The microbiome is a collection of bacteria residing primarily in our digestive tract that plays a huge role in health promotion and disease prevention. We know that diseases such as obesity (1, 2), IBS (3, 4), diabetes (5, 6), asthma (7), eczema (8), and more are linked to an altered microbiome (a state that is known as dysbiosis), but how can we define a healthy microbiome? 

The profiles with alterations that are associated with diseases can be considered unhealthy microbiomes, right? Actually, we don’t know if the disturbances or changes in gut microbes that are associated with diseases are part of the cause or are factors contributing to the disease, or if these changes are simply effects of the disease pathway that is already ongoing (9). 

The studies that show links between disease and the microbiome find a common quality among the individuals with the disease being studied that differs from healthy controls. The challenge here is that healthy individuals being used as a comparison group differ immensely. They may have gut microbiomes that look completely different, yet all of the individuals can be considered “healthy.”  

There is a theory that grouping individuals into 3-4 enterotypes, or defined microbiome profiles, is one way to identify healthy versus less healthy microbiome makeups (10). Other researchers propose that a gradient approach where individuals fall somewhere on a scale of microbiome makeups is a better way to identify what qualities can be linked with health (11). While these strategies are useful for research and furthering our knowledge about the microbiome, not one of these microbiome enterotypes or one part of a microbiome gradient scale has been linked to being “healthier” or more ideal than the others (12).  

One quality we do know is associated with a healthy microbiome is the diversity of bacteria residing in the gut (13). It also seems the lack of diversity or depletion of microbial species could be predictive of increased disease risk (13). What factors are associated with this depletion of diversity? Low levels of physical activity and a diet high in salt and refined carbs that is also low in fiber (14, 15). 

The punchline here is that we still don’t know exactly what a healthy microbiome looks like, and it most likely looks different for everyone (16). We all have extremely different microbial makeups, which are more individual to us than our genes (17). The beauty of personalized nutrition is that we can better understand your biological responses to foods and diets and identify ways we can optimize your microbiome by offering precise recommendations that are right for you. 

Sources:

1. Turnbaugh PJ, Ley RE, Mahowald MA, et al. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027-1031. 
2. Bäckhed F, Manchester JK, Semenkovich CF, et al. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. PNAS. 2007;104(3):979-984.  
3. Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–11.   
4. Sartor RB. Mechanisms of disease: Pathogenesis of Crohn’s disease and ulcerative colitis. Nat Clin Pract Gastroenterol Hepatol. 2006;3:390–407.  
5. Larsen N, Vogensen FK, van den Berg FW, et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE. 2010;5:e9085. 
6. Siljander H, Honkanen J, Knip M. Microbiome and type 1 diabetes. EBioMedicine. 2019;46:512-521.  
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8. Kong HH, Andersson B, Clavel T, et al. Performing skin microbiome research: A method to the madness. J Invest Dermatol. 2017;137(3)561-568.  
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10. Arumugam, M., Raes, J., Pelletier, E. et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174–180.  
11. Koren O, Knights D, Gonzalez A, Waldron L, Segata N, et al. A Guide to Enterotypes across the Human Body: Meta-Analysis of Microbial Community Structures in Human Microbiome Datasets. PLOS Computational Biology. 2013;9(1):e1002863.  
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14. Fedacko J, Takahashi T, Singh RB, Pella D, Chibisov S, Hristova K, Pella D, Elkilany GN, Tomar RS, Juneja LR. Globalization of diets and risk of noncommunicable diseases, In: Watson R, Singh R, Takahashi T , editors The role of functional food security in global health, Associated Press, New York City. 2019. p. 87–107. 
15. Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, et al. Links between environment, diet, and the hunter-gatherer microbiome. Gut Microbes.2019;10(2):216–27. 
16. McBurney MI, Davis C, Fraser CM, et al.  Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions. The Journal of Nutrition. 2019;149(11):1882-1895. 
17. Ursell, LK, et al. Defining the human microbiome. Nutr Rev. 2012;70(Suppl 1):S38–S44.