Comparative Analysis of Primers Used for 16S rRNA Gene Sequencing in Oral Microbiome Studies

• Published in: Methods and protocols Vol. 6; no. 4; p. 71
• Main Authors: Song, Yuri, Yu, Yeuni, Chung, Jin
• Format: Journal Article
• Language: English
• Published: Basel MDPI AG 01.08.2023; MDPI
• Subjects: 16s RNA; Classification; Comparative analysis; gene sequencing; Genes; in silico; Microbiomes; Microbiota; Microorganisms; oral microbiome; Phylogenetics; Phylogeny; primer; Primers; RNA; rRNA 16S; Simulation methods; Trees; South Korea; United States > US
• ISSN: 2409-9279; 2409-9279
• DOI: 10.3390/mps6040071

Recent advances in genomic technologies have enabled more in-depth study of the oral microbiome. In this study, we compared the amplicons generated by primers targeting different sites of the 16S rRNA gene found in the Human Oral Microbiome Database (HOMD). Six sets of primer targeting V1–V2, V1–V3, V3–V4, V4–V5, V5–V7 and V6–V8 regions of 16S rRNA were tested via in silico simulation. Primers targeting the V1–V2, V3–V4, and V4–V5 regions generated more than 90% of the original input sequences. Primers targeting the V1–V2 and V1–V3 regions exhibited a low number of mismatches and unclassified sequences at the taxonomic level, but there were notable discrepancies at the species level. Phylogenetic tree comparisons showed primers targeting the V1–V2 and V3–V4 regions showed performances similar to primers targeting the whole 16s RNA region in terms of separating total oral microbiomes and periodontopathogens. In an analysis of clinical oral samples, V1–V2 primers showed superior performance for identifying more taxa and had better resolution sensitivity for Streptococcus than V3–V4 primers. In conclusion, primers targeting the V1–V2 region of 16S rRNA showed the best performance for oral microbiome studies. In addition, the study demonstrates the need for careful PCR primer selections.