The microorganisms naturally inhabiting the gastrointestinal tract, collectively known as the gut “microbiota”, serve as a natural barrier to prevent the invasion and expansion of pathogens, a function termed “colonization resistance”. Several processes have been proposed to explain such a host protection conferred by the microbiota including induction of immune responses, reduction of luminal oxygen, and production of microbiota-derived inhibitory compounds.
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Microbiome studies offer important potential to identify organisms associated with human disease. Longitudinal measures may further reveal the dynamics of the microbiome and its accumulating effects on health outcomes. However, microbiome data are complex in nature, involving high dimensionality, compositionality, zero inflation and taxonomic hierarchy. This complexity cannot be adequately addressed using existing statistical methods, leaving the power of microbiome data relatively unharnessed.