The Human Microbiome: Why You Need Pre- and Probiotics For Optimal Gut Wellness

Dr. Denise K. Hee (Mb BCh BAO, MRCS, CHC) discusses how pre- and probiotics play a significant role in keeping our intestines working properly:

The gateway to thriving health is through a properly functioning digestive tract.

It begins in the gut The lustre of your skin. The smell you emanate. These 2 things alone say so much about your state of health. We perceive health within moments of meeting someone. Are we in the presence of vitality?

Our digestive system is the root of our health, or lack thereof. Hippocrates said it best: “ All disease begins in the gut.” This is why gut wellness is the top priority of many practitioners in the world of clinical nutrition. The digestive tract is roughly 9 metres long: it starts in the mouth and ends at the anus.

Worldwide, millions of people suffer from some form of digestive upset somewhere along this tract, whether it is acid reflux, stomach ulcers, abdominal cramps or constipation. In the Australian Burden Of Disease Study , it is estimated that 70,000 people are living with inflammatory bowel disease and 1 in 10 people suffer from symptoms of irritable bowel syndrome. According to the Gut Foundation Research Institute, more than 15000 people were diagnosed with bowel cancer in 2012, making it the second most common cause of cancer-related death in Australia.

What Is The Gut Microbiome?

Previous estimates stated that the ratio of human to bacterial cells in our body was about 10 trillion to 100 trillion respectively. However, with scientific advancements, more accurate measurements now suggest that the average human male is made up of about 30 trillion cells and about 40 trillion bacteria live in his digestive tract. Excuse the pun, but does that fact bug you? Well, it shouldn’t -- as long as the good and bad microbes are living in harmony and balanced in the right quantities.

When I talk about the microbes present in the body, it's important to understand that there are many different types. The bacteria that we find in the gut may be transient (just passing through via what we eat) or colonising (like a seed that plants itself in the gut, it lives and multiplies there permanently in varying quantities). The bacteria may also be friendly or pathogenic. Examples of good bacteria are Lactobacillus, Bacteroides and Bifidobacterium, while E.coli would be an example of one we do not wish to have a lot of. The reason your immune system doesn’t get rid of all these foreign bacteria is because the friendly ones actually help our body function. Friendly bacteria help in digestion of food, absorption of vitamins and maintaining the integrity of the intestinal lining. Aside from bacteria, the gut microbiome may also consist of fungi like Candida or Saccharomyces and parasites like Entamoeba. It's a truly diverse ecosystem.

Unfortunately, an imbalance in the gut microbiome, a condition known as dysbiosis, is pretty common in today’s society. Dysbiosis describes the state in which there is either quantitative changes in the good and bad microbes, changes in their metabolic activity or a change in their distribution in the body. This can arise from:

• Diets high in sugar and processed foods
• Meat and dairy products that are pumped with hormones
• Taking too many antibiotics and medications
• Illness and aging
• Environmental mould and other toxins, and
• Chronic stress

Although the dysbiosis starts in the gut, an imbalanced microbiome leads to much more than just digestive issues. Some common symptoms include:

• Abdominal cramps
• Bloating and frequent passing of gas
• Food intolerances
• Malnourishment
• Changes in stool patterns
• Bad breath
• Indigestion and acid reflux
• Joint pains and inflammation
• Fatigue
• Brain fog or poor concentration
• Sinus infections
• Autoimmune conditions like Hashimoto’s thyroiditis and psoriasis
• Skin disorders and
• Acne

Because the effects of dysbiosis can be seen in so many different systems of the body, it would not be surprising if one or more of the symptoms listed above sound familiar to you. As the number of clinical studies that link dysbiosis to different diseases grows, it is impossible to estimate the number of people around the world who could be affected. However, with the causes of dysbiosis all around us, it’s probably not a question of whether someone is affected or not, but rather, to what degree.

The common pathway of how dysbiosis leads to disease is through increasing inflammation throughout the body. Our intestinal lining has tiny holes, called tight junctions, that allow it to filter and only absorb the nutrients it requires from our food. The rest of the toxins and waste stay in the intestine and pass out in our stool. When left unchecked, the increased number of bad microbes in the gut are capable of enlarging these holes. This is a condition known as Leaky Gut Syndrome. This means that other larger particles, toxins and sometimes the bacteria themselves, are able to pass out from the intestines and travel into the bloodstream causing damage to other organs.

In addition to irritable bowel disease, celiac disease and life threatening conditions like colon cancer, dysbiosis has also been linked to other non-gastrointestinal disorders like type 2 diabetes, autoimmune and mental health disorders. One study published in 2015 also showed that dysbiosis was linked to non-alcoholic fatty liver disease (NAFLD). Since 70% of the blood flow to the liver comes from a vein that is linked to the intestine, this is not surprising. Researchers found that patients with NAFLD had significantly more pro-inflammatory bacteria in their gut. These bacteria produced compounds, known as cytokines IL-6 and TNF-alpha, which caused damage to the liver and potentiate the progression of NAFLD. Studies like this highlight the gut-liver axis and demonstrate the potential for treatments that target the gut microbiome.

Other clinical studies have also showed a correlation between dysbiosis and mental health. There are a few possible pathways that the microbiome could affect the brain and mood including the direct connection between the brain and intestine via the vagus nerve , the availability of nutrients to support brain function from digestion and the production of certain hormones, like serotonin and tryptophan, that occurs in the gut.

How to Improve the Gut Microbiome Balance:

Probiotics:

Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit on the host.”

The most common groups of bacteria in probiotics are Lactobacillus and Bifidobacterium, which may be derived from human, dairy or fruit sources depending on the manufacturer. There are multiple different species within these genus that we are starting to associate with specific effects on the human system.

A new class of probiotic supplements becoming more common in the market use soil-based organisms or SBOs. These organisms are naturally resistant to stomach acid and do not need a special coating to ensure that enough of the organisms reach the intestine. SBOs can be likened to a seed - protected by a natural shell and thriving in warm, moist environments.

Humans evolved in intimate relationship with the soil, picking up good bacteria as they foraged for food and interacted with the eco-system. SBOs can be found in abundance on un-washed produce grown in a healthy soil. Unfortunately, the overuse of pesticides and fungicides in industrial agriculture has led to soil with an imbalance of micro-organisms, similar to that found in the guts of modern humans. This means that most people are not being exposed to nearly the amount of SBOs that we evolved with. The gold standard for obtaining more SBOs would be activities like gardening, eating unwashed local organic produce grown in healthy soil, barefoot time in nature, and-most importantly-mud wrestling. You can also supplement SBOs with products such as the Terraflora Synbiotic formula, a highly recommended and efficacious probiotic supplement.

Numerous clinical studies have confirmed that probiotics can help to relieve gastrointestinal discomfort, reduce systemic inflammation and deliver many other health benefits like lower cholesterol and weight. The strongest studies support their use in helping to cure infective diarrhoea, as well as antibiotic-associated diarrhoea. In antibiotic-associated diarrhoea, the culprit is normally a bacteria known as Clostridium Difficile. This bacteria surfaces when the good bacteria that normally keep it in check have been wiped out by the antibiotics and causes a debilitating, and possibly fatal, type of bloody diarrhoea. In emergency scenarios, fecal transplants through an enema or a colonoscopy have been successful in its treatment. More recently, the use of orally administered frozen encapsulated fecal material is being studied as well. The idea behind fecal transplants and ‘poop pills’ is bacterial interference and involves repopulating the gut with good bacteria. Personally, I believe it sounds a lot like what probiotics do, without the ick factor.

Unpasteurised fermented foods are a good source of probiotics. Examples include:

• Sauerkraut
• Yogurt (Sheep, Goat, Buffalo, or Grass-Fed Cow)
• Kimchi
• Kefir
• Kombucha

Which Probiotics?

If you prefer to take it as a supplement, and sometimes this is necessary to correct an imbalance, know that not all of the ones on the market are worth your money. For example, this report from Consumer Lab compares 46 different brands of probiotics (but note they are all US brands).

Generally speaking, try to find the ones with the most number of different strains of bacteria in them and with a minimum of 10 billion bacterial count. Look for probiotics that include L. Acidophilus, L. Plantarum L. Rhamnosus, B. Longum, B. Bifidum, B. Infantis, Saccharomyces boullardii and Streptococcus thermophilus.

Some specific probiotics like Cognibiotics that includes Lactobacillus brevis, Lactobacillus helveticus and Bifidobacterium animalis. These have been show to have nootropic effects including boosting BDNF, serotonin production and supporting cognitive performance.

And there are proteolytic probiotics like P3-OM that are specifically for digesting protein.

If you send away for a Viome or SmarGUT microbiome report, you can get personalised probiotic recommendations along with the diet to support them.

Bear in mind that companies will state the number of live units at the time of manufacture. This number may be a higher concentration that what your body benefits from by the time you buy it. Look for ‘shelf stability’ when deciding which brand to buy to ensure the number of organisms from the time of manufacture until the time it is sold in the shop varies as little as possible.

Choose supplements that come in coloured bottles which help protect the bacteria from sunlight and heat. Some brands also have a controlled-release delivery system that helps maximise the number of bacteria that reach the colon, instead of dying in the stomach.

Prebiotics: Feeding The Army Of Good Bacteria

Prebiotics and probiotics work together for optimal gut health. It's not enough to just dose on probiotics and think that the solution is in the pill. It's not all there.

Prebiotics are basically a type of indigestible fiber, also known as resistant starch, that we cannot digest and use for ourselves, but the good bacteria can. Inulin, oligosaccharides and fructo-oligosaccharides are included in this group of fibre. There are many foods rich in prebiotics including:

• Legumes, beans and peas
• Oats
• Raw bananas and plantains
• Asparagus
• Jerusalem artichokes
• Garlic and onion
• Berries
• Leeks
• Chicory
• Potato starch
• Green banana flour and
• Rice that has been cooked in coconut oil and cooled.

Once ingested, the prebiotics reach the large intestine undigested and are fermented by the microbes. They turn these fibres into a short-chain fatty acid known as butyrate , which has been shown to be anti-inflammatory and can help to prevent cancer growth.

Butyric acid in your colon is one of the by products of fermentation in your gut that is associated with centenarians.

Image source: http://suppversity.blogspot.com/2016/09/new-studies-on-gut-microbiome-and.html

4 Other Simple Steps To Maintaining Gut Health

1. In trying to correct digestive issues, meal quality and timing will clearly play a major role.

Your goal should be to make the food on your plate easy to digest. Remember that digestion begins in the mouth when you start chewing. The stomach gets involved later. Chewing is so important, yet highly disregarded in today’s rushed society. It is the start of the digestive system. Chewing breaks up the food into smaller particles, increasing surface area and helping more of the nutrients be absorbed. Furthermore, this study suggest slow eating (20 minutes) causes a lower glucose blood spike vs. fast eating (10 min). An obvious observation once it is pointed out!

Digestive enzymes are released when the food touches the tongue. Amylase, which is involved in the digestion of carbohydrates, and lingual lipase, involved in the digestion of fats, are examples of these enzymes.

Reductions in endogenous enzyme production and therefore food metabolism are noted from around age 27. More noticeable drops are seen from the 40 year mark. This is where supplementing with enzymes and HCL become powerful biohacks. We're aiming to take our digestive capacity back to what we had as teenagers and into our early twenties.

2. After eating, it takes about 20 minutes for our brain to register whether we are actually full or not.

Eating only until we are 70-80% full provides space in the stomach for the enzymes to properly move around and act to digest the food. This also avoids consumption of excess calories. Another reason to eat slowly. The longevity of Okinawans is partly attributed to this form of caloric restriction.

3. Stress triggers the ‘flight-or-fight’ response that occurs with increased cortisol and adrenaline

In this state, the body focuses on activities that it believes are more required at that moment including increasing the number of heartbeats and breathing rapidly. Digestion takes a backseat and slows down or even stops. Mindful eating is quickly becoming one of the most popular food trends and rightly so. When we slow down to appreciate our food using all our senses, are grateful for the food on our plate and eat without distractions, we help our body to relax before the meal. This allows our digestive system to work properly.

4. Many people suffer from food intolerances or sensitivities and don’t even realise it.

Symptoms of food sensitivities can manifest in 10 minutes or take as long as 72 hours. This is why it is important to keep a detailed food diary for 2 weeks. Your food diary should note what you ate for that particular meal, and how you felt afterwards. Physical symptoms you might note down include bloating, cramps, acne, change in stool, sinus infections, bags under the eyes, cravings for other foods, etc. Non-physical symptoms are also important. You might notice that you are more irritable, can’t sleep, have poor concentration, etc.

Some of the commonest foods that cause food sensitivities are wheat and other gluten-containing grains, dairy, eggs, corn, soy and nuts. If you do identify a possible food intolerance, you can try removing it from your diet for at least 2 weeks and see if the symptoms disappear. Removing refined sugars and processed foods from your diet is a quick way to start the process of identifying which foods you are sensitive to.

So, What’s The Take Home Message?

Now that you understand the significance of gut health to your overall wellness, cultivating healthy microflora should be a priority. The bacteria in our gut are living organisms and they are affected by the things we do or consume on a daily basis, just as we are. Things like the food we eat, whether our water contains chlorine, the presence of mercury in dental fillings, breathing in polluted air, exposure to radiation and taking medications are amongst the insults our body has to contend with. To sum up, take care of your bacteria and they will take care of you.

Author Bio:

Dr. Denise K. Hee

Mb BCh BAO, MRCS, CHC

Denise is a medical doctor and an intercollegiate member of the Royal College of Surgeons. She works as a health coach certified by the Institute of Integrative Nutrition and focuses on the clinical role of food in preventive medicine. She offers virtual coaching consultations on www.foodiedoc.com and applies nutrigenomics in her practice to identify the best foods for your body according to your DNA.

References:

1. Asge.org. (2016). ASGE: Human Digestive System . [online] Available at: http://www.asge.org/press/press.aspx?id=546 [Accessed 16 Oct. 2016].
2. World Gastroenterology, (2016). [online] Available at: http://www.worldgastroenterology.org/UserFiles/file/wdhd-2008-map-of-digestive-disorders.pdf [Accessed 16 Oct. 2016].
3. Australian Burden Of Disease Study, (2016). [online] Aihw.gov.au. Available at: http://www.aihw.gov.au/WorkArea/DownloadAsset.aspx?id=60129555176 [Accessed 16 Oct. 2016].
4. The Gut Foundation Australia. (2016). Treatment and prevention of gastrointestinal disease and conditions . [online] [Accessed 16 Oct. 2016].
5. Photograph Ian Cuming, A. (2016). How Many Cells Are in the Human Body—And How Many Microbes? . [online] News.nationalgeographic.com. Available at: http://news.nationalgeographic.com/2016/01/160111-microbiome-estimate-count-ratio-human-health-science/ [Accessed 16 Oct. 2016].
6. Hawrelak JA, Myers SP. The Causes of Intestinal Dysbiosis: A Review. Altern Med Rev 2004;9(2):180-197
7. MD, S. (2016). Dysbiosis Decoded: Symptoms, Why You Get It, and Link to Autoimmunity, Breast Cancer, Irritable Bowel Syndrome, Plus Other Common Conditions . [online] Sara Gottfried MD. Available at: http://www.saragottfriedmd.com/dysbiosis-symptoms-and-conditions/ [Accessed 16 Oct. 2016].
8. Carding, S., Verbeke, K., Vipond, D., Corfe, B. and Owen, L. (2015). Dysbiosis of the gut microbiota in disease. Microbial Ecology in Health & Disease , 26(0).
9. Sato, J., Kanazawa, A., Ikeda, F., Yoshihara, T., Goto, H., Abe, H., Komiya, K., Kawaguchi, M., Shimizu, T., Ogihara, T., Tamura, Y., Sakurai, Y., Yamamoto, R., Mita, T., Fujitani, Y., Fukuda, H., Nomoto, K., Takahashi, T., Asahara, T., Hirose, T., Nagata, S., Yamashiro, Y. and Watada, H. (2014). Gut Dysbiosis and Detection of “Live Gut Bacteria” in Blood of Japanese Patients With Type 2 Diabetes. Diabetes Care , 37(8), pp.2343-2350.
10. Campbell, A. (2014). Autoimmunity and the Gut. Autoimmune Diseases , 2014, pp.1-12.
11. Jiang, W., Wu, N., Wang, X., Chi, Y., Zhang, Y., Qiu, X., Hu, Y., Li, J. and Liu, Y. (2015). Dysbiosis gut microbiota associated with inflammation and impaired mucosal immune function in intestine of humans with non-alcoholic fatty liver disease. Sci. Rep. , 5, p.8096.
12. Logan, A. (2015). Dysbiotic drift: mental health, environmental grey space, and microbiota. J Physiol Anthropol , 34(1).
13. Leclercq, S., Matamoros, S., Cani, P., Neyrinck, A., Jamar, F., Stärkel, P., Windey, K., Tremaroli, V., Bäckhed, F., Verbeke, K., de Timary, P. and Delzenne, N. (2014). Intestinal permeability, gut-bacterial dysbiosis, and behavioral markers of alcohol-dependence severity. Proceedings of the National Academy of Sciences , 111(42), pp.E4485-E4493.
14. OptimOZ.com.au. (2016). The Gut and the Brain Work Together to Keep Us Healthy . [online] Available at: http://www.optimoz.com.au/blogs/news/81659079-the-gut-and-the-brain-work-together-to-keep-us-healthy [Accessed 16 Oct. 2016].
15. Hill, C., Guarner, F., Reid, G., Gibson, G., Merenstein, D., Pot, B., Morelli, L., Canani, R., Flint, H., Salminen, S., Calder, P. and Sanders, M. (2014). Expert consensus document: The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology , 11(8), pp.506-514.
16. Prescript-assist.com. (2016). Soil-Based Probiotics and Soil-Based Organisms | Prescript Assist . [online] Available at: http://www.prescript-assist.com/intestinal-health/soil-probiotics/ [Accessed 16 Oct. 2016].
17. Kris Gunnars, B. (2015). What are Probiotics and Why are They so Good For You? . [online] Authority Nutrition. Available at: https://authoritynutrition.com/probiotics-101/ [Accessed 16 Oct. 2016].
18. Allen, S., Martinez, E., Gregorio, G. and Dans, L. (2010). Probiotics for treating acute infectious diarrhoea. Cochrane Database of Systematic Reviews .
19. Hempel S, e. (2016). Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. - PubMed - NCBI . [online] Ncbi.nlm.nih.gov. Available at: https://www.ncbi.nlm.nih.gov/pubmed/22570464 [Accessed 16 Oct. 2016].
20. Edelstein, C. and Edelstein, C. (2015). Fecal transplant pills: Large-scale production begins following successful dosing study . [online] OpenBiome. Available at: http://www.openbiome.org/press-releases/2015/10/28/fecal-transplant-pills-large-scale-production-begins-following-successful-dosing-study [Accessed 16 Oct. 2016].
21. Consumerlab.com. (2016). Review of Probiotic Supplements and Kefirs . [online] Available at: https://www.consumerlab.com/reviews/Probiotic_Supplements_and_Kefir/probiotics/ [Accessed 16 Oct. 2016].
22. White, S. (2014). How to Choose a Good Probiotic . [online] LIVESTRONG.COM. Available at: http://www.livestrong.com/article/383282-how-to-choose-a-good-probiotic/ [Accessed 16 Oct. 2016].
23. Sarah Lewis, R. (2016). Probiotics and Prebiotics: What's the Difference? . [online] Authority Nutrition. Available at: https://authoritynutrition.com/probiotics-and-prebiotics/ [Accessed 16 Oct. 2016].
24. Flora, T. (2016). The Role of Prebiotics in Maintaining Healthy Gut Flora . [online] Dr. David Williams. Available at: http://www.drdavidwilliams.com/the-role-of-prebiotics-in-maintaining-healthy-gut-flora/ [Accessed 16 Oct. 2016].
25. Slavin, J. (2013). Fiber and Prebiotics: Mechanisms and Health Benefits. Nutrients , 5(4), pp.1417-1435.
26. Mercola.com. (2016). 7 Reasons Why Chewing Your Food Is Important . [online] Available at: http://articles.mercola.com/sites/articles/archive/2013/07/31/chewing-foods.aspx [Accessed 16 Oct. 2016].
27. Publications, H. (2011). Mindful eating - Harvard Health . [online] Harvard Health. Available at: http://www.health.harvard.edu/staying-healthy/mindful-eating [Accessed 16 Oct. 2016].
28. Thecenterformindfuleating.org. (2016). The Center for Mindful Eating - Principles . [online] Available at: http://thecenterformindfuleating.org/principles [Accessed 16 Oct. 2016].
29. Whfoods.com. (2016). Food Sensitivities . [online] Available at: http://www.whfoods.com/genpage.php?tname=faq&dbid=30 [Accessed 16 Oct. 2016].
30. Allergyuk.org. (2016). Identifying your Food Intolerances - Allergy UK . [online] Available at: https://www.allergyuk.org/food-intolerance/identifying-your-food-intolerances [Accessed 16 Oct. 2016].