What is the gut microbiome?
The human gut microbiome also called the gut flora or microbiota is a complex ecosystem of microorganisms that populate the human gastrointestinal tract (GI), including the principal organs of digestion, such as the stomach and small and large intestine. It is a mass collection of bacteria, archaea and eukaryotes that have co-evolved over thousands of years to form an intricate and mutually beneficial relationship.1
The microbiota offers immeasurable benefits to the human body through a range of physiological, psychological and metabolic functions, such as
Figure: Benefits of Microbiota
Created by Aastha Malik
However, an altered microbial composition, known as dysbiosis, can affect the functioning of the gut's microorganisms, which disrupts those mechanisms aforementioned. Dysbiosis means a greater proportion of "bad" bacteria in the gut than under normal symbiotic conditions. With this in mind, more studies have been conducted on the role of microbiota in modern-day society, where newly emerging, lifestyle-induced diseases are becoming increasingly prevalent.7
There are three different types of gut bacteria, categorised as 'beneficial' ("good"), 'harmful' ("bad"), and opportunistic, each with different mechanisms and effects on your body.8 This article aims to describe the causes and symptoms of a bad gut microbiome and how to reduce "bad" bacteria to optimise your gut health.
Good gut microbiome
There are many examples of ‘good bacteria’ in the gut that contribute to overall health maintenance:
- Lactobacilli: oral administration of commensal Lactobacilli has been shown to alleviate anxiety, anxiety-related behaviour and stress.9
- Bifidobacterium Longum: supplementation of Bifidobacterium Longum has been linked to weight loss in obese individuals, reducing constipation, and maintaining gut symbiosis.10
- Lactobacillus helviticus: studies have shown that Lactobacillus helviticus could prevent gastrointestinal infection, protect against pathogens, regulate host cell immunity, enhance the bioavailability of nutrients, and remove allergens from food.11
- Bifidobacteria: Bifidobacteria has proved successful in protecting against bone and connective tissue loss, the treatment of intestinal conditions, as well as reducing inflammatory markers.12
A good gut microbiome is inhabited by trillions of microorganisms,13 each living mutually exclusively to influence physiology, metabolism, nutrition and immune function. No two individuals have the same gut microbiome, affected by life history and environmental conditions.
A healthy functioning digestive system indicates good gut health, showing no reaction to certain foods or external influences, such as stress or the environment. You are less susceptible to inflammation, autoimmune conditions, or skin disorders like psoriasis and acne.
Bad gut bacteria
Gut bacteria can be harmful when the gut microbiome undergoes abnormal change. Dysbiosis - an imbalance in the microbiota - changes the functional composition of the gut’s bacteria, metabolic activity and distribution,14 leading to a host of issues. Examples of “bad” bacteria include
- Staphylococcus: which inhibits health by causing infections, is resistant to antimicrobial therapies and attacks host cell defences. It can produce bacterial toxins that permeate plasma membranes.15
- Helicobacter pylori: can damage the epithelial lining of the stomach and small intestine, allowing stomach acid to create open sores (ulcers).16
Methanobrevibacter smithii is an archaeon and not a bacterium. However, it influences the specificity and efficiency of the bacteria in the GI tract. They have been linked to malnutrition17 and inflammatory responses, where their abundance is higher in inflammatory bowel diseases (IBD).18
What causes bad bacteria in the gut?
Changes in gut microbiota composition are directly correlated to several factors:
- Antibiotic use: probably the most significant effect on the gut microbiome is the use of antibiotics. Antibiotics kill the "good" and "bad" bacteria during treatment.19 As a result, the number of "good" bacteria in the body that aid physiological function decrease, which can cause GI dysbiosis and digestion issues.
- Geographical location: those who live in non-Western countries, who are less likely to adopt the Western diet, have greater gut biodiversity and better overall gut health.20 Another study found that children living in urban environments have more 'bad' bacteria and less 'good' bacteria than rural children.21
- Diet: a diet composed of ultra-processed foods, refined carbohydrates, sugar, high intake of fat, low intake of fibre and low intake of fruits and vegetables can change the gut microbiome and cause local and systemic inflammation.22 In addition, artificial sweeteners can induce glucose intolerance and dysbiosis by altering the function of gut bacteria.23
- Stress: changes to the gut microbiome due to stress are associated with changes in the permeability of the gut barrier (which can induce leaky gut) immune response. The theory of the gut microbiome-brain axis suggests that dysbiosis is involved in anxiety disorders, depression, autism, Alzheimer's disease and Parkinson's disease.24
- Inactivity: whilst the impact of inactivity on gut bacteria is largely unknown, some research suggests that inactivity is a major determinant of the health of the gut microbiome.25 Inactivity has been shown to disrupt the balance of "good" and "bad" bacteria in the intestines, leading to possible adverse health effects.
- Lack of sleep: just like humans, the bacteria in the gut possess a circadian rhythm, which response to feeding and fasting cycles. Jet lag, shortened sleep durations and sleep fragmentation cause gut dysbiosis, leading to an overgrowth of 'bad' gut bacteria.26
What are the symptoms of bad bacteria in the gut?
An unhealthy gut is associated with many symptoms throughout the body, such as:
- Bloating: bloating is associated with the dysbiosis of normal gut bacteria.27
- Abdominal pain: if you experience persistent abdominal pain, it could be a sign of Irritable bowel syndrome (IBS), an inflammation of the large intestines. Gut dysbiosis contributes to the pathophysiology of IBS by inducing the gut's immune system and low-grade inflammation.27
- Food cravings: consuming too much sugar can lead to the accumulation of "bad" bacteria in the GI tract, causing dysbiosis.28 By limiting your sugar intake - both refined and natural - you are more likely to have a predominance of beneficial, healthy bacteria.
- Constipation: evidence suggests that dysbiosis of healthy and unhealthy gut microbiota contributes to constipation and constipation-type IBS.29
- Weight changes: a typical western diet high in fat, refined carbohydrates, and sugar and low in fibre promotes an overgrowth of "bad" bacteria linked to obesity.30
Effects of bad bacteria on gut health
The symptoms aforementioned indicate issues with digestive health and the immune system. Dysbiosis of the gut bacteria can cause many diseases, including
- Inflammatory Bowel Disease (IBD): IBD is a chronic and reoccurring inflammatory disorder of the gut. A shift in the balance of the gut microbiota, namely, reduced diversity of the "good" bacteria, can trigger chronic inflammatory responses.31
- Metabolic conditions: diseases such as Type-2 diabetes are strongly associated with changes in gut bacteria. High-fat, Western diet-induced diabetes is associated with gut dysbiosis, thus triggering inflammation that contributes to the development of insulin resistance.14
- Leaky gut: Leaky gut syndrome, commonly referred to as "gastrointestinal permeability", is a condition in which the epithelial cells that constitute the 'wall' of the small intestine become loose and hyperpermeable. This forms passages that allow bacteria, toxins and allergens to 'leak' through the intestines and into the bloodstream.32 A healthy gut lining is pivotal for gut health.
- Crohn's disease: abnormally high levels of the "bad" strain of bacteria in the GI tract may occur when Crohn's Disease develops, triggering an atypical immune response that causes inflammation.33
How to starve bad gut bacteria?
If you are experiencing gut dysbiosis - an imbalance of the "good" and "bad" bacteria - or an overgrowth of small intestinal bacteria (SIBO), then starving the "bad" gut bacteria is pivotal in treating your gut health. Many fundamental lifestyle changes have been recommended to promote wider biodiversity and improve gut health.
Lifestyle factors that support your gut
Exercise, sleep, and stress management all affect digestive health. Regarding physical activity, studies have shown that regular exercise resulted in greater gut microbiome diversity and prevalence of "good" bacteria in active people compared to sedentary individuals.34 Another study found that regular physical activity was positively associated with increased "good" bacteria diversity and the availability of food sources for these beneficial bacteria.35 In addition, reduced sleep fragmentation, consistent sleep durations and bedtime 'unwinding' are associated with a gut symbiosis.26 Metabolic disturbances due to sleep disruption can also induce overgrowth of the "bad" gut bacteria. It is clear that the practice of anxiety and stress management techniques influences the gut microbiota, and gut microbiota on stress modulation is apparent for different stressors. Stress management maintains the symbiotic relationship between the "good" and "bad" bacteria in the gut, which not only reduces the risk and incidence of stress-related disorders but prevents an overgrowth of "bad" bacteria and associated inflammation.24
To maintain a healthy gut, eat a typical 'anti-inflammatory diet', which means eating to control inflammation, blood glucose levels and allergic and intolerance responses. A standard Western diet includes refined sugar, alcohol, highly processed carbohydrates and a lack of fibre, all leading to inflammation in the body. These inflammatory foods feed the "bad" bacteria in the gut, leading to symptoms of an unhealthy gut and damage to the gut lining - the basis of the leaky gut syndrome. Anti-inflammatory foods that you'd find in the Mediterranean diet or fermented foods can help starve unhealthy bacteria and improve overall gut health.
The Mediterranean diet includes fresh vegetables, fresh meat and fish, olive oil, whole grains and legumes, which have anti-inflammatory properties, can aid the growth of "good" gut bacteria, and strengthen the intestinal lining.36
Fermented foods have emerged as highly important in developing good gut health. They contain live bacteria that contribute to increased gut biodiversity, which supports a healthy gut flora. Foods such as sauerkraut, kimchi, and kombucha, as well as probiotic supplements, provide the gut with beneficial bacteria.37
Antibiotic and antimicrobial treatments have detrimental effects on gut biodiversity. Pharmaceuticals cannot distinguish between the harmful inflammatory bacteria in the gut from the healthy beneficial bacteria upon treatment. Prolonged antibiotic negatively impacts the gut microbiota by reducing diversity, altering metabolic activity, and creating harmful antibiotic-resistant strains.38 Over time, the "good" bacteria in the gut become eradicated, and the conditions facilitate the growth of unhealthy bacteria that cause a whole host of health issues.
You may wish to use more holistic medicinal approaches to heal the gut via supplementation, functional foods or probiotic intake. The prebiotic properties in garlic capsules have shown effectiveness in increasing gut microbial diversity and the number of "good" bacteria (39). Similarly, oregano supplementation can potentially reduce the population of "bad" bacteria in the GI tract.40
How long does it take to repopulate the gut with good bacteria?
Research has shown that the gut microbiome can change within two to four days of nutritional intervention.41 This study also found that subjects' gut microbiota reverted to a 'normal', 'healthy' structure two days after ending an animal-based diet. However, to fully repopulate the gut, it is recommended that the appropriate intervention is implemented for at least six months to a year. To maintain a healthy gut microbiome, intervention strategies should be implemented long-term.
How to improve gut health
Various lifestyle changes can be made to heal and improve your gut.
- Eat a diverse range of fruits and vegetables: fresh fruit and vegetables contain lots of fibre that stimulate the growth and diversity of the "good" bacteria in the gut and reduce inflammation.42 Leafy greens such as spinach, kale, Bak Choy, Swiss chard and collard greens, as well as broccoli, fennel, beetroot and carrots, have beneficial gut-supporting fibre.43
- Eat fermented and prebiotic foods: Fermented foods like kombucha, sauerkraut, kimchi and yoghurt have prebiotic effects, which feed the "good" gut bacteria and reduce overall inflammation. One study found that those who eat yoghurt have more "good" gut bacteria Lactobacilli, and fewer inflammatory bacteria.44
- Eat whole grains and legumes: fibre-rich wholegrains and legumes alter the gut microbiome by increasing the number of "good" gut bacteria, which confers protective effects on gut health.45 Wholegrains such as whole oats, quinoa, buckwheat and brown rice, as well as lentils, kidney beans and edamame, should all be included.
- Limit artificial sweeteners and refined carbohydrates: removing refined carbohydrates and artificial sweeteners prevent gut dysbiosis, inflammation, and an overgrowth of the 'bad' gut bacteria.22,23,28
- Regular physical activity: physical activity helps maintain the symbiotic relationship between the 'good' and 'bad' gut bacteria.25
- Reduce stress: stress management helps support the gut microbiome-brain axis by maintaining symbiosis, which is essential for minimising the incidence of anxiety disorders, depression, autism, Alzheimer's disease and Parkinson's disease.24
- Reduce alcohol intake: alcohol changes the proportion and diversity of microbiota, which is directly linked to gut inflammation and secondary psychiatric conditions.46 Alcohol induces dysbiosis, which alters microbiome-derived metabolites and neurotransmitters such as GABA, dopamine and serotonin. Limiting your alcohol intake would protect against emotional behaviour, memory changes, sleep alterations and depressive episodes.46
The microorganisms that populate the GI tract form the gut microbiome. These microorganisms benefit our physiology, metabolism, psychology, health, and well-being.
Lifestyle changes such as stress, smoking, and a poor diet can induce dysbiosis - an imbalance of the "good" and "bad" gut bacteria - leading to diseases such as IBD, leaky gut syndrome, diabetes and psychiatric disorders.
Starving these ‘bad’ gut bacteria can be achieved through proper nutrition, lifestyle changes, reduced antibiotic use, and incorporating probiotic supplementation into your diet. The number of "bad" gut bacteria can be changed within a few days to a few months. However, it is recommended that you maintain the recommended lifestyle interventions for life to support a long-term happy, healthy gut!
- Backhed F. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–1920.
- Den Besten G, Van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. Journal of lipid research. 2013;54(9):2325-2340.
- Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Science. 2016;352(6285):539-544.
- Capuco A, Urits I, Hasoon J, Chun R, Gerald B, Wang JK, Kassem H, Ngo AL, Abd-Elsayed A, Simopoulos T, Kaye AD. Current perspectives on gut microbiome dysbiosis and depression. Advances in therapy. 2020;37(4):1328-1346.
- Natividad JM, Verdu EF. Modulation of intestinal barrier by intestinal microbiota: pathological and therapeutic implications. Pharmacological research. 2013;69(1):42-51.
- Karasov WH, Martinez del Rio C, Caviedes-Vidal E. Ecological physiology of diet and digestive systems. Annual review of physiology. 2011;73(1):69-93.
- Schroeder BO, Bäckhed F. Signals from the gut microbiota to distant organs in physiology and disease. Nature medicine. 2016;22(10):1079-1089.
- Otsuka Pharmaceutical Co., Ltd. The surprising facts about dietary fibre: Typical intestinal bacteria [Internet]. [cited 2022 July 31]. Available from: https://www.otsuka.co.jp/en/health-and-illness/fiber/for-body/intestinal-flora.
- Frankiensztajn LM, Elliott E, Koren O. The microbiota and the hypothalamus-pituitary-adrenocortical (HPA) axis, implications for anxiety and stress disorders. Current Opinion in Neurobiology. 2020;62:76-82.
- Amenta M, Cascio MT, Di Fiore P, Venturini I. Diet and chronic constipation. Benefits of oral supplementation with symbiotic zir fos (Bifidobacterium longum W11+ FOS Actilight). ACTA BIOMEDICA-ATENEO PARMENSE. 2006;77(3):157.
- Taverniti V, Guglielmetti S. Health-promoting properties of Lactobacillus helveticus. Frontiers in microbiology. 2012;3:392.
- Oliveira LF, Salvador SL, Silva PH, Furlaneto FA, Figueiredo L, Casarin R, et al. Benefits of Bifidobacterium animalis subsp. lactis probiotic in experimental periodontitis. Journal of Periodontology. 2017;88(2):197-208.
- Cresci GA, Bawden E. Gut microbiome: what we do and don't know. Nutrition in Clinical Practice. 2015;30(6):734-746.
- Zhang YJ, Li S, Gan RY, Zhou T, Xu DP, Li HB. Impacts of gut bacteria on human health and diseases. International Journal of Molecular Sciences. 2015;16(4):7493-7519.
- Yoong P, Torres VJ. The effects of Staphylococcus aureus leukotoxins on the host: cell lysis and beyond. Current opinion in microbiology. 2013;16(1):63-69.
- Peterson WL. Helicobacter pylori and peptic ulcer disease. New England Journal of Medicine. 1991;324(15):1043-8.
- Camara A, Konate S, Tidjani Alou M, Kodio A, Togo AH, Cortaredona S, et al. Clinical evidence of the role of Methanobrevibacter smithii in severe acute malnutrition. Scientific reports. 2021;11(1):1.
- Neuman H, Koren O. The Gut Microbiome. Encyclopaedia of Cell Biology. 2016;2:799-808.
- Cammarota G, Ianiro G, Bibbo S, Gasbarrini A. Gut microbiota modulation: probiotics, antibiotics or fecal microbiota transplantation?. Internal and emergency medicine. 2014;9(4):365-373.
- Deering KE, Devine A, O’Sullivan TA, Lo J, Boyce MC, Christophersen CT. Characterizing the composition of the pediatric gut microbiome: a systematic review. Nutrients. 2019;12(1):16.
- Shi Z. Gut microbiota: An important link between western diet and chronic diseases. Nutrients. 2019;11(10):2287.
- Suez J, Korem T, Zeevi D, Zilberman-Schapira G, Thaiss CA, Maza O, et al. Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature. 2014;514(7521):181-186.
- Basson AR, Rodriguez-Palacios A, Cominelli F. Artificial Sweeteners: History and New Concepts on Inflammation. Frontiers in Nutrition. 2021;8:746247.
- Tetel MJ, De Vries GJ, Melcangi RC, Panzica G, O'Mahony SM. Steroids, stress and the gut microbiome‐brain axis. Journal of neuroendocrinology. 2018;30(2):548.
- Jollet M, Nay K, Chopard A, et al. Does Physical Inactivity Induce Significant Changes in Human Gut Microbiota? New Answers Using the Dry Immersion Hypoactivity Model. Nutrients. 2021;13(11):3865.
- Matenchuk BA, Mandhane PJ, Kozyrskyj AL. Sleep, circadian rhythm, and gut microbiota. Sleep medicine reviews. 2020;53:101340.
- Menees S, Chey W. The gut microbiome and irritable bowel syndrome. F1000Research. 2018;7.
- Alcock J, Maley CC, Aktipis CA. Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. Bioessays. 2014;36(10):940-949.
- Ohkusa T, Koido S, Nishikawa Y, Sato N. Gut microbiota and chronic constipation: a review and update. Frontiers in medicine. 2019:19.
- Davis C. The Gut Microbiome and Its Role in Obesity. Nutrition Today. 2016;51(4):167-174.
- Matsuoka K, Kanai T. The gut microbiota and inflammatory bowel disease. InSeminars in immunopathology 2015;37(1):47-55.
- Fasano A. Leaky Gut and Autoimmune Diseases. Clinical Reviews in Allergy & Immunology. 2012;42:71–78.
- Bhattacharjee A. Oral micro-particulate colon targeted drug delivery system for the treatment of Crohn’s disease: A review. International Journal of Life Science and Pharma Research. 2012;1:31–39.
- Dorelli B, Gallè F, De Vito C, et al. Can Physical Activity Influence Human Gut Microbiota Composition Independently of Diet? A Systematic Review. Nutrients. 2021;13(6):1890.
- Ortiz-Alvarez L, Xu H, Martinez-Tellez B. Influence of exercise on the human gut microbiota of healthy adults: A systematic review. Clinical and Translational Gastroenterology. 2020;11(2).
- Illescas O, Rodríguez-Sosa M, Gariboldi M. Mediterranean Diet to Prevent the Development of Colon Diseases: A Meta-Analysis of Gut Microbiota Studies. Nutrients. 2021;13(7):2234.
- Taylor BC, Lejzerowicz F, Poirel M, Shaffer JP, Jiang L, Aksenov A, et al. Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome. Msystems. 2020;5(2):901-919.
- Ramirez J, Guarner F, Bustos Fernandez L, Maruy A, Sdepanian VL, Cohen H. Antibiotics as major disruptors of gut microbiota. Frontiers in cellular and infection microbiology. 2020;10:572912.
- Ried K. Garlic lowers blood pressure in hypertensive subjects, improves arterial stiffness and gut microbiota: A review and meta-analysis. Experimental and Therapeutic Medicine. 2020;19(2):1472-1478.
- Criste RD, Panaite TD, Tabuc C, Saracila M, Soica C, Olteanu M. Effect of oregano and rosehip supplements on broiler (14-35 days) performance, carcass and internal organs development and gut health. AgroLife Scientific Journal. 2017;6(1):75-83.
- David LA, Maurice CF, Carmody RN, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature. 2014;505(7484):559-563.
- van der Merwe M. Gut microbiome changes induced by a diet rich in fruits and vegetables. International Journal of Food Sciences and Nutrition. 2021;72(5):665-669.
- Mathis A. These Are the Best Vegetables for Gut Health, According to a Doctor [Internet]. 2021 [updated: 2021 Mar 03; cited 2022 Jul 31]. Available from: https://www.eatingwell.com/article/7891357/the-best-vegetables-for-gut-health/.
- Adolfsson O, Meydani SN, Russell RM. Yogurt and Gut Function. The American Journal of Clinical Nutrition. 2004; 80(2):245-256.
- Rebello CJ, Greenway FL, Finley JW. Whole grains and pulses: A comparison of the nutritional and health benefits. Journal of agricultural and food chemistry. 2014;62(29):7029-4709.
- Qamar N, Castano D, Patt C, Chu T, Cottrell J, Chang SL. Meta-analysis of alcohol induced gut dysbiosis and the resulting behavioral impact. Behavioural Brain Research. 2019;376:112196.