1
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Ahmad P, Moussa DG, Siqueira WL. Metabolomics for dental caries diagnosis: Past, present, and future. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38940512 DOI: 10.1002/mas.21896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/22/2024] [Accepted: 06/15/2024] [Indexed: 06/29/2024]
Abstract
Dental caries, a prevalent global infectious condition affecting over 95% of adults, remains elusive in its precise etiology. Addressing the complex dynamics of caries demands a thorough exploration of taxonomic, potential, active, and encoded functions within the oral ecosystem. Metabolomic profiling emerges as a crucial tool, offering immediate insights into microecosystem physiology and linking directly to the phenotype. Identified metabolites, indicative of caries status, play a pivotal role in unraveling the metabolic processes underlying the disease. Despite challenges in metabolite variability, the use of metabolomics, particularly via mass spectrometry and nuclear magnetic resonance spectroscopy, holds promise in caries research. This review comprehensively examines metabolomics in caries prevention, diagnosis, and treatment, highlighting distinct metabolite expression patterns and their associations with disease-related bacterial communities. Pioneering in approach, it integrates singular and combinatory metabolomics methodologies, diverse biofluids, and study designs, critically evaluating prior limitations while offering expert insights for future investigations. By synthesizing existing knowledge, this review significantly advances our comprehension of caries, providing a foundation for improved prevention and treatment strategies.
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Affiliation(s)
- Paras Ahmad
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Dina G Moussa
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, SK, Canada
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2
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Duitama González C, Rangavittal S, Vicedomini R, Chikhi R, Richard H. aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets. iScience 2023; 26:108057. [PMID: 37876815 PMCID: PMC10590965 DOI: 10.1016/j.isci.2023.108057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/04/2023] [Accepted: 09/22/2023] [Indexed: 10/26/2023] Open
Abstract
Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over 89.53 % sensitivity and 94.00 % specificity. On real datasets, aKmerBroom shows higher read retainment (+ 60 % on average) than other methods. We anticipate aKmerBroom will be a valuable tool for the processing of ancient oral samples as it will prevent contaminated datasets from being completely discarded in downstream analyses.
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Affiliation(s)
- Camila Duitama González
- Institut Pasteur, 75015 Paris, France
- Sorbonne Université, Université Paris Cité, 75005 Paris, France
| | | | | | | | - Hugues Richard
- MF1 - Genome Competence Center, Robert Koch Institute, 13353 Berlin, Germany
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3
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Wilkin S, Hommel P, Ventresca Miller A, Boivin N, Pedergnana A, Shishlina N, Trifonov V. Curated cauldrons: Preserved proteins from early copper-alloy vessels illuminate feasting practices in the Caucasian steppe. iScience 2023; 26:107482. [PMID: 37744407 PMCID: PMC10517358 DOI: 10.1016/j.isci.2023.107482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 09/26/2023] Open
Abstract
Large metal and metal-alloy cauldrons first appear on the far western steppe and Caucasus region during the Maykop period (3700-2900 BCE); however, the types of foods or beverages cooked in and served from these vessels have remained mysterious. Here, we present proteomic analysis of nine residues from copper-alloy cauldrons from Maykop burial contexts where we identify muscle, blood, and milk proteins specific to domesticated, and possibly wild, ruminants. This study clearly demonstrates that the earliest, large-volume feasting vessels contained both primary and secondary animal products, likely prepared in the form of a stew.
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Affiliation(s)
- Shevan Wilkin
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Max Planck Institute of Geoanthropology, Jena, Germany
- Australian Research Centre for Human Evolution (ARCHE), Griffith University, Brisbane, QLD, Australia
| | - Peter Hommel
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK
| | - Alicia Ventresca Miller
- Department of Anthropology, University of Michigan, Ann Arbor, MI, USA
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI, USA
| | - Nicole Boivin
- Max Planck Institute of Geoanthropology, Jena, Germany
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- School of Social Science, University of Queensland, Brisbane, QLD, Australia
- Griffith Sciences, Griffith University, Brisbane, QLD, Australia
| | | | - Natalia Shishlina
- State Historical Museum, Moscow, Russia
- Peter the Great Museum of Anthropology and Ethnography (the Kunstkamera), St Petersburg, Russia
| | - Viktor Trifonov
- Institute for the History of Material Culture, St Petersburg, Russia
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4
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Badillo-Sanchez D, Serrano Ruber M, Davies-Barrett A, Jones DJ, Hansen M, Inskip S. Metabolomics in archaeological science: A review of their advances and present requirements. SCIENCE ADVANCES 2023; 9:eadh0485. [PMID: 37566664 PMCID: PMC10421062 DOI: 10.1126/sciadv.adh0485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/11/2023] [Indexed: 08/13/2023]
Abstract
Metabolomics, the study of metabolites (small molecules of <1500 daltons), has been posited as a potential tool to explore the past in a comparable manner to other omics, e.g., genomics or proteomics. Archaeologists have used metabolomic approaches for a decade or so, mainly applied to organic residues adhering to archaeological materials. Because of advances in sensitivity, resolution, and the increased availability of different analytical platforms, combined with the low mass/volume required for analysis, metabolomics is now becoming a more feasible choice in the archaeological sector. Additional approaches, as presented by our group, show the versatility of metabolomics as a source of knowledge about the human past when using human osteoarchaeological remains. There is tremendous potential for metabolomics within archaeology, but further efforts are required to position it as a routine technique.
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Affiliation(s)
| | - Maria Serrano Ruber
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Anna Davies-Barrett
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Donald J. L. Jones
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester, UK
- The Leicester van Geest MultiOmics Facility, University of Leicester, Leicester, UK
| | - Martin Hansen
- Environmental Metabolomics Lab, Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Sarah Inskip
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
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5
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Riboni N, Bianchi F, Mattarozzi M, Peracchia M, Meleti M, Careri M. Ultra-high performance liquid chromatography high-resolution mass spectrometry for metabolomic analysis of dental calculus from Duke Alessandro Farnese and Maria D'Aviz. Sci Rep 2023; 13:8967. [PMID: 37268814 DOI: 10.1038/s41598-023-36177-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
Dental calculus is a valuable resource for the reconstruction of dietary habits and oral microbiome of past populations. In 2020 the remains of Duke Alessandro Farnese and his wife Maria D'Aviz were exhumed to get novel insights into the causes of death. This study aimed to investigate the dental calculus metabolome of the noble couple by untargeted metabolomics. The pulverized samples were decalcified in a water-formic acid mixture, extracted using methanol/acetonitrile and analyzed by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) using a reversed-phase separation followed by electrospray ionization and full scan in positive and negative ion mode. Waters Synapt-G2-Si High-Definition hybrid quadrupole time-of-flight mass spectrometer was used. Significant features were then identified using MSE acquisition mode, recording information on exact mass precursor and fragment ions within the same run. This approach, together with data pre-treatment and multivariate statistical analysis allowed for the identification of compounds able to differentiate between the investigated samples. More than 200 metabolites were identified, being fatty acids, alcohols, aldehydes, phosphatidylcholines, phosphatidylglycerols, ceramides and phosphatidylserines the most abundant classes. Metabolites deriving from food, bacteria and fungi were also determined, providing information on the habits and oral health status of the couple.
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Affiliation(s)
- Nicolo' Riboni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy.
| | - Federica Bianchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy.
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy
| | - Marianna Peracchia
- Department of Medicine and Surgery, Centro Universitario di Odontoiatria, University of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Marco Meleti
- Department of Medicine and Surgery, Centro Universitario di Odontoiatria, University of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy
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6
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Klapper M, Hübner A, Ibrahim A, Wasmuth I, Borry M, Haensch VG, Zhang S, Al-Jammal WK, Suma H, Fellows Yates JA, Frangenberg J, Velsko IM, Chowdhury S, Herbst R, Bratovanov EV, Dahse HM, Horch T, Hertweck C, González Morales MR, Straus LG, Vilotijevic I, Warinner C, Stallforth P. Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic. Science 2023; 380:619-624. [PMID: 37141315 DOI: 10.1126/science.adf5300] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. Here, we investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans spanning 100 kya to the present and reconstructed 459 bacterial metagenome-assembled genomes (MAGs). We identified a biosynthetic gene cluster (BGC) shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites we name paleofurans. This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.
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Affiliation(s)
- Martin Klapper
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Anan Ibrahim
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Ina Wasmuth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Veit G Haensch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Shuaibing Zhang
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Walid K Al-Jammal
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Harikumar Suma
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - James A Fellows Yates
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Jasmin Frangenberg
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Somak Chowdhury
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Rosa Herbst
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Evgeni V Bratovanov
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Hans-Martin Dahse
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Therese Horch
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Manuel Ramon González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, 39071 Santander, Spain
| | - Lawrence Guy Straus
- Department of Anthropology, University of New Mexico, Albuquerque, NM 87131, USA
- Grupo I+D+i EvoAdapta, Departmento de Ciencias Históricas, Universidad de Cantabria, 39005 Santander, Spain
| | - Ivan Vilotijevic
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Associated Research Group of Archaeogenetics, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Faculty of Biological Sciences, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Pierre Stallforth
- Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knöll Institute, 07745 Jena, Germany
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
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7
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Badillo-Sanchez DA, Jones DJL, Inskip SA, Scheib CL. Human Archaeological Dentin as Source of Polar and Less Polar Metabolites for Untargeted Metabolomic Research: The Case of Yersinia pestis. Metabolites 2023; 13:588. [PMID: 37233629 PMCID: PMC10223108 DOI: 10.3390/metabo13050588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/05/2023] [Accepted: 04/19/2023] [Indexed: 05/27/2023] Open
Abstract
Metabolomic approaches, such as in clinical applications of living individuals, have shown potential use for solving questions regarding the past when applied to archaeological material. Here, we study for the first time the potential of this Omic approach as applied to metabolites extracted from archaeological human dentin. Dentin obtained from micro sampling the dental pulp of teeth of victims and non-victims of Yersinia pestis (plague) from a 6th century Cambridgeshire site are used to evaluate the potential use of such unique material for untargeted metabolomic studies on disease state through liquid chromatography hyphenated to high-resolution mass spectrometry (LC-HRMS). Results show that small molecules of both likely endogenous and exogenous sources are preserved for a range of polar and less polar/apolar metabolites in archaeological dentin; however, untargeted metabolomic profiles show no clear differentiation between healthy and infected individuals in the small sample analysed (n = 20). This study discusses the potential of dentin as a source of small molecules for metabolomic assays and highlights: (1) the need for follow up research to optimise sampling protocols, (2) the requirements of studies with larger sample numbers and (3) the necessity of more databases to amplify the positive results achievable with this Omic technique in the archaeological sciences.
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Affiliation(s)
| | - Donald J L Jones
- Leicester Cancer Research Centre, RKCSB, University of Leicester, Leicester LE1 7RH, UK
- The Leicester van Geest MultiOmics Facility, University of Leicester, Leicester LE1 7RH, UK
| | - Sarah A Inskip
- School of Archaeology and Ancient History, University of Leicester, Leicester LE1 7RH, UK
| | - Christiana L Scheib
- Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge CB2 3ER, UK
- St. John's College, University of Cambridge, Cambridge CB2 1TP, UK
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8
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Tang L, Wilkin S, Richter KK, Bleasdale M, Fernandes R, He Y, Li S, Petraglia M, Scott A, Teoh FK, Tong Y, Tsering T, Tsho Y, Xi L, Yang F, Yuan H, Chen Z, Roberts P, He W, Spengler R, Lu H, Wangdue S, Boivin N. Paleoproteomic evidence reveals dairying supported prehistoric occupation of the highland Tibetan Plateau. SCIENCE ADVANCES 2023; 9:eadf0345. [PMID: 37043579 PMCID: PMC10096579 DOI: 10.1126/sciadv.adf0345] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/13/2023] [Indexed: 06/19/2023]
Abstract
The extreme environments of the Tibetan Plateau offer considerable challenges to human survival, demanding novel adaptations. While the role of biological and agricultural adaptations in enabling early human colonization of the plateau has been widely discussed, the contribution of pastoralism is less well understood, especially the dairy pastoralism that has historically been central to Tibetan diets. Here, we analyze ancient proteins from the dental calculus (n = 40) of all human individuals with sufficient calculus preservation from the interior plateau. Our paleoproteomic results demonstrate that dairy pastoralism began on the highland plateau by ~3500 years ago. Patterns of milk protein recovery point to the importance of dairy for individuals who lived in agriculturally poor regions above 3700 m above sea level. Our study suggests that dairy was a critical cultural adaptation that supported expansion of early pastoralists into the region's vast, non-arable highlands, opening the Tibetan Plateau up to widespread, permanent human occupation.
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Affiliation(s)
- Li Tang
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Center for Archaeological Science, Sichuan University, Chengdu, China
- Institute for Prehistoric and Protohistoric Archaeology, Kiel University, Kiel, Germany
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, Australia
- Institute for Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - Kristine Korzow Richter
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, USA
| | - Madeleine Bleasdale
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Archaeology, University of York, York, UK
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Faculty of Arts, Masaryk University, Brno, Czech Republic
- Climate Change and History Research Initiative, Princeton University, Princeton, NJ, USA
| | - Yuanhong He
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
| | - Shuai Li
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
- Center for Tibetan Studies, Sichuan University, Chengdu, China
| | - Michael Petraglia
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, Australia
- School of Social Science, University of Queensland, Brisbane, Australia
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Ashley Scott
- Department of Anthropology, Harvard University, Cambridge, USA
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fallen K.Y. Teoh
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Yan Tong
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Tinlei Tsering
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Yang Tsho
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Lin Xi
- Shaanxi Academy of Archaeology, Xian, China
| | - Feng Yang
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
- Center for Tibetan Studies, Sichuan University, Chengdu, China
| | - Haibing Yuan
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
| | - Zujun Chen
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- School of Social Science, University of Queensland, Brisbane, Australia
- isoTROPIC Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Wei He
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Robert Spengler
- Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
- Domestication and Anthropogenic Evolution Research Group, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Hongliang Lu
- Center for Archaeological Science, Sichuan University, Chengdu, China
- School of Archaeology and Museology, Sichuan University, Chengdu, China
- Center for Tibetan Studies, Sichuan University, Chengdu, China
| | - Shargan Wangdue
- Tibetan Cultural Relics Conservation Institute, Lhasa, China
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, University of Queensland, Brisbane, Australia
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
- Griffith Sciences, Griffith University, Brisbane, Australia
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9
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Alqahtani SM, Gokhale ST, Elagib MFA, Shrivastava D, Nagate RR, Alshmrani BAM, Alburade AMA, Alqahtani FMA, Nagarajappa AK, Natoli V, Srivastava KC. Assessment and Correlation of Salivary Ca, Mg, and pH in Smokers and Non-Smokers with Generalized Chronic Periodontitis. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59040765. [PMID: 37109723 PMCID: PMC10141299 DOI: 10.3390/medicina59040765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/12/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023]
Abstract
Background and Objectives: Diagnostic evaluation with the aid of biomarkers has reached newer heights to assess disease activity. Salivary calcium, magnesium, and pH are one of the biochemical parameters which can be helpful in assessing the progression of periodontal disease. Smokers are at topnotch threat for having oral diseases, predominantly periodontal diseases. The aim of this study was to assess the salivary calcium, magnesium, and pH levels in smokers compared with non-smokers with chronic periodontitis. Materials and Methods: The current study was conducted on 210 individuals affected with generalized chronic periodontitis, with the age group between 25 and 55 years. Based on their smoking habit, an equal number of patients were categorized into two groups; namely, group I consisted of non-smokers and group II consisted of smokers. The clinical parameters that were measured included Plaque Index (PI), Gingival Index (GI), Probing Pocket Depth (PPD), and Clinical Attachment Loss (CAL). The biochemical variables that were evaluated in the current study included salivary calcium, magnesium, and pH using an AVL9180 electrolyte analyzer (Roche, Germany). The gathered data were analyzed with an unpaired t test was using SPSS 20.0. Results: A statistically significant higher PPD (p < 0.01), CAL (p < 0.05), and salivary calcium levels (p < 0.001) were observed in the smokers' compared with their non-smoking counterparts. Among the biochemical parameters, calcium showed a significantly (p < 0.001) higher level in smokers (5.79 ± 1.76) in contrast to non-smokers (3.87 ± 1.03). Additionally, a significant negative correlation (p < 0.05) between calcium and PPD was observed in non-smokers, whereas a non-significant inverse relation (p > 0.05) was seen in smokers. Conclusions: The present study indicates that the salivary calcium level can be a potential biochemical parameter to assess the progression of periodontal disease in smokers and non-smokers. Within the limitations of the current study, the salivary biomarkers appear to have an essential role in the identification and indication of the status of periodontal diseases.
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Affiliation(s)
- Saad Mohammad Alqahtani
- Department of Periodontics and Community Sciences (PCS), College of Dentistry, King Khalid University, Abha 62529, Saudi Arabia
| | - Shankar T Gokhale
- Department of Periodontics and Community Sciences (PCS), College of Dentistry, King Khalid University, Abha 62529, Saudi Arabia
| | - Mohamed Fadul A Elagib
- Department of Periodontics and Community Sciences (PCS), College of Dentistry, King Khalid University, Abha 62529, Saudi Arabia
| | - Deepti Shrivastava
- Department of Preventive dentistry, College of Dentistry, Jouf University, Sakaka 72345, Saudi Arabia
| | - Raghavendra Reddy Nagate
- Department of Periodontics and Community Sciences (PCS), College of Dentistry, King Khalid University, Abha 62529, Saudi Arabia
| | - Badar Awadh Mohammad Alshmrani
- Department of Periodontics and Community Sciences (PCS), College of Dentistry, King Khalid University, Abha 62529, Saudi Arabia
| | | | - Fares Mufreh Abdullah Alqahtani
- Department of Periodontics and Community Sciences (PCS), College of Dentistry, King Khalid University, Abha 62529, Saudi Arabia
| | - Anil Kumar Nagarajappa
- Department of Oral Maxillofacial Surgery & Diagnostic Sciences, College of Dentistry, Jouf University, Sakaka 72345, Saudi Arabia
| | - Valentino Natoli
- Department of Dentistry, School of Biomedical and Health Sciences, European University of Madrid, 28670 Madrid, Spain
- Private Dental Practice, 72015 Fasano, Italy
| | - Kumar Chandan Srivastava
- Department of Oral Maxillofacial Surgery & Diagnostic Sciences, College of Dentistry, Jouf University, Sakaka 72345, Saudi Arabia
- Department of Oral Medicine and radiology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 602105, India
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10
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He XF, Wang H, Tian Y, Zhang T, Qiu ZP, Cui XJ, Zhou JS, Yan XL, Wu YW, Pan YS, Ning YB, Chen L, Zhang KL, Zhao WH, Sharma D, Tan XD, Zhang MB. Evaluation of Copper Levels in Dental Calculus of OSF Patients with Chewing Dried Areca-Nut Quids in Hunan Province of Mainland China. Biol Trace Elem Res 2023; 201:677-682. [PMID: 35332437 DOI: 10.1007/s12011-022-03210-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/15/2022] [Indexed: 01/21/2023]
Abstract
Dental calculus is a potential material that can be used for assessing chronic exposure to trace heavy metals in oral cavity as it is a long-term reservoir. The aim of this study was to investigate the correlation between dental calculus copper levels and risk of oral submucous fibrosis (OSF) due to chewing dried areca-nut quids in Mainland China. This study included 34 OSF (grade 1) sufferers with dried areca-nut quids chewing as the patient group and 23 healthy individuals without areca-nut chewing as the control group. The dental calculus sample was obtained from all 57 participants and evaluated by inductively coupled plasma mass spectrometry (ICP-MS) for dental calculus level of copper. This work revealed that the mean copper level of dental calculus was significantly higher in OSF (grade 1) sufferers with areca-nut chewing than those in healthy individuals without areca-nut chewing (p < 0.001). This work provided an evidence to support that there may be a positive correlation between elevated levels of copper in dental calculus caused by chewing dried areca-nut quids and an increased risk of developing OSF in Mainland China.
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Affiliation(s)
- Xi-Fan He
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
- Department of Stomatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
- Department of Stomatology, First Affiliated Hospital of Hunan College of Traditional Chinese Medicine (Zhuzhou Hospital of Traditional Chinese Medicine), Zhuzhou, People's Republic of China
| | - Hui Wang
- Changsha Institute for Food and Drug Control & National Alcohol Products Quality Supervision and Inspection Center, Changsha, Hunan, People's Republic of China
| | - Ye Tian
- Hunan Provincial Key Laboratory of Chemical Power Sources, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan, People's Republic of China
| | - Te Zhang
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Zhi-Peng Qiu
- Changsha Institute for Food and Drug Control & National Alcohol Products Quality Supervision and Inspection Center, Changsha, Hunan, People's Republic of China
| | - Xiao-Jiao Cui
- Changsha Institute for Food and Drug Control & National Alcohol Products Quality Supervision and Inspection Center, Changsha, Hunan, People's Republic of China
| | - Jing-Sha Zhou
- Changsha Institute for Food and Drug Control & National Alcohol Products Quality Supervision and Inspection Center, Changsha, Hunan, People's Republic of China
| | - Xin-Lan Yan
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Yi-Wei Wu
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Yi-Sha Pan
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Yang-Bo Ning
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Lin Chen
- Department of Stomatology, Second Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Kun-Lun Zhang
- Hanwoo DNA Solutions Co., Ltd, Changsha, People's Republic of China
| | - Wei-Hao Zhao
- Hanwoo DNA Solutions Co., Ltd, Changsha, People's Republic of China
| | - David Sharma
- Hanwoo DNA Solutions Co., Ltd, Changsha, People's Republic of China
| | - Xiao-Dan Tan
- Hanwoo DNA Solutions Co., Ltd, Changsha, People's Republic of China
- Hunan Legal Forensic Center, Changsha, People's Republic of China
| | - Michael Bo Zhang
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China.
- Hanwoo DNA Solutions Co., Ltd, Changsha, People's Republic of China.
- Hunan Legal Forensic Center, Changsha, People's Republic of China.
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11
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Examination of human osteoarchaeological remains as a feasible source of polar and apolar metabolites to study past conditions. Sci Rep 2023; 13:696. [PMID: 36639564 PMCID: PMC9839756 DOI: 10.1038/s41598-023-27401-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/02/2023] [Indexed: 01/15/2023] Open
Abstract
Metabolomics is a modern tool that aids in our understanding of the molecular changes in organisms. Archaeological science is a branch of archaeology that explores different archaeological materials using modern analytical tools. Human osteoarchaeological material are a frequent finding in archaeological contexts and have the potential to offer information about previous human populations, which can be illuminating about our current condition. Using a set of samples comprising different skeletal elements and bone structures, here we explore for the first time the possibility of extracting metabolites from osteoarchaeological material. Here, a protocol for extraction and measurement of extracted polar and less-polar/apolar metabolites by ultra-high performance liquid chromatography hyphenated to high resolution mass spectrometry is presented to measure the molecules separated after a reversed phase and hydrophilic interaction liquid chromatography column. Molecular information was obtained, showing that osteoarchaeological material is a viable source of molecular information for metabolomic studies.
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12
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Li Q, Luo K, Su Z, Huang F, Wu Y, Zhou F, Li Y, Peng X, Li J, Ren B. Dental calculus: A repository of bioinformation indicating diseases and human evolution. Front Cell Infect Microbiol 2022; 12:1035324. [PMID: 36579339 PMCID: PMC9791188 DOI: 10.3389/fcimb.2022.1035324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Dental calculus has long been considered as a vital contributing factor of periodontal diseases. Our review focuses on the role of dental calculus as a repository and discusses the bioinformation recently reported to be concealed in dental calculus from three perspectives: time-varying oral condition, systemic diseases, and anthropology at various times. Molecular information representing an individual's contemporary oral health status could be detected in dental calculus. Additionally, pathogenic factors of systemic diseases were found in dental calculus, including bacteria, viruses and toxic heavy metals. Thus, dental calculus has been proposed to play a role as biological data storage for detection of molecular markers of latent health concerns. Through the study of environmental debris in dental calculus, an overview of an individual's historical dietary habits and information about the environment, individual behaviors and social culture changes can be unveiled. This review summarizes a new role of dental calculus as a repository of bioinformation, with potential use in the prediction of oral diseases, systemic diseases, and even anthropology.
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Affiliation(s)
- Qinyang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Kaihua Luo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhifei Su
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fangting Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yajie Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fangjie Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China,*Correspondence: Jiyao Li, ; Biao Ren,
| | - Biao Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China,*Correspondence: Jiyao Li, ; Biao Ren,
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13
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Velsko IM, Semerau L, Inskip SA, García-Collado MI, Ziesemer K, Ruber MS, Benítez de Lugo Enrich L, Molero García JM, Valle DG, Peña Ruiz AC, Salazar-García DC, Hoogland MLP, Warinner C. Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology. PNAS NEXUS 2022; 1:pgac148. [PMID: 36714834 PMCID: PMC9802386 DOI: 10.1093/pnasnexus/pgac148] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023]
Abstract
Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.
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Affiliation(s)
- Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany
| | - Sarah A Inskip
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Maite I García-Collado
- GIPYPAC, Department of Geography, Prehistory and Archaeology, University of the Basque Country, Leioa 48940, Spain.,BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Kirsten Ziesemer
- University Library, Vrije Universiteit, Einsteinweg 2, Amsterdam 1081 HV, The Netherlands
| | - Maria Serrano Ruber
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Luis Benítez de Lugo Enrich
- Departmento de Prehistoria, Historia Antigua y Arqueología, Universidad Complutense de Madrid, Madrid 28040, Spain
| | | | - David Gallego Valle
- Facultad de Letras, Universidad de Castilla-La Mancha, Ciudad Real 13004, Spain
| | | | - Domingo C Salazar-García
- Departament de Prehistòria, Historia i Arqueología, Universitat de València, València 46010, Spain.,Department of Geological Sciences, University of Cape Town, Rondebosch 7701, South Africa
| | - Menno L P Hoogland
- Faculty of Archaeology, Leiden University, Einsteinweg, Leiden 2333 CC, The Netherlands
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
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14
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Maruyama Y, Nishimoto Y, Umezawa K, Kawamata R, Ichiba Y, Tsutsumi K, Kimura M, Murakami S, Kakizawa Y, Kumagai T, Yamada T, Fukuda S. Comparison of oral metabolome profiles of stimulated saliva, unstimulated saliva, and mouth-rinsed water. Sci Rep 2022; 12:689. [PMID: 35027617 PMCID: PMC8758762 DOI: 10.1038/s41598-021-04612-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/20/2021] [Indexed: 12/16/2022] Open
Abstract
Saliva includes a substantial amount of biological information, which has enabled us to understand the relationship between oral metabolites and various oral and systemic disorders. However, collecting saliva using a controlled protocol is time-consuming, making saliva an unsuitable analyte in large cohort studies. Mouth-rinsed water (MW), the water used to rinse the mouth, can be collected easily in less time with less difference between subjects than saliva and could be used as an alternative in oral metabolome analyses. In this study, we investigated the potential of MW collection as an efficient alternative to saliva sample collection for oral metabolome profiling. MW, stimulated saliva, and unstimulated saliva were collected from 10 systemically healthy participants. The samples were subjected to metabolome analysis using capillary electrophoresis time-of-flight mass spectrometry, and the types and amounts of metabolites in the samples were compared. Qualitatively, MW contained the same metabolites as unstimulated and stimulated saliva. While the quantity of the metabolites did not drastically change between the sampling methods, all three reflected individual differences, and the features of MW were the same as those of the unstimulated saliva. Overall, these results suggest that MW may be an appropriate alternative to saliva in oral metabolome profile analysis.
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Affiliation(s)
- Yuki Maruyama
- Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Yuichiro Nishimoto
- Metabologenomics, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Kouta Umezawa
- Hiyoshi Oral Health Clinics, 2-1-16 Hiyoshi-cho, Sakata, Yamagata, 998-0037, Japan
| | - Ryosuke Kawamata
- Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Yuko Ichiba
- Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Kota Tsutsumi
- Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Mitsuo Kimura
- Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Shinnosuke Murakami
- Metabologenomics, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.,Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan
| | - Yasushi Kakizawa
- Research and Development Headquarters, Lion Corporation, 7-2-1 Hirai, Edogawa-ku, Tokyo, 132-0035, Japan
| | - Takashi Kumagai
- Hiyoshi Oral Health Clinics, 2-1-16 Hiyoshi-cho, Sakata, Yamagata, 998-0037, Japan
| | - Takuji Yamada
- Metabologenomics, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan.,Department of Life Science and Technology, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro, Tokyo, 152-8550, Japan
| | - Shinji Fukuda
- Metabologenomics, Inc., 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan. .,Institute for Advanced Biosciences, Keio University, 246-2 Mizukami, Kakuganji, Tsuruoka, Yamagata, 997-0052, Japan. .,Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki, Kanagawa, 210-0821, Japan. .,Transborder Medical Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8575, Japan.
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15
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Granehäll L, Huang KD, Tett A, Manghi P, Paladin A, O’Sullivan N, Rota-Stabelli O, Segata N, Zink A, Maixner F. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. MICROBIOME 2021; 9:197. [PMID: 34593021 PMCID: PMC8485483 DOI: 10.1186/s40168-021-01132-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/01/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE). RESULTS We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. CONCLUSIONS We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.
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Affiliation(s)
- Lena Granehäll
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
- Faculty of Biology, Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Kun D. Huang
- CIBIO Department, University of Trento, 38123 Trento, Italy
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
| | - Adrian Tett
- CIBIO Department, University of Trento, 38123 Trento, Italy
- CUBE - Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Paolo Manghi
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Alice Paladin
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Niall O’Sullivan
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, 38123 Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
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16
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Trends in deamidation across archaeological bones, ceramics and dental calculus. Methods 2021; 200:67-79. [PMID: 34450289 DOI: 10.1016/j.ymeth.2021.08.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/04/2021] [Accepted: 08/14/2021] [Indexed: 11/23/2022] Open
Abstract
The accumulation of post-translational modifications (PTMs) in proteins throughout the lifecycle has been studied for decades, particularly more so with the advent of soft-ionization mass spectrometry-based proteomic techniques. However, particular PTMs, such as the deamidations of asparagine and glutamine residues, continue to accumulate in proteins that remain into the forensic, archaeological, and palaeontological records. The accurate measurement of these ancient 'molecular timers' has been proposed as a method to not only differentiate between exogenous and endogenous proteins within complex mixtures (i.e., contamination), but also as a method of providing relative age estimations into geological time. In this study we explored the extent to which deamidation varies with chronological age across different proteins in bones, as well as investigated differences between proteins across dental calculus and archaeological ceramics. We also analysed the relationships between the observed extent of deamidation and the protein primary structure. We found that collagen obtained from archaeological bones showed a chronological dependence on the extent of deamidation observed, but only when they were from similar environments, supporting prior suggestions about 'thermal age' being a major influence on the deamidation observed. Our study on non-collagenous proteins (NCPs) in archaeological bones showed that while biglycan, and to a lesser extent chondroadherin, showed positive correlations between geological age and the extent of deamidation, others including fetuin-A and serum albumin did not. However, despite the well-known dependence of deamidation on the three-dimensional structure of the peptides, we were unable to find any clear correlation between the structural motifs of the peptides in archaeological bones and the extent of deamidation observed. Our analysis of a set of food proteins obtained from Neolithic archaeological ceramics in Çatalhöyük also showed similar deamidation levels irrespective of the protein structure. Overall, our results suggest that deamidation in archaeological samples could be useful for obtaining additional information beyond identification of species and tissue type, be that as a measure of protein endogeneity and potential contamination, or a measure of protein degradation, or as an indicator of thermal age and for relative dating; however, further research needs to be undertaken to understand why particular proteins are better for this than others, going beyond simple consideration of their secondary structure.
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17
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La Nasa J, Modugno F, Degano I. Liquid chromatography and mass spectrometry for the analysis of acylglycerols in art and archeology. MASS SPECTROMETRY REVIEWS 2021; 40:381-407. [PMID: 32643188 DOI: 10.1002/mas.21644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/29/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Lipid characterization in art and archeology, together with the study of lipid degradation processes, is an important research area in heritage science. Lipid-based materials have been used as food since ancient times, but also employed as illuminants and as ingredients in cosmetic, ritual, and pharmaceutical preparations. Both animal and plant lipids have also been processed to produce materials used in art and crafts, such as paint binders, varnishes, waterproofing agents, and coatings. Identifying the origin of the lipid materials is challenging when they are found in association with artistic historical objects. This is due to the inherent complex composition of lipids, their widespread occurrence, and the chemical alterations induced by ageing. The most common approach for lipid characterization in heritage objects entails profiling fatty acids by gas chromatography/mass spectrometry after saponification or transesterification. New developments in high-performance liquid chromatography coupled with mass spectrometry (HPLC-MS) for the characterization of acylglycerols, together with more efficient sample treatments, have fostered the introduction of liquid chromatography for characterizing the lipid profile in heritage objects. This review reports the latest developments and applications of HPLC-MS for the characterization of lipid materials in the field of heritage science. We describe the various approaches for sample pretreatment and highlight the advantages and limitations of HPLC-MS in the analysis of paint and archeological samples. © 2020 John Wiley & Sons Ltd.
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Affiliation(s)
- Jacopo La Nasa
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, 56124, Italy
| | - Francesca Modugno
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, 56124, Italy
| | - Ilaria Degano
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Giuseppe Moruzzi 13, Pisa, 56124, Italy
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18
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Nodari R, Drancourt M, Barbieri R. Paleomicrobiology of the human digestive tract: A review. Microb Pathog 2021; 157:104972. [PMID: 34029658 DOI: 10.1016/j.micpath.2021.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/23/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.
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Affiliation(s)
- Riccardo Nodari
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, 20133, Italy
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rémi Barbieri
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; UMR 7268, Anthropologie Bioculturelle, Droit, Ethique et Santé, Aix Marseille Univ., 11 CNRS, EFS, ADES, Marseille, France.
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19
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Rogóż J, Podbielska M, Szpyrka E, Wnuk M. Characteristics of Dietary Fatty Acids Isolated from Historic Dental Calculus of the 17th- and 18th-Century Inhabitants of the Subcarpathian Region (Poland). Molecules 2021; 26:molecules26102951. [PMID: 34063539 PMCID: PMC8155891 DOI: 10.3390/molecules26102951] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 11/17/2022] Open
Abstract
Dental calculus analysis can be a valuable source of archaeological knowledge, since it preserves not only microbial and host biomolecules but also dietary and environmental debris, as well as metabolic products likely originating from dietary and craft activities. Here we described GC-MS analysis of a set of historic dental calculus samples from the front teeth of the mandibles of seven individuals found in 17th- and 18th-century graves in the city of Rzeszow, located in South-eastern Poland. We have found that only saturated fatty acids, which are characteristic for fats of animal origin, were present in the tested samples. Our preliminary results indicate that the diet of modern-period inhabitants of Rzeszow was rich in animal products, such as meat and dairy products.
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Affiliation(s)
- Joanna Rogóż
- Institute of Archaeology, University of Rzeszow, Aleja Rejtana 16c, 35-959 Rzeszow, Poland;
| | - Magdalena Podbielska
- Department of Biotechnology, University of Rzeszow, Aleja Rejtana 16c, 35-959 Rzeszow, Poland; (M.P.); (E.S.)
| | - Ewa Szpyrka
- Department of Biotechnology, University of Rzeszow, Aleja Rejtana 16c, 35-959 Rzeszow, Poland; (M.P.); (E.S.)
| | - Maciej Wnuk
- Department of Biotechnology, University of Rzeszow, Aleja Rejtana 16c, 35-959 Rzeszow, Poland; (M.P.); (E.S.)
- Correspondence:
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20
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Tanasi D, Cucina A, Cunsolo V, Saletti R, Di Francesco A, Greco E, Foti S. Paleoproteomic profiling of organic residues on prehistoric pottery from Malta. Amino Acids 2021; 53:295-312. [PMID: 33582869 PMCID: PMC7910365 DOI: 10.1007/s00726-021-02946-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 01/22/2021] [Indexed: 11/02/2022]
Abstract
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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Affiliation(s)
- Davide Tanasi
- Department of History, University of South Florida, SOC107 4202 E. Fowler Ave, Tampa, FL, 33620, USA
| | - Annamaria Cucina
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Vincenzo Cunsolo
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy.
| | - Rosaria Saletti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Antonella Di Francesco
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| | - Enrico Greco
- Aix-Marseille Université, Institut de Chimie Radicalaire, Service 512, Avenue Escadrille Normandie Niemen, 13013, Marseille, France
| | - Salvatore Foti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
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21
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Sørensen LK, Hasselstrøm JB, Larsen LS, Bindslev DA. Entrapment of drugs in dental calculus - Detection validation based on test results from post-mortem investigations. Forensic Sci Int 2020; 319:110647. [PMID: 33341470 DOI: 10.1016/j.forsciint.2020.110647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/26/2022]
Abstract
For prospective investigation of drugs and metabolites in archaeological and contemporary dental calculus, a sensitive, broadly applicable ultra-high-performance liquid chromatography-tandem mass spectrometry method using pneumatically assisted electrospray ionisation (UHPLC-ESI-MS/MS) was developed. The dental calculus was treated with citric acid and the dissolution extracts were cleaned using weak and strong polymeric cation-exchange sorbents. The method was validated on hydroxyapatite for the analysis of 67 drugs and metabolites. Typically, the lower limits of quantification were in the range of 0.01-0.05ng for the sample mass extracted. The general applicability of the method was tested using dental calculus material sampled from 10 corpses undergoing forensic autopsy. The calculus material was washed several times before dissolution to remove residual substances originating from saliva, gingival crevicular fluid and blood. The wash extracts and the calculus samples (cleaned calculus material) were analysed using the same instrumental conditions. The dry mass of the calculus samples ranged from 1 to 10mg. The total number of drug detections was 131 in the dental calculus samples and 117 in the whole blood samples. From the analyses of the wash extracts and calculus samples, it was proven that drug residues were trapped in the interior of the calculus material. In 82 of the drug detections, the drug concentrations were higher in the dental calculus than in the blood. Among substances detected in the dental calculus but not in the blood were cocaine, heroin, 6-MAM and THCA-A.
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Affiliation(s)
- Lambert K Sørensen
- Section for Forensic Chemistry, Department of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
| | - Jørgen B Hasselstrøm
- Section for Forensic Chemistry, Department of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Line S Larsen
- Section of Dental Pathology, Operative Dentistry and Endodontics, Health, Aarhus University, Vennelyst Boulevard 9, 8000, Aarhus C, Denmark
| | - Dorthe A Bindslev
- Section for Forensic Pathology, Department of Forensic Medicine, Aarhus University, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
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22
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Bostanci N, Grant M, Bao K, Silbereisen A, Hetrodt F, Manoil D, Belibasakis GN. Metaproteome and metabolome of oral microbial communities. Periodontol 2000 2020; 85:46-81. [PMID: 33226703 DOI: 10.1111/prd.12351] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The emergence of high-throughput technologies for the comprehensive measurement of biomolecules, also referred to as "omics" technologies, has helped us gather "big data" and characterize microbial communities. In this article, we focus on metaproteomic and metabolomic approaches that support hypothesis-driven investigations on various oral biologic samples. Proteomics reveals the working units of the oral milieu and metabolomics unveils the reactions taking place; and so these complementary techniques can unravel the functionality and underlying regulatory processes within various oral microbial communities. Current knowledge of the proteomic interplay and metabolic interactions of microorganisms within oral biofilm and salivary microbiome communities is presented and discussed, from both clinical and basic research perspectives. Communities indicative of, or from, health, caries, periodontal diseases, and endodontic lesions are represented. Challenges, future prospects, and examples of best practice are given.
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Affiliation(s)
- Nagihan Bostanci
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Melissa Grant
- Biological Sciences, School of Dentistry, Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
| | - Kai Bao
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Angelika Silbereisen
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Franziska Hetrodt
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Manoil
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Georgios N Belibasakis
- Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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23
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Fotakis AK, Denham SD, Mackie M, Orbegozo MI, Mylopotamitaki D, Gopalakrishnan S, Sicheritz-Pontén T, Olsen JV, Cappellini E, Zhang G, Christophersen A, Gilbert MTP, Vågene ÅJ. Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190584. [PMID: 33012227 PMCID: PMC7702802 DOI: 10.1098/rstb.2019.0584] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Sean D Denham
- Museum of Archaeology, University of Stavanger, Stavanger, Norway
| | - Meaghan Mackie
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway.,Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Miren Iraeta Orbegozo
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Dorothea Mylopotamitaki
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Jesper V Olsen
- Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.,BGI-Shenzhen, 518083 Shenzhen, People's Republic of China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, People's Republic of China.,Centre for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, People's Republic of China
| | | | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway.,NTNU University Museum, Trondheim, Norway
| | - Åshild J Vågene
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
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24
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Drotleff B, Roth SR, Henkel K, Calderón C, Schlotterbeck J, Neukamm MA, Lämmerhofer M. Lipidomic profiling of non-mineralized dental plaque and biofilm by untargeted UHPLC-QTOF-MS/MS and SWATH acquisition. Anal Bioanal Chem 2020; 412:2303-2314. [PMID: 31942654 PMCID: PMC7118048 DOI: 10.1007/s00216-019-02364-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/29/2019] [Accepted: 12/18/2019] [Indexed: 12/22/2022]
Abstract
Dental plaque is a structurally organized biofilm which consists of diverse microbial colonies and extracellular matrix. Its composition may change when pathogenic microorganisms become dominating. Therefore, dental biofilm or plaque has been frequently investigated in the context of oral health and disease. Furthermore, its potential as an alternative matrix for analytical purposes has also been recognized in other disciplines like archeology, food sciences, and forensics. Thus, a careful in-depth characterization of dental plaque is worthwhile. Most of the conducted studies focused on the screening of microbial populations in dental plaque. Their lipid membranes, on the other hand, may significantly impact substance (metabolite) exchange within microbial colonies as well as xenobiotics uptake and incorporation into teeth. Under this umbrella, a comprehensive lipidomic profiling for determination of lipid compositions of in vivo dental plaque samples and of in vitro cultivated biofilm as surrogate matrix to be used for analytical purposes has been performed in this work. An untargeted lipidomics workflow utilizing a ultra-high-performance liquid chromatography (UHPLC)-quadrupole-time-of-flight (QTOF) platform together with comprehensive SWATH (sequential window acquisition of all theoretical fragment ion mass spectra) acquisition and compatible software (MS-DIAL) that comprises a vast lipid library has been adopted to establish an extensive lipidomic fingerprint of dental plaque. The main lipid components in dental plaque were identified as triacylglycerols, followed by cholesterol, cholesteryl esters as well as diacylglycerols, and various phospholipid classes. In vivo plaque is a rare matrix which is usually available in very low amounts. When higher quantities for specific research assays are required, efficient ways to produce an appropriate surrogate matrix are mandatory. A potential surrogate matrix substituting dental plaque was prepared by cultivation of in vitro biofilm from saliva and similarities and differences in the lipidomics profile to in vivo plaque were mapped by statistical evaluation post-analysis. It was discovered that most lipid classes were highly elevated in the in vitro biofilm samples, in particular diacylglycerols, phosphatidylglycerols, and phosphatidylethanolamines (PEs). Furthermore, an overall shift from even-chain lipid species to odd-chain lipids was observed in the cultivated biofilms. On the other hand, even-chain phosphatidylcholines (PCs), lysoPCs, cholesteryl esters, and cholesterol-sulfate were shown to be specifically increased in plaque samples. Graphical abstract ![]()
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Affiliation(s)
- Bernhard Drotleff
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Simon R Roth
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstraße 9, 79104, Freiburg, Germany
| | - Kerstin Henkel
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstraße 9, 79104, Freiburg, Germany
| | - Carlos Calderón
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Jörg Schlotterbeck
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Merja A Neukamm
- Institute of Forensic Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstraße 9, 79104, Freiburg, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
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25
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Al Ankily M, Makkeyah F, Bakr M, Shamel M. Effect of different scaling methods and materials on the enamel surface topography: An in vitro SEM study. J Int Oral Health 2020. [DOI: 10.4103/jioh.jioh_121_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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26
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Lewis CM, McCall LI, Sharp RR, Spicer PG. Ethical priority of the most actionable system of biomolecules: the metabolome. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2019; 171:177-181. [PMID: 31643083 PMCID: PMC7003909 DOI: 10.1002/ajpa.23943] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 09/26/2019] [Accepted: 10/01/2019] [Indexed: 11/06/2022]
Abstract
The metabolome is a system of small biomolecules (metabolites) and a direct result of human bioculture. Consequently, metabolomics is well poised to impact anthropological and biomedical research for the foreseeable future. Overall, we provide a perspective on the ethical, legal, and social implications (ELSI) of metabolomics, which we argue are often more alarming than those of genomics. Given the current mechanisms to fund research, ELSI beyond human DNA is stifled and in need of considerable attention.
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Affiliation(s)
- Cecil M Lewis
- University of Oklahoma (OU) College of Arts and Sciences, Norman, OK.,OU Center on the Ethics of Indigenous Genomic Research, Norman, OK.,OU Stephenson Cancer Center, Norman, OK.,OU Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK.,OU Department of Anthropology, Norman, OK
| | - Laura-Isobel McCall
- University of Oklahoma (OU) College of Arts and Sciences, Norman, OK.,OU Stephenson Cancer Center, Norman, OK.,OU Laboratories of Molecular Anthropology and Microbiome Research, Norman, OK.,OU Department of Chemistry and Biochemistry, Norman, OK.,OU Department of Microbiology and Plant Biology, Norman, OK
| | | | - Paul G Spicer
- University of Oklahoma (OU) College of Arts and Sciences, Norman, OK.,OU Center on the Ethics of Indigenous Genomic Research, Norman, OK.,OU Stephenson Cancer Center, Norman, OK.,OU Department of Anthropology, Norman, OK
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27
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Zhang B, Tan X, He X, Yang H, Wang Y, Zhang K. Evaluation of Cadmium Levels in Dental Calculus of Male Oral SCC Patients with Betel-Quid Chewing in Hunan Province of China. Biol Trace Elem Res 2019; 191:348-353. [PMID: 30659512 DOI: 10.1007/s12011-019-1639-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/11/2019] [Indexed: 01/01/2023]
Abstract
Cadmium (Cd) is a widespread trace toxic heavy metal with long biological half-life and may induce higher risk of cancer on multiple organs of human body. Recent studies have confirmed that dental calculus has enormous potential for investigation of exposure to Cd in the human mouth by acting as a time capsule. We aimed to examine relationship between Cd levels in dental calculus due to betel-quid chewing and risk of oral cancer. This study included 85 male oral squamous cell carcinoma (SCC) cases with betel-quid chewing and smoking as observation subjects (group A) and 67 healthy people with smoking but without betel-quid chewing as control subjects (group B) in Hunan province of Mainland China. Cd levels in calcified dental calculus samples from all participants were measured by inductively coupled plasma mass spectrometry (ICP-MS). The results of this study indicated that cadmium levels in dental calculus were significantly higher in male oral SCC patients with betel-quid chewing and smoking than that in healthy individuals without habit of betel-quid chewing and with smoking (p < 0.0001). This study gives some evidence to support that there may be a positive relationship between cadmium in dental calculus due to betel-quid chewing and risk of oral SCC.
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Affiliation(s)
- Bo Zhang
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China.
- Hanwoo DNA Solutions Co., Ltd, Changsha, China.
- Hunan Legal Forensic Center, Changsha, China.
| | - Xiaodan Tan
- Hanwoo DNA Solutions Co., Ltd, Changsha, China
- Hunan Legal Forensic Center, Changsha, China
| | - Xifan He
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Hanlin Yang
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Yuehui Wang
- Department of Oral and Maxillofacial Surgery, Hunan Provincial People's Hospital and The First Affiliated Hospital of Hunan Normal University, Changsha, Hunan, People's Republic of China
| | - Kunlun Zhang
- Hanwoo DNA Solutions Co., Ltd, Changsha, China
- Hunan Legal Forensic Center, Changsha, China
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28
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Peters DL, Wang W, Zhang X, Ning Z, Mayne J, Figeys D. Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome. Proteomics 2019; 19:e1800363. [PMID: 31321880 DOI: 10.1002/pmic.201800363] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/27/2019] [Indexed: 12/14/2022]
Abstract
The gut microbiome has been shown to play a significant role in human healthy and diseased states. The dynamic signaling that occurs between the host and microbiome is critical for the maintenance of host homeostasis. Analyzing the human microbiome with metaproteomics, metabolomics, and integrative multi-omics analyses can provide significant information on markers for healthy and diseased states, allowing for the eventual creation of microbiome-targeted treatments for diseases associated with dysbiosis. Metaproteomics enables functional activity information to be gained from the microbiome samples, while metabolomics provides insight into the overall metabolic states affecting/representing the host-microbiome interactions. Combining these functional -omic platforms together with microbiome composition profiling allows for a holistic overview on the functional and metabolic state of the microbiome and its influence on human health. Here the benefits of metaproteomics, metabolomics, and the integrative multi-omic approaches to investigating the gut microbiome in the context of human health and diseases are reviewed.
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Affiliation(s)
- Danielle L Peters
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Wenju Wang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Janice Mayne
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada.,Canadian Institute for Advanced Research, 661 University Ave, Toronto, ON, M5G 1M1, Canada.,The University of Ottawa and Shanghai Institute of Materia Medica Joint Research Center on Systems and Personalized Pharmacology, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
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29
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Velsko IM, Fellows Yates JA, Aron F, Hagan RW, Frantz LAF, Loe L, Martinez JBR, Chaves E, Gosden C, Larson G, Warinner C. Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage. MICROBIOME 2019; 7:102. [PMID: 31279340 PMCID: PMC6612086 DOI: 10.1186/s40168-019-0717-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/24/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates. RESULTS Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins. CONCLUSIONS Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.
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Affiliation(s)
- Irina M Velsko
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK.
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Richard W Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, OX2 0ES, UK
| | | | - Eros Chaves
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma City, 73117, OK, USA
- Current address: Pinellas Dental Specialties, Largo, FL, 33776, USA
| | - Chris Gosden
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma City, 73117, OK, USA.
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
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30
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Selection of Appropriate Metagenome Taxonomic Classifiers for Ancient Microbiome Research. mSystems 2018; 3:mSystems00080-18. [PMID: 30035235 PMCID: PMC6050634 DOI: 10.1128/msystems.00080-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/20/2018] [Indexed: 02/01/2023] Open
Abstract
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. Metagenomics enables the study of complex microbial communities from myriad sources, including the remains of oral and gut microbiota preserved in archaeological dental calculus and paleofeces, respectively. While accurate taxonomic assignment is essential to this process, DNA damage characteristic of ancient samples (e.g., reduction in fragment size and cytosine deamination) may reduce the accuracy of read taxonomic assignment. Using a set of in silico-generated metagenomic data sets, we investigated how the addition of ancient DNA (aDNA) damage patterns influences microbial taxonomic assignment by five widely used profilers: QIIME/UCLUST, MetaPhlAn2, MIDAS, CLARK-S, and MALT. In silico-generated data sets were designed to mimic dental plaque, consisting of 40, 100, and 200 microbial species/strains, both with and without simulated aDNA damage patterns. Following taxonomic assignment, the profiles were evaluated for species presence/absence, relative abundance, alpha diversity, beta diversity, and specific taxonomic assignment biases. Unifrac metrics indicated that both MIDAS and MetaPhlAn2 reconstructed the most accurate community structure. QIIME/UCLUST, CLARK-S, and MALT had the highest number of inaccurate taxonomic assignments; false-positive rates were highest by CLARK-S and QIIME/UCLUST. Filtering out species present at <0.1% abundance greatly increased the accuracy of CLARK-S and MALT. All programs except CLARK-S failed to detect some species from the input file that were in their databases. The addition of ancient DNA damage resulted in minimal differences in species detection and relative abundance between simulated ancient and modern data sets for most programs. Overall, taxonomic profiling biases are program specific rather than damage dependent, and the choice of taxonomic classification program should be tailored to specific research questions. IMPORTANCE 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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Differential preservation of endogenous human and microbial DNA in dental calculus and dentin. Sci Rep 2018; 8:9822. [PMID: 29959351 PMCID: PMC6026117 DOI: 10.1038/s41598-018-28091-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/14/2018] [Indexed: 12/11/2022] Open
Abstract
Dental calculus (calcified dental plaque) is prevalent in archaeological skeletal collections and is a rich source of oral microbiome and host-derived ancient biomolecules. Recently, it has been proposed that dental calculus may provide a more robust environment for DNA preservation than other skeletal remains, but this has not been systematically tested. In this study, shotgun-sequenced data from paired dental calculus and dentin samples from 48 globally distributed individuals are compared using a metagenomic approach. Overall, we find DNA from dental calculus is consistently more abundant and less contaminated than DNA from dentin. The majority of DNA in dental calculus is microbial and originates from the oral microbiome; however, a small but consistent proportion of DNA (mean 0.08 ± 0.08%, range 0.007–0.47%) derives from the host genome. Host DNA content within dentin is variable (mean 13.70 ± 18.62%, range 0.003–70.14%), and for a subset of dentin samples (15.21%), oral bacteria contribute > 20% of total DNA. Human DNA in dental calculus is highly fragmented, and is consistently shorter than both microbial DNA in dental calculus and human DNA in paired dentin samples. Finally, we find that microbial DNA fragmentation patterns are associated with guanine-cytosine (GC) content, but not aspects of cellular structure.
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Hutchins PD, Russell JD, Coon JJ. LipiDex: An Integrated Software Package for High-Confidence Lipid Identification. Cell Syst 2018; 6:621-625.e5. [PMID: 29705063 DOI: 10.1016/j.cels.2018.03.011] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/30/2018] [Accepted: 03/14/2018] [Indexed: 12/31/2022]
Abstract
State-of-the-art proteomics software routinely quantifies thousands of peptides per experiment with minimal need for manual validation or processing of data. For the emerging field of discovery lipidomics via liquid chromatography-tandem mass spectrometry (LC-MS/MS), comparably mature informatics tools do not exist. Here, we introduce LipiDex, a freely available software suite that unifies and automates all stages of lipid identification, reducing hands-on processing time from hours to minutes for even the most expansive datasets. LipiDex utilizes flexible in silico fragmentation templates and lipid-optimized MS/MS spectral matching routines to confidently identify and track hundreds of lipid species and unknown compounds from diverse sample matrices. Unique spectral and chromatographic peak purity algorithms accurately quantify co-isolation and co-elution of isobaric lipids, generating identifications that match the structural resolution afforded by the LC-MS/MS experiment. During final data filtering, ionization artifacts are removed to significantly reduce dataset redundancy. LipiDex interfaces with several LC-MS/MS software packages, enabling robust lipid identification to be readily incorporated into pre-existing data workflows.
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Affiliation(s)
- Paul D Hutchins
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jason D Russell
- Morgridge Institute for Research, Madison, WI 53715, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA; Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Bravenec AD, Ward KD, Ward TJ. Amino acid racemization and its relation to geochronology and archaeometry. J Sep Sci 2018; 41:1489-1506. [DOI: 10.1002/jssc.201701506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Revised: 02/15/2018] [Accepted: 02/15/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Ardith D. Bravenec
- School of GeoSciences; Grant Institute; University of Edinburgh; Edinburgh UK
| | - Karen D. Ward
- Department of Chemistry and Biochemistry; Keck Center for Instrumental and Biochemical Comparative Archaeology; Millsaps College; Jackson MS USA
| | - Timothy J. Ward
- Department of Chemistry and Biochemistry; Keck Center for Instrumental and Biochemical Comparative Archaeology; Millsaps College; Jackson MS USA
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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