Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing

Shashank Gupta, Martin S. Mortensen, Susanne Schjørring, Urvish Trivedi, Gisle Vestergaard, Jakob Stokholm, Hans Bisgaard, Karen A. Krogfelt, Søren J. Sørensen*

*Corresponding author af dette arbejde

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    Abstrakt

    Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs. However, are we really ready for this transition? Here we compare the diagnostic efficiency of the two methods using a large number of samples (n = 1,748 fecal and n = 1,790 hypopharyngeal), among healthy children at different time points. Here we show that bacteria identified by NGS represented 75.70% of the unique bacterial species cultured in each sample, while TCM only identified 23.86% of the bacterial species found by amplicon sequencing. We discuss the pros and cons of both methods and provide perspective on how NGS can be implemented effectively in clinical settings.

    OriginalsprogEngelsk
    Artikelnummer291
    Sider (fra-til)291
    TidsskriftCommunications Biology
    Vol/bind2
    Udgave nummer1
    DOI
    StatusUdgivet - 1 dec. 2019

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