Metaproteomic analysis adds a functional glimpse into host–microbe succession in an infant's GI

Succession is a fundamental concept in ecology, describing the process by which pioneering species colonize a new environmental niche, paving the way for increasingly complex, yet stable ecosystems. The human gut—among the most complex ecosystems known—develops from a nearly sterile state as newborns to a thriving functional network of trillions of organisms living in concert with the host. Recent microbiome analyses have begun to characterize the identities of the microbes during this period of colonization. However, the biochemical processes that govern the stages of interorganism succession remains a poorly understood, yet exciting frontier. Toward the goal of learning how host–microbe symbiosis arises and is maintained, Young et al. ( Proteomics 2015, 15 , 3463–3473) present a longitudinal metaproteomic case study of an infant during her second and third weeks of life. In the first such analysis of its kind, Young et al. portray overlapping stages of protein production by both the microbiota and the host consistent with their increasing complexity, and deepening interactions.