Community genomics in microbial ecology and evolution

Genomic analyses of microbial communities can reveal the metabolic potential of uncultivated microorganisms.Community genomics emphasizes the analysis of natural coexisting species populations through cultivation-independent environmental genome sequencing. The approach enables post-genomic functional assays to be carried out to understand the ecology and evolution of microbial consortia.It possible to reconstruct near-complete, and possibly complete, genome sequences directly from environmental samples. However, heterogeneity in gene content and sequence identity, and genomic rearrangements in strain populations presents a fundamental challenge in reconstructing species genomes from mixed communities. Resolution of strain-level genomic heterogeneity is a fundamental goal of community genomic analysis. Comparative genome assembly that uses a sequenced strain as an assembly scaffold is a rapid and efficient method for analysis of the corresponding environmental population.Comparative genomics of DNA sequences from members of strain populations can reveal the extent to which individuals are representative of their associated populations, the form of genomic heterogeneity, and the importance of processes such as lateral gene transfer and recombination in genome evolution over relatively short timescales.Genomic data from communities can enable analyses of metabolic activity using gene-expression-array-based and proteomic methods. Analyses that evaluate gene expression have the potential to reveal the extent to which metabolic functions are partitioned among community members and how this changes as communities establish and develop.To understand the processes of adaptation and evolution, it is important to find ways in which genome and environmental change can be placed on the same timescale.