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

TY - JOUR

T1 - Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing

AU - Gupta, Shashank

AU - Mortensen, Martin S

AU - Schjørring, Susanne

AU - Trivedi, Urvish

AU - Vestergaard, Gisle

AU - Stokholm, Jakob

AU - Bisgaard, Hans

AU - Krogfelt, Karen A

AU - Sørensen, Søren J

PY - 2019/12/1

Y1 - 2019/12/1

N2 - 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.

AB - 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.

U2 - 10.1038/s42003-019-0540-1

DO - 10.1038/s42003-019-0540-1

M3 - Journal article

C2 - 31396571

SN - 2399-3642

VL - 2

SP - 1

EP - 7

JO - Communications Biology

JF - Communications Biology

M1 - 291

ER -