Data_Sheet_7_Rigorous Plasma Microbiome Analysis Method Enables Disease Association Discovery in Clinic.csv

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.

血液微生物组对于探究微生物与宿主之间的相互作用及其对全身免疫失调的影响具有重要意义。然而，由于微生物生物量低和背景伪迹的存在，此项研究面临着重大挑战。在当前研究中，我们采用了微生物16S DNA测序技术来分析血浆微生物组。我们开发了一种质量过滤策略，以评估和排除血浆微生物16S DNA测序分析中的低水平微生物序列、潜在污染和伪迹。此外，我们将该技术应用于三个队列，包括吸烟者、HIV感染者以及系统性红斑狼疮（SLE）患者，以及相应的对照组。通过严格的质控策略分析，我们移除了超过97%的总序列数据；这些被移除的扩增子序列变异体（ASVs）包括低水平微生物序列、污染和伪迹。在吸烟者、HIV感染者和SLE患者的血浆中，我们识别出了特异性富集的病原菌ASVs，而在对照组中并未发现。这些ASVs与疾病发病机制之间的关联得到了证实。此外，我们还进一步在体外验证了某些鉴定出的细菌的病理活性。我们提出了一种质量过滤策略，以识别与发病机制相关的血浆微生物组。我们的方法为研究亚临床微生物感染的诊断以及理解微生物组与宿主相互作用在疾病发病机制中的作用提供了一种途径。