Gut microbiome

The totality of microorganisms that colonize the intestine (microbiota), along with their structural elements, metabolites, and signaling molecules, as well as the surrounding environmental conditions; see also microbiome. The microbiota includes bacteria, fungi, single-celled and multicellular organisms, and viruses. Approximately 100 trillion bacteria—representing up to 1,000 different species—colonize the human gut. 

The composition of the gut microbiome is influenced by diet, as well as by genetic factors, the birth process, and exocrine pancreatic function; age also plays a role in the composition of the microbiome; see also oral microbiome. 

The gut microbiome possesses a broader spectrum of metabolic enzymes than the human body: Humans have slightly more than 10 enzymes for breaking down carbohydrates, whereas some gut bacteria produce more than 200 enzymes for carbohydrate breakdown. The gut microbiome influences numerous diseases, including those of the gastrointestinal tract, as well as immune disorders and metabolic diseases such as diabetes mellitus, insulin resistance, obesity, atherosclerosis, cardiovascular diseases, cancers, and numerous mental health conditions. Components of the bacteria, as well as their metabolic byproducts such as short-chain fatty acids, can trigger inflammation. On the other hand, gut bacteria protect against harmful microorganisms. 

The influence on the autonomic and central nervous systems is bidirectional, forming what is known as the gut-brain axis.

1. Frost F (2022) Introduction to the Microbiome. Inn Med (Heidelb);63(10):1015-1021. German. doi: 10.1007/s00108-022-01395-9. Published online September 2, 2022. PMID: 36053301.
2. Al Bander Z et al. (2020) The Gut Microbiota and Inflammation: An Overview. Int J Environ Res Public Health 19;17(20):7618. doi: 10.3390/ijerph17207618. PMID: 33086688; PMCID: PMC7589951.
3. Halmos T et al. (2016) Physiological patterns of intestinal microbiota. The role of dysbiosis in obesity, insulin resistance, diabetes, and metabolic syndrome. Orv Hetil 3;157(1):13–22. Hungarian. doi: 10.1556/650.2015.30296. PMID: 26708682.
4. He C et al. (2015) Targeting gut microbiota as a possible therapy for diabetes. Nutr Res;35(5):361–7. doi: 10.1016/j.nutres.2015.03.002. Epub 2015 Mar 14. PMID: 25818484.
5. Belizário JE et al. (2018) Microbiome and Gut Dysbiosis. Exp Suppl;109:459-476. doi: 10.1007/978-3-319-74932-7_13. PMID: 30535609.
6. de Vos WM et al. (2022) Gut microbiome and health: mechanistic insights. Gut;71(5):1020–1032. doi: 10.1136/gutjnl-2021-326789. Epub 2022 Feb 1. PMID: 35105664; PMCID: PMC8995832.
7. Berg G et al. (2020) Microbiome definition revisited: old concepts and new challenges. Microbiome 30;8(1):103. doi: 10.1186/s40168-020-00875-0. 
8. Shabani et al. (2025) The relationship between the gut microbiome and human diseases: mechanisms, predisposing factors, and potential interventions. Front Cell Infect Microbiol 6;15:1516010. doi: 10.3389/fcimb.2025.1516010. PMID: 40395507; PMCID: PMC12089137.
9. Pausan MR et al. Bidirectional interactions between herbal medicines and the gut microbiome: New research approaches (2022) ZPT; 43(01): 9–13. DOI: 10.1055/a-1651-6981
10. Schwiertz A et al. (2022) The Microbiome and Plants. The Microbiome and Plant-Based Nutrition. ZPT; 43(01): 5–8
11. DOI: 10.1055/a-1736-2627