Why Diversity is the Key to a Happy + Healthy Microbiome

Why Diversity is the Key to a Happy + Healthy Microbiome

30 Different Plant-Based Foods per week

The importance of including plant-based fiber and carbohydrates in a healthy diet is not a new concept. However, new studies suggest that dietary intake of plant foods can have significant benefits to your gut microbiome. The American Gut Project is an active research effort that has studied the gut flora composition of over 10,000 average citizens with the goal of examining the potential influences of diet, lifestyle, and disease on microbial diversity. The project found a direct correlation between the number of different plants incorporated into a person's diet and the number of different bacteria types present in their gut. Participants who consumed 30 or more different types of plant foods per week had significantly more diverse microbiomes than those that consumed fewer than 10 types of plants, regardless of adherence to varied specialized diets.1

“Participants who consumed 30 or more different types of plant foods per week had significantly more diverse microbiomes”

How do Plant-Based Foods Affect our Gut Bacteria?

Plants, in the form of fruits, vegetables, nuts, legumes, herbs, and spices provide us with two important nutritive components: carbohydrates and dietary fibers. While carbohydrates are digested by human enzymes in the small intestine, dietary fibers pass through to the colon where Carbohydrate-Activated Enzymes (CAZymes) break down these fibers into fermentable monosaccharides. The major end products of fermentation are metabolites known as the short-chain fatty acids (SCFAs) acetate, butyrate, and propionate. SCFAs are rapidly absorbed by intestinal epithelial cells where they are intrinsic to several cellular and regulatory processes.2 Microbes play a key part in every step along the way.

The human genome only provides us with 17 different digestive enzymes to break down carbohydrate nutrients. The microbes in our gut make up for our biological deficiency by encoding enzymes - CAZymes - to metabolize our complex repertoire of dietary polysaccharides and glycosides.3 In other words, gut microbial diversity ensures its host a wide range of metabolic abilities, and maintaining diversity protects the functionality of metabolic pathways as the microbiome adjusts to variations of dietary intake and environmental stressors.

Microbiota-Accessible Carbohydrates (MACs): A Different type of Carbohydrate

Soluble fiber is defined as an edible carbohydrate polymer with three or more monomeric units that are resistant to human digestive enzymes. They are neither hydrolyzed nor absorbed in the small intestine; instead, these microbiota-accessible carbohydrates (MACs) end up in the colon where they provide substrates for microbial growth and specific population regulation. A diet low in MACs can lead to the depletion of certain bacteria taxa and has been linked to the development of chronic inflammatory diseases such as intestinal bowel disease, colorectal cancer, allergies, and autoimmune diseases.4 Furthermore, when amino acids are the main substrate over MACs for bacterial fermentation, the end products are pro-inflammatory metabolites such as branched-chain fatty acids (ammonia and amines), sulfides, and indolic compounds. An overproduction of these molecules has been linked to the development of various chronic diseases.5

Soluble non-starch polysaccharides (NSPs) are a type of plant-based MAC that possess many advantageous properties including water dispersibility, bulking factors, fermentability into SCFAs, and a viscosity effect. The viscous nature of NSPs acts to coat the intestinal epithelial cells with a gel-like substance, decreasing permeability and delaying glucose absorption; therefore lowering inflammatory reactions and oxidative stress.6

Short-Chain Fatty Acids (SCFAs): The 3:1:1 Ratio

Acetate, butyrate, and propionate are ideally produced in a 3:1:1 ratio within the gut. The abundance of SCFAs in the gut signifies a healthy population of ideal bacterial fermenters. SCFAs also directly influence host metabolism, modulate the immune system, and direct cell proliferation. Specifically, butyrate plays an important role in brain function, has anti-cancer properties, and works to maintain the intestinal barrier. Propionate and acetate regulate immune response and stimulate the secretion of appetite-regulating hormones. Furthermore, the production of SCFAs enhances mucus and anti-microbial peptide production and increases the expression of tight junction proteins within the gut.7

Diversity in Diet = Diversity in Microbes

Long-term lifestyle and patterned dietary habits of consuming varied sources of plant-derived protein and fiber are associated with higher microbial diversity, colonization resistance, immune homeostasis, a healthy mucus layer and gut barrier, and higher SCFA levels. Participants in the American Gut Project that consumed more than 30 types of vegetables per week specifically had an abundance of putative SCFA fermenting bacterial species, and because different bacteria have different carbohydrate-binding molecules and encode different metabolizing enzymes, dietary intake of various fibers and microbiota accessible carbohydrates likely supports a resilient and diverse microbiome.8

“Long-term lifestyle and patterned dietary habits of consuming varied sources of plant-derived protein and fiber are associated with higher microbial diversity, colonization resistance, immune homeostasis, a healthy mucus layer and gut barrier, and higher SCFA levels.”

Luckily, incorporating 30 different plant-based foods per week into your diet is easier than it seems. Meal planning and thoughtful shopping practices can alleviate guesswork and ensure that you are meeting your weekly plant-based quota.9 Single pot recipes such as stews, soups, and baked casseroles are a great way to get multiple veggies in one shot, preparation and clean-up are easier, and these types of recipes also lend well to preparing ahead of time and freezing. Stir-fry is a great way to combine and utilize on-hand leftovers in a quick and tasty meal ready in minutes. Learning basic traditional cooking techniques can make you more versatile in the kitchen and give you the ability to use those weird veggies in your co-op delivery box!

Multi-ingredient, one-hit wonders are also achievable at breakfast time in the form of smoothies and warm cereal grain bowls filled with nuts, seeds, and dried fruits. Remember that spices and herbs also count - another excuse to explore flavorful cooking techniques and make those meals colorful and garnished.

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  1. McDonald D, Hyde E, Debelius JW, et al. American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems. 2018;3(3). doi:10.1128/mSystems.00031-18
  2. Mills S, Stanton C, Lane JA, Smith GJ, Ross RP. Precision Nutrition and the Microbiome, Part I: Current State of the Science. Nutrients. 2019;11(4). doi:10.3390/nu11040923
  3. Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13(4):260-270. doi:10.1038/nrg3182
  4. Makki K, Deehan EC, Walter J, Bäckhed F. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe. 2018;23(6):705-715. doi:10.1016/j.chom.2018.05.012
  5. Zhao L, Zhang F, Ding X, et al. Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes. Science. 2018;359(6380):1151-1156. doi:10.1126/science.aao5774
  6. Node K, Inoue T. Postprandial hyperglycemia as an etiological factor in vascular failure. Cardiovasc Diabetol. 2009;8:23. doi:10.1186/1475-2840-8-23
  7. Feng Y, Wang Y, Wang P, Huang Y, Wang F. Short-Chain Fatty Acids Manifest Stimulative and Protective Effects on Intestinal Barrier Function Through the Inhibition of NLRP3 Inflammasome and Autophagy. Cell Physiol Biochem. 2018;49(1):190-205. doi:10.1159/000492853
  8. Daïen CI, Pinget GV, Tan JK, Macia L. Detrimental Impact of Microbiota-Accessible Carbohydrate-Deprived Diet on Gut and Immune Homeostasis: An Overview. Front Immunol. 2017;8:548. Published 2017 May 12. doi:10.3389/fimmu.2017.00548
  9. Crawford D, Ball K, Mishra G, Salmon J, Timperio A. Which food-related behaviours are associated with healthier intakes of fruits and vegetables among women? Public Health Nutr. 2007;10(3):256-265. doi:10.1017/S1368980007246798