By: Mary Schroeder, ND, LAc

If you’re struggling with digestion and searching for answers, it may be time to investigate a vast world in your belly: the gut microbiome. 

Over the past decade, an explosion of research into this crucial ecosystem has illuminated key elements of healthy microbial communities as well as ways we can shape them with diet and lifestyle. In this article, we will discuss recent findings about the gut microbiome, and lay out ways in which you can cultivate your own resident microbes. 

The gut microbiome is home to 10¹⁴ resident microorganisms, including bacteria, viruses, fungi and protozoa.¹ The majority of these organisms reside in the large intestine, though smaller, niche communities exist in the mouth, stomach, and small intestine.  As a whole, these organisms weigh about as much as a human heart. 

From digestive health to hormone regulation, the impacts of these microbial communities are manifold. Microbiome degradation is associated with a host of chronic conditions, including allergies, autoimmunity, gastrointestinal disorders, cardiovascular disease, anxiety, and depression. Because of its critical importance to our physiology, many argue that the gut microbiome constitutes another human organ, an extension of ourselves. 

Symbiosis

Over time, the gut microbiome has developed a mutually dependent relationship with its human host. In exchange for food, our resident microbes help harvest many of the nutrients we need to thrive. They also provide protection from infection and help regulate our immune, hormone and nervous systems. 

Like plants that use bacteria and fungi to fix essential elements, humans depend on our microbial residents to glean certain nutrients. After food makes it through the small intestine, where the majority of our nutrients are absorbed, it is shuttled to the large intestine. There, gut microbes go to town on undigested plant fibers and produce short-chained fatty acids, which are the primary food source for the cells that line the large intestine. By maintaining a healthy intestinal barrier, these molecular morsels help quell local and systemic immune responses and reduce the risk of colon cancer.² Besides short-chained fatty acids, gut microbes also produce significant quantities of b-vitamins, vitamin K, and essential amino acids.^1,2 

We also depend on our microbes for protection. Like trees of an old growth forest that shade out competitors with their canopy, a healthy, diverse microbiome holds court in the digestive tract and prevents colonization by potentially deadly intestinal infections. It is when we clear-cut this forest that we are most vulnerable to invaders. Colostridium difficile, for example, is a type of deadly intestinal infection that is most common after multiple rounds of broad-spectrum antibiotics. In this way, a robust, diverse microbiome is a safeguard against infectious disease. 

Early Development

Despite its obvious importance, the composition of the ideal microbiome remains unclear. What we do know is that, as in most ecosystems, diversity is one element that makes some gut microbiomes more resilient than others.³ We also know that our microbial communities develops in early childhood, and key factors that shape the ecosystem can have major impacts on our health long term.⁴ 

Our first dose of probiotics comes in the birth canal, via vaginal microbes.⁴ Breast milk is another important source of both probiotics and prebiotics; it contains the pioneer species of the gut ecosystem, Bifidobacterium infantis, in addition to specific type of carbohydrate, oligosaccharides, that is their primary food source. Disruptions to these first stages of microbiome development may have significant consequences later in life, and there is some evidence that suggests that swabbing newborns with fluids from their mother’s birth canal may mitigate some of the loss of microbial diversity from c-section deliveries.  

Our exposure to microbes at an early age may also have a lasting influence on the complexity of our gut microbiomes.^3,4 Interaction with dogs, for example, is one way to diversify a child’s microbes. Some research also suggests that growing up on a farm may yield a richer gut microbiome that reduces the risk of inflammatory respiratory diseases relative to children raised in more urban environments. On the flip side, a more sanitized environment and less interaction with soil may hinder the development of a robust intestinal ecosystem. 

Cultivating the Microbiome

Once we reach adulthood, our microbial communities remain relatively static. At this point, it is important to maintain the diversity and integrity of the ecosystem. Microbiome cultivation is one of the key ways we can optimize our health over time.  Here are some of the ways we can support our microbes in daily life:

1. Avoid antibiotics when possible.  Antibiotics can profoundly impact our gut microbiome.^3,4 Due to increasing concerns about their impacts on the microbiome and about antimicrobial resistance, most doctors are prescribing antibiotics more conservatively than in previous decades. However, there is a time and place for these medicines. When you do need antibiotics for a bacterial infection, it is important to…
2. Eat your probiotics. Probiotics, whether in capsule or through fermented foods, are especially important when you have a disturbance in your gut microbes. Encapsulated probiotic strains such as Lactobacillus, Bifidobacterium, Saccharomyces, Streptococcus, Enterococcus, and/or Bacillus can be used to treat antibiotic-associated diarrhea.⁵ Rather than repopulating the intestines, these microbes can act as a “cover crop” of sorts; they act as space holders and prevent overgrowth of opportunistic and harmful bacteria. Fermented milk products, such as yogurt and kefir, and fermentic vegetables, like kimchi and sauerkraut, are significant sources of Lactobacillus spp. and are great options for daily doses of probiotics. 
3. Eat organic. Another source of antibiotic exposure is through non-organic dairy, meat and eggs.³ Farmers use antibiotics in animals to prevent the spread of disease in crowded conditions, and small antibiotic residues can end up on our breakfast plate. Certain herbicides and insecticides used in vegetable production are also associated with microbiome disruptions.³ So, aiming for organic or local animal products and produce that don’t use antibiotics is one way to reduce your exposure. 
4. Avoid plastics when possible. Phthalates, a type of chemical found in many plastics, cosmetics and synthetic fragrances, can also contribute to dysbiosis.³ While it is nearly impossible to avoid these substances in daily life, avoiding heating your food in plastic and opting for natural cosmetics is one way to support your microbes. 
5. Eat fresh, unprocessed food. Preservatives are put in foods to kill microbes. While this is incredibly useful in preventing contamination, it can exact a toll on our microbes over time. Look out for preservatives like sorbic acid, benzoic acid, and proprionic acid on labels and avoid them when possible.³ Unprocessed vegetables are also a great source of fiber, the ultimate food for your microbes. 
6. Fiber, fiber, fiber. Did I mention fiber? As we discussed before, tough plant fibers are essential for microbial and intestinal health.^1,2 Dubbed “prebiotics,” these indigestible fibers are a crucial source of food for bacteria. Sources include soy beans, whole oats, flax seed, green leafy vegetables and apples.² Inulin is one major prebiotic that is found in high amounts in dandelion greens, jeruselum artichokes and chicory root. 
7. Embrace the rainbow. In addition to their fiber content, colorful fruits and vegetables contain flavonoids and polyphenols.^1,2 These plant compounds have been shown to favorably influence microbial communities and you can find them in significant amounts in dark chocolate, berries, currants, cherries, red wine, coffee, tea, and certain vegetables like spinach and artichokes. 

The implications of your microbiome and gut health are far-reaching. At Prosper, we have a variety of tools for assessing your microbiome and we consider it a key component of holistic health. If you are struggling with persistent gas and bloating, constipation or diarrhea, or even anxiety and depression, it may be time to dig deeper and discover the root cause. Reach out for a consultation today. We are here to help.  

References

1. Singh, R. K., Chang, H. W., Yan, D., Lee, K. M., Ucmak, D., Wong, K., Abrouk, M., Farahnik, B., Nakamura, M., Zhu, T. H., Bhutani, T., & Liao, W. (2017). Influence of diet on the gut microbiome and implications for human health. Journal of translational medicine, 15(1), 73. https://doi.org/10.1186/s12967-017-1175-y
2. Milani C, Ferrario C, Turroni F, Duranti S, Mangifesta M, van Sinderen D, Ventura M. The human gut microbiota and its interactive connections to diet. J Hum Nutr Diet. 2016 Oct; 29(5):539-46. doi: 10.1111/jhn.12371. Epub 2016 May 10. PMID: 27161433.
3. Flandroy, L., Poutahidis T., Berg G., Clarke G., Dao M. (2018). The impact of human activities and lifestyles on the interlinked microbiota and health of humans and of ecosystems. Science of The Total Environment. 627 (1018-1038). https://doi.org/10.1016/j.scitotenv.2018.01.288.
4. Dore, A. (2020). The hunt for a healthy microbiome. Nature. https://www.nature.com/articles/d41586-020-00193-3
5. Hempel S, Newberry SJ, Maher AR, Wang Z, Miles JN, Shanman R, Johnsen B, Shekelle PG. Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. JAMA. 2012 May 9;307(18):1959-69. doi: 10.1001/jama.2012.3507. PMID: 22570464.

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