The microbiome is the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space. This microbial community is complex and abundant, with estimates of the total species that inhabit an individual ranging well into the thousands. Although it is evident that we understand only a small component of the human microbiome, there is growing recognition that resident microbial communities influence human nutrition, development and disease.
Much of our understanding of the human microbiome comes from culture-based approaches. Unfortunately, as much as 20% to 60% of the human-associated microbiome is presently uncultivable. Profiling bacterial communities by the culture-free, 16S rRNA gene sequencing approach has been enormously important in helping scientists identify the species present and quantify their abundance.
16S rRNA profiles can establish evolutionary relationships among bacteria but do not address gene content or gene expression. These limitations to the 16S rRNA gene sequencing have prompted efforts to examine the complexity of environmental samples by sequencing genomic libraries made from DNA extracted directly from the mixed sample, “metagenomics”, and from RNA,“transcriptomics”.