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Published Online: 11 July 2022

Comparison Between Full-Length 16S rRNA Metabarcoding and Whole Metagenome Sequencing Suggests the Use of Either Is Suitable for Large-Scale Microbiome Studies

Publication: Foodborne Pathogens and Disease
Volume 19, Issue Number 7

Abstract

Since the number of studies of the microbial communities related to food and food-associated matrices almost completely reliant on next-generation sequencing techniques is rising, evaluations of these high-throughput methods are critical. Currently, the two most used sequencing methods to profile the microbiota of complex samples, including food and food-related matrices, are the 16S ribosomal RNA (rRNA) metabarcoding and the whole metagenome sequencing (WMS), both of which are powerful tools for the monitoring of foodborne pathogens and the investigation of the microbiome. Herein, the microbial profiles of 20 bulk tank milk filters from different dairy farms were investigated using both the full-length 16S (FL-16S) rRNA metabarcoding, a third-generation sequencing method whose application in food and food-related matrices is yet in its infancy, and the WMS, to evaluate the correlation and the reliability of these two methods to explore the microbiome of food-related matrices. Metabarcoding and metagenomic data were generated on a MinION platform (Oxford Nanopore Technologies) and on a Illumina NovaSeq 6000 platform, respectively. Our findings support the greater resolution of WMS in terms of both increased detection of bacterial taxa and enhanced detection of diversity; in contrast, FL-16S rRNA metabarcoding has proven to be a promising, less expensive, and more practical tool to profile most abundant taxa. The significant correlation of the two technologies both in terms of taxa diversity and richness, together with the similar profiles defined for both highly abundant taxa and core microbiomes, including Acinetobacter, Bacillus, and Escherichia genera, highlights the possible application of both methods for different purposes. This study allowed the first comparison of FL-16S rRNA sequencing and WMS to investigate the microbial composition of a food-related matrix, pointing out the advantageous use of FL-16S rRNA to identify dominant microorganisms and the superior power of WMS for the taxonomic detection of low abundant microorganisms and to perform functional analysis of the microbial communities.

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Information

Published In

cover image Foodborne Pathogens and Disease
Foodborne Pathogens and Disease
Volume 19Issue Number 7July 2022
Pages: 495 - 504
PubMed: 35819265

History

Published online: 11 July 2022
Published in print: July 2022

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Data Availability Statement

The datasets presented in this study can be found in the following online repository: https://www.ncbi.nlm.nih.gov/, BioProject ID PRJNA808865, PRJNA809009.

Authors

Affiliations

Selene Rubiola*
Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.
Guerrino Macori*
University College Dublin-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Dublin, Ireland.
Tiziana Civera
Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.
Séamus Fanning
University College Dublin-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Dublin, Ireland.
University College Dublin-Centre for Food Safety, School of Public Health, Physiotherapy & Sports Science, Dublin, Ireland.
Department of Veterinary Sciences, University of Turin, Grugliasco, Italy.

Notes

*
Both these authors contributed equally to this study.
Address correspondence to: Francesco Chiesa, DVM, PhD, Department of Veterinary Sciences, University of Turin, Largo Paolo Braccini 2, 10095 Grugliasco (TO), Italy [email protected]

Authors' Contributions

Writing—original draft, formal analysis, investigation, and conceptualization by S.R. Writing—review and editing, resources, validation, and conceptualization by G.M. Writing—review and editing, and funding acquisition by T.C. Writing—review and editing, and resources by S.F. Writing—review and editing, and formal analysis by M.M. Writing—review and editing, visualization, supervision, and conceptualization by F.C.

Disclosure Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Funding Information

This study was supported by Ministero dell'Istruzione, dell'Università e della Ricerca (MIUR) under the programme “Dipartimenti di Eccellenza ex L.232/2016” to the “Department of Veterinary Science, University of Turin.” This study was supported by European Regional Development Funds (FESR 2014-2020—D24I19000980002)—TECH4MILK.

Ethical Statement

This study does not require Institutional Review Board (IRB) approval.

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