Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. Franzosa Eric A,Hsu Tiffany,Sirota-Madi Alexandra,Shafquat Afrah,Abu-Ali Galeb,Morgan Xochitl C,Huttenhower Curtis Nature reviews. Microbiology High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring multiple 'omic' data types that better capture community functional activity, such as transcriptomics, proteomics and metabolomics; and combining multiple forms of omic data in an integrated framework. We highlight studies in which the 'multi-omics' approach has led to improved mechanistic models of microbial community structure and function. 10.1038/nrmicro3451