Abstract
Eukaryotes and their environments serve as petri dishes, hosting an abundant and a rich prokaryotic microbiome. The assemblage of a eukaryotic host and its microbiome is referred to as a holobiont. The holobiont's microbiome interacts within itself, with the environment, and with the host at the chemical level through production of specialized metabolites resulting in homeostasis or dysbiosis. These interactions are triggered by a multitude of factors, such as community composition, age, presence of nutrients, xenobiotics, and change in physical conditions, such as temperature and oxygen. Understanding how holobionts respond and adapt to diverse triggers is necessary to uncover mechanisms of resilience or susceptibility to dysbiosis and to modulate the collective functioning of microbiome in health and disease. This article highlights the challenges associated with uncovering chemical contributions of individual holobiont members and the applicability of metabolomics-based approaches to uncover chemical signatures of microbial processes in the natural environment.