Quantitative Assessment of Shotgun Metagenomics and 16S rDNA Amplicon Sequencing in the Study of Human Gut Microbiome.

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PubMed ID: 29652573

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Laudadio I, Fulci V, Palone F, Stronati L, Cucchiara S, Carissimi C

OMICS. Apr 2018. doi: 10.1089/omi.2018.0013


Next Generation Sequencing (NGS) is emerging as a powerful approach to microbiome investigation, allowing characterization of microbial communities at unprecedented resolution, without prior culturing. The taxonomic profile of a microbial community can be obtained either by shotgun analysis of random DNA fragments or through 16S ribosomal RNA gene (rDNA) amplicon sequencing. Amplicon sequencing of 16S rDNA yields quantitatively and qualitatively different results compared to shotgun metagenomics when the two techniques are used to assess microbial community composition on the same samples.

However, most of such comparisons were either based on the recovery of 16S rDNA sequences in the shotgun metagenomics data or limited to a single microbiome or synthetic samples. Direct comparison of shotgun metagenomics and 16S rDNA amplicon sequencing on the same samples was performed only once in the recent literature, suggesting that the two methods yield comparable results.

In this article the authors set out to compare the outcome of these two alternative approaches to the microbiome characterization in human gut microbiomes from stool samples. To this end, they processed six different samples with both techniques and they report that shotgun next generation sequencing metagenomics allows much deeper characterization of the microbiome complexity, allowing identification of a larger number of species for each sample, compared to 16S rDNA amplicon sequencing.

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Javier Velasco