Quantitative PCR provides a simple and accessible method for quantitative microbiota profiling


Autoři: Ching Jian aff001;  Panu Luukkonen aff002;  Hannele Yki-Järvinen aff002;  Anne Salonen aff001;  Katri Korpela aff001
Působiště autorů: Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland aff001;  Minerva Foundation Institute for Medical Research, Helsinki, Finland aff002;  Department of Medicine, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland aff003
Vyšlo v časopise: PLoS ONE 15(1)
Kategorie: Research Article
doi: 10.1371/journal.pone.0227285

Souhrn

The use of relative abundance data from next generation sequencing (NGS) can lead to misinterpretations of microbial community structures, as the increase of one taxon leads to the concurrent decrease of the other(s) in compositional data. Although different DNA- and cell-based methods as well as statistical approaches have been developed to overcome the compositionality problem, and the biological relevance of absolute bacterial abundances has been demonstrated, the human microbiome research has not yet adopted these methods, likely due to feasibility issues. Here, we describe how quantitative PCR (qPCR) done in parallel to NGS library preparation provides an accurate estimation of absolute taxon abundances from NGS data and hence provides an attainable solution to compositionality in high-throughput microbiome analyses. The advantages and potential challenges of the method are also discussed.

Klíčová slova:

Bacteria – DNA extraction – Flow cytometry – Microbiome – Next-generation sequencing – Polymerase chain reaction – Ribosomal RNA – Statistical data


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