Genomic and ecological studies to understand bifidobacterial adaptation to the human gastro-intestinal tract

The Bifidobacterium genus comprises a high GC Gram positive bacteria belonging to the Actinobacteria phylum, which has been found to represent a common inhabitant of the gastro-intestinal tract (GIT) of mammals. In particular focusing on the GIT of human, the overall microorganisms that colonize such environment represent the †œgut microbiota†�. The human gut microbiota is an extremely complex microbial community whose functions are believed to have a significant impact on human physiology. Different ecological relationships with their host might be developed by bifidobacteria ranging from opportunistic pathogens (e.g., the case of Bifidobacterium dentium species) to health promoting features (e.g., the case of Bifidobacterium bifidum and Bifidobacterium breve species). Among health promoting microorganisms, also known as probiotic microorganisms, bifidobacteria represent one of the dominant group and some bifidobacterial species are frequently used as healthy components in many functional foods. However, despite the generally accepted importance of bifidobacteria as constituent of human microbiota, there is only a limited body of information about their phylogenetic position, physiology and genetics. Moreover, host-microbiota interaction as well as the cross-talk between the different components of the gut ecosystem are far to be completely known although they represent a crucial point in human physiology. The aim of this Ph.D. thesis research is to shed light into the genetic and functional features of bifidobacteria residing in the human GIT with the use of genomics and ecological based tools. This study offers first evidences about the contribution of bifidobacteria to the human gut microbiota and also it provides insights into the genetic functions explaining their presence in the particular ecological environment of the GIT of human beings.