Human Microbiome Analysis via the 16s rRNA Gene
Jonathan McCafferty and Anthony Fodor
from: Bioinformatics and Data Analysis in Microbiology (Edited by: Özlem Taştan Bishop). Caister Academic Press, U.K. (2014)
The human associated microbiota has been linked to an ever-expanding set of diseases including obesity, cancer and inflammatory bowel disease. While the decreasing cost of sequencing is making whole-genome metagenomic shotgun sequencing more feasible, 16S rRNA based sequencing studies remain the most commonly utilized method to characterize a microbial community. In this review, we consider different methods to characterize a mixed microbial community by examination of the 16S rRNA gene. We discuss older, low-resolution methods such as Terminal Restriction Length Polymorphisms (T-RFLP) and Automated Ribosomal Intergenic Spacer Analysis (ARISA), which yield low-cost "snapshots" of the microbial community that can be generated rapidly. We next consider current high-throughput sequencing technology from 454 Life Sciences and Illumina. These techniques generate large amounts of data and careful consideration must be given to how low-quality sequences and PCR chimeras are removed from downstream consideration. We examine algorithms for clustering sequences into Operational Taxonomic Units (OTUs) and for assigning taxonomy. Finally, we consider methods for assigning statistical significance to differences between different microbial communities read more ...