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<p>Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including <i>Prevotella</i> spp. and <i>Mycoplasma pneumoniae</i>, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (&gt;1%) in BALF were underrepresented (&lt;0.1%) in OP, highlighting OP’s limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.</p>

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Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年7月7日

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  • Chun Wang,
  • Li Zhang,
  • Chuanwen Kan,
  • Junyan He,
  • Weijie Liang,
  • Ruiyan Xia,
  • Linyu Zhu,
  • Jing Yang,
  • Xuan Jiang,
  • Wentai Ma,
  • Zhihang Liang,
  • Zhiqing Xiao,
  • Juanjuan Zhang,
  • Jiaxin Zhong,
  • Xiao Sun,
  • De Chang,
  • Zhang Wang,
  • Guoliang Zhang,
  • Mingkun Li

摘要

Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP’s limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.