Rigorous Plasma Microbiome Analysis Method Enables Disease Association Discovery in Clinic

Zhenwu Luo, Alexander V. Alekseyenko, Elizabeth Ogunrinde, Min Li, Quan Zhen Li, Lei Huang, Betty P. Tsao, Diane L. Kamen, Jim C. Oates, Zihai Li, Gary S. Gilkeson, Wei Jiang

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

Abstract

Blood microbiome is important to investigate microbial-host interactions and the effects on systemic immune perturbations. However, this effort has met with major challenges due to low microbial biomass and background artifacts. In the current study, microbial 16S DNA sequencing was applied to analyze plasma microbiome. We have developed a quality-filtering strategy to evaluate and exclude low levels of microbial sequences, potential contaminations, and artifacts from plasma microbial 16S DNA sequencing analyses. Furthermore, we have applied our technique in three cohorts, including tobacco-smokers, HIV-infected individuals, and individuals with systemic lupus erythematosus (SLE), as well as corresponding controls. More than 97% of total sequence data was removed using stringent quality-filtering strategy analyses; those removed amplicon sequence variants (ASVs) were low levels of microbial sequences, contaminations, and artifacts. The specifically enriched pathobiont bacterial ASVs have been identified in plasmas from tobacco-smokers, HIV-infected individuals, and individuals with SLE but not from control subjects. The associations between these ASVs and disease pathogenesis were demonstrated. The pathologic activities of some identified bacteria were further verified in vitro. We present a quality-filtering strategy to identify pathogenesis-associated plasma microbiome. Our approach provides a method for studying the diagnosis of subclinical microbial infection as well as for understanding the roles of microbiome-host interaction in disease pathogenesis.

Original languageEnglish (US)
Article number613268
JournalFrontiers in Microbiology
Volume11
DOIs
StatePublished - Jan 8 2021

Keywords

  • contaminations and artifacts
  • microbiome-host interaction
  • pathogenic bacteria
  • plasma microbiome
  • quality-filtering strategies

ASJC Scopus subject areas

  • Microbiology
  • Microbiology (medical)

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