The term “microbiota” refers to microorganisms that colonise a given ecological niche. Recent studies in the field of molecular biology have provided at least partial insight into complex interactions between microorganisms themselves and between the microflora and host organism. Particularly favourable conditions for bacteria to proliferate are found in the large intestine, mainly due to slow intestinal passage. The weight of the systemic microbiota is estimated at even 2 kg. Despite such a numerous and diversified commensal flora, no inflammatory reactions are elicited since there are numerous mechanisms that protect against excessive proliferation of commensal bacteria and their penetration beyond the gastrointestinal tract. The microbiota has various significant functions in the organism. For instance, it enables effective energy assimilation, participates in vitamin synthesis, magnesium, calcium and iron ion absorption and strengthens intestinal integrity. By occupying the niche and stimulating the immune system, it protects from the proliferation of potential pathogens. The relationship of the microbiome with specific disease entities has been recently underlined. Studies on the intestinal flora composition in patients with gastrointestinal diseases, such as non-specific inflammatory bowel disease, have delivered important information. It has been suggested that there is a relationship between the commensal flora composition and obesity, allergy, cancer or autism. The human microbiome undergoes various changes in response to external and internal factors. The most abrupt disorders are called dysbiosis. Its major causes include antibiotic therapy with its unfavourable influence on the human organism that can persist for several months or even years.