456 Beneficial Microbes 1 (4) kinds of bifidobacteria that establish in the gut of a given child. The second chapter gives an overview of genomics of bifidobacteria, where we stand now and where we are going. It describes how during recent years microbiological research has been fundamentally changed by the everincreasing number of publicly available bacterial wholegenome sequences. This sequence information has largely affected our understanding of the metabolic capabilities, genetics and phylogeny of bifidobacteria. Due to their perceived positive contribution to maintaining a balanced gut homeostasis, bifidobacteria represent a developing area of scientific interest with respect to genomics, molecular biology, genetics and physiology. Recent genome sequencing of different bifidobacterial species has provided the complete genetic make-up of these bacteria. The chapter discusses how genomic data has provided insights into bifidobacterial evolution, while at the same time revealing genetic functions that explain their presence in the particular ecological environment of the gastro-intestinal tract, such as the infant gut. This concept is taken a step further in Chapter 3, where ecological niches are correlated with the presence of specific genes in the genome of certain species. Also, the core genome sequences for bifidobacteria can be derived from the available genome sequences. Thus, recent genome sequencing has provided detailed insights into the genetic make-up of some members of the genus Bifidobacterium, although it represents only the first step in moving towards a better understanding of the biology and metabolic capabilities of these bacteria, and further comparative analyses of these genomes are necessary to increase our understanding of the physiological and metabolic behaviour of these microorganisms, in particular with regard to the way in which bifidobacteria have adapted to the intestinal environment.

Chapter 4 describes the metabolism of bifidobacteria, focusing on oligosaccharide metabolism, as these are the major carbohydrate polymers that are available in the otherwise nutrient-limited environment. Interestingly, infant-associated bifidobacterial phylotypes appear to have evolved the ability to ferment milk oligosaccharides, whereas adult-associated species utilise plant oligosaccharides, consistent with what they encounter in their respective environments. The metabolism of prebiotics that should mimic human milk oligosaccharides is also discussed. Apart from carbohydrate metabolism, the chapter reviews nitrogen and iron metabolism. Chapter 13 describes the molecular tools that are available to study the physiology of bifidobacteria. The current knowledge on the mobile genetic elements of bifidobacteria (phages, plasmids, and transposons) is presented, and the chapter reviews the different types of vectors available for the Bifidobacterium species, together with the transformation procedures for introducing DNA into bifidobacterial cells.