16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls

By J. Janda, S. Abbott. Journal of Clinical Microbiology, 2007

2,053 citations recorded by the source corpus.

Subfields: Clinical Biochemistry, Epidemiology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/485efa3d2eb4ca7af347e6f116a660bdd41c31f2

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Citations in the corpus

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation (2017, neutral): “Unlike 16S rRNA gene sequencing 3 , whole metagenome shotgun sequencing 4 can identify chromosomes, plasmids and bacteriophages 5,6 .”
The Rebirth of Culture in Microbiology through the Example of Culturomics To Study Human Gut Microbiota (2015, background): “In fact, only 1,791 official bacterial species had been recognized in 1980, whereas currently, 12,000 species have been recorded (9).”
Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics (2017, background): “While providing valuable insights into the broad characteristics of FMTs, amplicons from the 16S ribosomal RNA gene do not offer the resolution to effectively identify populations that colonize recipients [27].”
Sphingomonas: from diversity and genomics to functional role in environmental remediation and plant growth (2020, background): “lowest or highest taxonomic ranks [48], primer mis-”
Current challenges and best-practice protocols for microbiome analysis (2019, methodology): “Most of the 16S rRNA-based genotyping protocols use V5–V6, V3–V4, or V4 hypervariable regions to identify and catalogue microbial profiles [17, 18].”
The Genus Aeromonas: Taxonomy, Pathogenicity, and Infection (2010, methodology): “From the advent of the approved lists in 1980 to September 2007, more than a 450% increase in the number of validly published bacterial species has occurred (145).”
The importance of dispersal related and local factors in shaping the taxonomic structure of diatom metacommunities (2009, background): “5% similarity) in these datasets above which there is universal agreement of what constitutes definitive and conclusive identification to the rank of species (Janda and Abbott 2007).”
Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing (2021, background): “regions interspersed with nine variable regions (V-regions), V1 to V9 (8, 9).”
Identification of Bacterial Fish Pathogens in Brazil by Direct Colony PCR and 16S rRNA Gene Sequencing (2015, methodology): “For this reason, methods based on 16S rRNA ribosomal gene amplification and sequencing have been widely explored [13].”
The Hologenome Concept: Human, Animal and Plant Microbiota (2014, background): “…the main ones being: (1) its presence in almost all cells; (2) the function of the rRNA gene over time has not changed, suggesting that random sequence changes are an accurate measure of time (evolution); and (3) the rRNA gene is large enough for informatics purposes (Janda and Abbott 2007).”