Sequencing the human microbiome in health and disease

Abstract

Molecular techniques have revolutionized the practice of standard microbiology. In particular, 16S rRNA sequencing, whole microbial genome sequencing and metagenomics are revealing the extraordinary diversity of microorganisms on Earth and their vast genetic and metabolic repertoire. The increase in length, accuracy and number of reads generated by high-throughput sequencing has coincided with a surge of interest in the human microbiota, the totality of bacteria associated with the human body, in both health and disease. Traditional views of host/pathogen interactions are being challenged as the human microbiota are being revealed to be important in normal immune systemfunction, to diseases not previously thought to have amicrobialcomponent and to infectious diseaseswith unknown aetiology. In this review,weintroduce the nature of the human microbiota and application of these three key sequencing techniques for its study, highlighting both advances and challenges in the field. We go on to discuss how further adoption of additional techniques, also originally developed in environmental microbiology, will allow the establishment of disease causality against a background of numerous, complex and interacting microorganisms within the human host. © The Author 2013.