The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research
Open accessAbstract
Ancient biomolecules from oral and gut microbiome samples have been shown to be preserved in the archaeological record. Studying ancient microbiome communities using metagenomic techniques offers a unique opportunity to reconstruct the evolutionary trajectories of microbial communities through time. DNA accumulates specific damage over time, which could potentially affect taxonomic classification and our ability to accurately reconstruct community assemblages. It is therefore necessary to assess whether ancient DNA (aDNA) damage patterns affect metagenomic taxonomic profiling. Here, we assessed biases in community structure, diversity, species detection, and relative abundance estimates by five popular metagenomic taxonomic classification programs using in silico -generated data sets with and without aDNA damage. Damage patterns had minimal impact on the taxonomic profiles produced by each program, while false-positive rates and biases were intrinsic to each program. Therefore, the most appropriate classification program is one that minimizes the biases related to the questions being addressed.
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The sensitivity and specificity of taxonomic assignment largely depends on the representation characteristics of the comparative database but are robust to post-mortem DNA damage.
“The sensitivity and specificity of taxonomic assignment largely depends on the representation characteristics of the comparative database but are robust to post-mortem DNA damage 238,239 .”
From Ancient DNA analysis (2021) · cites this paper as [238]
The Discussion (page not available) says database biases strongly affect profiling of abundant species and that ancient-DNA damage does not substantially affect which dominant taxa are identified. But it also reports that damage increases false-positive assignments, particularly for low-abundance taxa. Thus, describing taxonomic assignment as broadly robust to post-mortem damage omits an important qualification. (LLM, conf=0.88)
Experimental — accuracy not yet measuredNew advances in de novo genomic and metagenomic assembly hold promise for moving beyond reference-based mapping and towards more accurate and complete reconstruction of ancient microbial genomes and metagenomes, including improved strain separation, genomic architecture reconstruction, and identification and recovery of novel genes.
“New advances in de novo genomic and metagenomic assembly likewise hold promise for moving beyond reference-based mapping and towards a more accurate and complete reconstruction of ancient microbial genomes and metagenomes 238 , including improved strain separation, genomic architecture reconstruction, and the identification and recovery of novel genes.”
From Ancient DNA analysis (2021) · cites this paper as [238]
The Introduction and Discussion address taxonomic classification of ancient microbiome reads and biases in reference databases, not advances in de novo assembly. Searches for de novo assembly, strain separation, genomic architecture, and novel genes found no passage supporting the claimed improvements in ancient genome reconstruction. (LLM, conf=0.72)
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Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
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Self-citationVelsko, I. M., Fellows Yates, J. A., Aron, F., Hagan, R. W., Frantz, L. A. F., Loe, L., Martinez, J. B. R., Chaves, E., Gosden, C., Larson, G., et al. (2019) · Microbiome · doi:10.1186/s40168-019-0717-3 · Cited by 170
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Metadata
- Authors
- Velsko, I. M., Frantz, L. A. F., Herbig, A., Larson, G., & Warinner, C.
- Affiliations
- University of Oxford (GB)
- Queen Mary University of London (GB)
- Max Planck Institute of Geoanthropology (DE)
- Venue
- mSystems
- Publisher
- American Society for Microbiology
- Published
- 2018-08-28
- Volume
- 3
- Issue
- 4
- ISSN
- 2379-5077 (ISSN-L)
- PMC
- PMC6050634
- OpenAlex
- W2953251663
- Cited by
- 68
- References
- 10
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 11 · 2023: 6 · 2022: 22 · 2021: 5 · 2020: 6 · 2019: 10 · 2018: 1
- FWCI
- 1.72
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mSystems (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Oxford University Research Archive (ORA) (University of Oxford) (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Max Planck Digital Library (submittedVersion, other-oa)
- MPG.PuRe (Max Planck Society) (submittedVersion, cc-by)
- MPG.PuRe (Max Planck Society) (submittedVersion, other-oa)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion, cc-by)
- Funders
- University of Oxford Fell Fund (143/108)
- Wellcome Trust (210119/Z/18/Z)
- HHS | National Institutes of Health (2R01GM089886)
- National Science Foundation (BCS-1516633, BCS-1643318)
- Oxford University | Wolfson College, University of Oxford
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Social Sciences › Arts and Humanities › Archeology (arts and humanities) › Paleopathology and ancient diseases
- Keywords
- ancient microbiome, dental calculus, paleofeces, oral microbiota, gut microbiota, MetaPhlAn2, MIDAS, malt, species detection, alpha and beta diversity, relative abundance estimation
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