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Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
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Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
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Journal Article
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
2015
Overview
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.
Publisher
Nature Publishing Group UK,Nature Publishing Group
Subject
/ Dental Calculus - microbiology
/ DNA
/ E coli
/ Female
/ Gastrointestinal Microbiome - genetics
/ High-Throughput Nucleotide Sequencing - methods
/ Humanities and Social Sciences
/ Humans
/ Male
/ Methanobrevibacter - classification
/ Methanobrevibacter - genetics
/ Primers
/ RNA, Ribosomal, 16S - chemistry
/ RNA, Ribosomal, 16S - genetics
/ rRNA 16S
/ Science
/ Taxonomy
