Inflammatory Bowel Diseases (IBD) are a group of chronic gastrointestinal tract disorders, affecting more than 3.6 million people worldwide (Edward et al. 2004), with cases in North America and Europe doubling every decade. In developing countries, IBDs have expanded since the 1990s, with a higher incidence of ulcerative colitis (UC) than Crohn’s disease (CD) (Molodecky et al., 2012). The IBDs mainly include UC and CD (Ye et al, 2015), these two phenotypes with distinct descriptions, UC being a continuous, mucosal limited inflammation located in the colon and CD characterized by discontinuous, transmural inflammation and may involve any part of the Intestine, but both tend to affect adolescents and young adults (Whelan and Quigley, 2015). Its pathogenesis is not yet well understood, but several factors have been related: genetic, environmental, immune and more recently intestinal microbiota and diet. The latter two are modifiable factors that are related to both prevention and treatment of the disease (Lee et al., 2015). The bowel microorganisms have effects on gastrointestinal physiology, as well as on pathologies, but these mechanisms are still unclear. The human microbiota is composed of approximately one thousand different species, including bacteria, fungi, bacteriophages and viruses, which live synergistically with the host (Scaldaferri et al., 2013). Current studies suggest that the altered profile of the intestinal microbiota is related to pathogenesis of IBD, characterized by low density of beneficial genera and high density of invasive genes. (Zhou et al, 2017). Microbial predominance includes 4 different phyla, the Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria, and the first two make up 90% of the intestinal flora (Dethlefsen et al., 2007; Barbara et al., 2016). Results from several studies have shown that commensal bacteria such as Escherichia coli, Bacterioides, Enterococcus and Klebsiella are involved in intestinal inflammation and in pathogenic proprieties (Lakatos et al., 2006; Yang and Jobin, 2014), whereas species of Lactobacillus, Bifidobacterium and Lactococcus promote intestinal barrier integrity, prevent bacterial translocation in the gut and reduces inflammation (DeGruttola et al, 2016). In addition, changes in the microbiological profile in these diseases include the reduction of the diversity of the microbiota and the phylum Firmicutes (especially in the Clostridium leptum group, highlighting the Faecalibacterium prausnitzii) and increase of Proteobacteria (Matsuoka and Kanai, 2015).