人类学学报 ›› 2022, Vol. 41 ›› Issue (04): 764-774.doi: 10.16359/j.1000-3193/AAS.2022.0025cstr: 32091.14.j.1000-3193/AAS.2022.0025
• • 上一篇
收稿日期:
2022-03-24
修回日期:
2022-05-09
出版日期:
2022-08-12
发布日期:
2022-08-10
作者简介:
崔银秋,教授,研究方向是古微生物学与人类遗传。Email: 基金资助:
CUI Yinqiu1,2(), ZHANG Hao2, WU Xiyan3, SUN Bing2, ZHOU Hui2
Received:
2022-03-24
Revised:
2022-05-09
Online:
2022-08-12
Published:
2022-08-10
摘要:
古代病原微生物基因组研究对病理学、微生物学、考古学等领域均具有重要的价值。在过去的十年里,高通量测序和靶向富集技术的发展和应用使古代微生物基因组的获取成为可能,通过对古代人群样本中获取的宏基因组进行筛查,使得引发古代疫情的相关病原体的基因组得以重建,为研究人类传染病的起源、传播和演化提供了一个独特的窗口。在当今全球化的背景下,新发及再发传染性疾病的出现频率促使我们回顾过去,以便更好地了解现代病原菌出现和古代病原菌重新出现的过程和生态环境。在这篇文章中,我们总结了近十年古代病原微生物基因组水平的研究进展,并提出了这项研究所面临的挑战以及未来的研究前景和方向。
中图分类号:
崔银秋, 张昊, 武喜艳, 孙冰, 周慧. 古代病原微生物基因组的研究进展[J]. 人类学学报, 2022, 41(04): 764-774.
CUI Yinqiu, ZHANG Hao, WU Xiyan, SUN Bing, ZHOU Hui. Progress in genomes of ancient pathogenic microorganisms[J]. Acta Anthropologica Sinica, 2022, 41(04): 764-774.
[1] | 肯尼思·F·基普尔. 剑桥世界人类疾病史[M]. 译者:张大庆. 上海: 上海科技教育出版社, 2007: 907-918 |
[2] | 西里尔·曼戈. 牛津拜占庭史[M]. 译者:陈志强,武鹏 北京: 北京师范大学出版社, 2015: 33-37 |
[3] | 乔万尼·薄迦丘. 十日谈[M]. 译者:钱鸿嘉,泰和庠,田青. 南京: 译林出版社, 2011: 17-19 |
[4] | [东汉]张仲景. 伤寒杂病论[M]. 北京: 中国中医药出版社, 2021: 1-4 |
[5] | [南朝·宋范晔]. 后汉书[M]. 北京: 中华书局, 2012: 194-197 |
[6] |
Arrizabalaga J. The Black Death, 1346-1353: The Complete History[J]. Bulletin of the History of Medicine, 2006, 80(1): 161-163
doi: 10.1353/bhm.2006.0002 URL |
[7] | Allison MJ, Mendoza D, Pezzia A. Documentation of a case of tuberculosis in pre-Columbian America[J]. The American review of respiratory disease, 1973, 107(6): 985-991 |
[8] | 周亚威, 高国帅. 性病梅毒的古病理学研究回顾[J]. 人类学学报, 2022, 41(1): 157-168 |
[9] |
Bos KI, Schuenemann VJ, Golding GB, et al. A draft genome of Yersinia pestis from victims of the Black Death[J]. Nature, 2011, 478(7370): 506-510
doi: 10.1038/nature10549 URL |
[10] |
Fu QM, Meyer M, Gao X, et al. DNA analysis of an early modern human from Tianyuan Cave, China[J]. Proc Natl Acad Sci USA, 2013, 110(6): 2223-2227
doi: 10.1073/pnas.1221359110 URL |
[11] |
Burbano HA, Hodges E, Green RE, et al. Targeted investigation of the Neandertal genome by array-based sequence capture[J]. Science, 2010, 328(5979): 723-725
doi: 10.1126/science.1188046 pmid: 20448179 |
[12] |
Bos KI, Kühnert D, Herbig A, et al. Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens[J]. Annu Rev Microbiol, 2019, 73: 639-666
doi: 10.1146/annurev-micro-090817-062436 URL |
[13] |
Devault AM, McLoughlin K, Jaing C, et al. Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array[J]. Scientific Reports, 2014, 4: 4245
doi: 10.1038/srep04245 pmid: 24603850 |
[14] | Sarkissian CD, Velsko IM, Fotakis AK, et al. Ancient Metagenomic Studies: Considerations for the Wider Scientific Community[J]. mSystems, 2021, 6(6): e01315-21 |
[15] |
Irving-Pease EK, Muktupavela R, Dannemann M, et al. Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution?[J]. Frontiers in Genetics, 2021, 12: 703541
doi: 10.3389/fgene.2021.703541 URL |
[16] |
Duchêne S, Ho SYW, Carmichael AG, et al. The Recovery, Interpretation and Use of Ancient Pathogen Genomes[J]. Current Biology, 2020, 30(19): R1215-R1231
doi: 10.1016/j.cub.2020.08.081 URL |
[17] | 武喜艳. 新疆古代致病菌基因组学与进化历史研究[D]. 长春: 吉林大学, 2020: 1-13 |
[18] | Tyler AJ, Pe'er I. An Introduction to Whole-Metagenome Shotgun Sequencing Studies[J]. Methods in Molecular Biology, 2021, 2243: 107-122 |
[19] |
Gaeta R. Ancient DNA and paleogenetics: risks and potentiality[J]. Pathologica, 2021, 113(2): 141-146
doi: 10.32074/1591-951X-146 URL |
[20] | 吴斯豪. 新疆塔里木盆地南缘铁器时代人群的基因组学研究[D]. 长春: 吉林大学, 2020: 13-18 |
[21] |
Firth C, Lipkin WI. The genomics of emerging pathogens[J]. Annual Review of Genomics and Human Genetics, 2013, 14: 281-300
doi: 10.1146/annurev-genom-091212-153446 URL |
[22] |
Warinner C, Herbig A, Mann A, et al. A Robust Framework for Microbial Archaeology[J]. Annual Review of Genomics and Human Genetics, 2017, 18: 321-356
doi: 10.1146/annurev-genom-091416-035526 URL |
[23] | Kılınç GM, Kashuba N, Koptekin D, et al. Human population dynamics and Yersinia pestisin ancient northeast Asia[J]. Science Advances, 2021, 7(2): eabc4587 |
[24] |
Salo WL, Aufderheide AC, Buikstra J, et al. Identification of Mycobacterium tuberculosis DNA in a pre-Columbian Peruvian mummy[J]. Proc Natl Acad Sci USA, 1994, 91(6): 2091-2094
doi: 10.1073/pnas.91.6.2091 URL |
[25] |
Monot M, Honoré N, Garnier T, et al. Comparative genomic and phylogeographic analysis of Mycobacterium leprae[J]. Nature Genetics, 2009, 41(12): 1282-1289
doi: 10.1038/ng.477 pmid: 19881526 |
[26] | Vradenburg JA. The role of treponematoses in the development of prehistoric cultures and the bioarchaeology of proto-urbanism of the central coast of Peru[M]. Columbia: University of Missouri-Columbia, 2001 |
[27] |
Immel A, Key FM, Szolek A, et al. Analysis of Genomic DNA from Medieval Plague Victims Suggests Long-Term Effect of Yersinia pestis on Human Immunity Genes[J]. Molecular Biology and Evolution, 2021, 38(10): 4059-4076
doi: 10.1093/molbev/msab147 URL |
[28] |
Spyrou MA, Bos KI, Herbig A, et al. Ancient pathogen genomics as an emerging tool for infectious disease research[J]. Nature Reviews Genetics, 2019, 20(6): 323-340
doi: 10.1038/s41576-019-0119-1 pmid: 30953039 |
[29] | Hansen HB, Damgaard PB, Margaryan A, et al. Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum[J]. PLoS One, 2017, 12(1): e0170940 |
[30] |
Bos KI, Harkins KM, Herbig A, et al. Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis[J]. Nature, 2014, 514(7523): 494-497
doi: 10.1038/nature13591 URL |
[31] |
Schuenemann VJ, Singh P, Mendum TA, et al. Genome-wide comparison of medieval and modern Mycobacterium leprae[J]. Science, 2013, 341(6142): 179-183
doi: 10.1126/science.1238286 pmid: 23765279 |
[32] | Schuenemann VJ, Lankapalli AK, Barquera R, et al. Historic Treponema pallidum genomes from Colonial Mexico retrieved from archaeological remains[J]. PLoS Neglected Tropical Diseases, 2018, 12(6): e0006447 |
[33] | Vågene ÅJ, Herbig A, Campana MG, et al. Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico[J]. Nature Ecology & Evolution, 2018, 2(3): 520-528 |
[34] |
Marciniak S, Prowse TL, Herring DA, et al. Plasmodium falciparum malaria in 1st-2nd century CE southern Italy[J]. Current Biology, 2016, 26(23): R1220-R1222
doi: 10.1016/j.cub.2016.10.016 URL |
[35] |
Maixner F, Kyora BK, Turaev D, et al. The 5300-year-old Helicobacter pylori genome of the Iceman[J]. Science, 2016, 351(6269): 162-165
doi: 10.1126/science.aad2545 pmid: 26744403 |
[36] |
Duggan AT, Perdomo MF, Piombino-Mascali D, et al. 17th Century Variola Virus Reveals the Recent History of Smallpox[J]. Current Biology, 2016, 26(24): 3407-3412
doi: S0960-9822(16)31324-0 pmid: 27939314 |
[37] |
Biagini P, Thèves C, Balaresque P, et al. Variola virus in a 300-year-old Siberian mummy[J]. N Engl J Med, 2012, 367(21): 2057-2059
doi: 10.1056/NEJMc1208124 URL |
[38] |
Carpenter ML, Buenrostro JD, Valdiosera C, et al. Pulling out the 1%: whole-genome capture for the targeted enrichment of ancient DNA sequencing libraries[J]. American Journal Of Human Genetics, 2013, 93(5): 852-864
doi: 10.1016/j.ajhg.2013.10.002 pmid: 24568772 |
[39] |
Key FM, Posth C, Krause J, et al. Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication[J]. Trends in genetics, 2017, 33(8): 508-520
doi: 10.1016/j.tig.2017.05.005 URL |
[40] | Harbeck M, Seifert L, Hänsch S, et al. Yersinia pestis DNA from skeletal remains from the 6(th) century AD reveals insights into Justinianic Plague[J]. PLoS Pathogens, 2013, 9(5): e1003349 |
[41] |
Giffin K, Lankapalli AK, Sabin S, et al. A treponemal genome from an historic plague victim supports a recent emergence of yaws and its presence in 15th century Europe[J]. Scientific reports, 2020, 10(1): 9499
doi: 10.1038/s41598-020-66012-x pmid: 32528126 |
[42] |
Rasmussen S, Allentoft ME, Nielsen K, et al. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago[J]. Cell, 2015, 163(3): 571-582
doi: 10.1016/j.cell.2015.10.009 pmid: 26496604 |
[43] |
Valtueña AA, Mittnik A, Key FM, et al. The Stone Age Plague and Its Persistence in Eurasia[J]. Current Biology, 2017, 27(23): 3683-3691
doi: 10.1016/j.cub.2017.10.025 URL |
[44] | Luhmann N, Doer D, Chauve C. Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestisgenomes[J]. Microbial Genomics, 2017, 3(9): e000123 |
[45] |
Song YJ, Wang J, Yang RF, et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis[J]. Proc Natl Acad Sci USA, 2013, 110(2): 577-582
doi: 10.1073/pnas.1205750110 URL |
[46] | Wagner DM, Keim PS, Scholz HC, et al. Yersinia pestis and the three plague pandemics--authors' reply[J]. The Lancet Infectious Diseases, 2014, 14(10): 919 |
[47] |
Damgaard PdB, Marchi N, Rasmussen S, et al. 137 ancient human genomes from across the Eurasian steppes[J]. Nature, 2018, 557(7705): 369-374
doi: 10.1038/s41586-018-0094-2 URL |
[48] | Kirk MD, Pires SM, Black RE, et al. World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data Synthesis[J]. PLoS Medicine, 2015, 12(12): e1001921 |
[49] |
Zhou ZM, Lundstrøm I, Tran-Dien A, et al. Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia[J]. Current Biology, 2018, 28(15): 2420-2428
doi: 10.1016/j.cub.2018.05.058 URL |
[50] | Key FM, Posth C, Esquivel-Gomez LR, et al. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process[J]. Nature Ecology & Evolution, 2020, 4(3): 324-333 |
[51] | Wu XY, Ning C, Key FM, et al. A 3,000-year-old basal S. enterica lineage from Bronze Age Xinjiang suggests spread along the Proto-Silk Road[J]. PLoS Pathogens, 2021, 17(9): e1009886 |
[52] |
Spyrou MA, Keller M, Tukhbatova RI, et al. Phylogeography of the second plague pandemic revealed through analysis of historical Yersinia pestis genomes[J]. Nature Communications, 2019, 10(1): 4470
doi: 10.1038/s41467-019-12154-0 pmid: 31578321 |
[53] |
Susat J, Lübke H, Immel A, et al. A 5,000-year-old hunter-gatherer already plagued by Yersinia pestis[J]. Cell Reports, 2021, 35(13): 109278
doi: 10.1016/j.celrep.2021.109278 URL |
[54] |
Stephens JC, Reich DE, Goldstein DB, et al. Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes[J]. American Journal of human genetics, 1998, 62(6): 1507-1515
pmid: 9585595 |
[55] | Sabeti PC, Walsh E, Schaffner SF, et al. The case for selection at CCR5-Delta32[J]. PLoS Biology, 2005, 3(11): e378 |
[56] | Lindo J, Huerta-Sanchez E, Nakagome S, et al. Demographic and immune-based selection shifts before and after European contact inferred from 50 ancient and modern exomes from the Northwest Coast of North America[J]. BioRxiv 051078 |
[57] |
Kyora BK, Nutsua M, Boehme L, et al. Ancient DNA study reveals HLA susceptibility locus for leprosy in medieval Europeans[J]. Nature Communications, 2018, 9(1): 1569
doi: 10.1038/s41467-018-03857-x URL |
[58] |
Guellil M, Keller M, Dittmar JM, et al. An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim[J]. Genome Biology, 2022, 23(1): 22
doi: 10.1186/s13059-021-02580-z pmid: 35109894 |
[59] | Spyrou MA, Tukhbatova RI, Feldman M, et al. Historical Y. pestis Genomes Reveal the European Black Death as the Source of Ancient and Modern Plague Pandemics[J]. Cell Host & Microbe, 2016, 19(6): 874-881 |
[60] |
Gansauge MT, Meyer M. Selective enrichment of damaged DNA molecules for ancient genome sequencing[J]. Genome research, 2014, 24(9): 1543-1549
doi: 10.1101/gr.174201.114 URL |
[61] |
Ginolhac A, Rasmussen M, Gilbert MT, et al. mapDamage: testing for damage patterns in ancient DNA sequences[J]. Bioinformatics, 2011, 27(15): 2153-2155
doi: 10.1093/bioinformatics/btr347 URL |
[62] |
Hübler R, Felix MK, Warinner C, et al. HOPS: automated detection and authentication of pathogen DNA in archaeological remains[J]. Genome biology, 2019, 20(1): 280
doi: 10.1186/s13059-019-1903-0 pmid: 31842945 |
[63] |
Kumar S, Stecher G, Peterson D, et al. MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis[J]. Bioinformatics, 2012, 28(20): 2685-2686
doi: 10.1093/bioinformatics/bts507 URL |
[64] |
Warinner C, Speller C, Collins MJ. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome[J]. Philos Trans R Soc Lond B Biol Sci, 2015, 370(1660): 20130376
doi: 10.1098/rstb.2013.0376 URL |
[1] | 丁曼雨, 何伟, 王恬怡, 夏格旺堆, 张明, 曹鹏, 刘峰, 戴情燕, 付巧妹. 中国西藏拉托唐古墓地古代居民线粒体全基因组研究[J]. 人类学学报, 2021, 40(01): 1-11. |
[2] | 李春香, 张帆, 马鹏程, 王立新, 崔银秋. 线粒体全基因组揭示嫩江流域史前人群遗传结构的动态变化[J]. 人类学学报, 2020, 39(04): 695-705. |
[3] | 王恬怡, 赵东月, 张明, 乔诗雨, 杨帆, 万杨, 杨若薇, 曹鹏, 刘峰, 付巧妹. 古DNA捕获新技术与中国南方早期人群遗传研究新格局[J]. 人类学学报, 2020, 39(04): 680-694. |
[4] | 张明;付巧妹. 史前古人类之间的基因交流及对当今现代人的影响[J]. 人类学学报, 2018, 37(02): 206-218. |
[5] | 王广结,王钢,刘益平,方根,张俊玲,丁齐虹,翟晓平,尚锦青,魏庭萱,唐晏立,杨世荣,刁玉英. 内蒙古蒙古族Kell、Rh血型分布[J]. 人类学学报, 1993, 12(01): 88-91. |
[6] | 曾溢滔,黄淑帧,任兆瑞,周霞娣,仇效坤. 中国人血红蛋白 HbQ-Thailand 的研究[J]. 人类学学报, 1985, 4(03): 259-263. |
阅读次数 | ||||||
全文 |
|
|||||
摘要 |
|
|||||