Related Experiment Video
Updated: May 27, 2026

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing
Published on: August 25, 2018
Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and
Simon Roux1, François Enault, Gisèle Bronner
1Clermont Université, Université Blaise Pascal, Clermont-Ferrand, France.
Abstract:
PCR amplification of the rRNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein-coding genes compared to 16S rRNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected (rplB, pyrG, fusA, leuS and rpoB) and compared with 16S rRNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as Actinobacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16S rRNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of rRNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.
Related Concept Videos
Modern Molecular Taxonomy
Applications of Molecular Taxonomy
Phylogenetic Species Concept in Microbiology
Diversity of Archaea I
Methods to Assess Microbial Communities
Diversity of Archaea II

