Stable isotope probing: uses in metagenomics
Ondrej Uhlik, Lucie Musilova, Katerina Demnerova, Tomas Macek and Martina Mackova
from: Metagenomics: Current Innovations and Future Trends (Edited by: Diana Marco). Caister Academic Press, U.K. (2011)
Until recently, investigating functions of microbial populations was restricted to thorough studying of pure cultures. Molecular biology tools enabled scientists to take a much deeper insight into the phylogenetic as well as metabolic diversity but hardly allowed for linking the phylogenetic identity with the metabolic activity which the microbes disposed of. Stable isotope probing (SIP) was one of the first microbial ecology tools to enable such a linkage. SIP consists of providing the community with a stable isotope labelled substrate and subsequent extraction and analysis of the labelled biomarkers. This text summarizes why SIP is a technique of an outstanding importance for microbial ecology and related fields and further focuses on SIP using DNA as a biomarker since DNA is one of the few molecules that bears both phylogenetic and functional information. Much deeper insight into stable isotope labelled DNA has been allowed especially due to current advances in high-throughput sequencing technologies. Metagenomic analyses, however, profit from stable isotope probing as well by reduced complexity of studied DNA (only populations actively performing a particular process). Therefore, when DNA-SIP is used in metagenomics, it is much easier to reconstruct individual genomes of key uncultured microbes as well as detect genes of interest read more ...