The dental calculus metabolome in modern and historic samples

Velsko, Irina M.; Overmyer, Katherine A.; Speller, Camilla; Collins, Matthew J.; Loe, Louise; Frantz, Laurent; Martinez, Juan Bautista Rodriguez; Chavez, Eros; Klaus, Lauren; Sankaranarayanan, Krithivasan; Lewis, Cecil M.; Coon, Joshua J.; Larson, Greger; Warinner, Christina

doi:10.1101/136176

Cited by 8 publications

(15 citation statements)

References 80 publications

(46 reference statements)

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“…All reads assigned to the 7 false-positive genera in set of historic calculus samples from the Radcliffe Infirmary burial ground (ca. 1770-1855; Oxford, England) (3) were searched against the NCBI nt database using BLASTn to identify the likely species of origin for the reads. Many of the biases in read assignment observed in the in silico datasets were also observed in the real calculus samples (Table S4), i.e., in silico-generated reads assigned to Enterococcus by QIIME were from taxa in the order Lactobacialles , and historic calculus reads assigned to Enterococcus by QIIME also had best BLAST hits to the order Lactobacialles.…”

Section: Resultsmentioning

confidence: 99%

“…The simulated ancient metagenomic datasets we generated were modeled after data generated from archaeological dental calculus (3), and we selected 5M reads for the in silico samples because this was the lowest read count in these samples. However, McIntyre, et al 2017 (25) have shown that as read depth increases the performance of metagenomic classifier tools changes, and this should be kept in mind for studies with higher sequencing depth.…”

Section: Discussionmentioning

confidence: 99%

“…Palaeomicrobiology uses archaeological material to trace the emergence and spread of microorganisms throughout history and prehistory. Archaeological dental calculus and palaeofeces are promising substrates for ancient human microbiome studies, as they have been shown to preserve DNA (1), proteins (1, 2), and small molecule metabolites (3) from the resident microbes and the host. During life, these dense microbial communities contain hundreds of species, predominantly composed of bacteria (4), but also including archaea (4), viruses (5), fungi (6), and protists (7).…”

Section: Introductionmentioning

confidence: 99%

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Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research

Velsko

Frantz

Herbig

et al. 2018

Preprint

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30Metagenomics enables the study of complex microbial communities from myriad sources, 31 including the remains of oral and gut microbiota preserved in archaeological dental calculus and 32 paleofeces, respectively. While accurate taxonomic assignment is essential to this process, DNA 33 damage, characteristic to ancient samples (e.g. reduction in fragment size), may reduce the 34 accuracy of read taxonomic assignment. Using a set of in silico-generated metagenomic datasets 35 we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial 36 taxonomic assignment by five widely-used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, 37 CLARK-S, and MALT (BLAST-X-mode). In silico-generated datasets were designed to mimic 38 dental plaque, consisting of 40, 100, and 200 microbial species/strains, both with and without 39 simulated aDNA damage patterns. Following taxonomic assignment, the profiles were evaluated 40 for species presence/absence, relative abundance, alpha-diversity, beta-diversity, and specific 41 taxonomic assignment biases. Unifrac metrics indicated that both MIDAS and MetaPhlAn2 42 provided the most accurate community structure reconstruction. QIIME/UCLUST, CLARK-S, 43and MALT had the highest number of inaccurate taxonomic assignments; however, filtering out 44 species present at <0.1% abundance greatly increased the accuracy of CLARK-S and MALT. All 45 programs except CLARK-S failed to detect some species from the input file that were in their 46 databases. Ancient DNA damage resulted in minimal differences in species detection and relative 47 abundance between simulated ancient and modern datasets for most programs. In conclusion, 48 taxonomic profiling biases are program-specific rather than damage-dependent, and the choice of 49 taxonomic classification program to use should be tailored to the research question. 50 51 Importance 52 Ancient biomolecules from oral and gut microbiome samples have been shown to preserve 53 in the archaeological record. Studying ancient microbiome communities using metagenomic 54 techniques offer a unique opportunity to reconstruct the evolutionary trajectories of microbial 55 communities through time. DNA accumulates specific damage over time, which could potentially 56 affect taxonomic classification and our ability to reconstruct community assemblages accurately. 57It is therefore necessary to assess whether ancient DNA (aDNA) damage patterns affect 58 metagenomic taxonomic profiling. Here, we assessed biases in community structure, diversity, 59 species detection, and relative abundance estimates by five popular metagenomic taxonomic 60

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research

Velsko

Frantz

Herbig

et al. 2018

Preprint

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“…Velsko et al. presented a comprehensive metabolomic characterization of human dental calculus using wide range of metabolic categories (amino acids, carbohydrates, cofactors and vitamins, energy, lipids, nucleic acids, peptides, and xenobiotics) . Another area of innovation that intersects AAR dating is the use of chiral amino acids as biomarkers of diseases/disorders, which has received growing interest in recent years.…”

Section: Future Directionsmentioning

confidence: 99%

“…A potential new trend in AAR lies in lipidomics, a branch of metabolomics, which provides a "systems-based study of all lipids, the molecules with which they interact, and their function within the cell" [180]. Velsko et al presented a comprehensive metabolomic characterization of human dental calculus using wide range of metabolic categories (amino acids, carbohydrates, cofactors and vitamins, energy, lipids, nucleic acids, peptides, and xenobiotics) [181]. Another area of innovation that intersects AAR dating is the use of chiral amino acids as biomarkers of diseases/disorders, which has received growing interest in recent years.…”

Section: Future Directionsmentioning

confidence: 99%

Amino acid racemization and its relation to geochronology and archaeometry

Bravenec

Ward

2018

J of Separation Science

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Amino acid racemization, used as a method of relative and quantitative dating of fossils, evaluates the degree of postmortem conversion of l to d amino acid enantiomers. While extensively utilized, this method has garnered confusion due to controversial age estimates for human fossils in North America in the 1970s. This paper explains the age controversy and aftermath, current chromatographic methods used in research, mathematical calibration models, and a short synopsis of other dating techniques in geochronology and archaeometry.

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Paleoproteomic profiling of organic residues on prehistoric pottery from Malta

et al. 2021

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Mass spectrometry-based approaches have been successfully applied for identifying ancient proteins in bones and other tissues. On the contrary, there are relatively few examples of the successful recovery and identification of archeological protein residues from ceramic artifacts; this is because ceramics contain much lower levels of proteins which are extensively degraded by diagenetic effects. In this paper, we report the results of the characterization of proteins extracted from pottery of the Maltese site of Baħrija, the guide-site for the Baħrija period (half of 9th–second half of eighth century BCE), recently identified as the final part of the Borġ in-Nadur culture. Proteomic data here reported confirm that one of the major issue of these kind of studies is represented by contamination of animal and human agents that may complicate endogenous protein identification and authentication. The samples tested included a small group of ceramic forms, namely three tableware and six coarse ware thought to have been used in food preparation and/or storage. In this context, the limited availability of paleobotanical and archeozoological analyses may be compensated by the outcomes of the first proteomics profiling which, even if obtained on a limited selection of vessels, revealed the centrality of wheat in the diet of the ancient community of Baħrija. The data have been deposited to the ProteomeXchange with identifier < PXD022848 > .

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The dental calculus metabolome in modern and historic samples

Cited by 8 publications

References 80 publications

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research

Selection of appropriate metagenome taxonomic classifiers for ancient microbiome research

Amino acid racemization and its relation to geochronology and archaeometry

Paleoproteomic profiling of organic residues on prehistoric pottery from Malta

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