The Omics Era and Host Microbiomes

Abstract

Advancement in ‘omics’ technologies permits the quantitative monitoring of the plethora of biological molecules in natural systems in a high-throughput manner. Such technologies allow determination of the variation between different biological states (RNA, DNA and protein) on a genomic scale. From a fundamental knowledge perspective, no single omics technique can completely disentangle the complexities of host microbiomes. As a result, several ‘omics’ platforms have been developed in order to better understand the systems biology of host-microbiome interactions (Zhang et al. 2010). For instance, metagenomics, meta-transcriptomics, meta-proteomics and metabolomics methods provide information on the meta-genome. Overall changes in the mRNA or proteins levels of the host microbiome can be determined dynamic changes of all classes of molecules within a microbiome over a given time period. Integration of different layers of information obtained from multi-omics approaches are required in order to paint a meaningful canvas of functional and dynamic interactions of host-microbiome communities. To date, the application of more than one -omics technology have been applied to different host microbiomes, including in plant and humans (Tlaskalova-Hogenova et al. 2011; Fernandez et al. 2013; Tkacz and Poole 2015; Addis et al. 2016; Lareen et al. 2016). Application of multi-omics approaches to the microbiome of these hosts unravels their essential functions, which are key throughout the host’s life cycle; thus, associated microbial communities are sometimes referred to as the ‘secondary genome’ of the host (Siboni et al. 2008). This perspective chapter briefly describes what has been unveiled so far and what still needs to be done in order to better understand human and plant microbiomes.