A variety of species are found within the microbiome. Organisms like Bifidobacteria, Lactobacillus, Akkermansia muciniphilia and Fecalibacterium prausnitzii compose the beneficial strains. Bacteroides and Escherichia coli may be categorized as commensal or opportunistic strains. They play a role in the digestive tract, but can become problematic if the environment changes and they overgrow. Finally, pathogenic strains such as Desulfovibrio and Bilophila Wadsworthia can proliferate under certain conditions and cause dysfunction.
An imbalanced ecosystem creates dysbiosis. The name is as it sounds-an alteration of bacterial populations that disrupts normal function. If there is a decline in the number of healthy species and a rise in commensal or pathogenic ones, the body’s homeostasis may become impaired.
In a healthy microbiome, digestion, absorption and assimilation of nutrients occur normally. Normal digestion might best be defined as a lack of signs and symptoms. Gas, bloating, abdominal pain, loose stools, constipation, food sensitivity/allergy and gastroparesis are all indications that your digestion isn’t working properly. While there can be a myriad of causes, a common thread seen throughout many such complaints is dysbiosis.
When populations of beneficial bacteria decline, pathogenic or opportunistic species increase and create symptoms that are quite unpleasant. Many of these symptoms arise from the production of gasses released by the bacteria when they ferment foods that did not completely digest somewhere along the GI tract. Lactose intolerance is a good example. Lactose is a large sugar that needs to be broken down into smaller sugars before being absorbed by the body. If this does not occur, lactose can become fuel for certain bacteria leading to the unpleasant production of gas.
Yeast and fungus also play roles in the digestive tract. Their populations are normally limited by beneficial bacteria and a lower pH in the colon. If dysbiosis occurs and concentrations of beneficial bacteria decline, this can subsequently lead to an increase in pH which allows for an overgrowth of yeasts and fungi. Think of how weeds appear in places where there is no grass. If the grass is healthy and full, weeds don’t have the room and resources to develop. If the grass dies, however, weeds can proliferate and take over the yard. This phenomenon is not limited to the digestive system. The skin, vagina, urinary tract and sinuses can also harbor an overgrowth of the wrong kinds of microorganisms.
Antibiotics [5], NSAIDs [6], PPI’s [7] and potentially anti-microbial herbs can all exert negative effects on populations of beneficial bacteria. A diet that is high in refined carbohydrates (sugars, sweets and starches) and low in fiber also sets the stage for dysbiosis [8].
Butyrate and colonic pH
Certain strains of bacteria in the GI tract produce a Short Chain Fatty Acid (SCFA) known as butyrate. As the description suggests, butyrate is acidic in nature. Studies suggest that a colonic environment with an acidic pH range of 5.5 is optimal for maintaining proper function [9]. Pathogenic strains and yeasts prefer a more neutral or alkaline pH. The presence of butyrate then, may be protective against microbial imbalances which lead to the rise of dysbiosis.
Methanobrevibacter smithii is a bacterial strain that produces a gas called methane. Increased methane production has been associated with constipation and altered bowel motility [10]. Decreased levels of butyrate may allow for concentrations of M. smithii to rise and result in digestive dysfunction [11]. Strains like F. Prausnitzii and R. intestinalis metabolize fiber into SCFA’s like butyrate and can help to limit the growth of M. smithii.
In addition to constipation, there may be a potential association between a neutral colon pH and colon cancer [12]. Researchers found that the introduction of butyrate affected carcinogenic cells positively [13]. Higher butyrate concentrations may lead to a shift in cellular functioning that promotes a more normative phenotype [14].
The importance of SCFA’s in the colonic environment cannot be overstated. They nourish colonocytes, promote optimal pH and confer protective qualities which allow for proper function.
Fiber as prebiotic
Beneficial bacteria of the colon derive their food from fiber sources. Fiber is typically composed of chains of glucose or fructose molecules joined together by saccharide bonds. The human body does not have the enzymes necessary to break apart these bonds, but beneficial bacteria in the colon do. They possess enzymes which hydrolyze saccharide bonds and convert them to smaller sugars. The bacteria then feed on these sugars and produce butyrate as a byproduct. Increasing concentrations of butyrate results in a drop of colonic pH making the environment more hospitable to beneficial microbes and less likely to support pathogenic ones.
Fiber is therefore considered a prebiotic. It serves as a food source for the beneficial bacteria and enables them to grow. Increasing the number of beneficial strains can crowd out pathogenic organisms and facilitate a return to eubiosis.
There are actually many different types of fiber. Inulin, fructooligosaccharides (FOS), galactooligosacharides (GOS), psyllium husk, partially hydrolyzed guar gum, pectin and konjac glucomannan are a few examples. Plant based foods will offer various types of fiber while supplements contain others.
It’s important to understand that fiber is selective. Each type will support the growth of a different strain of bacteria. Lactobacillus, for instance, has been shown to thrive on Konjac glucomannan [15] while fructooligosaccharides (FOS) may induce growth of Bifidobacteria [16]. There are conditions, such as Small Intestinal Bacterial Overgrowth (SIBO), which may affect fiber tolerance. Organisms that migrate to the Small Intestine from the colon may consume prebiotic food sources and produce unwanted gas. The presence of SIBO in some individuals may necessitate the exploration of additional interventions.
Probiotics
Probiotics are microorganisms found in fermented foods and supplements. Cultures of bacteria digest sugars in these foods and produce lactic acid, which leads to the formation of a sour flavor. Kefir made from the addition of kefir grains to milk is a good example. The grains consist of bacterial cultures which consume sugars in the milk and boost levels of probiotics. Not everyone is able to drink kefir because it still contains dairy proteins. For those who can, however, kefir may confer numerous benefits.
Probiotics are also available in supplement form. They are grown, harvested, then packaged into capsules, liquids or tablets. Despite commonly held beliefs, it’s doubtful that probiotics actually “re-seed” or colonize the gut on a permanent basis [17]. They do, however, offer other benefits such as the displacement of pathogenic organisms [18]; modulation of the body’s immune system [19], increased production of anti-inflammatory messengers and decreased permeability of the intestinal mucosa [20].
But just like all fiber isn’t the same, all probiotics are not the same. Each strain of bacteria may exert a different effect in the GI Tract. Strain specificity is key in utilizing the right probiotic for the particular set of symptoms or conditions.
Polyphenols
Polyphenols are molecular substances which provide plants with numerous benefits. They are usually known for their antioxidant properties and can help to protect plants against the effects of ultraviolet radiation and pathogens [21]. Flavonoids, stilbenes and anthocyanidins are all good examples. Foods rich in these beneficial phytochemicals include fruits, vegetables, herbs, teas, some grains, beans and chocolate (cacao).
In addition to fiber, polyphenols may serve as a food source for strains of colonic bacteria. It’s been estimated that 90% of polyphenols pass through the upper GI tract undigested and reach the colon [22]. Akkermansia muciniphilia, for example, has been shown to thrive on red polyphenols [23]. Foods such as apple skins, pomegranate, cranberries and raspberries may help to increase concentrations. Reduced levels of this strain have been associated with Inflammatory Bowel Disease (IBD), Autism, atopy (allergic tendencies) and obesity [24]. A. muciniphilia may possess anti-inflammatory properties which help to maintain a beneficial colonic environment and offer protection against such conditions.
A diet rich in polyphenols can nourish the microbiome and increase species diversity. GI tracts dominated by a few species are more likely to exhibit dysfunctional characteristics or conditions [25]. Microbial richness, however, has been associated with better overall health [26]. Polyphenols are often times best derived from food-based sources rather than supplements as concentrated extracts may be problematic in higher doses [27].
Analyzing your microbiome
Current estimates put the number of different microorganisms in the GI tract at over 1,000 [28]. We’re only beginning to understand each individual strain and its role in contributing to overall homeostasis.
An analysis of the microbiome can yield important clues into gut health and allow clinicians to better understand the etiology contributing to current health challenges. Autoimmune presentations [29], ulcerative colitis [30], IBD [31], IBS [32], visceral pain [33] and colon cancer [34] all have likely associations to bacterial imbalances in the GI tract. An evaluation of the microbiome allows for more targeted recommendations involving the use of specific fibers or polyphenol containing foods. By supplementing your ecosystem with the right interventions, depressed populations of beneficial bacteria can be revived and help to rebalance the body towards optimal health.
If you’d like to have your microbiome analyzed, contact Chris Bramich at consultation@vitalfoundations.com or visit www.vitalfoundations.com
Chris Bramich graduated with distinction from the University of Western States with a Master’s (MS) in Human Nutrition and Functional Medicine. He is a Nutritional Therapy Practitioner (NTP) and is Board Certified in Holistic Nutrition (BCHN). He practices in the Dallas/Fort Worth area of Texas.
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