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...

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Autores principales:	Francesco Durazzi, Claudia Sala, Gastone Castellani, Gerardo Manfreda, Daniel Remondini, Alessandra De Cesare
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/5d06a0ab160c4b69b32e7bdfe9894a8f
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spelling	oai:doaj.org-article:5d06a0ab160c4b69b32e7bdfe9894a8f2021-12-02T14:06:11ZComparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota10.1038/s41598-021-82726-y2045-2322https://doaj.org/article/5d06a0ab160c4b69b32e7bdfe9894a8f2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-82726-yhttps://doaj.org/toc/2045-2322Abstract 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.Francesco DurazziClaudia SalaGastone CastellaniGerardo ManfredaDaniel RemondiniAlessandra De CesareNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-10 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Francesco Durazzi Claudia Sala Gastone Castellani Gerardo Manfreda Daniel Remondini Alessandra De Cesare Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
description	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.
format	article
author	Francesco Durazzi Claudia Sala Gastone Castellani Gerardo Manfreda Daniel Remondini Alessandra De Cesare
author_facet	Francesco Durazzi Claudia Sala Gastone Castellani Gerardo Manfreda Daniel Remondini Alessandra De Cesare
author_sort	Francesco Durazzi
title	Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
title_short	Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
title_full	Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
title_fullStr	Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
title_full_unstemmed	Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota
title_sort	comparison between 16s rrna and shotgun sequencing data for the taxonomic characterization of the gut microbiota
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/5d06a0ab160c4b69b32e7bdfe9894a8f
work_keys_str_mv	AT francescodurazzi comparisonbetween16srrnaandshotgunsequencingdataforthetaxonomiccharacterizationofthegutmicrobiota AT claudiasala comparisonbetween16srrnaandshotgunsequencingdataforthetaxonomiccharacterizationofthegutmicrobiota AT gastonecastellani comparisonbetween16srrnaandshotgunsequencingdataforthetaxonomiccharacterizationofthegutmicrobiota AT gerardomanfreda comparisonbetween16srrnaandshotgunsequencingdataforthetaxonomiccharacterizationofthegutmicrobiota AT danielremondini comparisonbetween16srrnaandshotgunsequencingdataforthetaxonomiccharacterizationofthegutmicrobiota AT alessandradecesare comparisonbetween16srrnaandshotgunsequencingdataforthetaxonomiccharacterizationofthegutmicrobiota
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Comparison between 16S rRNA and shotgun sequencing data for the taxonomic characterization of the gut microbiota

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