The Gut Microbiome: This Changes Everything

Today’s understanding of the gut microbiome has profound implications on our entire body and mind.

gut microbiome

A study published recently in Nature investigated the importance of the gut microbiome in contributing to insulin resistance and therefore increasing the risk of type 2 diabetes.

© T.L. Furrer |

Something astonishing has been happening in medicine that is completely changing how we view health and disease. Today’s understanding of the microscopic life inside our gut—microbiome, as it’s known—has profound implications for managing not only our digestive health, but also that of the entire body and mind.[4]

The microbiome is the richly diverse community of bacteria that each and every one of us carries in and on our bodies. Your microbiome is unique to you. It contains 10 times more cells and 100 times more genes than you have in your whole body, and it accounts for three to six pounds of your total weight.

Your microbiome doesn’t just sit there, doing nothing. It performs many vital jobs in the body, talks to the brain, and even influences your behavior.[2,3] In fact, the microbiome is essentially a newly discovered organ in the human body.

Perhaps most important is the fact that you can change your microbiome, and thus your physical and mental health, through diet, lifestyle, and natural medicine.

Diseases Linked to Alterations in the Microbiome

When your healthy, balanced microbiome gets significantly disrupted or impaired, you have what is referred to as dysbiosis. Although there is still no standard ­definition of this term, a number of seemingly random diseases are directly linked to dysbiosis. For example, alterations in the microbiome are clearly associated with:

  • Irritable bowel syndrome (IBS)[8]
  • Asthma[9]
  • Food allergies[10]
  • Inflammatory bowel disease (IBD), ulcerative colitis, Crohn’s disease[11]
  • Obesity[1]
  • Type 2 diabetes[12]
  • Metabolic syndrome[13]
  • Atherosclerosis[14]
  • Liver diseases: non-alcoholic fatty liver disease (NAFLD), alcoholic liver disease, primary sclerosing cholangitis (PSC), primary biliary cirrhosis (PBC), autoimmune hepatitis[1]
  • Autism[15]
  • Celiac disease[16]
  • Parkinson’s disease[17]
  • Cancer[18]
  • Depression[19]
  • Schizophrenia[20]
  • Autoimmune diseases[21]

The clear implication for anyone ­suffering from one of these disorders (and probably from many other illnesses) is to carefully examine the possibility of poor gut health being an unsuspected underlying cause. This discovery could very well lead to the corrective action needed to restore health: optimizing the gut microbiome. We’ll discuss just how to do that in this article.

Examining the Gut Microbiome

Because of very recent scientific developments in genetics, we are finally able to identify and quantify the microorganisms that live within our gastrointestinal systems. New gene-based tests have determined that there are more than 1,000 species of microorganisms and that 150 to 170 predominate in a given person.

We’re beginning to understand what makes up a healthy gut microbiome in terms of these species, their numbers, and their relationships to one another. In general, a high diversity and total number of gut microorganisms is associated with relatively good health, while low diversity has been associated with states of disease or chronic dysfunction. Some species of microorganisms are very important because of their specific, unique functions. Even those organisms that are typically present in smaller numbers in the healthy gut microbiome have considerable potential to influence our health.[22,23]

How to Have Your Microbiome Tested

To get detailed information on your own microbiome, you can order a test kit yourself through the company uBiome or the crowd-source-funded American Gut. Or your doctor can order testing through functional/integrative laboratories such as Genova Diagnostics. These tests allow you to compare the microbes in your gut to those in the guts of other people. They can provide information about the diversity and abundance of microbes, but the tests do not diagnose disease. Monitoring your microbiome over time also provides insight into the impact of medications, supplements, diet, and lifestyle interventions on your current and future health.

Some labs also test for important compounds that your gut microorganisms produce. For instance, many labs measure short-chain fatty acids (SCFAs), which are created when certain gut microorganisms ferment fiber for fuel. SCFAs are the primary form of nourishment for cells of the colon wall and are thus crucial for gut health.

How to Eat to Improve the Health of Your Gut Microbiome

Dietary changes are the primary treatment for optimizing your microbiome. The Western dietary pattern, characterized as high in fat, sugar, red meat, and processed/refined foods, has been associated in numerous studies with a microbiome more geared toward obesity, inflammation, and other less desirable consequences.

In contrast, diets higher in fiber, fruits, and vegetables have been associated with more favorable microbial communities.

  • Eat more fiber, fruits and vegetables/less sugar and processed foods. The way to most profoundly alter your microbiome, therefore, appears to be to lower your intake of refined, processed, sugar- and fat-laden foods while simultaneously increasing your intake of fruits and vegetables. ­Indigestible carbohydrates (fiber) are the main food for gut microbes. All plant foods—fruits, vegetables, nuts, seeds, legumes, and whole grains—contain beneficial fiber. Always introduce high-fiber foods gradually to avoid exacerbation of GI symptoms.
  • Eat more high-polyphenol foods. Polyphenols improve the gut microbiota by increasing the relative abundance of friendly species such as bifidobacteria and lactobacilli.[1] The gut microbiota, in turn, plays a critical role in transforming polyphenols into absorbable, biologically active species that perform health-promoting functions.[1] Include plenty of polyphenol-rich berries, cocoa, tea, and red wine in your diet.
  • Eat seaweed and fermented foods. Seaweeds, such as nori, can significantly alter the gut microbiota.5 ­Fermented foods, such as kefir, sauerkraut, and kimchi, can increase the beneficial lactic acid bacteria in the gut and should also be eaten regularly.[23]

Supplements That Benefit the Gut

To promote and sustain beneficial gut microbes, consider taking probiotics (especially Lactobacillus and Bifido­bacteria). Probiotics are all unique living organisms and their health-promoting traits may be strain-specific. While the research is in its infancy, some specific strains have been studied and found to be effective for certain populations:24

For IBS, VSL#3 (an 8-strain combination of Lactobacillus, Bifidobacterium and Streptococcus) and Bifido­bacterium infantis 35624 (used in Proctor and Gamble’s Align), have both been found to be beneficial.

  • For cholesterol lowering, Lacto­bacillus reuteri NCIMB 30242 (sold as Cardio­viva) appears effective.
  • For obesity, 100 billion cells of Lacto­bacillus gasseri SBT2055 (specific strain not available in US) reduced visceral and abdominal fat.
  • For colds and acute respiratory infections, Lactobacillus plantarum HEAL9 and Lactobacillus paracasei 8700:2 (found in Metagenics Ultra Flora Immune Booster) has been found effective.
  • For anxiety and depression, the combination of Bifidobacterium longum R0175 and Lactobacillus helveticus R0052, sold by Jamieson as Probiotic Sticks, is beneficial.


Prebiotics are a specific type of dietary fiber that increases the relative abundance of beneficial bacteria, such as bifidobacteria, or certain bacteria that produce SCFAs such as butyrate. In animal studies, supplementation with prebiotics prevents or treats many diseases, including inflammatory bowel disease, IBS, colon cancer, obesity, type 2 diabetes, and cardiovascular disease.[1]

The most-studied prebiotic supplements include:

  • Psyllium
  • Oat bran
  • Oligofructose
  • Fructooligosaccharide (FOS)
  • Inulin
  • Beta-glucan
  • Arabinogalactan

Take as directed on the label, starting with a low dose and slowly working up to the full recommended dose.


Studies have linked the microbiome to human mood and behavior, as well as gut health, metabolic disorders, and many other chronic diseases.

All people can improve their microbiome by eating a whole-foods diet that includes plenty of prebiotics and probiotics.

For a more individualized approach, your doctor can order testing for you or you can self test through uBiome or American Gut.

If you self test, be sure to share your results with a naturopathic or functional medicine practitioner who is experienced in interpreting the tests and can help lead to a diagnosis and/or provide information on diet, lifestyle, supplements, and other natural strategies that are targeted specifically to you.

1. Gut. 2015 Sep 2. pii: gutjnl-2015-309990.
2. Clin Sci (Lond). 2015 Dec;129(12):1083-96.
3. Int J Neuropsychopharmacol. 2015 Oct 4. pii: pyv114.
4. The Naturopathic Approach to Digestive Disorders. AANP. Nov 1, 2012.
5. World J Gastroenterol. 2015 Aug 7; 21(29): 8787–8803.
6. Nutrients. 2015 Apr; 7(4): 2839–2849.
7. Eur J Nutr. 2015; 54(3): 325–341.
8. J Clin Gastroenterol. 2015 Nov-Dec;49 Suppl 1:S56-9.
9. J Allergy Clin Immunol. 2015 Jan;135(1):25-30.
10. Pediatr Clin North Am. 2015 Dec;62(6):1479-92.
11. Diabetes Metab J. 2015 Jun; 39(3): 198–203.
12. Nutr Clin Pract. 2015 Dec;30(6):760-79.
13. Front Physiol. 2015; 6: 341.
14. Nat Commun. 2012;3:1245.
15. Drug Metab Dispos. 2015 Oct;43(10):1557-71.
16. Nutrients. 2015;7(8):6900-6923.
17. Mov Disord. 2015 Sep;30(10):1351-60.
18. Rev Esp Enferm Dig. 2015 Nov;107(11).
19. Clin Psychopharmacol Neurosci. 2015 Dec 31;13(3):239-244.
20. Prog Neuropsychopharmacol Biol Psychiatry. 2015 Jan 2;56:155-60.
21. Gut. 2015 Feb;64(2):332-41.
22. Appl Environ Microbiol. 2015 Jun; 81(11): 3655–3662.
23. Microb Ecol Health Dis. 2015; 26: 10.3402/mehd.v26.26164.
24. Product Review: Probiotics. Updated November 7, 2015.

Originally published in February 2016 and updated.

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