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1969-2019年血液微生物组研究纵览 | 血液微生物组

市场部-LZ 联川生物 2024-03-27


前情回顾

1、人的血液中有微生物吗?

2、血液中的微生物从何而来?

3、血液循环微生物DNA可作肿瘤标志物?


大量研究已将临床疾病与人类微生物群落组成的变化联系在一起,使得利用微生物作为诊断人类重大疾病成为可能。越来越多的证据表明,血液微生物特征可作为疾病相关性分子标志物。虽然血液中细菌DNA的浓度通常非常低,但日益成熟的分析技术(qPCR和NGS)证实健康人类的血液中存在“无害的”细菌类群(Paisse et al.,2016)。微生物组对非感染性疾病和各种癌症的发病机制和发展至关重要。微生物生态失调促进癌变,如结肠直肠癌、肝癌和肺癌等(Dejea et al.,2017)。从人血浆中分离出的循环微生物DNA(cmDNA)可作为一种非侵入性生物标志物,在肿瘤的早期诊断中起着越来越重要的作用(血液循环微生物DNA可作肿瘤标志物?)。


cmDNA可作为肿瘤标志物,对于人体其他疾病是否与血液微生物存在联系?细菌可以从健康人体的外周血中培养出来,微生物基因组DNA在血液中循环,循环微生物的改变可以作为很有价值的疾病生物标志物(Damgaard et al.,2017)。例如,在重症急性胰腺炎患者中,通过16S测序分析了血液微生物发现患者微生物多样性比健康人群少,并且在与健康对照组相比病例组的拟杆菌(Bacteroides)和梭状芽孢杆菌(Clostridium Prazmowski)丰度增加,放线菌(Actinomycete)和黄杆菌(Flavobacterium Bergey)减少(Li et al.,2018)。通过检测到这些优势菌群的强烈变化暗示了胰腺炎患者血液微生物群失调。除此之外,其他各项研究证明血液微生物群的改变与炎症性肠炎、心血管和糖尿病等发病率的增加有关,表1针对近些年来对血液微生物研究进行汇总:“1969-2019”年血液微生物组研究纵览。研究人员通过不同方法描述多种患者和健康人群的血液微生物群(如糖尿病、脓毒症、肝硬化、急性胰腺炎、精神分裂症、双相情感障碍症和哮喘患者等),供大家全景了解血液微生物组研究的方法和进展,更好地站在前人的肩膀上设计自己的血液微生物组课题。


以往对血液微生物的研究运用过很多种方法,但仍有很多局限性,如“血液循环微生物DNA可作肿瘤标志物?”中所述,特别是在污染菌干扰方面,“1969-2019”年血液微生物组研究纵览中的各文献中都提出污染菌去除及优化的问题,到2019-2020年Eisenhofer R和Deborah Nejman等人分别细化污染菌去除流程(Eisenhofer R.,2019)和优化低微生物生物量样本检测技术(5R 16S测序)(Deborah Nejman.,2020),污染菌去除流程详情可见“做肿瘤微生物检测,这些实验设计你都知道吗?”。5R 16S测序技术适合血液微生物的检测,根据我们近百个血液微生物组项目结果来看,对于低微生物生物量样本的检测的灵敏度和特异性更高,相比常规16S测序检出率更高。随着血液微生物的研究不断深入,会有更多的血液微生物被列为重要的检测项目,在疾病中的诊断价值中都具有重要的价值。


 表1 1969-2019年血液微生物研究纵览

 


参考文献


1.Païssé, S., Valle, C., Servant, F., Courtney, M., Burcelin, R., Amar, J., et al. (2016). Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing. Transfusion 56, 1138–1147. doi: 10.1111/trf.13477

2.C.M. Dejea, P. Fathi, J.M. Craig, A. Boleij, R. Taddese, A.L. Geis, X. Wu, C. E. DeStefano Shields, E.M. Hechenbleikner, D.L. Huso, R.A. Anders, F. M. Giardiello, E.C. Wick, H. Wang, S. Wu, D.M. Pardoll, F. Housseau, C.L. Sears, Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria, Science 359 (2018) 592–597.

3.C. Damgaard, K. Magnussen, C. Enevold, M. Nilsson, T. Tolker-Nielsen, P. Holmstrup, C.H. Nielsen, Viable bacteria associated with red blood cells and plasma in freshly drawn blood donations, PloS One 10 (2015), e0120826.

4.S.I. Kim, N. Kang, S. Leem, J. Yang, H. Jo, M. Lee, H.S. Kim, D.N. Dhanasekaran, Y.- K. Kim, T. Park, Y.S. Song, Metagenomic analysis of serum microbe-derived extracellular vesicles and diagnostic models to differentiate ovarian cancer and benign ovarian tumor, Cancers 12 (2020).

5.E.J. Cho, S. Leem, S.A. Kim, J. Yang, Y.B. Lee, S.S. Kim, J.Y. Cheong, S.W. Cho, J. W. Kim, S.M. Kim, J.H. Yoon, T. Park, Circulating microbiota-based metagenomic signature for detection of hepatocellular carcinoma, Sci. Rep. 9 (2019) 7536.

6.Z. Dong, B. Chen, H. Pan, D. Wang, M. Liu, Y. Yang, M. Zou, J. Yang, K. Xiao, R. Zhao, X. Zheng, L. Zhang, Y. Zhang, Detection of microbial 16S rRNA gene in the serum of patients with gastric cancer, Front. Oncol. 9 (2019) 608.

7.] G.D. Poore, E. Kopylova, Q. Zhu, C. Carpenter, S. Fraraccio, S. Wandro, T. Kosciolek, S. Janssen, J. Metcalf, S.J. Song, J. Kanbar, S. Miller-Montgomery, R. Heaton, R. McKay, S.P. Patel, A.D. Swafford, R. Knight, Microbiome analyses of blood and tissues suggest cancer diagnostic approach, Nature 579 (2020) 567–574.

8. Q. Xiao, W. Lu, X. Kong, Y.W. Shao, Y. Hu, A. Wang, H. Bao, R. Cao, K. Liu, X. Wang, X. Wu, S. Zheng, Y. Yuan, K. Ding, Alterations of circulating bacterial DNA in colorectal cancer and adenoma: a proof-of-concept study, Canc. Lett. 499 (2021) 201–208.

9. E. Zozaya-Valdes, S.Q. Wong, J. Raleigh, A. Hatzimihalis, S. Ftouni, A.T. Papenfuss, S. Sandhu, M.A. Dawson, S.J. Dawson, Detection of cell-free microbial DNA using a contaminant-controlled analysis framework, Genome Biol. 22 (2021) 187.

10.Deborah Nejman,Ilana Livyatan,Garold Fuks,The human tumor microbiome is composed of tumor type–specific intracellular bacteria[J]. Science, 368.

11.Tedeschi, G., Amici, D., and Paparelli, M. (1969). Incorporation of nucleosides and amino-acids in human erythrocyte suspensions: possible relation with a diffffuse infection of mycoplasms or bacteria in the L form. Nature 222, 1285–1286. doi: 10.1038/2221285a0

12.Domingue, G., and Schlegel, J. (1977). Novel bacterial structures in human blood: cultural isolation. Infect. Immun. 15, 621–627.

13.Nikkari, S., McLaughlin, I. J., Bi, W., Dodge, D. E., and Relman, D. A. (2001). Does blood of healthy subjects contain bacterial ribosomal DNA? J. Clin. Microbiol. 39, 1956–1959. doi: 10.1128/JCM.39.5.1956-1959.2001

14.McLaughlin, R. W., Vali, H., Lau, P. C., Palfree, R. G., De Ciccio, A., Sirois, M., et al. (2002). Are there naturally occurring pleomorphic bacteria in the blood of healthy humans? J. Clin. Microbiol. 40, 4771–4775. doi: 10.1128/JCM.40.12.4771-4775.2002

15.Moriyama, K., Ando, C., Tashiro, K., Kuhara, S., Okamura, S., Nakano, S., et al. (2008). Polymerase chain reaction detection of bacterial 16S rRNA gene in human blood. Microbiol. Immunol. 52, 375–382. doi: 10.1111/j.1348-0421.2008.00048.x

16.Amar, J., Lange, C., Payros, G., Garret, C., Chabo, C., Lantieri, O., et al. (2013). Blood microbiota dysbiosis is associated with the onset of cardiovascular events in a large general population: the DESIR study. PLoS ONE 8:e54461. doi: 10.1371/journal.pone.0054461

17.Amar, J., Serino, M., Lange, C., Chabo, C., Iacovoni, J., Mondot, S., et al. (2011). Involvement of tissue bacteria in the onset of diabetes in humans: evidence for a concept. Diabetologia 54, 3055–3061. doi: 10.1007/s00125-011-2329-8

18.Dinakaran, V., Rathinavel, A., Pushpanathan, M., Sivakumar, R., Gunasekaran, P., and Rajendhran, J. (2014). Elevated levels of circulating DNA in cardiovascular disease patients: metagenomic profifiling of microbiome in the circulation. PLoS

ONE. 9:e105221. doi: 10.1371/journal.pone.0105221

19.Damgaard, C., Magnussen, K., Enevold, C., Nilsson, M., Tolker-Nielsen, T., Holmstrup, P., et al. (2015). Viable bacteria associated with red blood cells and plasma in freshly drawn blood donations. PLoS ONE. 10:e0120826. doi: 10.1371/journal.pone.0120826

20.Païssé, S., Valle, C., Servant, F., Courtney, M., Burcelin, R., Amar, J., et al. (2016). Comprehensive description of blood microbiome from healthy donors assessed by 16S targeted metagenomic sequencing. Transfusion 56, 1138–1147.

doi: 10.1111/trf.13477

21.Gosiewski, T., Ludwig-Galezowska, A., Huminska, K., Sroka-Oleksiak, A., Radkowski, P., Salamon, D., et al. (2016). Comprehensive detection and identifification of bacterial DNA in the blood of patients with sepsis and healthy volunteers using next-generation sequencing method-the observation of DNAemia. Eur. J. Clin. Microbiol. Infect. Dis. 2016, 1–8. doi: 10.1007/s10096-016-2805-7

22.Traykova, D., Schneider, B., Chojkier, M., and Buck, M. (2017). Blood microbiome quantity and the hyperdynamic circulation in decompensated cirrhotic patients. PLoS ONE. 12:e0169310. doi: 10.1371/journal.pone.0169310

23.Kowarsky, M., Camunas-Soler, J., Kertesz, M., De Vlaminck, I., Koh, W., Pan, W., et al. (2017). Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA. Proc Natl Acad Sci

U S A. 114, 9623–9628. doi: 10.1073/pnas.1707009114

24.Li, Q., Wang, C., Tang, C., Zhao, X., He, Q., and Li, J. (2018). Identifification and characterization of blood and neutrophil-associated microbiomes in patients with severe acute pancreatitis using next-generation sequencing. Front. Cell Infect. Microbiol. 8:5. doi: 10.3389/fcimb.2018.00005

25.Panaiotov, S., Filevski, G., Equestre, M., Nikolova, E., and Kalfifin, R. (2018). Cultural isolation and characteristics of the blood microbiome of healthy individuals. Adv. Microbiol. 8:406. doi: 10.4236/aim.2018.85027

26.Loohuis, L. M. O., Mangul, S., Ori, A. P., Jospin, G., Koslicki, D., Yang, H. T., et al. (2018). Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia. Transl. Psychiatry. 8:96. doi: 10.1038/s41398-018-0107-9

27.Whittle, E., Leonard, M. O., Harrison, R., Gant, T. W., and Tonge, D. P. (2018). Multi-method characterization of the human circulating microbiome. Front. Microbiol. 9:3266. doi: 10.3389/fmicb.2018.03266

28.Qiu, J., Zhou, H., Jing, Y., and Dong, C. (2019). Association between blood microbiome and type 2 diabetes mellitus: a nested case-control study. J. Clin. Lab. Anal. e22842. doi: 10.1002/jcla.22842

29.Sato, J., Kanazawa, A., Ikeda, F., Yoshihara, T., Goto, H., Abe, H., et al. (2014). Gut dysbiosis and detection of “live gut bacteria” in blood of Japanese patients with type 2 diabetes. Diabetes Care. 37, 2343–2350. doi: 10.2337/dc13-2817.

30.Eisenhofer R, Minich JJ, Marotz C, et al. Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations. Trends Microbiol. 2019 Feb;27(2):105-117.


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