虽然循环无细胞DNA(cfDNA)正在成为液体活检标本中感染性病原体的非侵入性鉴定的强大标记,对于临床宏基因组学中微生物cfDNA测序结果的正确解释,健康个体中的微生物cfDNA基线是迫切需要的.因为非侵入性产前检测(NIPT)与宏基因组学的测序方案有许多相似之处,我们利用基于标准低通全基因组测序的NIPT建立健康人的微生物cfDNA基线.回顾性收集了总共107,763份接受NIPT筛查的健康孕妇外周血样本的测序数据,并对微生物组DNA筛查进行了重新分析。发现超过95%的外源cfDNA来自细菌,3%来自真核生物,0.4%来自病毒,表明许多微生物的肠道/环境起源。总体和区域丰度模式得到了很好的说明,具有巨大的区域多样性和复杂性,并观察到了TORCH生物的独特种间和共生关系(弓形虫,其他[梅毒螺旋体{引起梅毒},乙型肝炎病毒{HBV},和人类细小病毒B19{HPV-B19}],风疹病毒,巨细胞病毒[CMV],和单纯疱疹病毒[HSV])和另一种常见病毒,EB病毒(EBV)。总而言之,我们的研究揭示了基线循环微生物cfDNA的复杂性,并表明微生物cfDNA测序结果需要以更全面的方式解释。重要性虽然循环无细胞DNA(cfDNA)已成为液体活检标本中感染性病原体的非侵入性鉴定的有力标记,临床宏基因组学中微生物cfDNA测序结果的正确解释迫切需要健康个体中微生物cfDNA的基线.基于标准低通全基因组测序的NIPT与宏基因组学测序方案有许多相似之处,可以在健康人中提供微生物cfDNA基线;因此,我们建立了人类微生物组的参考cfDNA数据集,其测序数据来自接受NIPT筛查的健康孕妇的总共107,763份外周血样本.我们的研究揭示了循环微生物cfDNA的复杂性,并表明微生物cfDNA测序结果需要以更全面的方式解释,特别是在地理模式和共存网络方面。
While circulating cell-free DNA (cfDNA) is becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a microbial cfDNA baseline in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Because noninvasive prenatal testing (NIPT) shares many similarities with the sequencing protocol of metagenomics, we utilized the standard low-pass whole-genome-sequencing-based NIPT to establish a microbial cfDNA baseline in healthy people. Sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening were retrospectively collected and reanalyzed for microbiome DNA screening. It was found that more than 95% of exogenous cfDNA was from bacteria, 3% from eukaryotes, and 0.4% from viruses, indicating the gut/environment origins of many microorganisms. Overall and regional abundance patterns were well illustrated, with huge regional diversity and complexity, and unique interspecies and symbiotic relationships were observed for TORCH organisms (Toxoplasma gondii, others [Treponema pallidum {causing syphilis}, hepatitis B virus {HBV}, and human parvovirus B19 {HPV-B19}], rubella virus, cytomegalovirus [CMV], and herpes simplex virus [HSV]) and another common virus, Epstein-Barr virus (EBV). To sum up, our study revealed the complexity of the baseline circulating microbial cfDNA and showed that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner. IMPORTANCE While circulating cell-free DNA (cfDNA) has been becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a baseline for microbial cfDNA in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Standard low-pass whole-genome-sequencing-based NIPT shares many similarities with the sequencing protocol for metagenomics and could provide a microbial cfDNA baseline in healthy people; thus, a reference cfDNA data set of the human microbiome was established with sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening. Our study revealed the complexity of circulating microbial cfDNA and indicated that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner, especially with regard to geographic patterns and coexistence networks.