Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA.
Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA.
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通过无创产前检测进行外周血微生物组分析揭示循环微生物无细胞 DNA 的复杂性
DOI：
10.1128/spectrum.00414-22
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发表时间：
2022-06-29
影响因子：
3.7
通讯作者：
中科院分区：
文献类型：
--
作者：
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.
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影响因子：
3.7
作者：
Wang T;He Q;Li H;Ding J;Wen P;Zhang Q;Xiang J;Li Q;Xuan L;Kong L;Mao Y;Zhu Y;Shen J;Liang B;Li H
通讯作者：
Li H
DOI：
10.3390/v13112322
发表时间：
2021-11-21
期刊：
Viruses
影响因子：
--
作者：
Cebriá-Mendoza M;Bracho MA;Arbona C;Larrea L;Díaz W;Sanjuán R;Cuevas JM
通讯作者：
Cuevas JM
基于元测序的微生物组分析揭示了医院环境中空气传播真菌的高度多样性。
影响因子：
4.6
作者：
Tong X;Xu H;Zou L;Cai M;Xu X;Zhao Z;Xiao F;Li Y
通讯作者：
Li Y
WGCNA：用于加权相关网络分析的 R 包。
影响因子：
3
作者：
Langfelder P;Horvath S
通讯作者：
Horvath S
影响因子：
12.3
作者：
Grumaz S;Stevens P;Grumaz C;Decker SO;Weigand MA;Hofer S;Brenner T;von Haeseler A;Sohn K
通讯作者：
Sohn K