Current understanding of human microbiome influence on health

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By Carolina Brooks, BA, IFMCP

The gut microbiome has gained recognition in conventional medicine for its importance to overall health and function. However, microbiomes exist throughout the body and each have a specific influence on human health.

A 2014 article in Frontiers in Medicine describes the human microbiome are consisting of over one thousand species of trillions of organisms. The gut microbiome is the most widely studied, more so than its urogenital, lung, or oral counterparts. Probiotics have been used for many years to treat irritable bowel syndrome, to replenish the microbiota after antibiotic therapy, and to treat intestinal permeability or vaginal thrush. Researchers continue to recognize the significance of our microbiome, including their influence on the development and prevention of chronic disease, in maintaining immune homeostasis, and regulating metabolic function. A healthy gut microbiome also produces neurotransmitters and neurotransmitter precursors, as well as producing certain vitamins and enhancing nutrient absorption.

Ensuring diversity of commensal bacteria is crucial to limit the growth of pathogenic and enterotoxigenic strains and pathobionts. Gram-negative bacteria produce pro-inflammatory endotoxins, which induce inflammation, higher circulating levels of insulin, glucose, and triglycerides, and can drive weight gain.

A 2018 report in Current Diabetes Reports discusses the role of the microbiome in glycemic control and insulin sensitivity, lipid metabolism, and appetite control, in particular the role of butyrate, a key short chain fatty acid which is often either not present or present in low numbers in those eating a typically western diet of processed food and inflammatory fats. Key butyrate-producing strains include Faecalibacterium prausnitzii and Roseburia homini. Other protective species include Bifidobacterium, associated with a lower of insulin resistance, and another key protective strain includes mucin degrading Akkermansia muciniphila, which protects against intestinal permeability, is associated with leanness, and a healthier, more diverse microbiome.

The vaginal microbiota favors a low pH and low diversity, which can inhibit the growth of pathobionts, leading to bacterial vaginosis, fungal overgrowths, and other infections that can negatively impact fertility and fetal implantation. The vaginal microbiome is dominated by lactic acid producing species, including Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jenseni.

A 2019 review in Frontiers of Microbiology describes the five community states dominated by these differing strains, which influence how other bacteria or yeasts can colonize. A 2020 mini review in American Society for Microbiology also discussed the protective role of Lactobacillus crispatus against uropathogens, such as Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis in the urogenital tract. Both Klebsiella pneumoniae and Proteus mirabilis have been linked with the development of systemic autoimmune diseases.

Many clinicians use probiotics rather like antibiotics, in that they often use a broad-spectrum combination of multiple clinically relevant species and strains and hope that that’s enough. However, what often happens is that the doses that are appropriate for the patient’s condition simply are not present in high enough doses to have a therapeutic effect. There are also many products on the market that are not stable in gastric acid or when exposed to bile salts.

Probiotics often only colonize temporarily. The “weed, seed, and feed” gut paradigm seems redundant, as I have seen countless patients end up at my clinic who have been put through expensive courses of mismatched probiotics and aggressive and unnecessary herbal protocols, only to feel worse than they did when they started. Probiotics are strain and not species-specific and it’s important for clinicians to do their research to check that they are using a targeted product and dosing at the correct level.

Humans have been consuming fermented foods for years. Certainly in the Mediterranean culture in which I was raised, olives and preserved chilis, goat’s yogurt, and cheeses are a stable of the Cypriot diet. However, pasteurized fermented foods confer no health benefits, so I actively encourage my patients to drink coconut kefir, or buy artisanal or home-made fermented foods. I send them recipes for cashew-based dairy products and direct them where they can buy local kombuchas that aren’t full of residual sugar.

I use a great deal of butyrate supplements and suggest both prebiotic foods containing fructooligosaccharides (FOS) and inulin, such as asparagus, dandelion, endive, leeks, and Jerusalem artichokes, as well as supplementation of these compounds. I also recommend a plant-heavy, varied diet rich in fiber and polyphenol-containing foods such as berries, brightly pigmented vegetables, nuts, and seeds, as well as avoiding processed foods and inflammatory omega-6 fats. This will not only improve gut health but shift the genitourinary microbiome and improve epithelial health overall. More specific advice I would give related to the genitourinary microbiota is to avoid using non-organic tampons and menstrual cups, as these can negatively impact vaginal ecology.

Shifting the microbiome, in combination with adjusting sleep, stress management, and other lifestyle habits, can dramatically reduce many health risks. I’ve seen patients reduce cardiovascular disease risk, lower trimethylamine N-oxide (TMAO) levels, and come off long-term medications. While such results depend on the patient, I believe they illustrate the importance of maintaining a healthy microbiome

References

Aydin Ö, Nieuwdorp M, Gerdes V (2018) The Gut Microbiome as a Target for the Treatment of Type 2 Diabetes. Current diabetes reports, 18(8), 55. Retrieved from: https://doi.org/10.1007/s11892-018-1020-6

De Seta F, Campisciano G, Zanotta N, Ricci G,  Comar M (2019) The Vaginal Community State Types Microbiome-Immune Network as Key Factor for Bacterial Vaginosis and Aerobic Vaginitis. Frontiers in microbiology, 10, 2451. Retrieved from: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6831638/

Neugent ML, Hulyalkar NV, Nguyen VH, Zimmern PE, De Nisco NJ (2020) Advances in Understanding the Human Urinary Microbiome and Its Potential Role in Urinary Tract Infection. American Society for Microbiology. Apr 2020, 11 (2) e00218-20; Retrieved from: https://mbio.asm.org/content/11/2/e00218-20

Zatorski H, Fichna J (2014) What is the future of the gut microbiota-related treatment? Toward modulation of microbiota in preventive and therapeutic medicine. Frontiers in Medicine. 1:19. Retrieved from: https://www.frontiersin.org/articles/10.3389/fmed.2014.00019/full