The terms microbiome/microbiota have frequently been used lately. Microbiota includes all special species while microbiome includes genes of microorganisms which live commensally with human. Likewise genomic superiority, quantity ofmicroorganisms in human body is 10 times more than human cell quantity. Human microbiota consists of mainly bacteria and viruses, fungi and many eukaryotic microorganisms. Most of human microbiota is colonized particularly in gastrointestinal system but also in skin, genitourinary and respiratory system. Gastrointestinal system provides the most convenient environment with a large surface area and rich nutritional elements for colonization of microorganisms. Thus gut shelters more than 70% of all microorganisms in our body. In humans, intestinal microbiota starts to form right after birth and it continues to form according to many factors like type of birth, nutrition and environmental factors.

Not all of bacteria in intestinal microbiota could be cultured by current culturing methods. Because majority of intestinal microbiota members are anaerobic bacteria which are very difficult to culture, primarily “16S rRNA genes” are targeted as analysis method.

Differences in intestinal microbiota composition are detected in many cases like diabetes, allergy, autism, obesity, gastric cancer, hypertension and autoimmune diseases. Thus, regulation of healthy intestinal microbiota is a current treatment alternative in disease control. In immediate future, microbiota will frequently be used as a marker in diagnosis or as an approved treatment method by Food and Drug Administration (FDA). In this review formation and development of intestinal microbiota, its relationship with pathogenesis of diseases and current situation of fecal transplantation will be discussed.

Intestinal microbiota Microbiome Fecal transplantation