Proteomics

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Human dental calculus LC-MS/MS

ABSTRACT: The purpose of this study was to investigate oral microbiome and host proteins in archaeological human dental tissues using a shotgun proteomics approach. The research focuses on dental calculus (mineralized plaque), dentine, a carious lesion, and an alveolar bone abscess from the medieval site of Dalheim, Germany (ca. AD 950-1200). For comparison, proteins were also analyzed from archaeological faunal dental tissues and human dental calculus samples from modern Swiss dental patient controls. Protein extraction and generation of tryptic peptides from tooth and dental calculus specimens was performed using a filter-aided sample preparation (FASP) protocol, modified for mineralized and degraded samples. Total protein extraction was performed on a total of fourteen samples: four ancient human calculus samples (indicated as: G12, B71, B61, and B78), four ancient human tooth root samples (indicated as: G12, B17, B61, and B78), one carious lesion (indicated as: B17), one alveolar bone abscess (indicated as: B17), two ancient fauna crown cementum/calculus samples (indicated as: F1 [sheep] and F5 [cattle]), and two modern dental calculus samples from clinical patients (indicated as: P1 and P2). All samples were extracted at the Centre for Evolutionary Medicine (ZEM) at the University of Zürich with the exception of dental calculus from G12, P1, and P2, which were extracted at the Center for GeoGenetics (CGG) at the University of Copenhagen. Two samples (G12 and B61 calculus) were extracted a second time in an independent laboratory at the University of York (YORK) for comparison. Sample extracts were then sequenced (LC-MS/MS) at the Functional Genomics Center Zürich (FGCZ) using an LTQ-Orbitrap Velos, at the Novo Nordisk Foundation Center for Protein Research (CPR) using a Q-Exactive Hybrid Quadrupole Orbitrap, and at the University of York’s Proteomics and Analytical Biochemistry Laboratories (PABL) using a MaXis UHR-Qq-TOF.

INSTRUMENT(S): maXis, LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human) Bos Taurus (bovine) Ovis

TISSUE(S): Alveolar Bone, Tooth, Dental Plaque

DISEASE(S): Periodontitis

SUBMITTER: Christina Warinner  

LAB HEAD: Christina G Warinner

PROVIDER: PXD000412 | Pride | 2014-01-29

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
20111024_QE4_QC_COLLAB_078CALCG12FR2CPM01.msm Other
20111024_QE4_QC_COLLAB_079CALCG12PTCPM01.msm Other
20111206_QE1_ChKe_COLLAB_082K-CALCFR2_01.msm Other
DB17_calc_Z27_F174395.dat Other
DB17_disalv_Z30_F182277.dat Other
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Publications

Pathogens and host immunity in the ancient human oral cavity.

Warinner Christina C   Rodrigues João F Matias JF   Vyas Rounak R   Trachsel Christian C   Shved Natallia N   Grossmann Jonas J   Radini Anita A   Hancock Y Y   Tito Raul Y RY   Fiddyment Sarah S   Speller Camilla C   Hendy Jessica J   Charlton Sophy S   Luder Hans Ulrich HU   Salazar-García Domingo C DC   Eppler Elisabeth E   Seiler Roger R   Hansen Lars H LH   Castruita José Alfredo Samaniego JA   Barkow-Oesterreicher Simon S   Teoh Kai Yik KY   Kelstrup Christian D CD   Olsen Jesper V JV   Nanni Paolo P   Kawai Toshihisa T   Willerslev Eske E   von Mering Christian C   Lewis Cecil M CM   Collins Matthew J MJ   Gilbert M Thomas P MT   Rühli Frank F   Cappellini Enrico E  

Nature genetics 20140223 4

Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii)  ...[more]

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