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

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 comp...

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Bibliographic Details
Published inScientific reports Vol. 11; no. 1; p. 3030
Main Authors Durazzi, Francesco, Sala, Claudia, Castellani, Gastone, Manfreda, Gerardo, Remondini, Daniel, De Cesare, Alessandra
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 04.02.2021
Nature Publishing Group
Nature Portfolio
Subjects
631/158/855
631/1647/514/2254
639/705/531
Bacteria - classification
Bacteria - genetics
Digestive system
Digestive tract
Gastrointestinal Microbiome - genetics
Genera
High-Throughput Nucleotide Sequencing - methods
Humanities and Social Sciences
Humans
Intestinal microflora
Invertebrates
Metagenome - genetics
Metagenomics
Microbiota
Microbiota - genetics
multidisciplinary
Phylogeny
Relative abundance
RNA, Ribosomal, 16S - genetics
rRNA 16S
Science
Science (multidisciplinary)
Sequence Analysis, DNA
Taxonomy
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Summary: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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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-021-82726-y