Genomic and ecological studies of key human microbiota members

The human microbiota is defined as the set of microorganisms residing on or within human tissues and biofluids. In last decades, the scientific community showed a huge interest in the study of the human microbiota, that represents one of the most complex bacterial community known and that have an important implication on human health. In this context, the genus Bifidobacterium represents one of the most important players of the human gut microbiota, especially in the early stages of life. In this Ph. D. thesis, different ecological and genomic aspects of this genus have been investigated. The first part of this thesis investigates genetic and ecological speciation between two important Bifidobacterium (sub)species, i.e. Bifidobacterium animalis subsp. lactis and Bifidobacterium animalis subsp. animalis taxa. Moreover, the Bifidobacterium inheritance from mothers to newborns is examined, through an in vivo study to evaluate the intriguing possible vertical transmission before delivery. Since different members of the Bifidobacterium genus are considered health-promoting bacteria, they should be totally safe to avoid the possible transmission of antibiotic resistance (AR) genes. Then, the resistome of bifidobacteria is explored in order to investigate the possible insurgence of AR genes in mobile genetic elements or close to them. Furthermore, a complete screening for the bifidobacterial Amoxicillin-Clavulanic acid (AMC) specific resistance is evaluated with the aim to understand the impact of this antibiotic in the human gut microbiota and especially versus this genus. Finally, the last part of this thesis concerns a detailed study regarding the vaginal microbiota, and more in specific the role of the Lactobacillus crispatus species in helping to preserve the healthy status of the host.