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Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing
- Source :
- Communications Biology, Gupta, S, Mortensen, M S, Schjørring, S, Trivedi, U, Vestergaard, G, Stokholm, J, Bisgaard, H, Krogfelt, K A & Sørensen, S J 2019, ' Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing ', Communications Biology, vol. 2, 291, pp. 1-7 . https://doi.org/10.1038/s42003-019-0540-1, Communications Biology, Vol 2, Iss 1, Pp 1-7 (2019)
- Publication Year :
- 2019
- Publisher :
- Nature Publishing Group UK, 2019.
-
Abstract
- 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.<br />Shashank Gupta, Martin Mortensen et al. compare the diagnostic efficiency of culturing and amplicon sequencing for studying the human microbiome. They show that amplicon sequencing identifies a greater number of species per sample, and can be implemented in clinical settings.
- Subjects :
- 0301 basic medicine
DNA, Bacterial
Male
Medicine (miscellaneous)
Clinical settings
Microbial communities
02 engineering and technology
Computational biology
Biology
Ribotyping
General Biochemistry, Genetics and Molecular Biology
Article
03 medical and health sciences
Feces
Predictive Value of Tests
Humans
Microbiome
lcsh:QH301-705.5
Phylogeny
Bacteriological Techniques
Bacteria
Human microbiome
Age Factors
Infant, Newborn
High-Throughput Nucleotide Sequencing
Infant
Reproducibility of Results
021001 nanoscience & nanotechnology
Healthy Volunteers
Gastrointestinal Microbiome
Hypopharynx
030104 developmental biology
lcsh:Biology (General)
Amplicon sequencing
Female
0210 nano-technology
General Agricultural and Biological Sciences
Subjects
Details
- Language :
- English
- ISSN :
- 23993642
- Volume :
- 2
- Database :
- OpenAIRE
- Journal :
- Communications Biology
- Accession number :
- edsair.doi.dedup.....882c9cefeff6c80d1627ec30c4c514da