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.

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

Durazzi, Francesco
Primo
Formal Analysis
;
Sala, Claudia
Secondo
Formal Analysis
;
Castellani, Gastone
Supervision
;
Manfreda, Gerardo
Supervision
;
Remondini, Daniel
Penultimo
Conceptualization
;
De Cesare, Alessandra
Ultimo
Conceptualization
2021

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.
Durazzi, Francesco; Sala, Claudia; Castellani, Gastone; Manfreda, Gerardo; Remondini, Daniel; De Cesare, Alessandra
File in questo prodotto:
File Dimensione Formato  
s41598-021-82726-y.pdf

accesso aperto

Tipo: Versione (PDF) editoriale
Licenza: Licenza per Accesso Aperto. Creative Commons Attribuzione (CCBY)
Dimensione 2.5 MB
Formato Adobe PDF
2.5 MB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11585/795739
Citazioni
  • ???jsp.display-item.citation.pmc??? 39
  • Scopus 66
  • ???jsp.display-item.citation.isi??? 63
social impact