For millions of years, immediately after birth humans and other mammals are turned into a scaffold for microorganisms' colonization. Environmentally exposed tissue like skin, mouth, gut and vagina are the most prominent colonized surfaces for microorganisms. It is estimated that over 100 trilion bacteria colonize the distal gut, fact that makes the human gut one of the most complex ecosystems of the world. It has been known for long that, gut is mainly colonized by symbiotic bacteria known for their beneficial properties to the host such as combating potential pathogenic microorganisms, providing nutrients, metabolizing undigested compounds and even promoting the development and function of the immune system. However, microbial imbalance, dysbiosis, can be caused by external factors such as antibiotic consumption, dietary changes, physical and psychological stress, resulting in gut enrichment with opportunistic microorganisms impairing host's wellness and homeostasis. The gastrointestinal microbial composition and host immune tolerance are subjected to a continuous interplay. Dysbiosis promotes the induction of host inflammatory responses and the onset of pathogenesis of a broad spectrum of diseases such as Inflammatory Bowel Disease (IBD), celiac disease, obesity, colorectal cancer, autism spectrum disorder and it is even associated with the modulation of host's brain function and epigenome. To this point, microbiome based new treatments have newly emerged, among them microbiome transplantation, prebiotic and probiotic consumption and metabolite-based (postbiotics) administration such as short chain fatty acids (SCFAs) have gained interest in combating above-mentioned diseases. Although, humans and especially socially close individuals share quite common gut microbiota composition, individuals genetic background and dietary habits play distinct role on personal gut microbiota. New diet acquisition has been a fundamental driver for the evolution of new species and the co-evolution of gut colonizing microorganisms. Hence, personalized medicine based on individual's microbiome (enterotype) and the development of precise dietary supplements is of imperative interest.

For the past years, new technologies have emerged allowing for the phylogenetical identification of gut microbiota by analyzing extracted nucleic acids (DNA and RNA). The majority of identification techniques are based on the amplification of 16S ribosomal RNA gene (rRNA) from genetic material isolated directly from stool samples. Although it is estimated that over 1014 microorganisms consist human gut microbiome including bacteria, viruses, fungi and protozoa, the most well studied group of organisms is bacteria. Metagenomics is defined the study analyzing all microbiota members found in environmental or biological specimens and entire ecosystems. In general, it includes the isolation of DNA from specimens, the construction of a metagenomic librady and then screening for target genes. This new field of metagenomics by-passes classical microbiology techniques as it enables sequencing and research of individual microorganisms without their previous isolation and cultivation. Application of metagenomic analysis is increasingly prominent in biotechnology, ecology, pharmaceutical and medical science providing a powerful tool to study all genomes of a biocommunity and its interactions improving the final products and accurate characterization of an ecosystem.