Humans consist only of our own somatic cells until birth, but over the first several years of life, our bodies, including the skin surface, mammary glands, placenta, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjuctiva and gastrointestinal tracts are colonized by an enormous variety of bacteria, archaea, protists, fungi and viruses, which form a community collectively known as the human microbiota. The human microbiome refers specifically to the collective genomes of resident microorganisms.

Until the middle of the 20th century, clinical microbiology was limited to bacterial cultures enabling the detection of pathogenic microorganisms. Traditional culture methods cultivate only 10-30% of gut microbiota. With the application of molecular biologic technology, especially metagenomic sequencing, progress has been made in the analysis of a large number of microorganisms in different environments and human body sites.

Metagenomics can be used to study  microbiome diversity and dysbiosis, as well as its relationship to health and disease. Moreover, functional metagenomics can identify novel functional genes, microbial pathways, antibiotic resistance genes, functional dysbiosis of the intestinal microbiome, and determine interactions and co-evolution between microbiota and host.

Differences in human microbiome composition appears exist across body sites and between individuals. Changes are also evident across the human lifespan, depending on the dietary habits, environmental and host genetic factors.

There are more than 1000 microbial species living in the complex human intestine. The gut microbial community plays an important role in protecting the host against pathogenic microbes, modulating immunity, regulating metabolic processes, and is even regarded as an endocrine organ.

Dysbiosis is defined as qualitative and quantitative changes in the intestinal flora; and modern diet and lifestyle, antibiotics, psychological and physical stress result in alterations in bacterial metabolism, as well as the overgrowth of potentially pathogenic microorganisms. All immune system components are directly or indirectly regulated by the microbiota. The nature of microbial exposure early in life appears to be important for the development of robust immune regulation; disruption of either the microbiota or the host response can trigger chronic inflammation. Dysbiosis is also an important clinical entity. Antibiotics, psychological and physical stress, and dietary factors contribute to intestinal dysbiosis.

Dysbiosis of the intestinal microbial community is associated with some diseases, including inflammatory bowel disease, obesity, diabetes, allergy, irritable bowel syndrome (IBS), colorectal cancer, liver cirrhosis, nonalcoholic steatohepatitis, neurodevelopmental disorders, cardiovascular disorders, cholesterol gallstones, diarrhea, malnutrition, kidney diseases, and colon polyps. Autoimmune diseases including diabetes, rheumatoid arthritis, muscular dystrophy, multiple sclerosis, and fibromyalgia are associated with dysfunctional microbiomes.

The resulting knowledge have shown that the human microbiome is highly variable between individuals, and its genetic capacity is far greater than the human genome. The future research will help us to understand our relationship with our microbial flora as well as its roles in human health and disease.


Corresponding author:
Dijana Varda Brkić,
Department for Clinical and Molecular Microbiology, University Hospital Centre Zagreb, Zagreb, Croatia

Creative Commons LicenseThis work is licensed under a Creative Commons Attribution 4.0 International License