Technology and techniques for microbial ecology via DNA sequencing

Abstract

High-throughput sequencing technology, coupled with the use of conserved marker genes, has allowed for the understanding of communities of microbes (both culturable and unculturable) as well as their phylogenetic placement. The recent explosion of sequencing data prompted the development of software that could process the vast amount of data generated and phylogenetically differentiate groups of samples. Host-associated microbial studies have revealed that microbes are highly varied between individuals and fluctuate within an individual. Large-scale studies are being undertaken that include collection of extensive environmental data to help uncover the forces that shape microbial communities.

Figure 1.

Total ribosomal small subunit sequences in GenBank by year. The nucleotide database was queried with ribosomal rRNA (rRNA; Feature key), “X” (publication date), and 16S (title) for each year from 1993 to 2012.

Figure 2.

Phylogenetic tree of 5,088 mouse (red) ceca-associated 16S rRNA sequences reported in this study and 11,831 human (blue) colon–associated 16S rRNA sequences. Scale bar indicates sequence convergence. Adapted by permission from Reference .