Sampling, analyzing, and integrating microbiome ‘omics data in a translational clinical setting

The intestinal microbiome is a complex assemblage of microorganisms that is critical for host health. It is highly individualized and associated with diseases, ranging from inflammatory bowel disease and obesity to cancers. Recent technological advances have allowed an unprecedented characterization of the microbiome using metagenomics, metatranscriptomics, and metabolomics methods, which have highlighted the microbiome as a target for personalized, precision medical interventions. These technologies generate an exponentially larger amount of data than that possible even a decade ago, resulting in analytical challenges. Moreover, integrating different ‘omics data to truly gain a translational, mechanistic understanding of the interaction between the microbiome and human host is a current challenge and active area of research. In this chapter, we discuss considerations associated with collecting samples for microbiome ‘omics research, analytical tools available for analysis of these data, and ongoing efforts to integrate various datasets, to understand the total systems biology of the host-microbe interactions.