Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

Abstract

In this paper we compared taxonomic results obtained by metataxonomics (16S rRNA gene sequencing) and metagenomics (whole shotgun metagenomic sequencing) to investigate their reliability for bacteria profiling, studying the chicken gut as a model system. The experimental conditions included two compartments of gastrointestinal tracts and two sampling times. We compared the relative abundance distributions obtained with the two sequencing strategies and then tested their capability to distinguish the experimental conditions. The results showed that 16S rRNA gene sequencing detects only part of the gut microbiota community revealed by shotgun sequencing. Specifically, when a sufficient number of reads is available, Shotgun sequencing has more power to identify less abundant taxa than 16S sequencing. Finally, we showed that the less abundant genera detected only by shotgun sequencing are biologically meaningful, being able to discriminate between the experimental conditions as much as the more abundant genera detected by both sequencing strategies.

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“…Bias may also be observed by the exclusive utilisation of 16 S rRNA gene sequencing. It has been shown in the gut microbiota that shotgun sequencing (also known as metagenomic sequencing) has more power to identify less abundant taxa, and the less abundant genera detected are biologically more meaningful [ 58 ]. Moreover, it is difficult to summarise the alpha diversity (species richness within a sample) and beta diversity (species richness between samples) due to different statistical and bioinformatics analyses being used across studies.…”

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“…Furthermore, the potential role of SCFA-producing microbiota underlines the importance of performing functional microbiota analysis by performing metagenomic sequencing or measuring microbial metabolites in the future. Furthermore, it would be worthwhile to use full length 16S sequencing or metagenomic sequencing to acquire even higher taxonomic resolutions when studies evolve from explorative pilot studies to more causal designs [35].…”

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“…On the contrary, shotgun metagenomics is based on DNA molecules, which are randomly broken into fragments that are then sequenced [90]. Hence, the shotgun metagenomic approach provides major information on the taxonomic composition and inferred functional genes, thus fully characterizing the sample, despite requested high coverage [91].…”