Genomic approaches to studying the human microbiota

Abstract

The human body is colonized by a vast array of microbes, which form communities of bacteria, viruses and microbial eukaryotes that are specific to each anatomical environment. Every community must be studied as a whole because many organisms have never been cultured independently, and this poses formidable challenges. The advent of next-generation DNA sequencing has allowed more sophisticated analysis and sampling of these complex systems by culture-independent methods. These methods are revealing differences in community structure between anatomical sites, between individuals, and between healthy and diseased states, and are transforming our view of human biology.

Figure 1. Data and analysis workflow for microbiome analysis

From a microbiota sample, DNA, RNA and protein can be extracted, and metadata and strains of bacteria obtained. Data from DNA can be supplemented with proteome and transcriptome analysis. During primary analysis, shotgun techniques can produce reads from DNA, which are then aligned to reference genomes to identify variants and community population genetics, assembled into contigs to make gene predictions or compared with databases. Alternatively, targeted sequencing such as 16S rRNA gene sequencing can be used to take a community census, and these data are then compared with databases to create tables of taxa and abundance, or analysed with software programs to cluster the reads into OTUs to create tables of abundance. The derivative data is used in secondary analysis for ecological metrics or competition and symbiosis analysis. In addition, shotgun reads and comparisons with reference genomes and databases can be used to build pathways and reconstruct the capabilities of a community. The combination of these analyses will contribute to understanding the differences within and between individuals.