A glimpse on the genomic evolution of bifidobacteria

The Bifidobacteriaceae family encompasses 54 (sub)species belonging to the Bifidobacterium genus as well as other 13 taxa distributed among the Aeriscardovia, Alloscardovia, Bombiscardovia, Gardnerella, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia genera (Whitman, 2012). While the majority of the 54 (sub)species of the Bifidobacterium genus colonize the gut of various animals, including humans, the remaining species are generally associated with human and animal dental caries, as well as human clinical samples of tonsils abscesses and bacterial vaginosis (Catlin, 1992, Mantzourani, et al., 2009, Turroni, et al., 2011). The relevance of bifidobacteria, as members of the human gut microbiota, has driven the interest of the scientific community into the understanding of the mechanisms responsible for colonization and persistence in the human gut. In fact, bifidobacteria have shown to exert host health-promoting activities such as degradation of diet-derived carbohydrates that cannot be digested by the host’s enzymes, vitamin production, maturation and stimulation of the immune system, development of the gastrointestinal tract and inhibition of the growth of other pathogenic bacteria (Turroni, et al., 2008, Turroni, et al., 2011). Furthermore, the highest average abundance of bifidobacterial species retrieved in new-borns, such as Bifidobacterium longum subsp. infantis, Bifidobacterium bifidum and Bifidobacterium breve, has opened a new frontier in the understanding of the mechanisms of vertical transmitted bacteria from mother to child. Due to these features and capabilities, bifidobacteria are currently used in many functional foods as probiotics. The aim of this Ph.D. thesis is to explore the genetic repertoire and evolutionary development of the members of the Bifidobacterium genus using next generation sequencing approaches and in silico analyses. Until now, only few species of the genus Bifidobacterium have been studied in detail, while in this thesis the entire repertoire of (sub)species has been take in account for genomic analyses, also encompassing metagenomics data to trace the presence of bifidobacteria in the gut of adults and infants. A complete investigation of the genetic repertoire of the Bifidobacterium genus (pan-genome) has been revealed through massive draft genome sequencing of all the members of this genus. Thanks to the pan-genome reconstruction, an identification of the bifidobacterial core genome sequences and the exploration of the evolutionary development of each (sub)species was performed. Dissecting the mobilome of this genus, bifidoprophage sequences as well as the resistome of bifidobacteria were identified within the bifidobacterial chromosomes. Furthermore, the development of an in silico pipeline for the genome assembly and gene’s annotation of (bifido)bacterial genomes allowed a more efficient way to analysed the (bifido)bacterial genomics. This approach was also applied to ancient metagenomics datasets (Tyrolean Iceman mummy Ötzi) in order to reconstruct the chromosomes of ancient human gut commensals.