Today in part 3 I’ll be exploring gut testing markers, in particular, functional digestive markers along with a review of the “keystone bacteria” that constitute a healthy microbiome.

Lastly we’ll look at re-feeding carbs for those who been low carb for a long time. If you’re just tuning in, it is helpful to read part 1 and part 2 beforehand for background.

TLDR:

1. Proper digestion or maldigestion effects everything downstream of it including absorption, fermentation and microbiome composition

2. Often the underlying cause of poor digestion, malabsorption and dysbiosis are chronically elevated cortisol and hypothyroidism

3. Keystone bacteria are critical to maintaining competitive inhibition of pathogens, optimal short chain fatty acids production and immunoregulation

4. Most people have the easiest time digesting and absorbing natural sugars like fruit, honey and maple syrup. In fewer cases starches are easier. It depends on your unique gut context.

These are the digestive markers tested in the GI Map, the gold standard functional medicine stool test. In particular, this test is for an eight year old boy with intermittent abdominal pain two-four hours after eating that I worked with.

Steatocrit measures the amount of fat in the stool. There shouldn’t be any. But if there’s a lack of bile release from the gallbladder (which emulsify fats), lipase release from the pancreas (which enzymatically break-down fats), low stomach acid, or improper chewing, fat will appear in the stool rather than be absorbed by the small intestine as fatty acids. This marker can also be high in celiac disease. Not only would a person with elevated steatocrit lack fatty acids as a macronutrient, they can also lack fat soluable vitamins that would accompany them and the excess fat would pathologically change the composition of the microbiome.

Elastase-1 is an enzyme exclusively excreted by the pancreas that offers a direct measure of pancreatic enzyme output. Since pancreatic enzymes and bile release are controlled by cholecystokinin (CCK) as a result of sufficient stomach acid, these markers are often correlated as we can see here with our little guy.

He is low in both and is likely also low in stomach acid. We can assume there is maldigestion leading to malabsorption and malnutrition. We also know from our previous articles that whenever you have undigested food traveling through the small intestine, the terrain for SIBO exists. This will cause gas and bloating from fermentation by those bacteria.

Chronically elevated cortisol, hypothyroidism and lack of micronutrients zinc and b vitamins (1,3,6,9,12) are the primary causes of low stomach acid. H. Pylori, a common opportunistic bacteria, can be a secondary cause taking hold in an environment of low stomach acid. Additionally, vegans and vegetarians are frequently low in stomach acid. This is due to a generally low protein diet, high alkaline foods and lack of B12.

Beta-Glucuronidase is an enzyme produced by pathogenic bacteria in cases of SIBO or dysbiosis. This enzyme causes elevated estrogen and blocks your liver’s ability to detoxify it. This is really important as excess estrogen is implicated in many cancers like breast and prostate as well as being the primary cause of hypothyroidism.

Psychologically, estrogen affects the amygdala, a key brain region for emotional processing and sensitives it. Estrogen also lowers GABA, the primary calming neurotransmitter, and increases Glutamate, the main excitatory neurotranmitter causing increased anxiety. Estrogen dominance also increases serotonin in many ways leading to hyper-emotional states and increased pain. To learn more about the negative effects of serotonin check out my article here.

For males, testosterone is meant to counter-point estrogen and for females that counter-point comes from progesterone. Both of these hormones are decreased by chronically elevated cortisol.

Anti-gliadin IgA refers to antibodies for gliadin (gluten). If elevated it indicates gluten sensitivity and potential celiac disease. For our guy this marker is low.

Eosinophil Activation Proteins elevate with various types of inflammation such as food allergies or parasites. He is also low here.

But his Secretory IgA is extremely low and this is something I’ve commonly seen with other clients, including myself. SIgA is the primary antibody produced in the intestinal lining and the first line of immune defense against pathogens in the gut. It is also the first-line of defense of the respiratory and uro-genital tract. If its low in the gut it is usually low on the other surfaces. Our guy has a history of susceptibility to respiratory infections.

Bet you can guess the biggest inhibitor of SIgA?…that’s right, chronically elevated cortisol! Whether its from lack of sleep, lack of calories, or overexercise cortisol consistently lowers immune function. This depression of the immune system by stress is what makes us vulnerable to infections. The gut-based immune suppression can lead to SIBO and dysbiosis further lowering SIgA.

Calprotectin is the most studied inflammatory marker in the gut and is frequently elevated in cases of SIBO, dysbiosis, food allergies and anti-nutrients. It also provides a possible diagnosis for irritable bowel syndrome (IBS). His is elevated.

This last panel, also part of the GI Map, shows us the Keystone Bacteria. They have been identified in all healthy human microbiomes regardless of location or diet and are essential for proper ecosystem functioning. I have found that if the Keystone bacteria are sufficient and appropriately balanced, dysbiosis is non-existent. And, if Akkermansia and Bifidobacteria families are supported, the other keystones follow. These are the core of a healthy microbiome and competitively inhibit the bad guys. In fact, it is these two families that are the first to boot up in infants who have had vaginal births and are breastfed.

As I mentioned last week, most soluble fiber indiscriminately feeds all bacteria, not just the good guys. Interestingly, researchers have found when investigating breastmilk that 20% of it acts as a prebiotic. This prebiotic is called Human Milk Oligosaccrides. HMOs are the third most abundant component of breast milk and play a crucial role in shaping the infant gut microbiota by selectively promoting the growth of two most important keystone families, Bifidobacterium and Akkermansia.

Furthermore, researchers at Cornell were able to identify these same oligosaccrides in cow milk, meaning they’re bioidentical. SuperHMO is my favorite solution for building up Akkermansia, Bifido and indirectly the rest of the Keystone Bacteria.

I personally use it for myself and my family once/year and complete a bottle. The keystones are crucial for producing short chain fatty acids, maintain gut barrier function and proper immunoregulation of the gut.

If you have gut symptoms, start at half the bottle dose and work your way up. If you already have decent gut function, you can probably start at bottle dose. Keep in mind that the more dysbiotic your microbiome, the more potential for die-off symptoms.

As I mentioned last week, eating carnivore and keto are elimination diets that can be effective in the short term but over the long term create problems like rapid aging from elevated stress hormones, lowered sex hormones and sleep issues to name a few. Usually the reason they are effective for symptom relief is because the fiber that was feeding dysbiosis and/or the anti-nutrients that were inflaming the gut are removed. Fiber is an amplifier of the microbiome, whatever the composition.

So, re-feeding carbohydrates, whether from sugars (fruit/honey/maple syrup) or starches (roots/tubers) is an experimental process of figuring out which you have an easier time in digesting and absorbing. In my case now, I’m eating about 50/50 sugars to starches and about 300g/day.

Generally speaking, the easiest carbs to digest are sugars that don’t have fiber - honey, maple syrup and fruit juice. The polyphenols in fruit juice are selectively prebiotic (for the good guys) and selectively antibiotic for the bad guys. On top of that and the carbs, juice is high in potassium of which most people are deficient.

After a period of time introducing those without issue, you’d want to incorporate whole and dried fruit (the fiber). If all is going well, continue on to starches like squashes, potatoes, sweet potatoes, cassava, white rice and maybe even sourdough bread.

If you start with sugars and get a flare up of symptoms, cut them out and try the starches in the order above. I know people that can’t eat fruit, only starches and vice versa.

The most important part of carb re-feeding is to go slow, 10-20g/week, until you get double your protein in grams while proportionalely titrating down your fat intake.

The formula for protein is .7-.8g x target body weight. Then doubling it for carbs (which optimizes stress hormones and thyroid function).

Next week in my final segment we’ll look at easy to spot symptoms that can help you generally assess where an issue is occurring in your gut as well as some of my favorite remedies.

Jonathan

This is for informational purposes only and should not replace professional medical advice. Consult with your physician or other health care professional if you have any concerns or questions about your health.

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How to Fix Your Gut, part 3