Bacteria have co-evolved with humans, adapting not only to genotypic idiosyncrasies, but also to behavioral and lifestyle changes. Together, the human and the microbiome we host form a ‘holobiont’, with these organisms playing a vital role in maintaining our physiology and health. Moreover, these dynamic communities form ecosystems within various niches in the human body, and by virtue of this lifestyle, are extremely responsive to shifts in the local environment. Thus, the microbiome acts as a ‘canary in the coal mine’. As a clinician and a microbial ecologist, my research focuses on harnessing the capabilities of the microbiome to promote health and to act as prognosticators of impending disease states as well as biomarkers of disease activity. For over a decade, our research group has explored the factors that shape this microbiome, with a view to identifying common microbial targets for therapeutic intervention as well as idiosyncratic features within this system.