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All known chlamydiae require a eukaryotic host cell to thrive. Using the environmental chlamydia\n            <jats:italic>Protochlamydia amoebophila<\/jats:italic>\n            within its natural host,\n            <jats:italic>Acanthamoeba castellanii<\/jats:italic>\n            , we investigated gene expression dynamics\n            <jats:italic>in vivo<\/jats:italic>\n            and throughout the complete chlamydial developmental cycle for the first time. This allowed us to infer how a major virulence mechanism, the type III secretion system, is regulated and employed, and we show that the physiology of chlamydiae undergoes a complete shift regarding carbon metabolism and energy generation. 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