Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing
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Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing. / Gupta, Shashank; Mortensen, Martin S; Schjørring, Susanne; Trivedi, Urvish; Vestergaard, Gisle; Stokholm, Jakob; Bisgaard, Hans; Krogfelt, Karen A; Sørensen, Søren J.
I: Communications Biology, Bind 2, 291, 2019, s. 1-7.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › fagfællebedømt
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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
Y1 - 2019
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
VL - 2
SP - 1
EP - 7
JO - Communications Biology
JF - Communications Biology
SN - 2399-3642
M1 - 291
ER -
ID: 225603869