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Background <p>This study investigated the bacterial community composition, phenotypes, and differentially abundant taxa in primary and secondary/persistent endodontic infections.</p> Methods <p>Bacterial profiles of 12 primary and 12 secondary/persistent endodontic infections were analyzed using 16&#xa0;S V3-V4 next-generation sequencing. Reads were processed into ASVs using DADA2 in Qiime2, and taxonomy was assigned with the SILVA dataset. Alpha and beta diversity were compared between groups using Kruskal-Wallis and PERMANOVA. LEfSe identified differentially abundant taxa (LDA &gt; 2), and Bugbase predicted community phenotypes, which were compared with the Mann-Whitney-Wilcoxon test.</p> Results <p>The alpha-diversity and beta-diversity are higher in the secondary/persistent group than in the primary one. In the primary group, anaerobic, Gram-negative, and potentially pathogenic microbes are dominant, whereas facultatively anaerobic, Gram-positive microbes are more prevalent in the secondary/persistent group. The bacterial metabolic phenotype is associated with the tooth condition. Linear discriminant analysis effect size analysis reveals that the relative abundance of genera <i>Clostridia_vadinBB60_group</i> and <i>Rothia</i> are higher in the primary group, while <i>Saccharimonadaceae</i>, <i>Veillonella</i>, <i>Actinomyces</i>, <i>Granulicatella</i>, <i>Haemophilus</i>, <i>Bergeyella</i>, <i>Leptotrichia</i>, <i>Capnocytophaga</i>, <i>TM7x</i>, <i>Neisseria</i>, <i>Centipeda</i>, and <i>Saccharimonadales</i> are more dominant in the secondary/persistent group.</p> Conclusion <p>Significant differences in species and abundance were present between primary and secondary/persistent endodontic infections, with the bacterial community being more diverse in secondary/persistent group than in primary one. The taxonomic and phenotypic information derived from microbiome analysis helps elucidate the microbial basis for primary and secondary/persistent infections, identify potential causes of treatment failure, and guide downstream irrigation protocol, retreatment strategy, and risk assessment.</p>

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Distinct bacteria profiles in primary and secondary/persistent endodontic infections: a 16S rRNA gene sequencing study

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年2月6日

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  • Kuan-Liang Chen,
  • I-Ching Liao,
  • Chao-An Chen,
  • Chih-Yin Kuo,
  • Yuan-Yuan Jiang,
  • Yu-Ching Lin,
  • Kuo Yuan,
  • Jrhau Lung

摘要

Background

This study investigated the bacterial community composition, phenotypes, and differentially abundant taxa in primary and secondary/persistent endodontic infections.

Methods

Bacterial profiles of 12 primary and 12 secondary/persistent endodontic infections were analyzed using 16 S V3-V4 next-generation sequencing. Reads were processed into ASVs using DADA2 in Qiime2, and taxonomy was assigned with the SILVA dataset. Alpha and beta diversity were compared between groups using Kruskal-Wallis and PERMANOVA. LEfSe identified differentially abundant taxa (LDA > 2), and Bugbase predicted community phenotypes, which were compared with the Mann-Whitney-Wilcoxon test.

Results

The alpha-diversity and beta-diversity are higher in the secondary/persistent group than in the primary one. In the primary group, anaerobic, Gram-negative, and potentially pathogenic microbes are dominant, whereas facultatively anaerobic, Gram-positive microbes are more prevalent in the secondary/persistent group. The bacterial metabolic phenotype is associated with the tooth condition. Linear discriminant analysis effect size analysis reveals that the relative abundance of genera Clostridia_vadinBB60_group and Rothia are higher in the primary group, while Saccharimonadaceae, Veillonella, Actinomyces, Granulicatella, Haemophilus, Bergeyella, Leptotrichia, Capnocytophaga, TM7x, Neisseria, Centipeda, and Saccharimonadales are more dominant in the secondary/persistent group.

Conclusion

Significant differences in species and abundance were present between primary and secondary/persistent endodontic infections, with the bacterial community being more diverse in secondary/persistent group than in primary one. The taxonomic and phenotypic information derived from microbiome analysis helps elucidate the microbial basis for primary and secondary/persistent infections, identify potential causes of treatment failure, and guide downstream irrigation protocol, retreatment strategy, and risk assessment.