From qualitative to quantitative data in microbiome analysis: Using metagenomics for qPCR validation

Michael Schloter 1,2,*,Gisle Vestergaard 1 , Anne Schoeler 1 , Stefanie Schulz 1 , Fabian Bergkemper 1
1 Helmholtz Zentrum München, Germany
2 Technical University of Munich, Germany

Microbial diversity in nature is enormous and even today we are unable to predict the correct number of species which are harboured by most ecosystems including our human body. This situation becomes even worse when not one marker gene is stud- ied, like in the case of the analysis of species richness, but complete metagemones and the related functional traits should be described. Here also most next generation sequencing approaches fail as sequencing efforts are needed to cover functional diversity which go far beyond 5 Tbases. Furthermore as still most of the func- tional traits are not well described and an annotation of reads towards predicted functions is hard to do or even impossible. In this presentation we describe an approach linking sequencing of metagenomes with a relative low coverage (10 Gbases or less), with the aim to identify key genes of interest which drive certain pro- cesses and to use this information to develop highly targeted primer pairs, which might be useful for in depth analysis of the diversity of those genes as well as a quantitative assessment. We consider this approach as “2nd generation full cycle” in microbial ecology.

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