What is the microbiome and what are the best herbs to keep it balanced and healthy? This article explores these questions.
What is the microbiome?
The human microbiome has been the subject of increased interest in recent years. The microbiome refers to the microorganisms that live within us and their genes. These microorganisms, also referred to as microbiota, are a diverse collection of not only bacteria but also viruses, fungi, protozoa and archaea that live and coexist in our bodies, especially in the gastrointestinal tract. Other body parts colonised by microbiota include the skin, oral and vaginal mucosa, the respiratory tract, the uterus, and the urinary tract (1).
The number of microbiota in a person is estimated to be around 39 trillion cells, and the human body has around 30 trillion cells, meaning there is approximately a 1:1 ratio of microbial cells to human cells! (2). Human cells and microbial cells coexist in a symbiotic relationship, with microorganisms contributing to metabolic functions such as synthesising B vitamins and some amino acids, stimulating the immune system, protecting against pathogens and breaking down toxic food metabolites amongst others (3). The human body in turn, supplies these microorganisms with the nutrients and environment they need to survive.
Each person has a unique complex and dynamic microbiome, and we need our microbiome to maintain healthy physiology. The human microbiome is determined by one’s DNA, it is acquired at birth and developed during the first year of life. The exact microbiota someone develops will be influenced by what microorganisms are in the breast milk they receive or the microbiota present in the person who gave birth to them (1). This acquired microbiota will then change during the course of one’s life depending on diet and environmental factors.
The microbiota in the gut is more diverse than that of other body sites, and it includes mainly anaerobic bacteria predominantly belonging to the Bacteroides, Bifidobacterium, Clostridium, Eubacterium, Lactobacillus and Streptococcus genera. Some anaerobes such as Escherichia coli are also present (4). Other agents that can alter the microbiota are biofilms. Biofilms are complex structures or aggregates of microorganisms that attach to internal surfaces (5). Bacterial biofilms are becoming a serious health concern because of their ability to tolerate antibiotics, contributing to chronic unresolved infections, and to the development of disease and inflammatory processes (5, 6).
When the usual microbiota composition of a certain body part is altered, this gives rise to ‘dysbiosis’. This can happen in any body part, namely gut dysbiosis, vaginal dysbiosis, endometrial dysbiosis, or dysbiosis in the respiratory tract (7). Dysbiosis can be caused by prolonged use of antibiotics, certain diets, infections, or stress, amongst other causes. There is research associating these imbalances in the microbiome with many diseases including autoimmune disorders, asthma, allergies, type 1 and type 2 diabetes, inflammatory bowel disease, multiple sclerosis and cancer (4).
Herbs for a healthy microbiome
So, what are the best herbs to keep our microbiome balanced and healthy?
A general herbal approach to correct dysbiosis to keep the microbiome healthy includes the following strategies (8):
- Prebiotic herbs and foods rich in polysaccharides, fructooligosaccharides and mucilage
- Probiotic supplementation
- Respiratory and/or gastrointestinal antimicrobial herbs
Slippery elm
The inner bark of slippery elm is considered a prebiotic, and prebiotics act as food for beneficial bacteria (8). Slippery elm is rich in mucilage, which is a water-soluble polysaccharide that has a gelatinous constituency when mixed with water. This gelatinous mucilage has a demulcent and emollient action inside the gut, and it helps soothe inflamed mucous membranes as well as feed good gut bacteria (8).
There are studies that have profiled stool cultures and shown that slippery elm changes the gut microbiota by increasing the number of beneficial bacteria including Bacteroides spp., Bifidobacterium spp. and Lactobacillus spp., and decreasing the number of potential pathogenic bacteria (9, 10).
Sadly, slippery elm is at risk of becoming extinct and it is recommended to source it from suppliers that can guarantee the tree has been cultivated from sustainable harvesting. Learn more about finding quality and sustainably sourced herbs in our article “Herbal quality & safety: What to know before you buy“. We also have an article section dedicated to sustainability and social welfare.
Dandelion
Dandelion leaves and root are rich in another prebiotic polysaccharide called inulin. The root of dandelion can contain inulin up to 45% (11). Inulin is a fibre containing fructo-oligosaccharides, a type of complex polysaccharide. These feed good bacteria and therefore have a positive impact on the microbiome by increasing the number of beneficial microorganisms, including bifidobacteria. Good bacteria will eat inulin and grow, populating different microbiomes in the body with those bacteria that we really need.
Inulin can also help stabilise blood sugar levels, so it can be used to help people with pre-diabetes or diabetes as part of a more comprehensive regimen (11).
Dandelion is also used by herbalists to assist with liver detoxification and improve bile flow, which will help with the absorption of fats (8).
Garlic
Garlic is another prebiotic food with the added benefit of having strong antibacterial properties as well as antifungal properties. The prebiotic component of garlic is not destroyed by the stomach and is used as food for beneficial bacteria in the intestines. Garlic feeds and increases numbers of the well-known beneficial bacteria Lactobacillus acidophilus (12).
As a broad-spectrum antibacterial, garlic can also be used to reduce harmful bacteria in small intestine bacterial overgrowth (SIBO). Garlic has a powerful antifungal activity against candida, so it is suited in cases of dysbiosis with this yeast (13).
Garlic needs to be used with caution as it can sometimes cause gut upset in some individuals. For example, for people suffering from irritable bowel syndrome (IBS) it is often recommended that they avoid garlic for some time as part of the FODMAP diet, as the prebiotic garlic contains can be an irritant in this gut condition.
Berberine-containing plants
Berberine is a bitter-tasting and yellow-coloured phytochemical that has a broad-spectrum antibacterial action, meaning it can inhibit the growth and/or kill many different types of bacteria (8). Berberine-containing plants such as barberry, mahonia or goldenseal are used to regulate the human microbiota ecosystem, as they seem to increase the abundance of beneficial bacteria like Bacteroides spp., whilst having an antibacterial action against Escherichia coli or Clostridium difficile for example (14).
Berberine-containing plants also seem to change the immunological profile of the intestine, inhibiting pro-inflammatory mediators and therefore reducing low-grade inflammation in the gut (15).
Green tea and grape seed extract
Polyphenols found in green tea and grape seed extract selectively inhibit the regrowth of pathogenic gut bacteria and encourage the growth of beneficial bacteria (8). Green tea polyphenols appear to inhibit the growth of pathogenic Bacteroides spp. and Clostridium spp., as well as promote the growth of good bacteria like Bifidobacterium and Lactobacillus (16).
Drinking green tea daily has a positive effect on gut dysbiosis, as it increases anaerobic bacteria like bifidobacteria. Studies have found that drinking at least 400 ml a day (or two or three mugs) of green tea changes the structure of the gut microbiome by correcting dysbiosis (8).
Oregano oil
Oregano essential oil is a strong antibacterial and can inhibit Escherichia choli, Salmonella, Staphylococcus aureus and Campylobacter (17). It can also be quite effective in treating Candida albicans and intestinal parasites (18, 19). Phenolic constituents such as thymol and carvacrol have been attributed to these antiseptic properties (8). Oregano essential oil also seems to be helpful in increasing the beneficial Lactobacillus species in the gut, contributing to a balanced microbiota.
Essential oils should not be ingested neat nor dissolved in water. They need to come in specific emulsified preparations that can be bought over the counter or dissolved in a carrier oil. If planning to use essential oils internally, it is recommended to do it under the guidance of an appropriately qualified healthcare professional.
References
- Ursell, L. K., Metcalf, J. L., Parfrey, L. W., & Knight, R. (2012). Defining the human microbiome. Nutrition reviews, 70(suppl_1), S38-S44.
- Kho, Z. Y., & Lal, S. K. (2018). The human gut microbiome–a potential controller of wellness and disease. Frontiers in microbiology, 1835.
- Den Besten, G., Van Eunen, K., Groen, A. K., Venema, K., Reijngoud, D. J., & Bakker, B. M. (2013). The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. Journal of lipid research, 54(9), 2325-2340.
- Lloyd-Price, J., Abu-Ali, G., & Huttenhower, C. (2016). The healthy human microbiome. Genome medicine, 8(1), 1-11.
- Sharma, D., Misba, L., & Khan, A. U. (2019). Antibiotics versus biofilm: an emerging battleground in microbial communities. Antimicrobial Resistance & Infection Control, 8(1), 1-10.
- Vestby, L. K., Grønseth, T., Simm, R., & Nesse, L. L. (2020). Bacterial biofilm and its role in the pathogenesis of disease. Antibiotics, 9(2), 59.
- Li, K. J., Chen, Z. L., Huang, Y., Zhang, R., Luan, X. Q., Lei, T. T., & Chen, L. (2019). Dysbiosis of lower respiratory tract microbiome are associated with inflammation and microbial function variety. Respiratory research, 20(1), 1-16.
- Bone, K. (2021). Functional Herbal Therapy: a modern paradigm for clinicians. Aeon books.
- Aleman, R. S., Paz, D., Cedillos, R., Tabora, M., Olson, D. W., & Aryana, K. (2023). Attributes of Culture Bacteria as Influenced by Ingredients That Help Treat Leaky Gut. Microorganisms, 11(4), 893.
- Peterson, C. T., Sharma, V., Uchitel, S., Denniston, K., Chopra, D., Mills, P. J., & Peterson, S. N. (2018). Prebiotic potential of herbal medicines used in digestive health and disease. The Journal of Alternative and Complementary Medicine, 24(7), 656-665.
- Wirngo, F. E., Lambert, M. N., & Jeppesen, P. B. (2016). The physiological effects of dandelion (Taraxacum officinale) in type 2 diabetes. The review of diabetic studies: RDS, 13(2-3), 113.
- Sunu, P., Sunarti, D., Mahfudz, L. D., & Yunianto, V. D. (2019). Prebiotic activity of garlic (Allium sativum) extract on Lactobacillus acidophilus. Veterinary World, 12(12), 2046.
- Khounganian, R. M., Alwakeel, A., Albadah, A., Nakshabandi, A., Alharbi, S., & Almslam, A. S. (2023). The Antifungal Efficacy of Pure Garlic, Onion, and Lemon Extracts Against Candida albicans. Cureus, 15(5).
- Habtemariam, S. (2020). Berberine pharmacology and the gut microbiota: A hidden therapeutic link. Pharmacological research, 155, 104722.
- Zhang, L., Wu, X., Yang, R., Chen, F., Liao, Y., Zhu, Z., … & Wang, L. (2021). Effects of berberine on the gastrointestinal microbiota. Frontiers in cellular and infection microbiology, 10, 588517.
- Pérez-Burillo, S., Navajas-Porras, B., López-Maldonado, A., Hinojosa-Nogueira, D., Pastoriza, S., & Rufián-Henares, J. Á. (2021). Green tea and its relation to human gut microbiome. Molecules, 26(13), 3907.
- Calo, J. R., Crandall, P. G., O’Bryan, C. A., & Ricke, S. C. (2015). Essential oils as antimicrobials in food systems–A review. Food control, 54, 111-119.
- Force, M., Sparks, W. S., & Ronzio, R. A. (2000). Inhibition of enteric parasites by emulsified oil of oregano in vivo. Phytotherapy Research, 14(3), 213-214.
- Manohar, V., Ingram, C., Gray, J., Talpur, N. A., Echard, B. W., Bagchi, D., & Preuss, H. G. (2001). Antifungal activities of origanum oil against Candida albicans. Molecular and cellular biochemistry, 228, 111-117.
