Culture vs. Amplicon sequencing: a large-scale comparative study between 3,538 samples from healthy children

Next-Generation Sequencing (NGS) of 16S rRNA gene is now 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. Based on the comparison, there was discordance between the two; TCMs identified up to 8 bacterial species per sample, whereas NGS identified up to 140 unique species per sample. 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.