstruction of the ribcage appeared to be wide and consistent with an individual having a large abdomen, similar to a gorilla, providing room for a long enough digestive tract to digest a mostly vegetable diet. Just as horses and cattle need a relatively large abdomen to provide a “fermentation vessel”, so too the gorilla (and A. sediba) have a skeletal structure to accommodate this structure. Later in the show, it was revealed that dental calculi (plaque) provided evidence of a vegetarian high-fiber diet. This validates my observation of the ribcage dimension and clinches, in my mind, that this ancestor was a veggie eater. The braincase suggests that this ancestor had not yet evolved the larger brain, particularly frontal lobes, characteristic of modern humans.

Scientists have identified two requirements for the evolution of large brains (termed “encephalizaton”). The first requirement is sociality, as much of the brain enlargement is frontal lobe and this part of the brain is where much of our social dynamic originates from. Executive functions, self control, altruism are frontal lobe functions for the most part. Species with large frontal lobes have advanced social societies (dolphins, whales, elephants are prime examples). The second requirement is DHA, an essential fatty acid found mostly in seafood but also in fats of prey animals.

It is thought by many research authors (see Ben-Dor and Jandhayala below in references) that mankind’s encephalization involved a shortening of the digestive tract to support eating more energy-dense foods like meats and fats. The consumption of plant material for a diet requires that most of the waking time be spent foraging and eating, and the digestive process depends on a large gut. The development of tools and weapons was a necessary step to becoming an omnivore, as was the development of social structure necessary to successfully hunt larger prey animals.

It is for these reasons that a diverse and unique gut bacteria were a critical component of our development. The gut bacteria help produce BDNF (brain derived neurotrophic factor), required for the development of new brain cells and is essential for plasticity and learning. High levels of DHA in the diet also help with BDNF production. The human brain requires essential fats in the diet to support both its energy requirements and its health. There is evidence that during the phases where early man was developing the large brain characteristic of our species, diet shifted from plant based to include meat and fat. Those near the ocean likely obtained all the DHA fats needed from seafood, while those dwelling inland may have obtained it from…brains and marrow fat. Fossil remains show that prey animals consumed by early man have been found with cranial vault damage suggesting that the brain was removed for consumption. Obviously, those living near the ocean had a much easier time of things, as clams do not run fast nor pose much of a threat! Ancient settlements near water are often characterized by large piles of seashells.

What this boils down to is that we developed our big and (usually) useful brains due to a dietary shift away from vegetarian to eating meat and animal fats. Accompanying this shift, and codependent on it, was a behavioral shift toward toolmaking, weapon use, and increased social interaction. It should also be noted that as I explained in The Symbiont Factor, a higher functioning brain is codependent on a diverse microbiome. More brain activity helps the gut become healthy and encourages a healthy microbiome, and vice versa. The modern Western diet has high levels of omega-6 fats, which displace DHA and increase inflammation, leading to more disease and less brain development! That type of diet is also typically very unheathy for the microbiome, further hindering brain function. A vegetarian or vegan diet can still be brain-healthy, but apparently not without additional supplementation of DHA as even the presence of healthy fats in vegetable sources does not provide enough DHA due to a low conversion rate. That subject is discussed at length in some of the references provided, and may be fodder for many who have strong opinions one way or the other.


The Symbiont Factor: http://tinyurl.com/ppyh9yr

Energetic and nutritional constraints on infant brain development: implications for brain expansion during human evolution:http://www.ncbi.nlm.nih.gov/pubmed/24928072

Docosahexaenoic acid, the aquatic diet, and hominin encephalization: difficulties in establishing evolutionary links. http://www.ncbi.nlm.nih.gov/pubmed/17160979

Encephalization is not a universal macroevolutionary phenomenon in mammals but is associated with sociality. http://www.ncbi.nlm.nih.gov/pubmed/21098277

Evidence for the unique function of docosahexaenoic acid during the evolution of
the modern hominid brain. http://www.ncbi.nlm.nih.gov/pubmed/10419087

Man the Fat Hunter: The Demise of Homo erectus and the Emergence of a New Hominin Lineage in the Middle Pleistocene (ca.400 kyr) Levant http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3235142/

New Insights into the Evolution of the Human Diet from Faecal Biomarker Analysis in Wild Chimpanzee and Gorilla Faeces http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4465628/

Docosahexaenoic Acid (DHA): An Ancient Nutrient for the Modern Human Brain http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3257695/

Role of the normal gut microbiota: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528021/




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!