Nested PCR to optimize rpoB metabarcoding for lowconcentration and host-associated bacterial DNA

Laëtitia Leclerc; Gabryelle Agoutin; Thierry Brévault; Antony Champion; Jean Mainguy; Nicolas Nègre; Sudeeptha Yainna; Géraldine Pascal; Sophie Gaudriault; Jean-Claude Ogier

doi:10.1186/s12866-019-1546

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Nested PCR to optimize rpoB metabarcoding for lowconcentration and host-associated bacterial DNA

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Nested PCR to optimize rpoB metabarcoding for lowconcentration and host-associated bacterial DNA

Laëtitia Leclerc, Gabryelle Agoutin, Thierry Brévault, Antony Champion, Jean Mainguy, Nicolas Nègre, Sudeeptha Yainna, Géraldine Pascal, Sophie Gaudriault and Jean-Claude Ogier

Microbiology Spectrum

12/08/2025

DOI: https://doi.org/10.1186/s12866-019-1546

PMID: 40792510

Abstract

metabarcoding

host-associated microbiota

rpoBnested PCR

insect

Spodoptera frugiperda

Housekeeping genes have proven to be effective taxonomic markers for characterizing bacterial microbiota in short-read amplicon metabarcoding studies. A region of the rpoB gene has been shown to minimize Operational Taxonomic Unit (OTU) overestimation bias with a high degree of accuracy, providing better species-level taxonomic resolution (

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Title: Nested PCR to optimize rpoB metabarcoding for lowconcentration and host-associated bacterial DNA
Creators - without role: Laëtitia Leclerc - Université de Montpellier, Diversité, Génomes et Interactions Microorganismes-Insectes - DGIMI
Gabryelle Agoutin - Génétique Physiologie et Systèmes d'Elevage
Thierry Brévault - Agroécologie
Antony Champion - Université de Montpellier, Diversité, Adaptation et Développement des plantes - DIADE
Jean Mainguy - BIO
Nicolas Nègre - Université de Montpellier, Diversité, Génomes et Interactions Microorganismes-Insectes - DGIMI
Sudeeptha Yainna - Université de Montpellier, Diversité, Génomes et Interactions Microorganismes-Insectes - DGIMI
Géraldine Pascal - Génétique Physiologie et Systèmes d'Elevage
Sophie Gaudriault - Université de Montpellier, Diversité, Génomes et Interactions Microorganismes-Insectes - DGIMI
Jean-Claude Ogier - Université de Montpellier, Diversité, Génomes et Interactions Microorganismes-Insectes - DGIMI
Publication Details: Microbiology Spectrum
Grant note: This work was funded by the SPE "MicroSpodoRice" grant from INRAE. Jean Mainguy's work was supported by "La Region Occitanie" and the European Union via the "Regional Platforms of Research and Innovation" call for proposals of the Occitanie Region as part of the Operational Program FEDER-FSE MIDI-PYRENEES ET GARONNE 2014-2020.
Identifiers: 9980054209311
Academic Unit: Diversité, Adaptation et Développement des plantes - DIADE; Diversité, Génomes et Interactions Microorganismes-Insectes - DGIMI
Language: English
Resource Type: Journal article
Local Fields: hal-05220858