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

Gupta, Shashank, 1989- (author)
Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
Mortensen, Martin S. (author)
Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
Schjørring, Susanne (author)
Department of Bacterial, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark.
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Trivedi, Urvish (author)
Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
Vestergaard, Gisle (author)
Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
Stokholm, Jakob (author)
Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, Copenhagen, Denmark
Bisgaard, Hans (author)
Copenhagen Prospective Studies on Asthma in Childhood, Faculty of Health Sciences, University of Copenhagen, Copenhagen University Hospital Gentofte, Copenhagen, Denmark
Krogfelt, Karen A. (author)
Department of Bacterial, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark; Virus and Microbiological diagnostics, Statens Serum Institut, Copenhagen S, Denmark
Sørensen, Søren J. (author)
Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark Department of Bacterial, Parasites and Fungi, Statens Serum Institut, Copenhagen S, Denmark (creator_code:org_t)
2019-08-05
2019
English.
In: Communications Biology. - : Springer Nature. - 2399-3642. ; 2:1
Related links:
https://doi.org/10.1...
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https://www.nature.c...
https://urn.kb.se/re...
https://doi.org/10.1...
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  • Journal article (peer-reviewed)
Abstract Subject headings
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  • 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.

Subject headings

NATURVETENSKAP  -- Biologi -- Mikrobiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Microbiology (hsv//eng)

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