Your Gut Microbiome – Miraculous and Mysterious – Part 5

Encouraging a Robust Gut Microbiome Continued

Part 4 of this article discussed the influence of diet on a healthy microbiome. Happily, there are even more factors within our own control that can affect the health of our gut. In this final part of the gut microbiome series, we’ll look into these other elements. Finally we’ll summarize all the ways that you can help your gut microbiome help you achieve optimum health.

Artificial Sweeteners
Animal studies have found that artificial sweeteners such as aspartame can impair glucose tolerance and increase the numbers of disease-causing bacteria in the gut (1). Similar results were found in humans with studies showing that artificial sweeteners such as saccharin, sucralose or aspartame could induce glucose intolerance possibly by altering the function of the gut microbiome (2). Further studies are warranted to discover the extent of these deleterious metabolic effects.

A 2011 investigation found that exercise has anti-inflammatory effects which improve gut health (3).
A 2014 study showed that athletes have a higher diversity of gut microbiota and lower inflammation in the gut compared to non-athletes (4).
A 2018 study discovered that exercise caused alterations of the gut microbiome that resulted in increased short-chain fatty acid production. This effect occurred only in lean subjects, not obese ones, and reversed once regular exercise ceased (5).

Emerging evidence shows that the gut microbiome can regulate the sleep of its host through the gut-brain axis. Microbiome exhibit cyclical changes in its abundance of microbes from day to night. The host has its own circadian rhythms. When these two sets of rhythms are in synergy relaxation and healthy sleep is promoted (6).

Chronic disturbances in host circadian rhythms can occur in many situations, some of which are alterations in sleeping routine, shift work, jet lag, Alzheimer’s disease and mental health conditions such as depression and anxiety. Disruptions in circadian rhythms not only cause poor sleep but also bring about changes in the composition of the gut microbiome that reduce the numbers of beneficial bacterial species such as Lactobacilli and increase the numbers of harmful species. These alterations in turn affect the metabolic function of the gut bacteria and may even produce metabolic syndrome (high blood pressure, high blood sugar, excess fat around the waist area, high blood triglycerides and cholesterol) which is a risk factor for cardiovascular disease and diabetes. It is unclear as yet whether or not gut microorganisms themselves can modify the circadian rhythm of the host or simply respond to disruptions in the pattern (6).

Instinctively we know that stress is related to the gut. Simple acknowledgement of pertinent phrases in our everyday language, “butterflies in the stomach”, “gutsy”, “gut feelings”, “gut-wrenching” and “gut instinct”, speaks to a strong relationship between the two. This should not be surprising. We know that the brain is closely linked to the gut through the gut-brain axis. Recent studies are showing that the intestinal microbiota is a major player in the control of this axis, especially during conditions of stress. Investigations reveal that psychological stress can adversely alter the composition of the gut microbiota, the permeability of the gut membrane, the function of the gastrointestinal system and cause changes in secretions produced in the intestines. The release of inflammatory substances called cytokines is thought to play a role in these detrimental effects. Our gut microbiota have been implicated in a variety of stress-related conditions, both short- and long-term, including anxiety, depression, inflammatory bowel disease (IBD), gastroesophageal reflux disease (GERD) and stomach ulcers.
On the other hand, specific strains of “good bacteria” such as Bifidobacteria, Lactobacilli and some Bacteroides species can have positive effects on emotions and mental health. The growth of these “good bacteria” is supported by eating a diet high in fiber from plants. Animal studies have found that diets high in saturated fat reduce numbers of Bifidobacteria, are associated with breakdown of the gut lining (“leaky gut”) and can worsen negative emotional states. Diet choices such as reducing saturated fat and increasing fiber emerge as important steps for preventing and combating the effects of stress. (7,8,9)

Antibiotics and other medications
Antibiotics can kill bacteria that are harming us. Unfortunately, they can also destroy the favourable bacteria that we require for full health. A gut microbiome may not recover for many months after being exposed to antibiotics and, in some cases, a healthy bacterial balance is never fully restored. Long-term changes in the microbiome may increase susceptibility to infections and disease and may also play a role in obesity, type-1 diabetes, inflammatory bowel disease, allergies and asthma. It is important to take antibiotics only when absolutely necessary. (10,11,12)

Proton pump inhibitors (PPIs) are a class of drugs used to decrease production of acid in the stomach. They are used for treating severe gastroesophageal reflux disease (GERD) and to help eradicate overgrowth of Helicobacter pylori in the stomach. Ideally these medications are for short-term use only. However, many people continue using PPIs for years. Unfortunately, even short-term use of these drugs cause dysbiosis in the gut. Bowel symptoms result (bloating, diarrhea and/or constipation) and risk for Clostridium difficile infections is increased due to significant alterations in the gut microbiota. Inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis can also be triggered.

Probiotics are defined by the International Life Sciences Institute Europe as “viable microbial food supplements which when taken in the right dose beneficially influence the health of the host” (14). Being “viable” means that they are alive and this is a necessary factor for probiotics to exert a beneficial health effect. Probiotics do not generally colonize the intestinal mucosa indefinitely. Rather they exert their benefits as they pass through, staying a short while, but eventually leaving no physical trace that they were ever there. Before they disappear however, probiotics are capable of many healthful effects.
Some of these are (14):
Inhibition of the replication of disease-causing microorganisms
Stabilization of the environment of the gut
Modulation of the immune system to decrease inflammation
Enhancing the strength of the gut’s permeability barrier
Increasing the production of mucins which reinforce the intestinal barrier
Controlling the balance between pro-inflammatory and anti-inflammatory cytokines

Evidence from Health Canada, the World Health Organization and internationally recognized expert committees on probiotics state that probiotics can be recommended in persons of all ages for the prevention of diseases that are associated with alterations of the intestinal microbiome.
Indications include (14,15,16);
The prevention of upper respiratory tract infections
The treatment of antibiotic-associated diarrhea, including Clostridium difficile infection
The reduction of risk for and the treatment of infectious diarrhea
The prevention and management of bacterial vaginosis
The treatment of eczema caused by allergy to cow’s milk

In addition, probiotics can manage constipation; decrease the risk of high cholesterol blood levels and in turn lower risk factors for cardiovascular disease; reduce recurrent urinary tract infections; improve irritable bowel syndrome symptoms; and lessen the side effects of antibiotics used in the eradication of Helicobacter pylori during treatment of stomach inflammation and gastric ulcers (15,17)

One warning about probiotics appeared following 2018 investigations. A study looked at the effects of a multi-strain probiotic on the recovery of the microbiome after antibiotic use. The probiotic treatment did indeed transiently increase bacterial numbers in the colon, however, only Bifidobacterium strains persisted after the probiotics were stopped. The presence of these introduced probiotic bacteria then seemed to act as a “placeholder” which significantly prolonged the disruption of the microbiome so that its recovery was markedly delayed compared to simply doing nothing and waiting for the microbiome to recover spontaneously. On the other hand, a fecal microbiome transplant (transplanting fecal matter from a person with a healthy microbiome into a person with a damaged microbiome) can induce a rapid and near-complete recovery of the microbiome within days of administration. (18)

In summary, probiotics have their place in the maintenance and recovery of a healthy intestinal tract. However, our microbiome is a complicated system and simply ingesting live bacteria from a probiotic does not replace the beneficial microbes that provide all the benefits of a balanced, robust microbiome. Sober thought will find this unsurprising. Our gut microbiome consists of trillions of microbes and encompasses over a thousand species while a probiotic contains relatively few of both of these elements. Healthy eating which includes fiber and prebiotic foods along with time for healing to take place is needed to allow a damaged microbiome to recover its previous healthful bacteria to their full vigour.

Fermented Foods
Fermentation occurs naturally in the gastrointestinal tract during digestion (19). Studies are now showing promising results for ingesting foods that are naturally fermented and contain live microbes. Such foods are a type of natural probiotic. Examples of fermented foods are sauerkraut, miso, tempeh, kimchi, yogurt, kombucha and kefir. These foods generally contain a greater variety of bacterial species than probiotic supplements. Fermented foods are especially rich in members of the healthy bacterial genus, lactobacillus (lactic acid bacteria). Fermented foods also contain abundant flavonoids (plant metabolites from highly coloured fruits and vegetables) which can protect the cardiovascular system and have anti-inflammatory, anti-diabetic, anti-obesity and anti-cancer effects (20).

Recently researchers discovered that a metabolite produced by lactic acid bacteria is capable of signalling the immune system. Investigators suggest that this interaction has anti-inflammatory effects and could explain how the microbiome exerts its benefit on inflammatory diseases (21).

Large, high quality scientific trials are needed to elucidate the exact relationship between these foods and a healthy gut microbiome (21,22).


Fostering a health-giving microbiome is not a mystery. Here are some steps to help make this happen.

Choose your meal ingredients mainly from the plant kingdom. A diet consisting of only plants and no animal-sourced food is the most beneficial for your gut microbiome.

Make sure you include lots of fiber, prebiotic foods and some fermented foods in your meal plans.

Eat from a wide range of plants to encourage broader diversity in the microbes in your gut.

Reduce your intake of saturated fat.

Avoid the use of artificial sweeteners.

Exercise regularly. Aim for about 30 minutes of moderate exercise a day or 150 minutes a week.

Employ good sleep hygiene. Make it a habit to fall asleep in bed, not in your chair while watching television. Decide on a reasonable bedtime and make it a consistent habit. Avoid looking at electronic devices (computers, cell phones, tablets) just before bedtime. The blue light that they emit boosts attention, increases wakefulness and is disruptive to sleep (23).

Avoid stress as much as possible. Relaxing activities such as yoga or meditation can help combat the effects of stress.

Resist the urge to take an antibiotic for minor, self-limiting conditions such as a cold or flu. If you must take one of these medications, you might choose to include a good probiotic along with it to help prevent damaging effects on your gut microbiome. However, more data is needed to determine the best course of action for gut microbiota recovery after antibiotic use (24).

Do not take PPIs for GERD any longer than 8 weeks. Long-term use is only recommended for serious esophageal problems such as pre-cancerous lesions, healing of recalcitrant ulcers, damage to the esophagus, eradication of resistant H. pylori infection and severe GERD not controlled by any other means (25). If you have been taking a PPI for a long time for simple GERD, work with your physician to discontinue the drug very slowly. Otherwise, once the PPI is discontinued, the stomach can rebound by overproducing stomach acid, leading to severe heartburn symptoms that might prevent you from discontinuing this drug at all (26).



1 Palmnäs, M.S., Cowan, T.E., Bomhof, M.R., Su, J., Reimer, R.A., Vogel, H.J., Hittel, D.S., Shearer, J. Low-dose aspartame consumption differentially affects gut microbiota-host metabolic interactions in the diet-induced obese rat. PLoS One. 2014 Oct 14;9(10):e109841.

2 Suez, J., Korem, T., Zilberman-Schapira, G., Segal, E., Elinav, E. Non-caloric artificial sweeteners and the microbiome: findings and challenges. Gut Microbes. 2015; 6(2): 149–155.

3 Gleeson, M., Bishop, N.C., Stensel, D.J., Lindley, M.R., Mastana, S.S., Nimmo, M.A. The anti-inflammatory effects of exercise: mechanisms and implications for the prevention and treatment of disease. Nat Rev Immunol. 2011; 11(9):607-615.

4 Clarke, S.F., Murphy, E.F.,O’Sullivan, O., Lucey, A.J., Humphreys, M. et al. Exercise and associated dietary extremes impact on gut microbial diversity. Gut. 2014; 63(12):1913-1920.

5 Allen, J.M., Mailing, L.J., Niemiro, G.M., Moore, R., Cook, M.D., White, B.A., Holscher, H.D., Woods, J.A. Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans. Med Sci Sports Exerc. 2018 Apr;50(4):747-757.

6 Li, Y., Hao, Y., Fan, F., Zhang, B. The Role of Microbiome in Insomnia, Circadian Disturbance and Depression. Front Psychiatry. 2018; 9: 669.

7 Rea, K., Dinan, T.G., Cryan, J.F. The microbiome: A key regulator of stress and neuroinflammation.
Neurobiology of Stress. October, 2016; 4:23-33.

8 Foster, J.A., Rinaman, L., Cryanc, J.F. Stress & the gut-brain axis: Regulation by the microbiome.
Neurobiol Stress. 2017 Dec; 7: 124–136.

9 Konturek, P.C., Brzozowski, T., Konturek, S.J. Stress and the gut: pathophysiology, clinical consequences, diagnostic approach and treatment options. J Physiol Pharmacol. 2011 Dec;62(6):591-599.

10 Blaser, M. Antibiotic Overuse: Stop the killing of beneficial bacteria. Nature. 2011; 476: 393-394.

11 Bailey, L.C., Forrest, C.B., Zhang, P., Richards, T.M., Livshits, A., DeRusso, P.A. Association of antibiotics in infancy with early childhood obesity. JAMA Pediatr. 2014 Nov;168(11):1063-1069.

12 Looft, T., Allen, H.K. Collateral effects of antibiotics on mammalian gut microbiomes. Gut Microbes. 2012 Sep 1; 3(5): 463–467.

13 Naito, Y., Kashiwagi, K., Takagi, T., Andoh, A., Inoue, R. Intestinal Dysbiosis Secondary to Proton-Pump Inhibitor Use. Digestion. 2018;97(2):195-204.

14 Salminen, S., Isolauri, E. Intestinal colonization, microbiota, and probiotics. The Journal of Pediatrics. November 2006; 149(5):S115-S120.

15 Taibi, A., Comelli, E.M. Practical approaches to probiotics use. Appl Physiol Nutr Metab. 2014 Aug;39(8):980-986.

16 Lenoir-Wijnkoop, I., Gerlier, L., Roy, D., Reid, G. The Clinical and Economic Impact of Probiotics Consumption on Respiratory Tract Infections: Projections for Canada. PLoS ONE. November, 2016; 11(11): e0166232.

17 Shimizu, M., Hashiguchi, M., Shiga, T., Tamura, H.O., Mochizuki, M. Meta-Analysis: Effects of Probiotic Supplementation on Lipid Profiles in Normal to Mildly Hypercholesterolemic Individuals.
PLoS One. 2015 Oct 16;10(10):e0139795. doi: 10.1371/journal.pone.0139795.

18 Suez, J., Zmora, N., Zilberman-Schapira, G., Halpern, Z. et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. September, 2018; 174(6):1406-1423.

19 van Hylckama Vlieg, J.E., Veiga, P., Zhang, C., Derrien, M., Zhao, L. Impact of microbial transformation of food on health – from fermented foods to fermentation in the gastro-intestinal tract. Curr Opin Biotechnol. 2011; 22(2):211-219.

20 Ballard, C.R., Maróstica Jr., M.R. Bioactive Compounds – Health Benefits and Potential Applications. Chapter 10 – Health Benefits of Flavonoids. Science Direct. 2019; Pages 1850201

21 Peters, A., Krumbholz, P., Jäger, E., Heintz-Buschart, A., Çakir, M.V., Rothemund, S., et al. Metabolites of lactic acid bacteria present in fermented foods are highly potent agonists of human hydroxycarboxylic acid receptor 3. PLoS Genet. 2019; 15(5): e1008145.

22 Klinder, A., Shen, Q., Heppel, S., Lovegrove, J.A., Rowland, I., Tuohy, K.M.. Impact of increasing fruit and vegetables and flavonoid intake on the human gut microbiota. Food Funct. 2016 Apr;7(4):1788-1796.


24 Langdon, A., Crook, N., Dantas, G. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome Med. 2016; 8: 39.


26 Reimer,C., Søndergaard, B., Hilsted, L., Bytzer, P. Proton-pump inhibitor therapy induces acid-related symptoms in healthy volunteers after withdrawal of therapy. Gastroenterology. 2009 Jul;137(1):80-87.

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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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