New technologies such as high-throughput methods and 13C-isotopologue-profiling
analysis are beginning to provide us with insight into the in vivo metabolism of
microorganisms, especially in the host cell compartments that are colonized by intracellular
bacterial pathogens. In this Review, we discuss the recent progress made in determining the
major carbon sources and metabolic pathways used by model intracellular bacterial
pathogens that replicate either in the cytosol or in vacuoles of infected host cells …

Bacterial metabolism has been studied intensively since the first observations of these
'animalcules' by Leeuwenhoek and their isolation in pure cultures by Pasteur. Metabolic
studies have traditionally focused on a small number of model organisms, primarily the
Gram negative bacillus Escherichia coli, adapted to artificial culture conditions in the
laboratory. Comparatively little is known about the physiology and metabolism of wild
microorganisms living in their natural habitats. For∼ 500–1000 species of commensals and …