ArticleScientific reports2015
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification.
Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 76 papers.
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Who cites it
76 citing papers in PubMed.
- Comparing the Performance of Double-Stranded and Single-Stranded DNA Libraries for Ancient Oral Microbiome Reconstruction.Molecular ecology resources · 2026Article
- Genetically Proxied Associations Among 473 Gut Microbial Taxa, 1,400 Circulating Metabolites, and Mental and Behavioral Disorders: A Mendelian Randomization Study.Journal of molecular neuroscience : MN · 2026Article
- The Oral Microbiome of King Richard III of England.American journal of biological anthropology · 2026Article
- Comparative Analysis of Quorum Sensing-Dependent Transcriptomic Responses in Phytopathogenic Burkholderia spp.The plant pathology journal · 2026Article
- Wet Lab Protocols Matter: Choice of DNA Extraction and Library Preparation Protocols Bias Ancient Oral Microbiome Recovery.Molecular ecology resources · 2025Article
- CarpeDeam: a de novo metagenome assembler for heavily damaged ancient datasets.Genome biology · 2025Article
- The Impact of Whole-Animal Fluid Preservation on the Observed Gut Microbiome of Vertebrates: Implications for the Use of Museum Specimens in Microbiome Research.Molecular ecology resources · 2025Article
- Validating a Target-Enrichment Design for Capturing Uniparental Haplotypes in Ancient Domesticated Animals.Molecular ecology resources · 2025Article
- An extensive archaeological dental calculus dataset spanning 5000 years for ancient human oral microbiome research.Data in brief · 2025Article
- Navigating Past Oceans: Comparing Metabarcoding and Metagenomics of Marine Ancient Sediment Environmental DNA.Molecular ecology resources · 2025Article
- Diet's impact on gut microbial assemblage in health and disease.The Journal of clinical investigation · 2025Review
- Microbiome characterization of a pre-Hispanic man from Zimapán, Mexico: Insights into ancient gut microbial communities.PloS one · 2025Article
- Article
- Impact of Quorum Sensing on the Virulence and Survival Traits ofPlants (Basel, Switzerland) · 2024Article
- Integration of Bite Mark Microbiome Analysis with Forensic DNA Profiling: Advancements, Challenges, and Synergistic Approaches.Rambam Maimonides medical journal · 2024Review
- Inferring diet, disease and antibiotic resistance from ancient human oral microbiomes.Microbial genomics · 2024Review
- Article
- Review
- decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.Microbiome · 2023Article
- Extraction Protocol for Parallel Analysis of Proteins and DNA from Ancient Teeth and Dental Calculus.Journal of proteome research · 2023Article
16 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
20 authors.
Funding
Abstract
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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