Work

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

Year: 2020

Type: article

Abstract: 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.

Source: PLoS ONE

DOI: 10.1371/journal.pone.0227285

Authors: Ching Jian, Panu Luukkonen, Hannele Yki-Järvinen, Anne Salonen, Katri Korpela

Institutions: University of Helsinki, Helsinki University Hospital, Minerva Foundation

Language: English

Topic: Gut microbiota and health

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: gold

Estimated APC paid: $1,695