An integrated workflow for analyzing microbial communities from different environments using high-throughput metaomic technologies. DNA, RNA, proteins, and/or metabolites are extracted from environmental samples for sequencing and protein/metabolite identification. At the same time, physiological, ecological, and functional information can be obtained via reference genomes and single-cell genomics, which helps with sequencing data analysis and functional annotation, generating useful information for microarray development, especially with novel genes. Microarray-based technologies can be used as a routine tool to address various microbial ecology questions in a rapid and cost-effective manner. Furthermore, metagenomic, metaproteomic, metametabolomic, stable isotope probing, and microarray data can be used alone or coupled with metadata for network analysis and modeling, understanding of microbial diversity, distribution and assembly mechanisms, and linking the microbial community structure with both environmental factors and ecosystem functioning.
mBio. 2015 Jan-Feb;6(1):e02288-14.