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The types of food that a person consumes can have a significant impact on gut microbiota.7 The Western diet, which is high in fat and low in fiber, is linked to a decrease in overall total bacteria and beneficial Bifidobacterium and Eubacterium species.8,9 This alteration can lead to mucus degradation, reduced levels of short-chain fatty acids, and increased susceptibility to invading pathogens.8,10 Bifidobacterium and Eubacterium species and overall total bacteria count are increased with high-fiber diets, such as the Mediterranean diet.8,9,11

  • Dietary fiber8,11:
    • Provides beneficial nutrients to gut microbiota
    • Increases bacterial richness
    • Boosts production of short-chain fatty acids
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Exposure to Pathogens

Infection is one of the most common causes of dysbiosis.12 Colonization by pathogenic bacteria can induce inflammation in the GI tract. This inflammatory state can destabilize the gut microbiota community, resulting in an imbalance in composition and function. In addition, pathogens can outcompete commensal bacteria, resulting in overgrowth of infectious bacteria.13

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Microbial diversity increases in early childhood and stabilizes at age 3.14-16 After age 70, immune system weakness and changes in physical activity, digestion, and nutrient intake can affect microbial composition. The resulting dysbiosis can trigger a proinflammatory state that may be linked to health issues, such as malnutrition and tumorgenesis.15,16

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Psychological Stress/Anxiety

Psychological stress can affect gut motility, visceral perception, GI secretion, and intestinal permeability. These effects on the GI tract can negatively alter the composition of gut microbiota.3,17

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Medication/Drug Use

Certain medications, such as antibiotics and proton pump inhibitors, can alter gut microbial composition.8,18 Proton pump inhibitors reduce acidity in the GI tract, creating a higher luminal pH, which can promote small intestinal bacterial overgrowth.8 Antibiotic use can diminish taxonomic diversity, which can persist over time.18,19

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Tobacco Use and Alcohol Consumption

Cigarette smoking has been linked to changes in the composition of gut microbiota. Analyses using high-throughput sequencing have shown profound and robust microbial shifts before and after smoking cessation.20 Alcohol consumption also has a known influence on gut microbiota composition and function, but more studies are needed to validate the impact.21,22

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Physical Activity

Habitual exercise is associated with increased diversity and abundance of gut microbiota and boosts production of beneficial short-chain fatty acids.16

Consequences of Gut Dysbiosis

Current research supports that gut microbiota, in some capacity, contribute not only to the maintenance of GI health but also to the development of many GI diseases.23

GI Conditions Linked to Gut Microbial Imbalance23-26

  • Irritable bowel syndrome
  • Inflammatory bowel disease
  • Chronic liver disease
  • Peptic ulcer disease
  • Clostridium difficile colitis
  • Celiac disease
  • Diverticular disease
  • GI cancers


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  2. Sommer F, Bäckhed F. The gut microbiota—masters of host development and physiology. Nat Rev Microbiol. 2013;11(4):227-238.
  3. Distrutti E, Monaldi L, Ricci P, Fiorucci S. Gut microbiota role in irritable bowel syndrome: new therapeutic strategies. World J Gastroenterol. 2016;22(7):2219-2241.
  4. Passos MDCF, Moraes-Filho JP. Intestinal microbiota in digestive diseases. Arq Gastroenterol. 2017;54(3):255-262.
  5. Ghoshal UC, Shukla R, Ghoshal U, Gwee KA, Ng SC, Quigley EM. The gut microbiota and irritable bowel syndrome: friend or foe? Int J Inflam. 2012;2012:151085.
  6. Blum HE. The human microbiome. Adv Med Sci. 2017;62(2):414-420.
  7. Cresci GA, Bawden E. Gut microbiome: what we do and don’t know. Nutr Clin Pract. 2015;30(6):734-746.
  8. Dong TS, Gupta A. Influence of early life, diet, and the environment on the microbiome. Clin Gastroenterol Hepatol. 2019;17(2):231-242.
  9. Singh RK, Chang HW, Yan D, et al. Influence of diet on the gut microbiome and implications for human health. J Transl Med. 2017;15(1):73.
  10. Desai MS, Seekatz AM, Koropatkin NM, et al. A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell. 2016;167(5):1339-1353.
  11. 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.
  12. Wang B, Yao M, Lv L, et al. The human microbiota in health and disease. Engineering. 2017;3(1):71-82.
  13. Pham TA, Lawley TD. Emerging insights on intestinal dysbiosis during bacterial infections. Curr Opin Microbiol. 2014;17:67-74.
  14. Flint HJ, Scott KP, Louis P, Duncan SH. The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol. 2012;9(10):577-589.
  15. Raskov H, Burcharth J, Pommergaard HC, Rosenberg J. Irritable bowel syndrome, the microbiota and the gut-brain axis. Gut Microbes. 2016;7(5):365-383.
  16. Rinninella E, Raoul P, Cintoni M, et al. What is the healthy gut microbiota composition? A changing ecosystem across age, environment, diet, and diseases. Microorganisms. 2019;7(1):14.
  17. Kennedy PJ, Cryan JF, Dinan TG, Clarke G. Irritable bowel syndrome: a microbiome-gut-brain axis disorder? World J Gastroenterol. 2014;20(39):14105-14125.
  18. Jandhyala SM, Talukdar R, Subramanyam C, Vuyyuru H, Sasikala M, Reddy DN. Role of the normal gut microbiota. World J Gastroenterol. 2015;21(29):8787-8803.
  19. Francino MP. Antibiotics and the human gut microbiome: dysbioses and accumulation of resistances. Front Microbiol. 2016;6:1543.
  20. Biedermann L, Zeitz J, Mwinyi J, et al. Smoking cessation induces profound changes in the composition of the intestinal microbiota in humans. PloS One. 2013;8(3):e59260.
  21. Shin A, Preidis GA, Shulman R, Kashyap PC. The gut microbiome in adult and pediatric functional gastrointestinal disorders. Clin Gastroenterol Hepatol. 2019;17(2):256-274.
  22. Mutlu EA, Gillevet PM, Rangwala H, et al. Colonic microbiome is altered in alcoholism. Am J Physiol Gastrointest Liver Physiol. 2012;302(9):G966-G978.
  23. Gorkiewicz G, Moschen A. Gut microbiome: a new player in gastrointestinal disease. Virchows Archiv. 2018;472(1):159-172.
  24. Nouvenne A, Ticinesi A, Tana C, et al. Digestive disorders and intestinal microbiota. Acta Biomed. 2018;89(9):47-51.
  25. Cho I, Blaser MJ. The human microbiome: at the interface of health and disease. Nat Rev Genet. 2012;13(4):260-270.
  26. Lanas A, Abad-Baroja D, Lanas-Gimeno A. Progress and challenges in the management of diverticular disease: which treatment? Therap Adv Gastroenterol. 2018;11. doi:10.1177/1756284818789055.
GI = gastrointestinal

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