1
|
Putrino A, Marinelli E, Galeotti A, Ferrazzano GF, Ciribè M, Zaami S. A Journey into the Evolution of Human Host-Oral Microbiome Relationship through Ancient Dental Calculus: A Scoping Review. Microorganisms 2024; 12:902. [PMID: 38792733 PMCID: PMC11123932 DOI: 10.3390/microorganisms12050902] [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: 03/29/2024] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/26/2024] Open
Abstract
One of the most promising areas of research in palaeomicrobiology is the study of the human microbiome. In particular, ancient dental calculus helps to reconstruct a substantial share of oral microbiome composition by mapping together human evolution with its state of health/oral disease. This review aims to trace microbial characteristics in ancient dental calculus to describe the evolution of the human host-oral microbiome relationship in oral health or disease in children and adults. Following the PRISMA-Extension for Scoping Reviews guidelines, the main scientific databases (PubMed, Scopus, Lilacs, Cochrane Library) have been drawn upon. Eligibility criteria were established, and all the data collected on a purpose-oriented collection form were analysed descriptively. From the initial 340 records, only 19 studies were deemed comprehensive enough for the purpose of this review. The knowledge of the composition of ancient oral microbiomes has broadened over the past few years thanks to increasingly well-performing decontamination protocols and additional analytical avenues. Above all, metagenomic sequencing, also implemented by state-of-the-art bioinformatics tools, allows for the determination of the qualitative-quantitative composition of microbial species associated with health status and caries/periodontal disease. Some microbial species, especially periodontal pathogens, do not appear to have changed in history, while others that support caries disease or oral health could be connected to human evolution through lifestyle and environmental contributing factors.
Collapse
Affiliation(s)
- Alessandra Putrino
- Dentistry Unit, Management Innovations, Diagnostics and Clinical Pathways, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.G.); (M.C.)
| | - Enrico Marinelli
- Department of Medico-Surgical Sciences and Biotechnologies, Sapienza University of Rome, 04100 Latina, Italy;
| | - Angela Galeotti
- Dentistry Unit, Management Innovations, Diagnostics and Clinical Pathways, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.G.); (M.C.)
- U.N.-E.U. INTERNATIONAL RESEARCH PROJECT ON HUMAN HEALTH-ORAL HEALTH SECTION, 1200 Géneve, Switzerland;
| | - Gianmaria Fabrizio Ferrazzano
- U.N.-E.U. INTERNATIONAL RESEARCH PROJECT ON HUMAN HEALTH-ORAL HEALTH SECTION, 1200 Géneve, Switzerland;
- UNESCO Chair in Health Education and Sustainable Development, Dentistry Section, University of Naples “Federico II”, 80138 Naples, Italy
- East-Asian-Pacific International Academic Consortium
| | - Massimiliano Ciribè
- Dentistry Unit, Management Innovations, Diagnostics and Clinical Pathways, Bambino Gesù Children’s Hospital, IRCCS, 00165 Rome, Italy; (A.G.); (M.C.)
| | - Simona Zaami
- Department of Anatomical, Histological, Forensic and Orthopedic Sciences, Sapienza University of Rome, 00161 Rome, Italy;
| |
Collapse
|
2
|
Gancz AS, Wright SL, Weyrich LS. Ancient human dental calculus metadata collection and sampling strategies: Recommendations for best practices. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24871. [PMID: 37994571 DOI: 10.1002/ajpa.24871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 09/26/2023] [Accepted: 10/18/2023] [Indexed: 11/24/2023]
Abstract
OBJECTIVES Ancient human dental calculus is a unique, nonrenewable biological resource encapsulating key information about the diets, lifestyles, and health conditions of past individuals and populations. With compounding calls its destructive analysis, it is imperative to refine the ways in which the scientific community documents, samples, and analyzes dental calculus so as to maximize its utility to the public and scientific community. MATERIALS AND METHODS Our research team conducted an IRB-approved survey of dental calculus researchers with diverse academic backgrounds, research foci, and analytical specializations. RESULTS This survey reveals variation in how metadata is collected and utilized across different subdisciplines and highlights how these differences have profound implications for dental calculus research. Moreover, the survey suggests the need for more communication between those who excavate, curate, and analyze biomolecular data from dental calculus. DISCUSSION Challenges in cross-disciplinary communication limit researchers' ability to effectively utilize samples in rigorous and reproducible ways. Specifically, the lack of standardized skeletal and dental metadata recording and contamination avoidance procedures hinder downstream anthropological applications, as well as the pursuit of broader paleodemographic and paleoepidemiological inquiries that rely on more complete information about the individuals sampled. To provide a path forward toward more ethical and standardized dental calculus sampling and documentation approaches, we review the current methods by which skeletal and dental metadata are recorded. We also describe trends in sampling and contamination-control approaches. Finally, we use that information to suggest new guidelines for ancient dental calculus documentation and sampling strategies that will improve research practices in the future.
Collapse
Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Sterling L Wright
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Laura S Weyrich
- Department of Anthropology, The Pennsylvania State University, University Park, Pennsylvania, USA
- One Health Microbiome Center, The Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| |
Collapse
|
3
|
Emam ِANM. Role of Forensic Odontology in Identification of Persons: A Review Article. Cureus 2024; 16:e56570. [PMID: 38523878 PMCID: PMC10957511 DOI: 10.7759/cureus.56570] [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] [Accepted: 03/19/2024] [Indexed: 03/26/2024] Open
Abstract
Forensic dentistry plays a pivotal role in identifying deceased individuals when visual or other means of identification are not possible, particularly in the aftermath of mass disasters or criminal activities. Accurate and timely identification of the deceased and injured becomes crucial following events like earthquakes, fires, transport accidents, gunshot incidents, floods, tsunamis, bomb blasts, and terrorist attacks. The process of creating a person's identity is a formidable task, often relying on prevalent methods such as dental, DNA, and fingerprint analyses. Forensic odontology, a specialized field within dentistry, assumes a significant role in identifying individuals in accidents, civil unrest, natural and mass disasters, and crimes related to genocide. In cases where natural teeth are absent, the marking or labeling of dentures becomes essential for personal identification. Teeth's resilience to destruction and decomposition makes dental identification feasible even under extreme conditions. The fundamental principle of forensic dentistry rests on the uniqueness of each individual's oral structure, emphasizing that no two mouths are identical, not even in the case of twins. The purpose of this review is to explore the role of forensic dentistry in identifying individuals through various methods such as denture labeling, cheiloscopy, radiographs, bite mark analysis, rugoscopy, salivary signature, age and sex estimation, dental DNA identification, individual characteristics, and denture marking. Based on detailed ante-mortem records from dental specialists, which are compared to postmortem data during investigations, forensic dentistry is a trustworthy technique for identifying deceased individuals and criminals.
Collapse
Affiliation(s)
- ِAbdel Naser M Emam
- Prosthetic Dental Science, Faculty of Dentistry, Najran University, Najran, SAU
| |
Collapse
|
4
|
Forshaw R. Windows into the past: recent scientific techniques in dental analysis. Br Dent J 2024; 236:205-211. [PMID: 38332093 PMCID: PMC10853062 DOI: 10.1038/s41415-024-7053-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/07/2023] [Accepted: 06/21/2023] [Indexed: 02/10/2024]
Abstract
Teeth are the hardest and most chemically stable tissues in the body, are well-preserved in archaeological remains and, being resistant to decomposition in the soil, survive long after their supporting structures have deteriorated. It has long been recognised that visual and radiographic examination of teeth can provide considerable information relating to the lifestyle of an individual. This paper examines the latest scientific approaches that have become available to investigate recent and ancient teeth. These techniques include DNA analysis, which can be used to determine the sex of an individual, indicate familial relationships, study population movements, provide phylogenetic information and identify the presence of disease pathogens. A stable isotopic approach can shed light on aspects of diet and mobility and even research climate change. Proteomic analysis of ancient dental calculus can reveal specific information about individual diets. Synchrotron microcomputed tomography is a non-invasive technique which can be used to visualise physiological impactful events, such as parturition, menopause and diseases in cementum microstructure - these being displayed as aberrant growth lines.
Collapse
Affiliation(s)
- Roger Forshaw
- KNH Centre for Biomedical Egyptology, Faculty of Biology, Medicine and Health, Stopford Building, Oxford Road, University of Manchester, Manchester, M13 9PL, UK.
| |
Collapse
|
5
|
Fiorin E, Roberts CA, Baldoni M, Connelly E, Lee C, Ottoni C, Cristiani E. First archaeological evidence for ginger consumption as a potential medicinal ingredient in a late medieval leprosarium at St Leonard, Peterborough, England. Sci Rep 2024; 14:2452. [PMID: 38291078 PMCID: PMC10827753 DOI: 10.1038/s41598-024-52422-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/18/2024] [Indexed: 02/01/2024] Open
Abstract
Leprosy was one of the most outwardly visible diseases in the European Middle Ages, a period during which leprosaria were founded to provide space for the sick. The extant documentary evidence for leprosy hospitals, especially in relation to diet, therapeutic, and medical care, is limited. However, human dental calculus stands to be an important source of information as it provides insight into the substances people were exposed to and accumulated in their bodies during their lives. In the present study, microremains and DNA were analysed from the calculus of individuals buried in the late medieval cemetery of St Leonard, a leprosarium located in Peterborough, England. The results show the presence of ginger (Zingiber officinale), a culinary and medicinal ingredient, as well as evidence of consumption of cereals and legumes. This research suggests that affected individuals consumed ingredients mentioned in medieval medical textbooks that were used to treat regions of the body typically impacted by leprosy. To the authors' knowledge, this is the first study which has identified Zingiber officinale in human dental calculus in England or on the wider European continent.
Collapse
Affiliation(s)
- Elena Fiorin
- Department of Oral and Maxillofacial Sciences, DANTE-Diet and Ancient Technology Laboratory, Sapienza University of Rome, 00161, Rome, Italy.
| | - Charlotte A Roberts
- Department of Archaeology, Durham University, Durham, DH1 3LE, United Kingdom
| | - Marica Baldoni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Erin Connelly
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Christina Lee
- School of English, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Claudio Ottoni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, 00133, Rome, Italy
| | - Emanuela Cristiani
- Department of Oral and Maxillofacial Sciences, DANTE-Diet and Ancient Technology Laboratory, Sapienza University of Rome, 00161, Rome, Italy
| |
Collapse
|
6
|
Kırdök E, Kashuba N, Damlien H, Manninen MA, Nordqvist B, Kjellström A, Jakobsson M, Lindberg AM, Storå J, Persson P, Andersson B, Aravena A, Götherström A. Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals. Sci Rep 2024; 13:22125. [PMID: 38238372 PMCID: PMC10796427 DOI: 10.1038/s41598-023-48762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/30/2023] [Indexed: 01/22/2024] Open
Abstract
Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
Collapse
Affiliation(s)
- Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin, Turkey.
| | - Natalija Kashuba
- Department of Archaeology and Ancient History, Uppsala University, Engelska Parken, Thunbergsvägen 3H Box 626, 751 26, Uppsala, Sweden
| | - Hege Damlien
- Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway
| | - Mikael A Manninen
- PAES, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science, University of Helsinki, Viikinkaari 1, P.O. Box 65, Helsinki, Finland
| | - Bengt Nordqvist
- Foundation War-Booty Site Finnestorp, Klarinettvägen 75, 434 75, Kungsbacka, Sweden
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Uppsala University, Evolutionsbiologiskt Centrum EBC Norbyvägen 18 A, Uppsala, Sweden
| | - A Michael Lindberg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Hus Vita, 44018, Kalmar, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Per Persson
- Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Insitutet, P.O. Box 285, 171 77, Stockholm, Sweden
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| |
Collapse
|
7
|
Lisman D, Drath J, Zielińska G, Zacharczuk J, Piątek J, van de Wetering T, Ossowki A. The evidential value of dental calculus in the identification process. Sci Rep 2023; 13:21666. [PMID: 38066060 PMCID: PMC10709568 DOI: 10.1038/s41598-023-48761-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
DNA analysis-based identification is by far the gold standard in forensic genetics and it should be performed in every case involving human remains or unidentified bodies. Bones and teeth are the preferred source of human DNA for genetic analysis. However, there are cases where the nature of the proceedings and historical significance prevent the disruption of skeletal structure. The remains may also be heavily degraded. In such situations, forensic geneticists seek alternative sources of human DNA. Teeth calculus has proven to be a viable source of DNA for identification purposes. The aim of this study was to assess the concentration of human DNA in teeth calculus and evaluate the usefulness of teeth calculus as a DNA source in the identification process. Teeth calculus was collected from skeletons exhumed between 2021 and 2022 by the PBGOT (Polish Genetic Database of Victims of Totalitarianism) team from the former Stalag IID prisoner-of-war camp in Stargard. Genetic analyses included the determination of autosomal and Y-STR markers. The total concentration of human DNA was also evaluated in samples from teeth calculus and teeth taken from the same individuals. The pilot study included 22 skeletons with a sufficient amount of calculus for isolation (specified in the protocol). Samples were taken from the largest areas of calculus deposited on lingual surfaces of mandibular incisors. The prepared samples underwent DNA extraction. Our study demonstrated that teeth calculus is a source of human DNA for remains from the World War II period. The obtained DNA concentration allowed for the determination of STR markers. It was shown that teeth calculus contains human DNA in an amount suitable for preliminary identification analyses.
Collapse
Affiliation(s)
- Dagmara Lisman
- Department of Forensic Genetic, Pomeranian Medical University, Szczecin, Poland.
| | - Joanna Drath
- Department of Forensic Genetic, Pomeranian Medical University, Szczecin, Poland
| | - Grażyna Zielińska
- Department of Forensic Genetic, Pomeranian Medical University, Szczecin, Poland
| | - Julia Zacharczuk
- Department of Forensic Genetic, Pomeranian Medical University, Szczecin, Poland
| | - Jarosław Piątek
- Department of Forensic Genetic, Pomeranian Medical University, Szczecin, Poland
| | - Thierry van de Wetering
- Department of Clinical and Molecular Biochemistry, Pomeranian Medical University, Szczecin, Poland
| | - Andrzej Ossowki
- Department of Forensic Genetic, Pomeranian Medical University, Szczecin, Poland
| |
Collapse
|
8
|
Gancz AS, Farrer AG, Nixon MP, Wright S, Arriola L, Adler C, Davenport ER, Gully N, Cooper A, Britton K, Dobney K, Silverman JD, Weyrich LS. Ancient dental calculus reveals oral microbiome shifts associated with lifestyle and disease in Great Britain. Nat Microbiol 2023; 8:2315-2325. [PMID: 38030898 DOI: 10.1038/s41564-023-01527-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/16/2023] [Indexed: 12/01/2023]
Abstract
The prevalence of chronic, non-communicable diseases has risen sharply in recent decades, especially in industrialized countries. While several studies implicate the microbiome in this trend, few have examined the evolutionary history of industrialized microbiomes. Here we sampled 235 ancient dental calculus samples from individuals living in Great Britain (∼2200 BCE to 1853 CE), including 127 well-contextualized London adults. We reconstructed their microbial history spanning the transition to industrialization. After controlling for oral geography and technical biases, we identified multiple oral microbial communities that coexisted in Britain for millennia, including a community associated with Methanobrevibacter, an anaerobic Archaea not commonly prevalent in the oral microbiome of modern industrialized societies. Calculus analysis suggests that oral hygiene contributed to oral microbiome composition, while microbial functions reflected past differences in diet, specifically in dairy and carbohydrate consumption. In London samples, Methanobrevibacter-associated microbial communities are linked with skeletal markers of systemic diseases (for example, periostitis and joint pathologies), and their disappearance is consistent with temporal shifts, including the arrival of the Second Plague Pandemic. This suggests pre-industrialized microbiomes were more diverse than previously recognized, enhancing our understanding of chronic, non-communicable disease origins in industrialized populations.
Collapse
Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - Andrew G Farrer
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Michelle P Nixon
- College of Information Sciences and Technology, The Pennsylvania State University, State College, PA, USA
| | - Sterling Wright
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - Luis Arriola
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Christina Adler
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Emily R Davenport
- Department of Biology, The Pennsylvania State University, State College, PA, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, USA
- Institute for Computational and Data Sciences, The Pennsylvania State University, State College, PA, USA
| | - Neville Gully
- School of Dentistry, Faculty of Health Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Alan Cooper
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- Gulbali Institute, Charles Sturt University, Albury, New South Wales, Australia
| | - Kate Britton
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, Aberdeen, UK
- Department of Archaeology, Faculty of Arts and Social Sciences, University of Sydney, Sydney, New South Wales, Australia
- Department of Archaeology, Classics and Egyptology, School of Histories, Languages and Cultures, University of Liverpool, Liverpool, UK
- Department of Archaeology, Faculty of Environment, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Justin D Silverman
- College of Information Sciences and Technology, The Pennsylvania State University, State College, PA, USA
- Institute for Computational and Data Sciences, The Pennsylvania State University, State College, PA, USA
- Department of Statistics, The Pennsylvania State University, State College, PA, USA
- Department of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Laura S Weyrich
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA.
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
- Huck Institutes of the Life Sciences, The Pennsylvania State University, State College, PA, USA.
| |
Collapse
|
9
|
Honap TP, Monroe CR, Johnson SJ, Jacobson DK, Abin CA, Austin RM, Sandberg P, Levine M, Sankaranarayanan K, Lewis CM. Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:542-556. [PMID: 37002784 DOI: 10.1002/ajpa.24735] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVES Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. MATERIALS AND METHODS Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. RESULTS Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains. DISCUSSION We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.
Collapse
Affiliation(s)
- Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cara R Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Center for the Ethics of Indigenous Genomics Research (CEIGR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Sarah J Johnson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Christopher A Abin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Rita M Austin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Paul Sandberg
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Marc Levine
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Duitama González C, Vicedomini R, Lemane T, Rascovan N, Richard H, Chikhi R. decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods. MICROBIOME 2023; 11:243. [PMID: 37926832 PMCID: PMC10626679 DOI: 10.1186/s40168-023-01670-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/13/2023] [Indexed: 11/07/2023]
Abstract
BACKGROUND The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices. RESULTS We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker. CONCLUSIONS decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.
Collapse
Affiliation(s)
- Camila Duitama González
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France.
| | - Riccardo Vicedomini
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France
- Université de Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Téo Lemane
- Université de Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Nicolas Rascovan
- Institut Pasteur, Université de Paris Cité, CNRS UMR 2000, Microbial Paleogenomics Unit, Paris, F-75015, France
| | - Hugues Richard
- Bioinformatics unit (MF1), Robert Koch Institute, Nordufer, 20, 13353, Berlin, Germany
| | - Rayan Chikhi
- Sequence Bioinformatics, Department of Computational Biology, Institut Pasteur, Université Paris Cité, Sorbonne Université, Paris, F-75015, France
| |
Collapse
|
12
|
Bader AC, Van Zuylen EM, Handsley-Davis M, Alegado RA, Benezra A, Pollet RM, Ehau-Taumaunu H, Weyrich LS, Anderson MZ. A relational framework for microbiome research with Indigenous communities. Nat Microbiol 2023; 8:1768-1776. [PMID: 37770743 DOI: 10.1038/s41564-023-01471-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 07/26/2023] [Indexed: 09/30/2023]
Abstract
Ethical practices in human microbiome research have failed to keep pace with scientific advances in the field. Researchers seeking to 'preserve' microbial species associated with Indigenous groups, but absent from industrialized populations, have largely failed to include Indigenous people in knowledge co-production or benefit, perpetuating a legacy of intellectual and material extraction. We propose a framework centred on relationality among Indigenous peoples, researchers and microbes, to guide ethical microbiome research. Our framework centres accountability to flatten historical power imbalances that favour researcher perspectives and interests to provide space for Indigenous worldviews in pursuit of Indigenous research sovereignty. Ethical inclusion of Indigenous communities in microbiome research can provide health benefits for all populations and reinforce mutually beneficial partnerships between researchers and the public.
Collapse
Affiliation(s)
- Alyssa C Bader
- Department of Anthropology, McGill University, Montreal, Quebec, Canada.
| | - Essie M Van Zuylen
- Department of Microbiology and Immunology, University of Otago, Dunedin North, Dunedin, New Zealand
- School of Product Design, University of Canterbury, Christchurch, New Zealand
| | - Matilda Handsley-Davis
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
| | - Rosanna A Alegado
- Department of Oceanography, University of Hawai'i Mānoa, Honolulu, HI, USA
| | - Amber Benezra
- Department of Science and Technology Studies, Stevens Institute of Technology, Hoboken, NJ, USA
| | | | - Hanareia Ehau-Taumaunu
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, State College, PA, USA
| | - Laura S Weyrich
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Wollongong, Wollongong, New South Wales, Australia
- Department of Anthropology, Pennsylvania State University, State College, PA, USA
| | - Matthew Z Anderson
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.
- Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA.
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
13
|
Hodgins HP, Chen P, Lobb B, Wei X, Tremblay BJM, Mansfield MJ, Lee VCY, Lee PG, Coffin J, Duggan AT, Dolphin AE, Renaud G, Dong M, Doxey AC. Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains. Nat Commun 2023; 14:5475. [PMID: 37673908 PMCID: PMC10482840 DOI: 10.1038/s41467-023-41174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023] Open
Abstract
The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.
Collapse
Affiliation(s)
- Harold P Hodgins
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Briallen Lobb
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Xin Wei
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Benjamin J M Tremblay
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Victoria C Y Lee
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Pyung-Gang Lee
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Coffin
- Department of Anthropology, University of Waterloo, Waterloo, ON, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Alexis E Dolphin
- Department of Anthropology, University of Waterloo, Waterloo, ON, Canada
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | - Andrew C Doxey
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada.
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Kaur Boparai A, Jain A, Arora S, Abullais Saquib S, Abdullah Alqahtani N, Fadul A Elagib M, Grover V. Dental calculus - An emerging bio resource for past SARS CoV2 detection, studying its evolution and relationship with oral microflora. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2023; 35:102646. [PMID: 36987442 PMCID: PMC10023199 DOI: 10.1016/j.jksus.2023.102646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 02/20/2023] [Accepted: 03/13/2023] [Indexed: 05/28/2023]
Abstract
The most grievous threat to human health has been witnessed worldwide with the recent outbreak of Corona virus disease 2019 (COVID-19). There is mounting evidence available regarding theconnect of COVID -19 and oral cavity, particularly periodontal disease. The current review provides an update on the diagnostic potential of dental calculus and how this bio resource may help in providing us huge amount of diagnostic regarding the causative virus. Contemporary standard method of diagnosis via nasopharyngeal swabs (NPS) is tedious, may enhance the risk of aerosol contamination by inducing sneezing and detects the presence of active infection only.However,dental calculus being a mineralized deposit serves as a reservoir for biomoleculesand provides detection of past SARS CoV2 infection. Further, the abundance of information that can be obtained from this remarkable mineralized deposit on teeth regarding the viral genome, its evolution and interactions with the oral microflora shall enhance the understanding of the viral disease process and its connection with the periodontal disease. Additional diagnostic information, which may be obtained from this simple bio reservoir can complement the contemporary diagnostic strategies adopted in the management of COVID-19pandemic and enhance our existing knowledge for developing improvised novel approaches to mitigate the effects of mutated variants of the infectious agent.
Collapse
Affiliation(s)
| | - Ashish Jain
- Department of Periodontology & Oral Implantology, Dr. H. S. J. lnstitute Dental Sciences & Hospital, Punjab University, Chandigarh, India
| | - Suraj Arora
- Department of Restorative Dental Sciences, College of Dentistry, King Khalid University, Abha 61321, Saudi Arabia
| | - Shahabe Abullais Saquib
- Periodontics and Community Dental Sciences, College of Dentistry, King Khalid University, Abha 61321, Saudi Arabia
| | - Nabeeh Abdullah Alqahtani
- Department of Periodontics and Community Dental Sciences, College of Dentistry, King Khalid University, Abha 61321, Saudi Arabia
| | | | - Vishakha Grover
- Department of Periodontology & Oral Implantology, Dr. H. S. J. lnstitute Dental Sciences & Hospital, Punjab University, Chandigarh, India
| |
Collapse
|
16
|
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: 3] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
17
|
Gancz AS, Weyrich LS. Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases. F1000Res 2023; 12:109. [PMID: 37065506 PMCID: PMC10090864 DOI: 10.12688/f1000research.129036.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2023] [Indexed: 01/31/2023] Open
Abstract
Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.
Collapse
Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
| | - Laura S Weyrich
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
| |
Collapse
|
18
|
Abstract
This perspective draws on the record of ancient pathogen genomes and microbiomes illuminating patterns of infectious disease over the course of the Holocene in order to address the following question. How did major changes in living circumstances involving the transition to and intensification of farming alter pathogens and their distributions? Answers to this question via ancient DNA research provide a rapidly expanding picture of pathogen evolution and in concert with archaeological and historical data, give a temporal and behavioral context for heath in the past that is relevant for challenges facing the world today, including the rise of novel pathogens.
Collapse
|
19
|
Gancz AS, Weyrich LS. Studying ancient human oral microbiomes could yield insights into the evolutionary history of noncommunicable diseases. F1000Res 2023; 12:109. [PMID: 37065506 PMCID: PMC10090864 DOI: 10.12688/f1000research.129036.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/05/2023] [Indexed: 04/19/2023] Open
Abstract
Noncommunicable diseases (NCDs) have played a critical role in shaping human evolution and societies. Despite the exceptional impact of NCDs economically and socially, little is known about the prevalence or impact of these diseases in the past as most do not leave distinguishing features on the human skeleton and are not directly associated with unique pathogens. The inability to identify NCDs in antiquity precludes researchers from investigating how changes in diet, lifestyle, and environments modulate NCD risks in specific populations and from linking evolutionary processes to modern health patterns and disparities. In this review, we highlight how recent advances in ancient DNA (aDNA) sequencing and analytical methodologies may now make it possible to reconstruct NCD-related oral microbiome traits in past populations, thereby providing the first proxies for ancient NCD risk. First, we review the direct and indirect associations between modern oral microbiomes and NCDs, specifically cardiovascular disease, diabetes mellitus, rheumatoid arthritis, and Alzheimer's disease. We then discuss how oral microbiome features associated with NCDs in modern populations may be used to identify previously unstudied sources of morbidity and mortality differences in ancient groups. Finally, we conclude with an outline of the challenges and limitations of employing this approach, as well as how they might be circumvented. While significant experimental work is needed to verify that ancient oral microbiome markers are indeed associated with quantifiable health and survivorship outcomes, this new approach is a promising path forward for evolutionary health research.
Collapse
Affiliation(s)
- Abigail S Gancz
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
| | - Laura S Weyrich
- Department of Anthropology, Pennsylvania State University, State College, PA, 16802, USA
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia, 5005, Australia
- Huck Institutes of the Life Sciences, Pennsylvania State University, State College, PA, 16802, USA
| |
Collapse
|
20
|
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: 0] [Impact Index Per Article: 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.
Collapse
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,
| |
Collapse
|
21
|
Warinner C. An Archaeology of Microbes. JOURNAL OF ANTHROPOLOGICAL RESEARCH 2022. [DOI: 10.1086/721976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Christina Warinner
- Department of Anthropology, Harvard University, Cambridge MA, USA 02138, and Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany 04103
| |
Collapse
|
22
|
Moraitou M, Forsythe A, Fellows Yates JA, Brealey JC, Warinner C, Guschanski K. Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species. Mol Biol Evol 2022; 39:6874787. [PMID: 36472532 PMCID: PMC9778846 DOI: 10.1093/molbev/msac263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/25/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022] Open
Abstract
Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.
Collapse
Affiliation(s)
| | | | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany
| | - Jaelle C Brealey
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany,Department of Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology Hans Knöll Institute, 07745 Jena, Germany,Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | | |
Collapse
|
23
|
Rabe A, Gesell Salazar M, Michalik S, Kocher T, Below H, Völker U, Welk A. Impact of different oral treatments on the composition of the supragingival plaque microbiome. J Oral Microbiol 2022; 14:2138251. [PMID: 36338832 PMCID: PMC9629129 DOI: 10.1080/20002297.2022.2138251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background Dental plaque consists of a diverse microbial community embedded in a complex structure of exopolysaccharides. Dental biofilms form a natural barrier against pathogens but lead to oral diseases in a dysbiotic state. Objective Using a metaproteome approach combined with a standard plaque-regrowth study, this pilot study examined the impact of different concentrations of lactoperoxidase (LPO) on early plaque formation, and active biological processes. Design Sixteen orally healthy subjects received four local treatments as a randomized single-blind study based on a cross-over design. Two lozenges containing components of the LPO-system in different concentrations were compared to a placebo and Listerine®. The newly formed dental plaque was analyzed by mass spectrometry (nLC-MS/MS). Results On average 1,916 metaproteins per sample were identified, which could be assigned to 116 genera and 1,316 protein functions. Listerine® reduced the number of metaproteins and their relative abundance, confirming the plaque inhibiting effect. The LPO-lozenges triggered mainly higher metaprotein abundances of early and secondary colonizers as well as bacteria associated with dental health but also periodontitis. Functional information indicated plaque biofilm growth. Conclusion In conclusion, the mechanisms on plaque biofilm formation of Listerine® and the LPO-system containing lozenges are different. In contrast to Listerine®, the lozenges led to a higher bacterial diversity.
Collapse
Affiliation(s)
- Alexander Rabe
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany,CONTACT Alexander Rabe University Medicine Greifswald, Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Felix-Hausdorff-Str. 8, 17489Greifswald, Germany
| | - Manuela Gesell Salazar
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Stephan Michalik
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Thomas Kocher
- Center for Dentistry, Oral and Maxillofacial Medicine, Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, Dental School of University Medicine Greifswald, Fleischmannstraße 42-44, 17489
| | - Harald Below
- Institute for Hygiene and Environmental Medicine, University Medicine Greifswald, Walter-Rathenau-Straße 49 A17475Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Felix-Hausdorff-Str. 8, 17475Greifswald, Germany
| | - Alexander Welk
- Center for Dentistry, Oral and Maxillofacial Medicine, Department of Restorative Dentistry, Periodontology, Endodontology, and Preventive and Pediatric Dentistry, Dental School of University Medicine Greifswald, Fleischmannstraße 42-44, 17489
| |
Collapse
|
24
|
van der Kuyl AC. Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens. EPIDEMIOLOGIA (BASEL, SWITZERLAND) 2022; 3:443-464. [PMID: 36547255 PMCID: PMC9778136 DOI: 10.3390/epidemiologia3040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.
Collapse
Affiliation(s)
- Antoinette C. van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; ; Tel.: +31-205-666-778
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
| |
Collapse
|
25
|
Remembering St. Louis individual-structural violence and acute bacterial infections in a historical anatomical collection. Commun Biol 2022; 5:1050. [PMID: 36192528 PMCID: PMC9527723 DOI: 10.1038/s42003-022-03890-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Incomplete documentary evidence, variable biomolecular preservation, and limited skeletal responses have hindered assessment of acute infections in the past. This study was initially developed to explore the diagnostic potential of dental calculus to identify infectious diseases, however, the breadth and depth of information gained from a particular individual, St. Louis Individual (St.LI), enabled an individualized assessment and demanded broader disciplinary introspection of ethical research conduct. Here, we document the embodiment of structural violence in a 23-year-old Black and/or African American male, who died of lobar pneumonia in 1930s St. Louis, Missouri. St.LI exhibits evidence of systemic poor health, including chronic oral infections and a probable tuberculosis infection. Metagenomic sequencing of dental calculus recovered three pre-antibiotic era pathogen genomes, which likely contributed to the lobar pneumonia cause of death (CoD): Klebsiella pneumoniae (13.8X); Acinetobacter nosocomialis (28.4X); and Acinetobacter junii (30.1X). Ante- and perimortem evidence of St.LI’s lived experiences chronicle the poverty, systemic racism, and race-based structural violence experienced by marginalized communities in St. Louis, which contributed to St.LI’s poor health, CoD, anatomization, and inclusion in the Robert J. Terry Anatomical Collection. These same embodied inequalities continue to manifest as health disparities affecting many contemporary communities in the United States. An investigation into the cause of death of St. Louis Individual, a 23-year old Black or African American male who died in the 1930s, reveals evidence of structural violence and the impact of systemic racism in historically marginalized communities.
Collapse
|
26
|
Changes in the oral status and periodontal pathogens in a Sardinian rural community from pre-industrial to modern time. Sci Rep 2022; 12:15895. [PMID: 36151274 PMCID: PMC9508227 DOI: 10.1038/s41598-022-20193-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 09/09/2022] [Indexed: 11/30/2022] Open
Abstract
The oral microbial profile in humans has evolved in response to lifestyle changes over the course of different eras. Here, we investigated tooth lesions and the microbial profile of periodontal bacteria (PB) in dental calculus of a Sardinian pre-industrial rural community. In total, 51 teeth belonging to 12 historical individuals buried in an ossuary in the early 1800s and 26 modern teeth extracted from 26 individuals from the same geographical area were compared to determine the oral health status, bacterial load and amount of most relevant PB. Total caries and bacterial genomes count appeared to be sex-related in historical samples. Historical females presented a higher incidence of caries, PB pathogens and a higher bacterial load than historical males. Furthermore, we compared the PB profile of the historical individuals with the modern ones, revealing a notable increase in modern individuals of PB belonging to “Red complex bacteria” often associated with periodontitis and other chronic diseases of modern life. Our findings could be explained through an analysis of environmental factors such as socioeconomic, hygienic and healthy conditions that can have a great impact on oral health and bacterial composition among individuals of the same and different eras.
Collapse
|
27
|
Abstract
Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human-animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.
Collapse
Affiliation(s)
- Christina Warinner
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Kristine Korzow Richter
- Department
of Anthropology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Matthew J. Collins
- Department
of Archaeology, Cambridge University, Cambridge CB2 3DZ, United Kingdom
- Section
for Evolutionary Genomics, Globe Institute,
University of Copenhagen, Copenhagen 1350, Denmark
| |
Collapse
|
28
|
Shibutani A, Aono T, Nagaya Y. Starch granules from human teeth: New clues on the Epi-Jomon diet. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.907666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study examined starch granules from the dental calculus of specimens from the Epi-Jomon (Zoku-Jomon in Japanese, ca. 350 BCE–350 CE) period in Japan for taxonomic identification of plant food items and the reconstruction of human socioeconomic practices. Dental calculus was extracted from 21 individuals across six Epi-Jomon sites in Hokkaido. Moreover, 12 starch granules and starch clusters were recovered from nine individuals. The morphologies of the extracted starch granules were then classified into five types: elliptical, angular circular, polygonal, pentagonal, and damaged. Morphometric analysis indicated that a small portion of these starch granules may have derived from acorns, nuts, and bulb or tuber plants, with one starch granule supposedly from rice. Although extracted starch granules are poor predictors of food diversity at the individual level, the results can identify potential food sources of the surveyed population. This is the first study to determine how well plant microremains in dental calculus reflect a plant diet in the Epi-Jomon population. The starch granules discovered at the surveyed sites provide essential information about the utilization of plant species and cultural contacts in Hokkaido during this period. This is of great significance in reconstructing the Epi-Jomon subsistence patterns in Hokkaido and exploring cultural interactions between hunting-gathering-fishing and agrarian societies.
Collapse
|
29
|
Nishimura L, Fujito N, Sugimoto R, Inoue I. Detection of Ancient Viruses and Long-Term Viral Evolution. Viruses 2022; 14:v14061336. [PMID: 35746807 PMCID: PMC9230872 DOI: 10.3390/v14061336] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 12/22/2022] Open
Abstract
The COVID-19 outbreak has reminded us of the importance of viral evolutionary studies as regards comprehending complex viral evolution and preventing future pandemics. A unique approach to understanding viral evolution is the use of ancient viral genomes. Ancient viruses are detectable in various archaeological remains, including ancient people's skeletons and mummified tissues. Those specimens have preserved ancient viral DNA and RNA, which have been vigorously analyzed in the last few decades thanks to the development of sequencing technologies. Reconstructed ancient pathogenic viral genomes have been utilized to estimate the past pandemics of pathogenic viruses within the ancient human population and long-term evolutionary events. Recent studies revealed the existence of non-pathogenic viral genomes in ancient people's bodies. These ancient non-pathogenic viruses might be informative for inferring their relationships with ancient people's diets and lifestyles. Here, we reviewed the past and ongoing studies on ancient pathogenic and non-pathogenic viruses and the usage of ancient viral genomes to understand their long-term viral evolution.
Collapse
Affiliation(s)
- Luca Nishimura
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Naoko Fujito
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Ryota Sugimoto
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
| | - Ituro Inoue
- Human Genetics Laboratory, National Institute of Genetics, Mishima 411-8540, Japan; (L.N.); (N.F.); (R.S.)
- Department of Genetics, School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
- Correspondence: ; Tel.: +81-55-981-6795
| |
Collapse
|
30
|
Power RC, Henry AG, Moosmann J, Beckmann F, Temming H, Roberts A, Le Cabec A. Synchrotron radiation-based phase-contrast microtomography of human dental calculus allows nondestructive analysis of inclusions: implications for archeological samples. J Med Imaging (Bellingham) 2022; 9:031505. [PMID: 35310450 PMCID: PMC8924454 DOI: 10.1117/1.jmi.9.3.031505] [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: 09/15/2021] [Accepted: 02/21/2022] [Indexed: 11/14/2022] Open
Abstract
Purpose: Dental calculus forms on teeth during the life of an individual and its investigation can yield information about diet, health status, and environmental pollution. Currently, the analytical techniques used to visualize the internal structure of human dental calculus and entrapped inclusions are limited and require destructive sampling, which cannot always be justified. Approach: We used propagation phase-contrast synchrotron radiation micro-computed tomography (PPC-SR- μ CT ) to non-destructively examine the internal organization of dental calculus, including its microstructure and entrapped inclusions, on both modern and archeological samples. Results: The virtual histological exploration of the samples shows that PPC-SR- μ CT is a powerful approach to visualize the internal organization of dental calculus. We identified several important features, including previously undetected negative imprints of enamel and dentine growth markers (perikymata and periradicular bands, respectively), the non-contiguous structure of calculus layers with multiple voids, and entrapped plant remains. Conclusions: PPC-SR- μ CT is an effective technique to explore dental calculus structural organization, and is especially powerful for enabling the identification of inclusions. The non-destructive nature of synchrotron tomography helps protect samples for future research. However, the irregular layers and frequent voids reveal a high heterogeneity and variability within calculus, with implications for research focusing on inclusions.
Collapse
Affiliation(s)
- Robert C Power
- Ludwig-Maximilians-University Munich, Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Munich, Germany.,Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, Leipzig, Germany
| | - Amanda G Henry
- Leiden University, Faculty of Archaeology, Leiden, The Netherlands
| | | | | | - Heiko Temming
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, Leipzig, Germany
| | - Anthony Roberts
- Cork University Dental School and Hospital, University College Cork, Ireland
| | - Adeline Le Cabec
- Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, Leipzig, Germany.,Univ. Bordeaux, CNRS, MCC, PACEA, UMR 5199, Pessac, France
| |
Collapse
|
31
|
Capo E, Monchamp ME, Coolen MJL, Domaizon I, Armbrecht L, Bertilsson S. Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential. Environ Microbiol 2022; 24:2201-2209. [PMID: 35049133 PMCID: PMC9304175 DOI: 10.1111/1462-2920.15913] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 11/30/2022]
Abstract
In‐depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo‐genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human‐induced global changes.
Collapse
Affiliation(s)
- Eric Capo
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Marie-Eve Monchamp
- Department of Biology, McGill University, Montréal, QC, H3A 1B1, Canada.,Groupe de recherche interuniversitaire en limnologie (GRIL)
| | - Marco J L Coolen
- Western Australia Organic and Isotope Geochemistry Centre (WA-OIGC), Curtin University, Bentley, 6102, Australia
| | - Isabelle Domaizon
- INRAE, Université Savoie Mont Blanc, CARRTEL, 74200 Thonon les Bains, France.,UMR CARRTEL, Pôle R&D ECLA, 74200 Thonon les Bains, France
| | - Linda Armbrecht
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia.,Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| |
Collapse
|
32
|
Dental calculus - oral health, forensic studies and archaeology: a review. Br Dent J 2022; 233:961-967. [PMID: 36494546 PMCID: PMC9734501 DOI: 10.1038/s41415-022-5266-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/09/2022] [Indexed: 12/13/2022]
Abstract
Dental calculus is recognised as a secondary aetiological factor in periodontal disease, and being a prominent plaque retentive factor, it is routinely removed by the dental team to maintain oral health. Conversely, dental calculus can potentially be useful in forensic studies by supplying data that may be helpful in the identification of human remains and assist in determining the cause of death. During the last few decades, dental calculus has been increasingly recognised as an informative tool to understand ancient diet and health. As an archaeological deposit, it may contain non-dietary debris which permits the exploration of human behaviour and activities. While optical and scanning electron microscopy were the original analytical methods utilised to study microparticles entrapped within the calcified matrix, more recently, molecular approaches, including ancient DNA (aDNA) and protein analyses, have been applied. Oral bacteria, a major component of calculus, is the primary target of these aDNA studies. Such analyses can detect changes in the oral microbiota, including those that have reflected the shift from agriculture to industrialisation, as well as identifying markers for various systemic diseases.
Collapse
|
33
|
Meta-proteomic analysis of two mammoth's trunks by EVA technology and high-resolution mass spectrometry for an indirect picture of their habitat and the characterization of the collagen type I, alpha-1 and alpha-2 sequence. Amino Acids 2022; 54:935-954. [PMID: 35434776 PMCID: PMC9213349 DOI: 10.1007/s00726-022-03160-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/27/2022] [Indexed: 12/30/2022]
Abstract
The recent paleoproteomic studies, including paleo-metaproteomic analyses, improved our understanding of the dietary of ancient populations, the characterization of past human diseases, the reconstruction of the habitat of ancient species, but also provided new insights into the phylogenetic relationships between extant and extinct species. In this respect, the present work reports the results of the metaproteomic analysis performed on the middle part of a trunk, and on the portion of a trunk tip tissue of two different woolly mammoths some 30,000 years old. In particular, proteins were extracted by applying EVA (Ethylene-Vinyl Acetate studded with hydrophilic and hydrophobic resins) films to the surface of these tissues belonging to two Mammuthus primigenus specimens, discovered in two regions located in the Russian Far East, and then investigated via a shotgun MS-based approach. This approach allowed to obtain two interesting results: (i) an indirect description of the habitat of these two mammoths, and (ii) an improved characterization of the collagen type I, alpha-1 and alpha-2 chains (col1a1 and col1a2). Sequence characterization of the col1a1 and col1a2 highlighted some differences between M. primigenius and other Proboscidea together with the identification of three (two for col1a1, and one for col1a2) potentially diagnostic amino acidic mutations that could be used to reliably distinguish the Mammuthus primigenius with respect to the other two genera of elephantids (i.e., Elephas and Loxodonta), and the extinct American mastodon (i.e., Mammut americanum). The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the "original" endogenous peptides from contaminant ones. The data have been deposited to the ProteomeXchange with identifier < PXD029558 > .
Collapse
|
34
|
Allende MKG, Samplonius A. Dental anthropological report: Exploring plant-based treatments through the analysis of dental calculus and sediment of dental caries in a woman from the Late Preceramic period, Peru. Ann Anat 2021; 240:151849. [PMID: 34699992 DOI: 10.1016/j.aanat.2021.151849] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/07/2021] [Accepted: 10/18/2021] [Indexed: 11/26/2022]
Abstract
Reconstructing plant-based healing treatments of past societies from a dental anthropological perspective is still challenging due to a wide range of plant species, many with both medicinal and nutritional properties, and limitations on plant-taxa identification. Starch grains and phytoliths retrieved in samples from dental calculus and sediment contained in the cavity of dental caries were examined to investigate the supply of a plant-based treatment in an individual buried in the Late Preceramic site of Huaca El Paraíso (2100-1500 BCE), whose osteological analysis reported the absence of any pathological condition at a bone tissue level. A variety of starch grains such as pumpkins, manioc, maize, and beans had an important role in the diet of the individual. The starch grains were embedded in their dental calculus, all of which, except for manioc, showed signs of cooking damage. Considering the context and characteristics of the crops, the nutritional properties of maize, pumpkins and beans are evident. However, parallel medicinal properties of manioc and maize could not be entirely denied. Phytoliths morphologically ascribed to the Asteraceae plant family, which suggest the consumption of medicinal plants of Andean vernacular use, were retrieved in the sediment of dental caries. Our results prove that the analysis of sediment obtained from dental caries is as valuable in tracing medicinal plant-based treatments as dental calculus in archaeological populations. There are still several limitations to approach this topic in dental anthropology, which are discussed in this report. The performance of both analyses -dental calculus and sediment of dental caries, is highly recommended.
Collapse
Affiliation(s)
- Maria Kolp-Godoy Allende
- Amt für Städtebau (AFS), Archäologie und Denkmalpflege, Stadtarchäologie Zürich & Kantonsarchäologie, St. Gallen, Switzerland.
| | - Anton Samplonius
- Dent. Surg. Universidad Nacional Mayor de San Marcos, Lima, Peru.
| |
Collapse
|
35
|
Shiba T, Komatsu K, Sudo T, Sawafuji R, Saso A, Ueda S, Watanabe T, Nemoto T, Kano C, Nagai T, Ohsugi Y, Katagiri S, Takeuchi Y, Kobayashi H, Iwata T. Comparison of Periodontal Bacteria of Edo and Modern Periods Using Novel Diagnostic Approach for Periodontitis With Micro-CT. Front Cell Infect Microbiol 2021; 11:723821. [PMID: 34616690 PMCID: PMC8488429 DOI: 10.3389/fcimb.2021.723821] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/17/2021] [Indexed: 11/07/2022] Open
Abstract
Ancient dental calculus, formed from dental plaque, is a rich source of ancient DNA and can provide information regarding the food and oral microbiology at that time. Genomic analysis of dental calculus from Neanderthals has revealed the difference in bacterial composition of oral microbiome between Neanderthals and modern humans. There are few reports investigating whether the pathogenic bacteria of periodontitis, a polymicrobial disease induced in response to the accumulation of dental plaque, were different between ancient and modern humans. This study aimed to compare the bacterial composition of the oral microbiome in ancient and modern human samples and to investigate whether lifestyle differences depending on the era have altered the bacterial composition of the oral microbiome and the causative bacteria of periodontitis. Additionally, we introduce a novel diagnostic approach for periodontitis in ancient skeletons using micro-computed tomography. Ancient 16S rDNA sequences were obtained from 12 samples at the Unko-in site (18th-19th century) of the Edo era (1603–1867), a characteristic period in Japan when immigrants were not accepted. Furthermore, modern 16S rDNA data from 53 samples were obtained from a database to compare the modern and ancient microbiome. The microbial co-occurrence network was analyzed based on 16S rDNA read abundance. Eubacterium species, Mollicutes species, and Treponema socranskii were the core species in the Edo co-occurrence network. The co-occurrence relationship between Actinomyces oricola and Eggerthella lenta appeared to have played a key role in causing periodontitis in the Edo era. However, Porphyromonas gingivalis, Fusobacterium nucleatum subsp. vincentii, and Prevotella pleuritidis were the core and highly abundant species in the co-occurrence network of modern samples. These results suggest the possibility of differences in the pathogens causing periodontitis during different eras in history.
Collapse
Affiliation(s)
- Takahiko Shiba
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keiji Komatsu
- Department of Lifetime Oral Health Care Sciences, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takeaki Sudo
- Institute of Education, Tokyo Medical and Dental University, Tokyo, Japan
| | - Rikai Sawafuji
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, Japan
| | - Aiko Saso
- Department of Physical Therapy, Faculty of Rehabilitation, Niigata University of Health and Welfare, Niigata, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Takayasu Watanabe
- Department of Chemistry, Nihon University School of Dentistry, Tokyo, Japan
| | - Takashi Nemoto
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Chihiro Kano
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takahiko Nagai
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yujin Ohsugi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Sayaka Katagiri
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yasuo Takeuchi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroaki Kobayashi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takanori Iwata
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| |
Collapse
|
36
|
Craig OE. Prehistoric Fermentation, Delayed-Return Economies, and the Adoption of Pottery Technology. CURRENT ANTHROPOLOGY 2021. [DOI: 10.1086/716610] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
37
|
|
38
|
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: 13] [Impact Index Per Article: 4.3] [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.
Collapse
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
| |
Collapse
|
39
|
Correlation between the Macronutrient Content of Dental Calculus and the FFQ-Based Nutritional Intake of Obese and Normal-Weight Individuals. Int J Dent 2021; 2021:5579208. [PMID: 34531913 PMCID: PMC8440092 DOI: 10.1155/2021/5579208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/28/2021] [Indexed: 11/18/2022] Open
Abstract
The growing epidemic of chronic diseases afflicting both developed and developing countries is related to diet and lifestyle. The current dietary assessment still has many constraints, particularly related to the objectivity of data gathering. Dental calculus, which is usually considered as medical waste in dental treatment, turns out to be a provider of abundant oral information. The objective of this study is to obtain the correlation between the macronutrient content of dental calculus and nutritional intake based on FFQ. This research is an analytic observational study with a case-control study design. Samples consisting of 35 obese individuals and 21 normal-weight individuals were taken using purposive sampling. The nutritional intake data were obtained using FFQ. The macronutrient content of dental calculus was checked using a colorimetric assay. The comparison between obese individuals and normal-weight individuals was tested using the Mann–Whitney test and T-test. The correlation between the macronutrient content of dental calculus and nutritional intake based on FFQ was measured using Spearman's rank-order correlation. The results showed there was a correlation between the macronutrient content of dental calculus and macronutrient intake based on FFQ. However, strong correlation was found only between fat intake with the total lipid content of dental calculus with rs = 0.521 and between carbohydrate intake with the total carbohydrate content of dental calculus with rs = 0.519. It was concluded that carbohydrate, protein, and lipid intake can be assessed using dental calculus. Dental calculus can be an alternative source of noninvasive, inexpensive, and specific dietary biomarkers.
Collapse
|
40
|
Cucina A, Cunsolo V, Di Francesco A, Saletti R, Zilberstein G, Zilberstein S, Tikhonov A, Bublichenko AG, Righetti PG, Foti S. Meta-proteomic analysis of the Shandrin mammoth by EVA technology and high-resolution mass spectrometry: what is its gut microbiota telling us? Amino Acids 2021; 53:1507-1521. [PMID: 34453585 PMCID: PMC8519927 DOI: 10.1007/s00726-021-03061-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 08/03/2021] [Indexed: 11/29/2022]
Abstract
During the last decade, paleoproteomics allowed us to open a direct window into the biological past, improving our understanding of the phylogenetic relationships of extant and extinct species, past human diseases, and reconstruction of the human diet. In particular, meta-proteomic studies, mainly carried out on ancient human dental calculus, provided insights into past oral microbial communities and ancient diets. On the contrary, very few investigations regard the analysis of ancient gut microbiota, which may enable a greater understanding of how microorganisms and their hosts have co-evolved and spread under the influence of changing diet practices and habitat. In this respect, this paper reports the results of the first-ever meta-proteomic analysis carried out on a gut tissue sample some 40,000 years old. Proteins were extracted by applying EVA (ethylene–vinyl acetate) films to the surface of the gut sample of a woolly mammoth (Mammuthus primigenus), discovered in 1972 close to the Shandrin River (Yakutia, Russia), and then investigated via a shotgun MS-based approach. Proteomic and peptidomic analysis allowed in-depth exploration of its meta-proteome composition. The results were validated through the level of deamidation and other diagenetic chemical modifications of the sample peptides, which were used to discriminate the “original” endogenous peptides from contaminant ones. Overall, the results of the meta-proteomic analysis here reported agreeing with the previous paleobotanical studies and with the reconstructed habitat of the Shandrin mammoth and provided insight into its diet. The data have been deposited to the ProteomeXchange with identifier < PXD025518 > .
Collapse
Affiliation(s)
- 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.
| | - Antonella Di Francesco
- 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
| | | | | | - Alexei Tikhonov
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab.1, Saint-Petersburg, 199034, Russia
| | - Andrey G Bublichenko
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab.1, Saint-Petersburg, 199034, Russia
| | - Pier Giorgio Righetti
- Department of Chemistry, Materials and Chemical Engineering ''Giulio Natta'', Politecnico di Milano, Via Mancinelli 7, 20131, Milan, Italy
| | - Salvatore Foti
- Laboratory of Organic Mass Spectrometry, Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125, Catania, Italy
| |
Collapse
|
41
|
Ottoni C, Borić D, Cheronet O, Sparacello V, Dori I, Coppa A, Antonović D, Vujević D, Price TD, Pinhasi R, Cristiani E. Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus. Proc Natl Acad Sci U S A 2021; 118:e2102116118. [PMID: 34312252 PMCID: PMC8364157 DOI: 10.1073/pnas.2102116118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.
Collapse
Affiliation(s)
- Claudio Ottoni
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Vitale Sparacello
- Department of Environmental and Life Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Irene Dori
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Verona, Rovigo e Vicenza, 37121 Verona, Italy
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
- Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA 02138
| | | | - Dario Vujević
- Department of Archaeology, University of Zadar, 23000 Zadar, Croatia
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Emanuela Cristiani
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
| |
Collapse
|
42
|
Flachs A, Orkin JD. On pickles: biological and sociocultural links between fermented foods and the human gut microbiome. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2021; 17:39. [PMID: 34107988 PMCID: PMC8188661 DOI: 10.1186/s13002-021-00458-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The composition of the human microbiome varies considerably in diversity and density across communities as a function of the foods we eat and the places we live. While all foods contain microbes, humans directly shape this microbial ecology through fermentation. Fermented foods are produced from microbial reactions that depend on local environmental conditions, fermentation practices, and the manner in which foods are prepared and consumed. These interactions are of special interest to ethnobiologists because they link investigations of how people shape and know the world around them to local knowledge, food traditions, local flora, and microbial taxa. METHODS In this manuscript, we report on data collected at a fermentation revivalist workshop in Tennessee. To ask how fermentation traditions are learned and influence macro and micro ecologies, we conducted interviews with eleven people and participated in a four-day craft fermentation workshop. We also collected 46 fermented food products and 46 stool samples from workshop participants eating those fermented foods. RESULTS We identified ten major themes comprised of 29 sub-themes drawn from 326 marked codes in the transcripts. In combination, this analysis allowed us to summarize key experiences with fermentation, particularly those related to a sense of authenticity, place, health, and the discovery of tactile work. From the 605 amplicon sequence variants (ASVs) shared between food and fecal samples, we identified 25 candidate ASVs that are suspected to have been transmitted from fermented food samples to the gut microbiomes of the workshop participants. Our results indicate that many of the foods prepared and consumed during the workshop were rich sources of probiotic microbes. CONCLUSIONS By combining these qualitative social and quantitative microbiological data, we suggest that variation in culturally informed fermentation practices introduces variation in bacterial flora even among very similar foods, and that these food products can influence gut microbial ecology.
Collapse
Affiliation(s)
- Andrew Flachs
- Department of Anthropology, Purdue University, West Lafayette, IN, USA.
| | - Joseph D Orkin
- Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain.
| |
Collapse
|
43
|
Hofreiter M, Sneberger J, Pospisek M, Vanek D. Progress in forensic bone DNA analysis: Lessons learned from ancient DNA. Forensic Sci Int Genet 2021; 54:102538. [PMID: 34265517 DOI: 10.1016/j.fsigen.2021.102538] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 03/07/2021] [Accepted: 05/25/2021] [Indexed: 01/18/2023]
Abstract
Research on ancient and forensic DNA is related in many ways, and the two fields must deal with similar obstacles. Therefore, communication between these two communities has the potential to improve results in both research fields. Here, we present the insights gained in the ancient DNA community with regard to analyzing DNA from aged skeletal material and the potential use of the developed protocols in forensic work. We discuss the various steps, from choosing samples for DNA extraction to deciding between classical PCR amplification and massively parallel sequencing approaches. Based on the progress made in ancient DNA analyses combined with the requirements of forensic work, we suggest that there is substantial potential for incorporating ancient DNA approaches into forensic protocols, a process that has already begun to a considerable extent. However, taking full advantage of the experiences gained from ancient DNA work will require comparative studies by the forensic DNA community to tailor the methods developed for ancient samples to the specific needs of forensic studies and case work. If successful, in our view, the benefits for both communities would be considerable.
Collapse
Affiliation(s)
- Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany.
| | - Jiri Sneberger
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Department of the History of the Middle Ages of Museum of West Bohemia, Kopeckeho sady 2, Pilsen 30100, Czech Republic; Nuclear Physics Institute of the CAS, Na Truhlarce 39/64, Prague 18086, Czech Republic
| | - Martin Pospisek
- Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Vinicna 5, Prague 2 12843, Czech Republic; Biologicals s.r.o., Sramkova 315, Ricany 25101, Czech Republic
| | - Daniel Vanek
- Forensic DNA Service, Janovskeho 18, Prague 7 17000, Czech Republic; Institute of Legal Medicine, Bulovka Hospital, Prague, Czech Republic; Charles University in Prague, 2nd Faculty of Medicine, Prague, Czech Republic.
| |
Collapse
|
44
|
Seguin-Orlando A, Costedoat C, Der Sarkissian C, Tzortzis S, Kamel C, Telmon N, Dalén L, Thèves C, Signoli M, Orlando L. No particular genomic features underpin the dramatic economic consequences of 17 th century plague epidemics in Italy. iScience 2021; 24:102383. [PMID: 33981971 PMCID: PMC8082092 DOI: 10.1016/j.isci.2021.102383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/25/2021] [Accepted: 03/29/2021] [Indexed: 10/26/2022] Open
Abstract
The 17th century plague epidemic had a particularly strong demographic toll in Southern Europe, especially Italy, where it caused long-lasting economical damage. Whether this resulted from ineffective sanitation measures or more pathogenic Yersinia pestis strains remains unknown. DNA screening of 26 skeletons from the 1629-1630 plague cemetery of Lariey (French Alps) identified two teeth rich in plague genetic material. Further sequencing revealed two Y. pestis genomes phylogenetically closest to those from the 1636 outbreak of San Procolo a Naturno, Italy. They both belonged to a cluster extending from the Alps to Northern Germany that probably propagated during the Thirty Years war. Sequence variation did not support faster evolutionary rates in the Italian genomes and revealed only rare private non-synonymous mutations not affecting virulence genes. This, and the more heterogeneous spatial diffusion of the epidemic outside Italy, suggests environmental or social rather than biological causes for the severe Italian epidemic trajectory.
Collapse
Affiliation(s)
- Andaine Seguin-Orlando
- Centre for Anthropobiology and Genomics of Toulouse CAGT, UMR 5288, CNRS, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France.,Institute for Advanced Study in Toulouse IAST, Université Toulouse I Capitole, Esplanade de l'Université, 31080 Toulouse cedex 06, France
| | - Caroline Costedoat
- Anthropologie bio-culturelle, droit, éthique et santé ADES, UMR 7268 CNRS EFS, Aix-Marseille Université, Faculté de Médecine, Secteur Nord Bâtiment A CS80011, Boulevard Pierre Dramard, 13344 Marseille Cedex 15, France
| | - Clio Der Sarkissian
- Centre for Anthropobiology and Genomics of Toulouse CAGT, UMR 5288, CNRS, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Stéfan Tzortzis
- Ministère de la Culture et de la Communication, Direction Régionale des Affaires Culturelles de PACA, Service Régional de l'Archéologie, 23 bd du Roi René, 13617 Aix-en-Provence cedex, France
| | - Célia Kamel
- Anthropologie bio-culturelle, droit, éthique et santé ADES, UMR 7268 CNRS EFS, Aix-Marseille Université, Faculté de Médecine, Secteur Nord Bâtiment A CS80011, Boulevard Pierre Dramard, 13344 Marseille Cedex 15, France
| | - Norbert Telmon
- Centre for Anthropobiology and Genomics of Toulouse CAGT, UMR 5288, CNRS, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Love Dalén
- Centre for Palaeogenetics, Svante Arrhenius väg 20C, 10691 Stockholm, Sweden.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Box 50007, 10405 Stockholm, Sweden
| | - Catherine Thèves
- Centre for Anthropobiology and Genomics of Toulouse CAGT, UMR 5288, CNRS, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France
| | - Michel Signoli
- Anthropologie bio-culturelle, droit, éthique et santé ADES, UMR 7268 CNRS EFS, Aix-Marseille Université, Faculté de Médecine, Secteur Nord Bâtiment A CS80011, Boulevard Pierre Dramard, 13344 Marseille Cedex 15, France
| | - Ludovic Orlando
- Centre for Anthropobiology and Genomics of Toulouse CAGT, UMR 5288, CNRS, Université Toulouse III Paul Sabatier, Faculté de Médecine Purpan, Bâtiment A, 37 allées Jules Guesde, 31000 Toulouse, France
| |
Collapse
|
45
|
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 > .
Collapse
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
| |
Collapse
|
46
|
Achtman M, Zhou Z. Metagenomics of the modern and historical human oral microbiome with phylogenetic studies on Streptococcus mutans and Streptococcus sobrinus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190573. [PMID: 33012228 PMCID: PMC7702799 DOI: 10.1098/rstb.2019.0573] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2020] [Indexed: 02/06/2023] Open
Abstract
We have recently developed bioinformatic tools to accurately assign metagenomic sequence reads to microbial taxa: SPARSE for probabilistic, taxonomic classification of sequence reads; EToKi for assembling and polishing genomes from short-read sequences; and GrapeTree, a graphic visualizer of genetic distances between large numbers of genomes. Together, these methods support comparative analyses of genomes from ancient skeletons and modern humans. Here, we illustrate these capabilities with 784 samples from historical dental calculus, modern saliva and modern dental plaque. The analyses revealed 1591 microbial species within the oral microbiome. We anticipated that the oral complexes of Socransky et al., which were defined in 1998, would predominate among taxa whose frequencies differed by source. However, although some species discriminated between sources, we could not confirm the existence of the complexes. The results also illustrate further functionality of our pipelines with two species that are associated with dental caries, Streptococcus mutans and Streptococcus sobrinus. They were rare in historical dental calculus but common in modern plaque, and even more common in saliva. Reconstructed draft genomes of these two species from metagenomic samples in which they were abundant were combined with modern public genomes to provide a detailed overview of their core genomic diversity. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
Collapse
Affiliation(s)
- Mark Achtman
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | | |
Collapse
|
47
|
Stone AC, Lewis CM, Schuenemann VJ. Insights into health and disease from ancient biomolecules. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190568. [PMID: 33012226 DOI: 10.1098/rstb.2019.0568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, 455 West Lindsey, Dale Hall Tower 521, Norman, OK 73019, USA
| | - Verena J Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| |
Collapse
|
48
|
Williams L, Cugini C, Duffy S. Two Nearly Complete Nosocomial Pathogen Genome Sequences Reconstructed from Early-Middle 20th-Century Dental Calculus. Microbiol Resour Announc 2020; 9:e00850-20. [PMID: 33093055 PMCID: PMC7585846 DOI: 10.1128/mra.00850-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/24/2020] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii and Stenotrophomonas maltophilia genomes were reconstructed from early-middle 20th-century human skeletal remains, maintained in natural history museums, using a metagenomic binning approach.
Collapse
Affiliation(s)
- LaShanda Williams
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| | - Carla Cugini
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, New Jersey, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, New Jersey, USA
| |
Collapse
|
49
|
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: 21] [Impact Index Per Article: 5.3] [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’.
Collapse
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
| |
Collapse
|
50
|
Pranata N, Maskoen AM, Sahiratmadja E, Widyaputra S. Dental Calculus as a Potential Biosource for Human Papillomavirus Detection in Oral Squamous Cell Carcinoma. Asian Pac J Cancer Prev 2020; 21:3093-3097. [PMID: 33112572 PMCID: PMC7798156 DOI: 10.31557/apjcp.2020.21.10.3093] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Indexed: 11/25/2022] Open
Abstract
OBJECTIVE The infection of human papillomaviruses (HPVs) plays a role in the development of oral squamous cell carcinoma (OSCC). A poor oral hygiene and dental calculus may cause the infection to persist. Therefore, this study aimed to assess whether this dental calculus could serve as a potential biosource in early detection of HPVs in patients with OSCC. METHODS DNA was isolated from the dental calculus of people diagnosed with OSCC, and MY09/11 primer set was used to detect the presence of HPV. The positive samples were further sequenced and aligned using megablast NCBI BLAST tool to identify the HPV genotype. RESULTS Electrophoresis examination showed that 4 of 14 samples collected (29%) had a clear single band, of which three had 97% to 99% similarity to a high-risk genotype HPV-58. Meanwhile, the other sample had 99% similarity to an unclassified papillomaviridae. CONCLUSION Dental calculus is a promising source of HPV in oral cavity and could be used as a biomarker for early detection.
Collapse
Affiliation(s)
- Natallia Pranata
- Graduate School of Biomedical Sciences, Master Program, Faculty of Medicine, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Department of Oral Biology, Faculty of Dentistry, Maranatha Christian University, Bandung, West Java, Indonesia
| | - Ani Melani Maskoen
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Jatinangor, West Java, Indonesia
| | - Edhyana Sahiratmadja
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Jatinangor, West Java, Indonesia
| | - Sunardhi Widyaputra
- Department of Oral Biology, Faculty of Dentistry, Universitas Padjadjaran, Jatinangor, West Java, Indonesia
| |
Collapse
|