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Background <p>Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy.</p> Results <p>Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20&#xa0;°C, and -80&#xa0;°C), revealed no significant impact on microbial composition. Additionally, the NEBNext® Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes.</p> Conclusions <p>These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.</p>

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Standardizing vaginal microbial profiling: evaluating swab materials, storage conditions, and host DNA depletion strategies

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2026年1月5日

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  • Jiwoo Seo,
  • Ruvie Pearl Araneta,
  • Jung Hwa Lee,
  • Jake Adolf Montecillo,
  • Heon Jong Yoo,
  • Yoo-Young Lee,
  • Chul Min Park,
  • Angela Cho,
  • Hyunsu Lee,
  • Hee Yeun Yoon,
  • Min Ju Kim,
  • Jong Mi Kim,
  • Yoon Hee Lee,
  • Nan Young Lee,
  • Nora Jee-Young Park,
  • Hyung Soo Han,
  • Incheol Seo,
  • Gun Oh Chong

摘要

Background

Studies on understanding female health from a microbial perspective have proliferated in recent years; however, validated protocols for swab materials, storage conditions, and host DNA depletion remain limited for vaginal microbiome studies. This study investigates these critical aspects to enhance microbial profiling accuracy.

Results

Three swab materials were evaluated, with minimal variations in bacterial composition observed across different swab materials. The DNA yield and host DNA contamination remained comparable. Mock samples, used to assess the effects of storage conditions (without freezing, -20 °C, and -80 °C), revealed no significant impact on microbial composition. Additionally, the NEBNext® Microbiome DNA Enrichment Kit demonstrated effective performance in host DNA removal and bacterial community recovery, even with reduced reagent volumes.

Conclusions

These findings underscore the importance of optimizing swab selection and host DNA depletion strategies to enhance microbiome profiling in clinical samples.