Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

被引:100
作者
Ziesemer, Kirsten A. [1 ]
Mann, Allison E. [2 ]
Sankaranarayanan, Krithivasan [2 ]
Schroeder, Hannes [1 ,3 ]
Ozga, Andrew T. [2 ]
Brandt, Bernd W. [4 ,5 ]
Zaura, Egija [4 ,5 ]
Waters-Rist, Andrea [1 ]
Hoogland, Menno [1 ]
Salazar-Garcia, Domingo C. [6 ,7 ,8 ]
Aldenderfer, Mark [9 ]
Speller, Camilla [10 ]
Hendy, Jessica [10 ]
Weston, Darlene A. [1 ,11 ]
MacDonald, Sandy J. [12 ]
Thomas, Gavin H. [12 ]
Collins, Matthew J. [10 ]
Lewis, Cecil M. [2 ]
Hofman, Corinne [1 ]
Warinner, Christina [2 ]
机构
[1] Leiden Univ, Fac Archaeol, NL-2333 CC Leiden, Netherlands
[2] Univ Oklahoma, Dept Anthropol, Norman, OK 73019 USA
[3] Univ Copenhagen, Ctr Geogenet, DK-1168 Copenhagen, Denmark
[4] Univ Amsterdam, Dept Prevent Dent, Acad Ctr Dent Amsterdam, NL-1012 WX Amsterdam, Netherlands
[5] Vrije Univ Amsterdam, Amsterdam, Netherlands
[6] Univ Cape Town, Dept Anthropol, ZA-7700 Rondebosch, South Africa
[7] Univ Valencia, Dept Prehist & Arqueol, E-46003 Valencia, Spain
[8] Max Planck Inst Evolutionare Anthropol, Dept Human Evolut, D-04103 Leipzig, Germany
[9] Univ Calif, Sch Social Sci Humanities & Arts, Merced, CA USA
[10] Univ York, Dept Archaeol, York YO10 5DD, N Yorkshire, England
[11] Univ British Columbia, Dept Anthropol, Vancouver, BC V5Z 1M9, Canada
[12] Univ York, Dept Biol, York YO10 5DD, N Yorkshire, England
来源
SCIENTIFIC REPORTS | 2015年 / 5卷
基金
欧洲研究理事会; 美国国家科学基金会; 英国惠康基金; 美国国家卫生研究院;
关键词
AVERAGE GENOME SIZE; GUT MICROBIOTA; BACTERIAL-DNA; SEQUENCE-ANALYSIS; COLON; HOST; BIAS; DIVERSITY; DATABASE; HEALTH;
D O I
10.1038/srep16498
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341-534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.
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页数:19
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