Your Gut Microbiome – Miraculous and Mysterious – Part 2

 What does the Microbiome Do For Us ?

Here is the essence of the gut microbiome in the simplest of terms. Bacteria in the gut that live in symbiosis with human beings and keep us healthy are known as “good bacteria” and they thrive on fruits, vegetables, grains and beans. In contrast, gut bacteria that contribute to disease are “bad bacteria” and like to feed on meat, dairy, eggs, seafood, junk food and fast food (1). The “good bacteria” in our gut have a myriad of health-promoting effects. Some of these include boosting our immune system; improving digestion and absorption; regulating energy metabolism; and inhibiting the growth of potential disease-causing microbes. On the other hand, “bad bacteria” can produce carcinogens and toxins; cause infections, low-grade inflammation, metabolic disorders such as diabetes, excess accumulation of fat and loss of insulin sensitivity; and decimate bowel function (2,3).

Gut microorganisms exert their beneficial effects in numerous ways. The mere presence of a healthy and rich growth of “good bacteria” will provide a barrier that can outcompete detrimental “bad bacteria” for nutrients, keeping them in check and limiting their harmful effects. If needed, the gut can warn the central nervous system about the threat of potentially damaging bacteria before any overt signs of inflammation occur. It can even instigate an anti-inflammatory response invoking the help of immune cells to decrease the danger. Gut microbes maintain a vast and complicated communication system with the central nervous system through the vagus nerve (as part of the gut-brain axis), the hypothalamic-pituitary-adrenal axis (our stress-response system which includes the hypothalamus in the brain along with the pituitary and adrenal glands), and also by producing chemical mediators such as neurotransmitters (serotonin, tryptophan, gamma-aminobutyric acid (GABA), dopamine, l-dopa, noradrenaline) and hormones (cortisol, ghrelin, leptin, glucagon-like peptide) (4,5). The microbiome also produces a plethora of neuroactive substances such as catecholamines, histamine and others that can interact directly with receptors within the gastrointestinal tract and be absorbed through the gut wall into the bloodstream (6).

It is important to note that differences in the content of a gut microbiome are not generally caused by the genetics of the person in which the microbiome resides. This has been shown through studies on twins who can have completely different microbiomes depending on physiological factors. For instance, in research on identical twin mice, the gut microbiomes of an obese mouse and its twin of healthy weight were significantly dissimilar (7). In people, it has been discovered that, though the gut microbiome among family members contains a core of shared microbial species, the microbiome in individuals varies with differing inputs (for example diet or antibiotics) and the state of health (for example presence of obesity, metabolic syndrome or diabetes) (8). A very large-scale study determined that only about 2% of variations in the microbiome come from the genetics of the host. Over 20% of the variability in the microbiomes of people is prompted by environmental factors such as diet and drugs (9).

We are discovering that our gut microbiota are involved in a great many functions of the human body. The following is an overview of some of these.


The Gut Microbiome and Metabolic Function

The gut microbiome performs vital metabolic and signalling functions that cannot be accomplished by the human body alone. Some examples of these functions are;

The digestion of otherwise indigestible starches and fibers such as cellulose and gums
The production of all B vitamins and vitamin K
The synthesis of essential amino acids
The use of bile in glucose and cholesterol metabolism
The production of anti-inflammatory short-chain fatty acids (butyrate, propionate and acetate) by gut microbes through the fermentation of fiber, the preferred energy source for the gut bacteria themselves (4).


The Gut Microbiome and the Immune System

The gastrointestinal system is our main contact with the outside world with all its potential benefits and harms. Eating can introduce destructive elements such as toxins and damaging microorganisms into our bodies. This is likely why almost 70% of the human immune system resides within or nearby our gastrointestinal system (10).

Immune mechanisms in the human digestive tract are very complex. Fermentation of fiber by gut microbes produces short-chain fatty acids that help to regulate the immune system and protect against the development of inflammatory diseases (11). A well-functioning immune system will analyze intestinal contents and either tolerate them or eliminate them according to their respective characteristics. Intestinal permeability (holes in the lining of the intestine) can be increased or decreased and the response to immune threats can be immediate if necessary (10). However, these immune functions must maintain a delicate balance. Dangers must be eliminated without imperiling normal and beneficial micro-inhabitants of the microbiome or healthy cells of the host body. The gut microbiome is adept at preserving this equilibrium (12).


The Gut Microbiome and Digestion of Fiber

Fiber is indeed a very important nutrient and its intake is closely associated with health and longevity. Recent data suggests there is a 15 to 30% decrease in all-cause and cardiovascular related mortality, and incidence of coronary heart disease, stroke incidence and mortality, type 2 diabetes, and colorectal cancer when comparing the highest dietary fibre consumers with the lowest (13). Intriguingly, the benefits of fiber for humans may come in an indirect manner. From fiber our healthy gut bacteria obtain their energy and produce the beneficial short-chain fatty acids that promote optimum intestinal function and many other valuable health effects (14).

When it comes to digesting fiber, the help of our gut microbiome is essential. Human beings on their own cannot process this nutrient. Surprisingly, the human genome contains only about seventeen genes dedicated to the digestion of fiber. On the other hand, our microbiome, with between 60,000 and 100,000 genes for processing fiber, takes over this activity for us (15).


Still to come…

In the next three parts of this article on the human gut we’ll examine what happens when the gut microbiome is disturbed and then show you ways to encourage your healthiest microbiome.



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2 Saulnier, D.M., Kolida, S., Gibson, G.R. Microbiology of the human intestinal tract and approaches for its dietary modulation. Curr Pharm Des. 2009;15(13):1403-1414.

3 Boulangé, C.L., Neves, A.L., Chilloux, J., Nicholson, J.K., Dumas, M.-E. Impact of the gut microbiota on inflammation, obesity, and metabolic disease. Genome Medicine. 2016; 8:Article number: 42.

4 Sidhu, M., Van der Poorten, D. The gut microbiome. Aust Fam Phys 2017; 46(4):206-211.

5 Forsythe, P., Bienenstock, J. Kunze, W.A. Vagal pathways for microbiome-brain-gut axis communication. Adv Exp Med Biol. 2014;817:115-133.

6 Lyte, M. Microbial Endocrinology in the Microbiome-Gut-Brain Axis: How Bacterial Production and Utilization of Neurochemicals Influence Behavior. PLoS Pathog. 2013 Nov; 9(11): e1003726.

7 Ridaura, V.K., Faith, J.J., Rey, F.E., Cheng, J., Duncan, A.E et al. Cultured gut microbiota from twins discordant for obesity modulate adiposity and metabolic phenotypes in mice. Science. September, 2013; 341(6150): 10.1126/science.1241214.

8 Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A. et al. A core gut microbiome in obese and lean twins. Nature. January, 2009; 457(7228):480-484.

9 Rothschild, D., Weissbrod, O., Barkan. E., et al. Environment dominates over host genetics in shaping human gut microbiota. Nature. February, 2018; 555:210-215.

10 Vighi, G., Marcucci, F., Sensi, L., DiCara, G., Frati, F. Allergy and the gastrointestinal system. Clin Exp Immunol. 2008 Sep; 153(Suppl 1): 3–6.

11 Maslowski, K.M., Vieira, A.T., Ng, A., Kranich, J., Sierro, F., Yu, D., Schilter, H.C., Rolph, M.S. et al. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature. 2009 Oct 29;461(7268):1282-1286.

12 Wu, H.-J., Wu, E. The role of gut microbiota in immune homeostasis and autoimmunity. Gut Microbes. 2012 Jan 1; 3(1): 4–14.

13 Reynolds, A., Mann, J., Cummings, J., Winter, N., Mete, E., Te Morenga, L. Carbohydrate quality and human health: a series of systematic reviews and meta-analyses. Lancet. 2019 Feb 2;393(10170):434-445.

14 Larsbrink, J., Rogers, T.E., Hemsworth, G.R., McKee, L.S., Tauzin, A.S. et al. A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes. Nature. 2014;506: 498-502.

15 Youtube – Understanding The Microbiome, Erica Sonnenburg, PhD. Jan 10, 2018.

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My name is Debra Harley (BScPhm) and I welcome you to my retirement project, this website. Over the course of a life many lessons are learned, altering deeply-rooted ideas and creating new passions.

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