Meet your Microbiome

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What is the microbiome?

The human microbiome is comprised of all the microorganisms that live on or inside us.

And here is why you should care about it:

The microbiome controls your weight!

Scientists found that mice who received a microbiome transplantation from obese people became fat even though they ate the same diet as their lean siblings [1, 2].

Transfer of microbes from either the obese twin leads to strong fat gain in mice [2]

Transfer of microbes from either the obese twin leads to strong fat gain in mice [2]

Imagine following scenario: Two genetically identical people decide to lose weight by going on a diet. The only difference between the two twins is that one of them was treated for 10 days with an antibiotic due to an infection, which kills many of the bacteria living in the gut. Will the twins lose weight equally?
Based on the evidence found by various studies, probably not [3, 4, 5, 6].

The functions and duties of the microbiome do not stop there!- It also helps regulate the immune system, which can help protect your brain.
There are case studies that have shown the progression of the auto-immune disease, Multiple Sclerosis, can be slowed by a change in nutrition and even reversed by a reset of the microbiome [7].


The Microbiome regulates the immune system

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In fact, there is an array of studies out there demonstrating the microbiome’s role in regulating the human immune system - And in the end, it is the immune system which is responsible for controlling most diseases [8, 9, 10, 11].

Here is alist of diseases that are impacted by the microbiome’s effect on the immune system:

  • Inflammatory diseaes [9, 12]
  • Constipation and diarrhea [13]
  • Obesity [1,2]
  • Allergies [14]
  • Heart Diseases [10, 15]
  • Diabetes [16, 17]
  • Colds and infections [21]

The Gut-Brain Axis



But it doesn’t stop here: our brains are also affected by our microbiome.
This so-called Gut-brain axis is a connection we have only started to understand. For most people, the influence of our microbes on our brains sounds like science fiction but more and more research shows us how our microbiome influences our mood, behavior, and even memory. Because of this many brain disorders are now analyzed within the context of the microbiome [7, 19, 20, 21].

Here is one example of how the microbiome can influence our behavior.
In one of my favorite studies, researchers from Canada deleted the microbiome from brave mice and introduced the microbiome of shy mice into them. Suddenly, the previously brave mice became less adventurous and much more reluctant to take a risk [19].

A diet high in fiber (HFD) increases the bone density (left) and reduces the number of osteclasts (right) [22]

A diet high in fiber (HFD) increases the bone density (left) and reduces the number of osteclasts (right) [22]

Frontline research from 2018 showed that the microbiome also had an effect on bone density. The researchers found that mice that ate more fiber have stronger bones than mice that ate less fiber [22].



Microbes produce vitamins

In Herbivorous animals, gut microbes provide a direct source of cobalamin [27]

In Herbivorous animals, gut microbes provide a direct source of cobalamin [27]

Another important feature of the microbiome is that our bacteria produce many vitamins including vitamin B1, B2, and B12 as well as Vitamin K, Biotin and Folate [23, 27].
The use of polyphenols, a group of anti-oxidants, that have been shown to possess anti-aging and anti-inflammatory properties and which are found in green and black teas, coffee, berries or red wine, also require a healthy microbiome [24, 25]. Researchers have shown that many polyphenols are basically of no use to the human body, as their bio-availability and activity depends on having the right bacteria in our gut that can convert the polyphenols to a form that can be used by human cells [26].

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  • The human DNA is 99.9% similar between individuals, but there are huge differences in the composition of the microbiome between different people. This might explain while somebody becomes overweight or develops a disease but somebody with the same DNA stays perfectly healthy.
  • With 100 trillion cells, the microbes in our guts outnumber our own cells.
  • These cells are extremely  diverse with more than 10,000 different species.
  • The microbiome provide a metabolic capacity 100 times greater than the liver.
  • We humans only possess 22,000 different genes, there are at least 3.3 million microbial genes.


"All disease begins in the gut"
- Hippocrates



  1. Turnbaugh et al., A core gut microbiome in obese and lean twins, Nature, 2009
  2. Ridaura et al., Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice, Science, 2013
  3. Angelakis et al., Abnormal weight gain and gut microbiota modifications are side effects of long-term doxycycline and hydoxychlroquine treament, American Society for Microbiology, 2014
  4. Scott et al., Administration of Antibiotics to Children Before Age 2 Years Increases Risk for Childhood Obesity, Gastroenterology. 2016
  6. Cho et al., Antibiotics in early life alter the murine colonic microbiome and adiposity, Nature, 2012
  7. Dr. David Perlmutter - Brain Maker
  8. Belkaid and Hand, Role of the Microbiota in Immunity and inflammation, Cell 2014
  9. Vaghef-Mehrabany et al., Probiotic supplementation improves inflammatory status in patients with rheumatoid arthritis, Nutrition 2014
  10. Wang et al., Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease, Nature, 2011
  11. Säemann et al., Anti-inflammatory effects of sodium butyrate on human monocytes: potent inhibition of IL-12 and up-regulation of IL-10 production, FASEB Journal, 2000
  12. Oliva et al., Randomised clinical trial: the effectiveness of Lactobacillus reuteri ATCC 55730 rectal enema in children with active distal ulcerative colitis, AP&T, 2012
  13. Cao et al., Dysbiosis contributes to chronic constipation development via regulation of serotonin transporter in the intestine, Sci Rep, 2017
  14. Huang and Boushey, The microbiome in Asthma, J Allergy Clin Immunol, 2015
  15. Koeth et al., Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis, Nat Med, 2013
  16. Cox et al., Increased intestinal permeability as a risk factor for type 2 diabetes, Diabetes Metab, 2017
  17. Jayashree et al., Increased circulatory levels of lipopolysaccharide (LPS) and zonulin signify novel biomarkers of proinflammation in patients with type 2 diabetes, Mol Cell Biochem, 2014
  18. Kamada et al., Control of pathogens and pathobionts by the gut microbiota, Nat Immunol, 2013
  19. Bercik et al., The Intestinal Microbiota Affect Central Levels of Brain-Derived Neurotropic Factor and Behavior in Mice, Gastroenterology, 2011
  20. O'Mahony et al., Serotonin, tryptophan metabolism and the brain-gut-microbiome axis, Behavioural Brain Research, 2015
  21. Desbonnet et al., The probiotic Bifidobacteria infantis: An assessment of potential antidepressant properties in the rat, Journal of psychiatric research, 2009
  22. Lucas et al., Short-chain fatty acids regulate systemic bone mass and protect from pathological bone loss, Nat Commun, 2018
  23. Biesalski, Nutrition meets the microbiome: micronutrients and the microbiota, Ann. N.Y. Acad. Sci, 2016
  24. Vieira et al., Effect of dietary phenolic compounds on apoptosis of human cultured endothelial cells induced by oxidized LDL, British Journal of Pharmacology, 1998
  25. Muldoon and Kritchevsky, Flavonoids and heart disease, BMJ, 1996
  26. Yuan and Liu, Metabolism of dietary soy isoflavones to equol by human intestinal microflora – implications for health, Mol Nutr Food Res, 2007
  27. Degnan et al., Vitamin B12 as a modulator of gut microbial ecology, Cell Metab, 2014