It is estimated that there are a total of 1014 microorganisms colonized in many organs and tissues in the human body. It is also estimated that there are trillions of bacteria in the human body, almost 10 times that of host cells. This new life association, which we define as microbiomes, has been shown to be essential for protection against enteric and systemic pathogens through many direct and indirect (immunologically mediated) mechanisms in preclinical studies. Dysbiosis or imbalance in the homeostasis of the intestinal microbiota has been associated with many different diseases such as diabetes, obesity, inflammatory bowel disease and rheumatoid arthritis. In general, intestinal microbiota in patients with sepsis following intensive care unit (ICU) follow-up is characterized by lower diversity and commensal species (such as Faecalibacterium, Blautia, Ruminococcus) and an increase in strains such as Escherichia, Shigella, Salmonella, Enterococcus, C. difficile or Staphylococcus. Current treatment methods are based on two principles, either to reduce the excess proliferation of potentially pathogenic microorganisms (decolonization strategies) or to re-supply the pool of beneficial organisms. As in all areas, research on microbiota-targeted treatment strategies in ICU continues.