Abstract
Investigation of microbial community structure and biology has been progressing with the help of high-throughput functional genomics which have proven to be irreplaceable for studying diverse microbial communities. In this chapter, we discuss emerging strategies for microbial community analysis through metagenomic profiling and beyond. These are complemented and expanded by innovative DNA sequencing approaches for identifying (below species) strain-level variations and sequential community dynamics; assessing RNA, cDNA, and proteins to capture community functional activity in a more effective way, such as metatranscriptomics and metaproteomics, by mapping DNA or RNA reads directly to databases of gene sequences. Such databases include: COGs (Clusters of Orthologous Groups) KEGG (Kyoto Encyclopedia of Genes and Genomes) Orthology, Pfam, NOGs (Nonsupervised Orthologous Groups), and UniRef (UniProt Reference) Clusters. In this chapter, we describe the skills, current technological advances, and unresolved challenges involved in the functional analysis of microbial communities.
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