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Wilkin S, Lanigan LT, Montes N, Sharma M, Avanzi C, Sejdiu D, Majander K, Pfrengle S, Chiang Y, Kunz L, Dittmann A, Rühli F, Singh P, Coll MF, Collins MJ, Taurozzi AJ, Schuenemann VJ. Sequential trypsin and ProAlanase digestions unearth immunological protein biomarkers shrouded by skeletal collagen. iScience 2024; 27:109663. [PMID: 38655200 PMCID: PMC11035369 DOI: 10.1016/j.isci.2024.109663] [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: 03/17/2023] [Revised: 09/30/2023] [Accepted: 04/02/2024] [Indexed: 04/26/2024] Open
Abstract
This study investigates the efficacy of proteomic analysis of human remains to identify active infections in the past through the detection of pathogens and the host response to infection. We advance leprosy as a case study due to the sequestering of sufferers in leprosaria and the suggestive skeletal lesions that can result from the disease. Here we present a sequential enzyme extraction protocol, using trypsin followed by ProAlanase, to reduce the abundance of collagen peptides and in so doing increase the detection of non-collagenous proteins. Through our study of five individuals from an 11th to 18th century leprosarium, as well as four from a contemporaneous non-leprosy associated cemetery in Barcelona, we show that samples from 2 out of 5 leprosarium individuals extracted with the sequential digestion methodology contain numerous host immune proteins associated with modern leprosy. In contrast, individuals from the non-leprosy associated cemetery and all samples extracted with a trypsin-only protocol did not. Through this study, we advance a palaeoproteomic methodology to gain insights into the health of archaeological individuals and take a step toward a proteomics-based method to study immune responses in past populations.
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Affiliation(s)
- Shevan Wilkin
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Max Planck Institute of Geoanthropology, Jena, Germany
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, QLD, Australia
| | - Liam T. Lanigan
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nuria Montes
- Unitat d'Antropologia Biològica, Departament de Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Mukul Sharma
- Microbial Pathogenesis and Genomics, National Institute of Research in Tribal Health, Jabalpur, MP, India
| | - Charlotte Avanzi
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Donikë Sejdiu
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Kerttu Majander
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Saskia Pfrengle
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Yun Chiang
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laura Kunz
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Antje Dittmann
- Functional Genomics Center Zurich, University of Zurich, Zurich, Switzerland
| | - Frank Rühli
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pushpendra Singh
- Microbial Pathogenesis and Genomics, National Institute of Research in Tribal Health, Jabalpur, MP, India
- Model Rural Health Research Unit, Badoni, Datia (MP), India
| | | | - Matthew J. Collins
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- McDonald Institute for Archaeological Research, University of Cambridge, West Tower, Downing St, Cambridge CB2 3ER, UK
| | - Alberto J. Taurozzi
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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2
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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.
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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;
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3
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Uchida-Fukuhara Y, Shimamura S, Sawafuji R, Nishiuchi T, Yoneda M, Ishida H, Matsumura H, Tsutaya T. Palaeoproteomic investigation of an ancient human skeleton with abnormal deposition of dental calculus. Sci Rep 2024; 14:5938. [PMID: 38467689 PMCID: PMC10928219 DOI: 10.1038/s41598-024-55779-y] [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: 08/03/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
Detailed investigation of extremely severe pathological conditions in ancient human skeletons is important as it could shed light on the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate an ancient human skeletal individual with severe oral pathology, focusing our research on bacterial pathogenic factors and host defense response. This female skeleton, from the Okhotsk period (i.e., fifth to thirteenth century) of Northern Japan, poses relevant amounts of abnormal dental calculus deposition and exhibits oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from the calculus of the subject. We identified two pathogenic or bioinvasive proteins originating from two of the three "red complex" bacteria, the core species associated with severe periodontal disease in modern humans, as well as two additional bioinvasive proteins of periodontal-associated bacteria. Moreover, we discovered defense response system-associated human proteins, although their proportion was mostly similar to those reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily more intense in ancient individuals with significant amounts of abnormal dental calculus deposition.
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Affiliation(s)
- Yoko Uchida-Fukuhara
- Department of Oral Morphology, Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8525, Japan.
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.
| | - Shigeru Shimamura
- Institute for Extra-Cutting-Edge Science and Technology Avant-Garde Research (X-STAR), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan
| | - Rikai Sawafuji
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
| | - Takumi Nishiuchi
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, 920-8640, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Okinawa, 903-0215, Japan
- Mt. Olive Hospital, Okinawa, 903-0804, Japan
| | - Hirofumi Matsumura
- School of Health Sciences, Sapporo Medical University, Hokkaido, 060-8556, Japan
| | - Takumi Tsutaya
- Research Center for Integrative Evolutionary Science, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa, 240-0193, Japan.
- Biogeochemistry Research Center (BGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, 237-0061, Japan.
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Fontani F, Boano R, Cinti A, Demarchi B, Sandron S, Rampelli S, Candela M, Traversari M, Latorre A, Iacovera R, Abondio P, Sarno S, Mackie M, Collins M, Radini A, Milani C, Petrella E, Giampalma E, Minelli A, Larocca F, Cilli E, Luiselli D. Bioarchaeological and paleogenomic profiling of the unusual Neolithic burial from Grotta di Pietra Sant'Angelo (Calabria, Italy). Sci Rep 2023; 13:11978. [PMID: 37488251 PMCID: PMC10366206 DOI: 10.1038/s41598-023-39250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023] Open
Abstract
The Neolithic burial of Grotta di Pietra Sant'Angelo (CS) represents a unique archaeological finding for the prehistory of Southern Italy. The unusual placement of the inhumation at a rather high altitude and far from inhabited areas, the lack of funerary equipment and the prone deposition of the body find limited similarities in coeval Italian sites. These elements have prompted wider questions on mortuary customs during the prehistory of Southern Italy. This atypical case requires an interdisciplinary approach aimed to build an integrated bioarchaeological profile of the individual. The paleopathological investigation of the skeletal remains revealed the presence of numerous markers that could be associated with craft activities, suggesting possible interpretations of the individual's lifestyle. CT analyses, carried out on the maxillary bones, showed the presence of a peculiar type of dental wear, but also a good density of the bone matrix. Biomolecular and micromorphological analyses of dental calculus highlight the presence of a rich Neolithic-like oral microbiome, the composition of which is consistent with the presence pathologies. Finally, paleogenomic data obtained from the individual were compared with ancient and modern Mediterranean populations, including unpublished high-resolution genome-wide data for 20 modern inhabitants of the nearby village of San Lorenzo Bellizzi, which provided interesting insights into the biodemographic landscape of the Neolithic in Southern Italy.
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Affiliation(s)
- Francesco Fontani
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy.
| | - Rosa Boano
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Alessandra Cinti
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Beatrice Demarchi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Sarah Sandron
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
| | - Simone Rampelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Marco Candela
- Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126, Bologna, Italy
| | - Mirko Traversari
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Adriana Latorre
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Rocco Iacovera
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Paolo Abondio
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Meaghan Mackie
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Torino, Italy
- Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, 2200, København, Denmark
- Faculty of Health and Medical Sciences, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, København, Denmark
- School of Archeology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matthew Collins
- Faculty of Health and Medical Sciences, The Globe Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, København, Denmark
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK
| | - Anita Radini
- School of Archeology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Chantal Milani
- SIOF - Italian Society of Forensic Odontology, Strada Degli Schiocchi 12, 41124, Modena, Italy
| | - Enrico Petrella
- Radiology Unit, Morgagni-Pierantoni Hospital, AUSL Romagna, Via Carlo Forlanini 34, 47121, Forlì, Italy
| | - Emanuela Giampalma
- Radiology Unit, Morgagni-Pierantoni Hospital, AUSL Romagna, Via Carlo Forlanini 34, 47121, Forlì, Italy
| | - Antonella Minelli
- Department of Humanities, Education and Social Sciences, University of Molise, Via Francesco De Sanctis, 86100, Campobasso, Italy
| | - Felice Larocca
- Speleo-Archaeological Research Group, University of Bari, Piazza Umberto I 1, 70121, Bari, Italy
- Speleo-Archaeological Research Centre "Enzo dei Medici", Via Lucania 3, 87070, Roseto Capo Spulico (CS), Italy
| | - Elisabetta Cilli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy
| | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Via Degli Ariani 1, 48121, Ravenna, Italy.
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5
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Riboni N, Bianchi F, Mattarozzi M, Peracchia M, Meleti M, Careri M. Ultra-high performance liquid chromatography high-resolution mass spectrometry for metabolomic analysis of dental calculus from Duke Alessandro Farnese and Maria D'Aviz. Sci Rep 2023; 13:8967. [PMID: 37268814 DOI: 10.1038/s41598-023-36177-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 05/30/2023] [Indexed: 06/04/2023] Open
Abstract
Dental calculus is a valuable resource for the reconstruction of dietary habits and oral microbiome of past populations. In 2020 the remains of Duke Alessandro Farnese and his wife Maria D'Aviz were exhumed to get novel insights into the causes of death. This study aimed to investigate the dental calculus metabolome of the noble couple by untargeted metabolomics. The pulverized samples were decalcified in a water-formic acid mixture, extracted using methanol/acetonitrile and analyzed by ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) using a reversed-phase separation followed by electrospray ionization and full scan in positive and negative ion mode. Waters Synapt-G2-Si High-Definition hybrid quadrupole time-of-flight mass spectrometer was used. Significant features were then identified using MSE acquisition mode, recording information on exact mass precursor and fragment ions within the same run. This approach, together with data pre-treatment and multivariate statistical analysis allowed for the identification of compounds able to differentiate between the investigated samples. More than 200 metabolites were identified, being fatty acids, alcohols, aldehydes, phosphatidylcholines, phosphatidylglycerols, ceramides and phosphatidylserines the most abundant classes. Metabolites deriving from food, bacteria and fungi were also determined, providing information on the habits and oral health status of the couple.
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Affiliation(s)
- Nicolo' Riboni
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy.
| | - Federica Bianchi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy.
| | - Monica Mattarozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy
| | - Marianna Peracchia
- Department of Medicine and Surgery, Centro Universitario di Odontoiatria, University of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Marco Meleti
- Department of Medicine and Surgery, Centro Universitario di Odontoiatria, University of Parma, Via Gramsci 14, 43126, Parma, Italy
| | - Maria Careri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy
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Ventresca Miller AR, Wilkin S, Bayarsaikhan J, Ramsøe A, Clark J, Byambadorj B, Vanderwarf S, Vanwezer N, Haruda A, Fernandes R, Miller B, Boivin N. Permafrost preservation reveals proteomic evidence for yak milk consumption in the 13 th century. Commun Biol 2023; 6:351. [PMID: 37002413 PMCID: PMC10066276 DOI: 10.1038/s42003-023-04723-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/17/2023] [Indexed: 04/04/2023] Open
Abstract
Domesticated yaks endure as iconic symbols of high-altitude frozen landscapes, where herding communities depend on their high-fat milk, transport, dung, and natural fibers. While there is established proteomic evidence for ancient consumption of ruminant and horse milk in the mountains and steppes of northern Eurasia, yak dairy products have yet to be detected. Yak domestication and the species' dispersal from Tibet into the mountainous zones to the north are also poorly resolved due to a paucity of zooarchaeological data. To examine the potential of paleoproteomics to shed light on domesticated yak in Mongolia, we analyzed human dental calculus from Mongol era elite individuals recovered from permafrost burials in Khovsgol province, where people continue to herd yak to this day. We report the first evidence for yak dairy consumption, linked to local resource control. In addition, we confirm a large diversity of recovered whey, curd, tissue, and blood proteins, likely reflecting the excellent preservation conditions found at permafrost sites.
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Affiliation(s)
- Alicia R Ventresca Miller
- Department of Anthropology, University of Michigan, Ann Arbor, 48109, MI, USA.
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, 48109, MI, USA.
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany.
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany.
- Institute for Evolutionary Medicine, Faculty of Medicine, University of Zürich, 8057, Zürich, Switzerland.
- Australian Research Centre for Human Evolution (ARCHE), Griffith University, Brisbane, 4111, QLD, Australia.
| | - Jamsranjav Bayarsaikhan
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
- National Museum of Mongolia, Juulchin Street-1, Ulaanbaatar, Mongolia
| | - Abigail Ramsøe
- Section for GeoGenetics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Julia Clark
- NOMAD Science, Glen, MT, USA
- Flinders University: Department of Archaeology, Flinders University, Bedford Park, 5042, Adelaide, SA, Australia
- Department of Sociology, Social Work and Anthropology, Utah State University, Logan, UT, USA
| | - Batsuren Byambadorj
- Department of Anthropology and Archaeology, National University of Mongolia, Baga toiruu-44, Ulaanbaatar, 46a, Mongolia
| | | | - Nils Vanwezer
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
| | - Ashleigh Haruda
- School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, UK
- Department of Archaeology, University of Exeter, Laver Building, North Parks Road, Exeter, UK
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
- School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, UK
- Faculty of Arts, Masaryk University, Arne Nováka 1, 602 00, Brno-střed, Czechia
| | - Bryan Miller
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, 48109, MI, USA
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
- History of Art Department University of Michigan, Ann Arbor, 48109, MI, USA
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
- School of Social Science, University of Queensland, Brisbane, QLD, Australia
- Department of Archaeology, University of Calgary, Calgary, AB, Canada
- Smithsonian Institution, New York, NY, USA
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7
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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.
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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
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8
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Zhao J, Yang Y, Xu H, Zheng J, Shen C, Chen T, Wang T, Wang B, Yi J, Zhao D, Wu E, Qin Q, Xia L, Qiao L. Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota. NPJ Biofilms Microbiomes 2023; 9:4. [PMID: 36693863 PMCID: PMC9873935 DOI: 10.1038/s41522-023-00373-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM. Data-independent acquisition (DIA) mass spectrometry (MS) has been an emerging quantitative technique in conventional proteomics, but is still at the early stage of development in the field of metaproteomics. Herein, we applied library-free DIA (directDIA)-based metaproteomics and compared the directDIA with other MS-based quantification techniques for metaproteomics on simulated microbial communities and feces samples spiked with bacteria with known ratios, demonstrating the superior performance of directDIA by a comprehensive consideration of proteome coverage in identification as well as accuracy and precision in quantification. We characterized human GM in two cohorts of clinical fecal samples of pancreatic cancer (PC) and mild cognitive impairment (MCI). About 70,000 microbial proteins were quantified in each cohort and annotated to profile the taxonomic and functional characteristics of GM in different diseases. Our work demonstrated the utility of directDIA in quantitative metaproteomics for investigating intestinal microbiota and its related disease pathogenesis.
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Affiliation(s)
- Jinzhi Zhao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Yi Yang
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, 311200, Hangzhou, China
| | - Hua Xu
- Department of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Jianxujie Zheng
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Chengpin Shen
- Shanghai Omicsolution Co., Ltd, 201100, Shanghai, China
| | - Tian Chen
- Changhai Hospital, The Naval Military Medical University, 200433, Shanghai, China
| | - Tao Wang
- Department of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Bing Wang
- College of Food Science and Technology, Shanghai Ocean University, 201306, Shanghai, China
| | - Jia Yi
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Dan Zhao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Enhui Wu
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China
| | - Qin Qin
- Changhai Hospital, The Naval Military Medical University, 200433, Shanghai, China.
| | - Li Xia
- Department of Core Facility of Basic Medical Sciences, and Department of Psychiatry of Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, Fudan University, 200000, Shanghai, China.
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9
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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.
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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
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10
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Li Q, Luo K, Su Z, Huang F, Wu Y, Zhou F, Li Y, Peng X, Li J, Ren B. Dental calculus: A repository of bioinformation indicating diseases and human evolution. Front Cell Infect Microbiol 2022; 12:1035324. [PMID: 36579339 PMCID: PMC9791188 DOI: 10.3389/fcimb.2022.1035324] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 11/11/2022] [Indexed: 12/14/2022] Open
Abstract
Dental calculus has long been considered as a vital contributing factor of periodontal diseases. Our review focuses on the role of dental calculus as a repository and discusses the bioinformation recently reported to be concealed in dental calculus from three perspectives: time-varying oral condition, systemic diseases, and anthropology at various times. Molecular information representing an individual's contemporary oral health status could be detected in dental calculus. Additionally, pathogenic factors of systemic diseases were found in dental calculus, including bacteria, viruses and toxic heavy metals. Thus, dental calculus has been proposed to play a role as biological data storage for detection of molecular markers of latent health concerns. Through the study of environmental debris in dental calculus, an overview of an individual's historical dietary habits and information about the environment, individual behaviors and social culture changes can be unveiled. This review summarizes a new role of dental calculus as a repository of bioinformation, with potential use in the prediction of oral diseases, systemic diseases, and even anthropology.
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Affiliation(s)
- Qinyang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Kaihua Luo
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhifei Su
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fangting Huang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yajie Wu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Fangjie Zhou
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xian Peng
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China,*Correspondence: Jiyao Li, ; Biao Ren,
| | - Biao Ren
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China,*Correspondence: Jiyao Li, ; Biao Ren,
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11
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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
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12
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The Hidden Secrets of the Dental Calculus: Calibration of a Mass Spectrometry Protocol for Dental Calculus Protein Analysis. Int J Mol Sci 2022; 23:ijms232214387. [PMID: 36430863 PMCID: PMC9698480 DOI: 10.3390/ijms232214387] [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: 10/19/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Dental calculus is a solid deposit that forms and accumulates on the tooth surface, entrapping oral microorganisms, biomolecules, and other micro-debris found in the oral cavity. A mass spectrometry analysis of its protein content opens a vista into the subject's diet, oral flora, and even some aspects of health, thus providing new insight and expanding our knowledge of archaic cultures. Multiple experimental protocols have been proposed for the optimal extraction of proteins from dental calculus. Herein, we compared various experimental conditions in order to calibrate and validate a protocol for protein extraction. Our results show that a high concentration of acetic acid followed by mechanical crushing and sonication provided the highest protein yield, while acetone precipitation enabled the identification of more distinct proteins. We validated this protocol using archeological samples, identifying human and microbial proteins in specimens from the eighth and seventeenth centuries (approximately 250-1300 years ago). These findings demonstrate that the developed protocol is useful for studying excavated archaeological samples and that it might be utilized to explore the biohistory, dietary habits, and microbiome of archaic populations.
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13
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Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave. Commun Biol 2022; 5:1262. [DOI: 10.1038/s42003-022-04190-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
AbstractRecent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.
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14
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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.
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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
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15
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Velsko IM, Semerau L, Inskip SA, García-Collado MI, Ziesemer K, Ruber MS, Benítez de Lugo Enrich L, Molero García JM, Valle DG, Peña Ruiz AC, Salazar-García DC, Hoogland MLP, Warinner C. Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology. PNAS NEXUS 2022; 1:pgac148. [PMID: 36714834 PMCID: PMC9802386 DOI: 10.1093/pnasnexus/pgac148] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/29/2022] [Indexed: 02/01/2023]
Abstract
Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.
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Affiliation(s)
- Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Lena Semerau
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany
| | - Sarah A Inskip
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Maite I García-Collado
- GIPYPAC, Department of Geography, Prehistory and Archaeology, University of the Basque Country, Leioa 48940, Spain.,BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Kirsten Ziesemer
- University Library, Vrije Universiteit, Einsteinweg 2, Amsterdam 1081 HV, The Netherlands
| | - Maria Serrano Ruber
- School of Archaeology and Ancient History, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Luis Benítez de Lugo Enrich
- Departmento de Prehistoria, Historia Antigua y Arqueología, Universidad Complutense de Madrid, Madrid 28040, Spain
| | | | - David Gallego Valle
- Facultad de Letras, Universidad de Castilla-La Mancha, Ciudad Real 13004, Spain
| | | | - Domingo C Salazar-García
- Departament de Prehistòria, Historia i Arqueología, Universitat de València, València 46010, Spain.,Department of Geological Sciences, University of Cape Town, Rondebosch 7701, South Africa
| | - Menno L P Hoogland
- Faculty of Archaeology, Leiden University, Einsteinweg, Leiden 2333 CC, The Netherlands
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany.,Faculty of Biological Sciences, Friedrich Schiller University, Jena 07743, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
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16
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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.
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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
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17
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Li Q, Zhou F, Su Z, Li Y, Li J. Corynebacterium matruchotii: A Confirmed Calcifying Bacterium With a Potentially Important Role in the Supragingival Plaque. Front Microbiol 2022; 13:940643. [PMID: 35875585 PMCID: PMC9298747 DOI: 10.3389/fmicb.2022.940643] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 05/30/2022] [Indexed: 02/05/2023] Open
Abstract
Corynebacterium matruchotii is a reported calcifying bacterium that can usually be isolated from dental calculus and induce mineralization in vitro. In recent years, based on in situ hybridization probe and sequencing technology, researchers have discovered the central "pillar" role of C. matruchotii in supragingival plaque, and many studies focused on bacterial interactions in the biofilm structure dominated by C. matruchotii have been conducted. Besides, C. matruchotii seems to be an indicator of "caries-free" oral status according to imaging and sequencing studies. Therefore, in this review, we summarize C. matruchotii 's role in supragingival plaque based on the structure, interactions, and potential connections with oral diseases.
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Affiliation(s)
- Qinyang Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,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, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,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, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,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
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.,Department of Cariology and Endodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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18
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SPIN enables high throughput species identification of archaeological bone by proteomics. Nat Commun 2022; 13:2458. [PMID: 35513387 PMCID: PMC9072323 DOI: 10.1038/s41467-022-30097-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 04/18/2022] [Indexed: 12/29/2022] Open
Abstract
Species determination based on genetic evidence is an indispensable tool in archaeology, forensics, ecology, and food authentication. Most available analytical approaches involve compromises with regard to the number of detectable species, high cost due to low throughput, or a labor-intensive manual process. Here, we introduce "Species by Proteome INvestigation" (SPIN), a shotgun proteomics workflow for analyzing archaeological bone capable of querying over 150 mammalian species by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Rapid peptide chromatography and data-independent acquisition (DIA) with throughput of 200 samples per day reduce expensive MS time, whereas streamlined sample preparation and automated data interpretation save labor costs. We confirm the successful classification of known reference bones, including domestic species and great apes, beyond the taxonomic resolution of the conventional peptide mass fingerprinting (PMF)-based Zooarchaeology by Mass Spectrometry (ZooMS) method. In a blinded study of degraded Iron-Age material from Scandinavia, SPIN produces reproducible results between replicates, which are consistent with morphological analysis. Finally, we demonstrate the high throughput capabilities of the method in a high-degradation context by analyzing more than two hundred Middle and Upper Palaeolithic bones from Southern European sites with late Neanderthal occupation. While this initial study is focused on modern and archaeological mammalian bone, SPIN will be open and expandable to other biological tissues and taxa.
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19
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Abstract
The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.
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Affiliation(s)
- Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, Maryland 20746, United States
| | - Mary H Schweitzer
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27695, United States.,North Carolina Museum of Natural Sciences, Raleigh, North Carolina 27605, United States.,Department of Geology, Lund University, Lund SE-221 00, Sweden
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20
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Granehäll L, Huang KD, Tett A, Manghi P, Paladin A, O’Sullivan N, Rota-Stabelli O, Segata N, Zink A, Maixner F. Metagenomic analysis of ancient dental calculus reveals unexplored diversity of oral archaeal Methanobrevibacter. MICROBIOME 2021; 9:197. [PMID: 34593021 PMCID: PMC8485483 DOI: 10.1186/s40168-021-01132-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 07/01/2021] [Indexed: 05/22/2023]
Abstract
BACKGROUND Dental calculus (mineralised dental plaque) preserves many types of microfossils and biomolecules, including microbial and host DNA, and ancient calculus are thus an important source of information regarding our ancestral human oral microbiome. In this study, we taxonomically characterised the dental calculus microbiome from 20 ancient human skeletal remains originating from Trentino-South Tyrol, Italy, dating from the Neolithic (6000-3500 BCE) to the Early Middle Ages (400-1000 CE). RESULTS We found a high abundance of the archaeal genus Methanobrevibacter in the calculus. However, only a fraction of the sequences showed high similarity to Methanobrevibacter oralis, the only described Methanobrevibacter species in the human oral microbiome so far. To further investigate the diversity of this genus, we used de novo metagenome assembly to reconstruct 11 Methanobrevibacter genomes from the ancient calculus samples. Besides the presence of M. oralis in one of the samples, our phylogenetic analysis revealed two hitherto uncharacterised and unnamed oral Methanobrevibacter species that are prevalent in ancient calculus samples sampled from a broad range of geographical locations and time periods. CONCLUSIONS We have shown the potential of using de novo metagenomic assembly on ancient samples to explore microbial diversity and evolution. Our study suggests that there has been a possible shift in the human oral microbiome member Methanobrevibacter over the last millennia. Video abstract.
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Affiliation(s)
- Lena Granehäll
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
- Faculty of Biology, Department of Biology II, Anthropology and Human Genomics, Ludwig-Maximilians-University of Munich, 82152 Planegg-Martinsried, Germany
| | - Kun D. Huang
- CIBIO Department, University of Trento, 38123 Trento, Italy
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
| | - Adrian Tett
- CIBIO Department, University of Trento, 38123 Trento, Italy
- CUBE - Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Paolo Manghi
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Alice Paladin
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Niall O’Sullivan
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Omar Rota-Stabelli
- Department of Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Center Agriculture Food Environment, University of Trento, 38123 Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, 38123 Trento, Italy
| | - Albert Zink
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, 39100 Bolzano, Italy
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21
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The degradation of intracrystalline mollusc shell proteins: A proteomics study of Spondylus gaederopus. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2021; 1869:140718. [PMID: 34506968 DOI: 10.1016/j.bbapap.2021.140718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/20/2021] [Accepted: 08/31/2021] [Indexed: 11/23/2022]
Abstract
Mollusc shells represent excellent systems for the preservation and retrieval of genuine biomolecules from archaeological or palaeontological samples. As a consequence, the post-mortem breakdown of intracrystalline mollusc shell proteins has been extensively investigated, particularly with regard to its potential use as a "molecular clock" for geochronological applications. But despite seventy years of ancient protein research, the fundamental aspects of diagenesis-induced changes to protein structures and sequences remain elusive. In this study we investigate the degradation of intracrystalline proteins by performing artificial degradation experiments on the shell of the thorny oyster, Spondylus gaederopus, which is particularly important for archaeological research. We used immunochemistry and tandem mass tag (TMT) quantitative proteomics to simultaneously track patterns of structural loss and of peptide bond hydrolysis. Powdered and bleached shell samples were heated in water at four different temperatures (80, 95, 110, 140 °C) for different time durations. The structural loss of carbohydrate and protein groups was investigated by immunochemical techniques (ELLA and ELISA) and peptide bond hydrolysis was studied by tracking the changes in protein/peptide relative abundances over time using TMT quantitative proteomics. We find that heating does not induce instant organic matrix decay, but first facilitates the uncoiling of cross-linked structures, thus improving matrix detection. We calculated apparent activation energies of structural loss: Ea (carbohydrate groups) = 104.7 kJ/mol, Ea (protein epitopes) = 104.4 kJ/mol, which suggests that secondary matrix structure degradation may proceed simultaneously with protein hydrolysis. While prolonged heating at 110 °C (10 days) results in complete loss of the structural signal, surviving peptide sequences were still observed. Eight hydrolysis-prone peptide bonds were identified in the top scoring shell sequence, the uncharacterised protein LOC117318053 from Pecten maximus. Interestingly, these were not the expected "weak" bonds based on published theoretical stabilities calculated for peptides in solution. This further confirms that intracrystalline protein degradation patterns are complex and that the overall microchemical environment plays an active role in protein stability. Our TMT approach represents a major stepping stone towards developing a model for studying protein diagenesis in biomineralised systems.
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Nodari R, Drancourt M, Barbieri R. Paleomicrobiology of the human digestive tract: A review. Microb Pathog 2021; 157:104972. [PMID: 34029658 DOI: 10.1016/j.micpath.2021.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/23/2021] [Accepted: 05/14/2021] [Indexed: 10/21/2022]
Abstract
The microbiota is a hot topic of research in medical microbiology, boosted by culturomics and metagenomics, with unanticipated knowledge outputs in physiology and pathology. Knowledge of the microbiota in ancient populations may therefore be of prime interest in understanding factors shaping the coevolution of the microbiota and populations. Studies on ancient human microbiomes can help us understand how the community of microorganisms presents in the oral cavity and the gut was shaped during the evolution of our species and what environmental, social or cultural changes may have changed it. This review cumulates and summarizes the discoveries in the field of the ancient human microbiota, focusing on the remains used as samples and techniques used to handle and analyze them.
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Affiliation(s)
- Riccardo Nodari
- Department of Biosciences and Pediatric Clinical Research Center "Romeo and Enrica Invernizzi", University of Milan, Milan, 20133, Italy
| | - Michel Drancourt
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Rémi Barbieri
- Aix-Marseille Univ., IRD, MEPHI, IHU Méditerranée Infection, Marseille, France; UMR 7268, Anthropologie Bioculturelle, Droit, Ethique et Santé, Aix Marseille Univ., 11 CNRS, EFS, ADES, Marseille, France.
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23
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Assessing the degradation of ancient milk proteins through site-specific deamidation patterns. Sci Rep 2021; 11:7795. [PMID: 33833277 PMCID: PMC8032661 DOI: 10.1038/s41598-021-87125-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/23/2021] [Indexed: 12/04/2022] Open
Abstract
The origins, prevalence and nature of dairying have been long debated by archaeologists. Within the last decade, new advances in high-resolution mass spectrometry have allowed for the direct detection of milk proteins from archaeological remains, including ceramic residues, dental calculus, and preserved dairy products. Proteins recovered from archaeological remains are susceptible to post-excavation and laboratory contamination, a particular concern for ancient dairying studies as milk proteins such as beta-lactoglobulin (BLG) and caseins are potential laboratory contaminants. Here, we examine how site-specific rates of deamidation (i.e., deamidation occurring in specific positions in the protein chain) can be used to elucidate patterns of peptide degradation, and authenticate ancient milk proteins. First, we characterize site-specific deamidation patterns in modern milk products and experimental samples, confirming that deamidation occurs primarily at low half-time sites. We then compare this to previously published palaeoproteomic data from six studies reporting ancient milk peptides. We confirm that site-specific deamidation rates, on average, are more advanced in BLG recovered from ancient dental calculus and pottery residues. Nevertheless, deamidation rates displayed a high degree of variability, making it challenging to authenticate samples with relatively few milk peptides. We demonstrate that site-specific deamidation is a useful tool for identifying modern contamination but highlight the need for multiple lines of evidence to authenticate ancient protein data.
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24
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Tsutaya T, Mackie M, Sawafuji R, Miyabe-Nishiwaki T, Olsen JV, Cappellini E. Faecal proteomics as a novel method to study mammalian behaviour and physiology. Mol Ecol Resour 2021; 21:1808-1819. [PMID: 33720532 PMCID: PMC8360081 DOI: 10.1111/1755-0998.13380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/28/2021] [Accepted: 03/10/2021] [Indexed: 11/30/2022]
Abstract
Mammalian faeces can be collected noninvasively during field research and provide valuable information on the ecology and evolution of the source individuals. Undigested food remains, genome/metagenome, steroid hormones, and stable isotopes obtained from faecal samples provide evidence on diet, host/symbiont genetics, and physiological status of the individuals. However, proteins in mammalian faeces have hardly been studied, which hinders the molecular investigations into the behaviour and physiology of the source individuals. Here, we apply mass spectrometry-based proteomics to faecal samples (n = 10), collected from infant, juvenile, and adult captive Japanese macaques (Macaca fuscata), to describe the proteomes of the source individual, of the food it consumed, and its intestinal microbes. The results show that faecal proteomics is a useful method to: (i) investigate dietary changes along with breastfeeding and weaning, (ii) reveal the taxonomic and histological origin of the food items consumed, and (iii) estimate physiological status inside intestinal tracts. These types of insights are difficult or impossible to obtain through other molecular approaches. Most mammalian species are facing extinction risk and there is an urgent need to obtain knowledge on their ecology and evolution for better conservation strategy. The faecal proteomics framework we present here is easily applicable to wild settings and other mammalian species, and provides direct evidence of their behaviour and physiology.
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Affiliation(s)
- Takumi Tsutaya
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan.,Biogeochemistry Research Center, Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Meaghan Mackie
- Evolutionary Genomics Section, The Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Rikai Sawafuji
- Department of Evolutionary Studies of Biosystems, The Graduate University for Advanced Studies, Hayama, Japan
| | | | - Jesper V Olsen
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Evolutionary Genomics Section, The Globe Institute, University of Copenhagen, Copenhagen, Denmark
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25
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Palmer KS, Makarewicz CA, Tishkin AA, Tur SS, Chunag A, Diimajav E, Jamsranjav B, Buckley M. Comparing the Use of Magnetic Beads with Ultrafiltration for Ancient Dental Calculus Proteomics. J Proteome Res 2021; 20:1689-1704. [PMID: 33596076 DOI: 10.1021/acs.jproteome.0c00862] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the past two decades, proteomic analysis has greatly developed in application to the field of biomolecular archaeology, coinciding with advancements in LC-MS/MS instrumentation sensitivity and improvements in sample preparation methods. Recently, human dental calculus has received much attention for its well-preserved proteomes locked in mineralized dental plaque which stores information on human diets and the oral microbiome otherwise invisible to other biomolecular approaches. Maximizing proteome recovery in ancient dental calculus, available only in minute quantities and irreplaceable after destructive analysis, is of paramount importance. Here, we compare the more traditional ultrafiltration-based and acetone precipitation approaches with the newer paramagnetic bead approach in order to test the influence of demineralization acid on recovered proteome complexity obtained from specimens as well as the sequence coverages matched for significant proteins. We found that a protocol utilizing EDTA combined with paramagnetic beads increased proteome complexity, in some cases doubling the number of unique peptides and number of proteins matched, compared to protocols involving the use of HCl and either acetone precipitation or ultrafiltration. Although the increase in the number of proteins was almost exclusively of bacterial origin, a development that has implications for the study of diseases within these ancient populations, an increase in the peptide number for the dairy proteins β-lactoglobulin and casein was also observed reflecting an increase in sequence coverage for these dietary proteins of interest. We also consider structural explanations for the discrepancies observed between these two key dietary proteins preserved in archaeological dental calculus.
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Affiliation(s)
- Karren S Palmer
- School of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Cheryl A Makarewicz
- Institute for Prehistoric and Protohistoric Archaeology, Kiel University, Johanna-Mestorf Strasse 2-6, D-24118 Kiel, Germany
| | - Alexey A Tishkin
- Department of Archeology, Ethnography, and Museology, Altai State University, Lenin Prospect 61, 656049 Barnaul, Russia
| | - Svetlana S Tur
- Department of Archeology, Ethnography, and Museology, Altai State University, Lenin Prospect 61, 656049 Barnaul, Russia
| | | | - Erdenebaatar Diimajav
- Department of Archaeology and History, Ulaanbataar State University, Luvsantseveen Street, 5th khoroo, 15th khorgoolol, Bayanzurk District 13343 Ulaanbaatar, Mongolia
| | - Bayarsaikhan Jamsranjav
- National Museum of Mongolia, Ulaanbaatar Mongolia, Juulchin Street-1, Ulaanbaatar 13343, Mongolia
| | - Michael Buckley
- School of Natural Sciences, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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26
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Bleasdale M, Richter KK, Janzen A, Brown S, Scott A, Zech J, Wilkin S, Wang K, Schiffels S, Desideri J, Besse M, Reinold J, Saad M, Babiker H, Power RC, Ndiema E, Ogola C, Manthi FK, Zahir M, Petraglia M, Trachsel C, Nanni P, Grossmann J, Hendy J, Crowther A, Roberts P, Goldstein ST, Boivin N. Ancient proteins provide evidence of dairy consumption in eastern Africa. Nat Commun 2021; 12:632. [PMID: 33504791 PMCID: PMC7841170 DOI: 10.1038/s41467-020-20682-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 12/10/2020] [Indexed: 11/09/2022] Open
Abstract
Consuming the milk of other species is a unique adaptation of Homo sapiens, with implications for health, birth spacing and evolution. Key questions nonetheless remain regarding the origins of dairying and its relationship to the genetically-determined ability to drink milk into adulthood through lactase persistence (LP). As a major centre of LP diversity, Africa is of significant interest to the evolution of dairying. Here we report proteomic evidence for milk consumption in ancient Africa. Using liquid chromatography tandem mass spectrometry (LC-MS/MS) we identify dairy proteins in human dental calculus from northeastern Africa, directly demonstrating milk consumption at least six millennia ago. Our findings indicate that pastoralist groups were drinking milk as soon as herding spread into eastern Africa, at a time when the genetic adaptation for milk digestion was absent or rare. Our study links LP status in specific ancient individuals with direct evidence for their consumption of dairy products.
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Affiliation(s)
- Madeleine Bleasdale
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
- Department of Archaeology, University of York, King's Manor, Exhibition Square, York, YO1 7EP, UK.
| | - Kristine K Richter
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Anneke Janzen
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Anthropology, University of Tennessee, Knoxville, TN, USA
| | - Samantha Brown
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ashley Scott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jana Zech
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Shevan Wilkin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jocelyne Desideri
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, Université de Genève, Geneva, Switzerland
| | - Marie Besse
- Laboratory of Prehistoric Archaeology and Anthropology, Department F.-A. Forel for Environmental and Aquatic Sciences, Université de Genève, Geneva, Switzerland
| | - Jacques Reinold
- Section française de la Direction des antiquités du Soudan, Khartoum, Sudan
| | - Mohamed Saad
- National Corporation for Antiquities and Museums of Sudan, M.Bolheim Bioarchaeology Laboratory, Khartoum, Sudan
| | - Hiba Babiker
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Robert C Power
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Pre-and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Emmanuel Ndiema
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Christine Ogola
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Fredrick K Manthi
- Department of Earth Sciences, National Museums of Kenya, Nairobi, Kenya
| | - Muhammad Zahir
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Archaeology, Hazara University, Mansehra, Pakistan
| | - Michael Petraglia
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DA, USA
| | - Christian Trachsel
- Functional Genomics Center, University of Zurich/ETH, Zurich, Switzerland
| | - Paolo Nanni
- Functional Genomics Center, University of Zurich/ETH, Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Center, University of Zurich/ETH, Zurich, Switzerland
| | - Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Alison Crowther
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
| | - Steven T Goldstein
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany.
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia.
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DA, USA.
- Department of Anthropology and Archaeology, University of Calgary, Calgary, AB, Canada.
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Hendy J. Ancient protein analysis in archaeology. SCIENCE ADVANCES 2021; 7:7/3/eabb9314. [PMID: 33523896 PMCID: PMC7810370 DOI: 10.1126/sciadv.abb9314] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 11/20/2020] [Indexed: 05/10/2023]
Abstract
The analysis of ancient proteins from paleontological, archeological, and historic materials is revealing insights into past subsistence practices, patterns of health and disease, evolution and phylogeny, and past environments. This review tracks the development of this field, discusses some of the major methodological strategies used, and synthesizes recent developments in archeological applications of ancient protein analysis. Moreover, this review highlights some of the challenges faced by the field and potential future directions, arguing that the development of minimally invasive or nondestructive techniques, strategies for protein authentication, and the integration of ancient protein analysis with other biomolecular techniques are important research strategies as this field grows.
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Affiliation(s)
- Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany.
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28
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Exotic foods reveal contact between South Asia and the Near East during the second millennium BCE. Proc Natl Acad Sci U S A 2020; 118:2014956117. [PMID: 33419922 DOI: 10.1073/pnas.2014956117] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Although the key role of long-distance trade in the transformation of cuisines worldwide has been well-documented since at least the Roman era, the prehistory of the Eurasian food trade is less visible. In order to shed light on the transformation of Eastern Mediterranean cuisines during the Bronze Age and Early Iron Age, we analyzed microremains and proteins preserved in the dental calculus of individuals who lived during the second millennium BCE in the Southern Levant. Our results provide clear evidence for the consumption of expected staple foods, such as cereals (Triticeae), sesame (Sesamum), and dates (Phoenix). We additionally report evidence for the consumption of soybean (Glycine), probable banana (Musa), and turmeric (Curcuma), which pushes back the earliest evidence of these foods in the Mediterranean by centuries (turmeric) or even millennia (soybean). We find that, from the early second millennium onwards, at least some people in the Eastern Mediterranean had access to food from distant locations, including South Asia, and such goods were likely consumed as oils, dried fruits, and spices. These insights force us to rethink the complexity and intensity of Indo-Mediterranean trade during the Bronze Age as well as the degree of globalization in early Eastern Mediterranean cuisine.
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29
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Froment C, Zanolli C, Hourset M, Mouton-Barbosa E, Moreira A, Burlet-Schiltz O, Mollereau C. Protein sequence comparison of human and non-human primate tooth proteomes. J Proteomics 2020; 231:104045. [PMID: 33189847 DOI: 10.1016/j.jprot.2020.104045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 10/23/2022]
Abstract
In the context of human evolution, the study of proteins may overcome the limitation of the high degradation of ancient DNA over time to provide biomolecular information useful for the phylogenetic reconstruction of hominid taxa. In this study, we used a shotgun proteomics approach to compare the tooth proteomes of extant human and non-human primates (gorilla, chimpanzee, orangutan and baboon) in order to search for a panel of peptides able to discriminate between taxa and further help reconstructing the evolutionary relationships of fossil primates. Among the 25 proteins shared by the five genera datasets, we found a combination of peptides with sequence variations allowing to differentiate the hominid taxa in the proteins AHSG, AMBN, APOA1, BGN, C9, COL11A2, COL22A1, COL3A1, DSPP, F2, LUM, OMD, PCOLCE and SERPINA1. The phylogenetic tree confirms the placement of the samples in the appropriate genus branches. Altogether, the results provide experimental evidence that a shotgun proteomics approach on dental tissue has the potential to detect taxonomic variation, which is promising for future investigations of uncharacterized and/or fossil hominid/hominin specimens. SIGNIFICANCE: A shotgun proteomics approach on human and non-human primate teeth allowed to identify peptides with taxonomic interest, highlighting the potential for future studies on hominid fossils.
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Affiliation(s)
- Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Clément Zanolli
- Laboratoire PACEA, UMR 5199 CNRS, Université de Bordeaux, Pessac, France
| | - Mathilde Hourset
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Andreia Moreira
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Catherine Mollereau
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), UMR 5288 CNRS, Université de Toulouse, UPS, Toulouse, France.
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30
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Fotakis AK, Denham SD, Mackie M, Orbegozo MI, Mylopotamitaki D, Gopalakrishnan S, Sicheritz-Pontén T, Olsen JV, Cappellini E, Zhang G, Christophersen A, Gilbert MTP, Vågene ÅJ. Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190584. [PMID: 33012227 PMCID: PMC7702802 DOI: 10.1098/rstb.2019.0584] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Mineralized dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. Here we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of sixteenth-century human dental calculus from an individual from Trondheim, Norway. When phylogenetically placed, this genome falls in branch 3I among the diversity of other contemporary ancient strains from Northern Europe. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. Mycobacterium leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual's dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early-stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Sean D Denham
- Museum of Archaeology, University of Stavanger, Stavanger, Norway
| | - Meaghan Mackie
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway.,Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Miren Iraeta Orbegozo
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Dorothea Mylopotamitaki
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Thomas Sicheritz-Pontén
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Jesper V Olsen
- Novo Nordisk Foundation Centre for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark.,BGI-Shenzhen, 518083 Shenzhen, People's Republic of China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, 650223 Kunming, People's Republic of China.,Centre for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, People's Republic of China
| | | | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway.,NTNU University Museum, Trondheim, Norway
| | - Åshild J Vågene
- Section for Evolutionary Genomics, GLOBE Institute, Faculty of Health and Medical Sciences, University of Stavanger, Stavanger, Norway
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31
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Cleland TP, Schroeter ER, Colleary C. Diagenetiforms: A new term to explain protein changes as a result of diagenesis in paleoproteomics. J Proteomics 2020; 230:103992. [PMID: 32992016 DOI: 10.1016/j.jprot.2020.103992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/11/2020] [Accepted: 09/18/2020] [Indexed: 12/14/2022]
Abstract
The term proteoform describes all combinations of change in a protein, as elucidated through intact mass proteomics. Paleoproteomic studies have begun using digestion-free and top-down techniques to access information from ancient and historical remains. However, to discuss protein changes that uniquely occur to archaeological and paleontological proteomes as the result of diagenesis (i.e., physical and chemical change imparted by burial), a novel term is needed that both addresses issues of combinatorics and distinguishes diagenetic-specific alteration. SIGNIFICANCE: The term diagenetiform provides the opportunity to communicate clearly the sets of diagenetic changes found on preserved proteins. The diagenetiform nomenclature will allow for top-down paleoproteomic studies to accurately describe the total changes detected on ancient proteins.
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Affiliation(s)
- Timothy P Cleland
- Museum Conservation Institute, Smithsonian Institution, Suitland, MD 20746, United States of America.
| | - Elena R Schroeter
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, United States of America
| | - Caitlin Colleary
- Department of Vertebrate Paleontology, Cleveland Museum of Natural History, Cleveland, OH 44106, United States of America
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32
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Lanigan LT, Mackie M, Feine S, Hublin JJ, Schmitz RW, Wilcke A, Collins MJ, Cappellini E, Olsen JV, Taurozzi AJ, Welker F. Multi-protease analysis of Pleistocene bone proteomes. J Proteomics 2020; 228:103889. [DOI: 10.1016/j.jprot.2020.103889] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/08/2020] [Accepted: 06/25/2020] [Indexed: 12/11/2022]
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Living off the land: Terrestrial-based diet and dairying in the farming communities of the Neolithic Balkans. PLoS One 2020; 15:e0237608. [PMID: 32817620 PMCID: PMC7444498 DOI: 10.1371/journal.pone.0237608] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/29/2020] [Indexed: 01/01/2023] Open
Abstract
The application of biomolecular techniques to archaeological materials from the Balkans is providing valuable new information on the prehistory of the region. This is especially relevant for the study of the neolithisation process in SE Europe, which gradually affected the rest of the continent. Here, to answer questions regarding diet and subsistence practices in early farming societies in the central Balkans, we combine organic residue analyses of archaeological pottery, taxonomic and isotopic study of domestic animal remains and biomolecular analyses of human dental calculus. The results from the analyses of the lipid residues from pottery suggest that milk was processed in ceramic vessels. Dairy products were shown to be part of the subsistence strategies of the earliest Neolithic communities in the region but were of varying importance in different areas of the Balkan. Conversely, milk proteins were not detected within the dental calculus. The molecular and isotopic identification of meat, dairy, plants and beeswax in the pottery lipids also provided insights into the diversity of diet in these early Neolithic communities, mainly based on terrestrial resources. We also present the first compound-specific radiocarbon dates for the region, obtained directly from absorbed organic residues extracted from pottery, identified as dairy lipids.
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Yang L, Fan W, Xu Y. Metaproteomics insights into traditional fermented foods and beverages. Compr Rev Food Sci Food Saf 2020; 19:2506-2529. [PMID: 33336970 DOI: 10.1111/1541-4337.12601] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/14/2020] [Accepted: 06/17/2020] [Indexed: 12/13/2022]
Abstract
Traditional fermented foods and beverages (TFFB) are important dietary components. Multi-omics techniques have been applied to all aspects of TFFB research to clarify the composition and nutritional value of TFFB, and to reveal the microbial community, microbial interactions, fermentative kinetics, and metabolic profiles during the fermentation process of TFFB. Because of the advantages of metaproteomics in providing functional information, this technology has increasingly been used in research to assess the functional diversity of microbial communities. Metaproteomics is gradually gaining attention in the field of TFFB research because it can reveal the nature of microorganism function at the protein level. This paper reviews the common methods of metaproteomics applied in TFFB research; systematically summarizes the results of metaproteomics research on TFFB, such as sauces, wines, fermented tea, cheese, and fermented fish; and compares the differences in conclusions reached through metaproteomics versus other omics methods. Metaproteomics has great advantages in revealing the microbial functions in TFFB and the interaction between the materials and microbial community. In the future, metaproteomics should be further applied to the study of functional protein markers and protein interaction in TFFB; multi-omics technology requires further integration to reveal the molecular nature of TFFB fermentation.
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Affiliation(s)
- Liang Yang
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenlai Fan
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education, Laboratory of Brewing Microbiology and Applied Enzymology, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan. PLoS One 2020; 15:e0226654. [PMID: 32130218 PMCID: PMC7055813 DOI: 10.1371/journal.pone.0226654] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 12/01/2019] [Indexed: 11/21/2022] Open
Abstract
Although there are many methods for reconstructing diets of the past, detailed taxon identification is still challenging, and most plants hardly remain at a site. In this study, we applied DNA metabarcoding to dental calculus of premodern Japan for the taxonomic identification of food items. DNA was extracted from 13 human dental calculi from the Unko-in site (18th–19th century) of the Edo period, Japan. Polymerase chain reaction (PCR) and sequencing were performed using a primer set specific to the genus Oryza because rice (Oryza sativa) was a staple food and this was the only member of this genus present in Japan at that time. DNA metabarcoding targeting plants, animals (meat and fish), and fungi were also carried out to investigate dietary diversity. We detected amplified products of the genus Oryza from more than half of the samples using PCR and Sanger sequencing. DNA metabarcoding enabled us to identify taxa of plants and fungi, although taxa of animals were not detected, except human. Most of the plant taxonomic groups (family/genus level) are present in Japan and include candidate species consumed as food at that time, as confirmed by historical literature. The other groups featured in the lifestyle of Edo people, such as for medicinal purposes and tobacco. The results indicate that plant DNA analysis from calculus provides information about food diversity and lifestyle habits from the past and can complement other analytical methods such as microparticle analysis and stable isotope analysis.
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37
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Jensen TZT, Niemann J, Iversen KH, Fotakis AK, Gopalakrishnan S, Vågene ÅJ, Pedersen MW, Sinding MHS, Ellegaard MR, Allentoft ME, Lanigan LT, Taurozzi AJ, Nielsen SH, Dee MW, Mortensen MN, Christensen MC, Sørensen SA, Collins MJ, Gilbert MTP, Sikora M, Rasmussen S, Schroeder H. A 5700 year-old human genome and oral microbiome from chewed birch pitch. Nat Commun 2019; 10:5520. [PMID: 31848342 PMCID: PMC6917805 DOI: 10.1038/s41467-019-13549-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/15/2019] [Indexed: 12/18/2022] Open
Abstract
The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.
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Affiliation(s)
- Theis Z T Jensen
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
- BioArch, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Jonas Niemann
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
- BioArch, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Katrine Højholt Iversen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens, Lyngby, 2800, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Anna K Fotakis
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Shyam Gopalakrishnan
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Åshild J Vågene
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Mikkel Winther Pedersen
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Mikkel-Holger S Sinding
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Martin R Ellegaard
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Morten E Allentoft
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Liam T Lanigan
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Alberto J Taurozzi
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Sofie Holtsmark Nielsen
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Michael W Dee
- Centre for Isotope Research, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Martin N Mortensen
- The National Museum of Denmark, I.C. Modewegs Vej, Brede, Kongens Lyngby, 2800, Denmark
| | - Mads C Christensen
- The National Museum of Denmark, I.C. Modewegs Vej, Brede, Kongens Lyngby, 2800, Denmark
| | - Søren A Sørensen
- Museum Lolland-Falster, Frisegade 40, Nykøbing Falster, 4800, Denmark
| | - Matthew J Collins
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, CB2 3ER, UK
| | - M Thomas P Gilbert
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
- University Museum, NTNU, 7012, Trondheim, Norway
| | - Martin Sikora
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark.
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Froment C, Hourset M, Sáenz-Oyhéréguy N, Mouton-Barbosa E, Willmann C, Zanolli C, Esclassan R, Donat R, Thèves C, Burlet-Schiltz O, Mollereau C. Analysis of 5000 year-old human teeth using optimized large-scale and targeted proteomics approaches for detection of sex-specific peptides. J Proteomics 2019; 211:103548. [PMID: 31626997 DOI: 10.1016/j.jprot.2019.103548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 08/30/2019] [Accepted: 10/07/2019] [Indexed: 12/27/2022]
Abstract
The study demonstrates the high potential of MS-based proteomics coupled to an iterative database search strategy for the in-depth investigation of ancient proteomes. An efficient targeted PRM MS-based approach, although limited to the detection of a single pair of sex-specific amelogenin peptides, allowed confirming the sex of individuals in ancient dental remains, an essential information for paleoanthropologists facing the issue of sex determination and dimorphism.
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Affiliation(s)
- Carine Froment
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Mathilde Hourset
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Nancy Sáenz-Oyhéréguy
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Claire Willmann
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Clément Zanolli
- Laboratoire PACEA, UMR 5199 CNRS, Université de Bordeaux, Pessac, France
| | - Rémi Esclassan
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France; Faculté de chirurgie dentaire de Toulouse, Université de Toulouse, UPS, Toulouse, France
| | - Richard Donat
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Catherine Thèves
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Catherine Mollereau
- Laboratoire d'Anthropobiologie Moléculaire et Imagerie de Synthèse (AMIS), Université de Toulouse, CNRS, UPS, Toulouse, France.
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Peters DL, Wang W, Zhang X, Ning Z, Mayne J, Figeys D. Metaproteomic and Metabolomic Approaches for Characterizing the Gut Microbiome. Proteomics 2019; 19:e1800363. [PMID: 31321880 DOI: 10.1002/pmic.201800363] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/27/2019] [Indexed: 12/14/2022]
Abstract
The gut microbiome has been shown to play a significant role in human healthy and diseased states. The dynamic signaling that occurs between the host and microbiome is critical for the maintenance of host homeostasis. Analyzing the human microbiome with metaproteomics, metabolomics, and integrative multi-omics analyses can provide significant information on markers for healthy and diseased states, allowing for the eventual creation of microbiome-targeted treatments for diseases associated with dysbiosis. Metaproteomics enables functional activity information to be gained from the microbiome samples, while metabolomics provides insight into the overall metabolic states affecting/representing the host-microbiome interactions. Combining these functional -omic platforms together with microbiome composition profiling allows for a holistic overview on the functional and metabolic state of the microbiome and its influence on human health. Here the benefits of metaproteomics, metabolomics, and the integrative multi-omic approaches to investigating the gut microbiome in the context of human health and diseases are reviewed.
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Affiliation(s)
- Danielle L Peters
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Wenju Wang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Janice Mayne
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada.,Canadian Institute for Advanced Research, 661 University Ave, Toronto, ON, M5G 1M1, Canada.,The University of Ottawa and Shanghai Institute of Materia Medica Joint Research Center on Systems and Personalized Pharmacology, 451 Smyth Road, Ottawa, ON, KIH 8M5, Canada
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40
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Velsko IM, Fellows Yates JA, Aron F, Hagan RW, Frantz LAF, Loe L, Martinez JBR, Chaves E, Gosden C, Larson G, Warinner C. Microbial differences between dental plaque and historic dental calculus are related to oral biofilm maturation stage. MICROBIOME 2019; 7:102. [PMID: 31279340 PMCID: PMC6612086 DOI: 10.1186/s40168-019-0717-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/24/2019] [Indexed: 05/19/2023]
Abstract
BACKGROUND Dental calculus, calcified oral plaque biofilm, contains microbial and host biomolecules that can be used to study historic microbiome communities and host responses. Dental calculus does not typically accumulate as much today as historically, and clinical oral microbiome research studies focus primarily on living dental plaque biofilm. However, plaque and calculus reflect different conditions of the oral biofilm, and the differences in microbial characteristics between the sample types have not yet been systematically explored. Here, we compare the microbial profiles of modern dental plaque, modern dental calculus, and historic dental calculus to establish expected differences between these substrates. RESULTS Metagenomic data was generated from modern and historic calculus samples, and dental plaque metagenomic data was downloaded from the Human Microbiome Project. Microbial composition and functional profile were assessed. Metaproteomic data was obtained from a subset of historic calculus samples. Comparisons between microbial, protein, and metabolomic profiles revealed distinct taxonomic and metabolic functional profiles between plaque, modern calculus, and historic calculus, but not between calculus collected from healthy teeth and periodontal disease-affected teeth. Species co-exclusion was related to biofilm environment. Proteomic profiling revealed that healthy tooth samples contain low levels of bacterial virulence proteins and a robust innate immune response. Correlations between proteomic and metabolomic profiles suggest co-preservation of bacterial lipid membranes and membrane-associated proteins. CONCLUSIONS Overall, we find that there are systematic microbial differences between plaque and calculus related to biofilm physiology, and recognizing these differences is important for accurate data interpretation in studies comparing dental plaque and calculus.
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Affiliation(s)
- Irina M Velsko
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK.
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Richard W Hagan
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, OX2 0ES, UK
| | | | - Eros Chaves
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma City, 73117, OK, USA
- Current address: Pinellas Dental Specialties, Largo, FL, 33776, USA
| | - Chris Gosden
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, OX1 3QY, UK
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Department of Periodontics, University of Oklahoma Health Sciences Center, Oklahoma City, 73117, OK, USA.
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
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Schiebenhoefer H, Van Den Bossche T, Fuchs S, Renard BY, Muth T, Martens L. Challenges and promise at the interface of metaproteomics and genomics: an overview of recent progress in metaproteogenomic data analysis. Expert Rev Proteomics 2019; 16:375-390. [PMID: 31002542 DOI: 10.1080/14789450.2019.1609944] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION The study of microbial communities based on the combined analysis of genomic and proteomic data - called metaproteogenomics - has gained increased research attention in recent years. This relatively young field aims to elucidate the functional and taxonomic interplay of proteins in microbiomes and its implications on human health and the environment. Areas covered: This article reviews bioinformatics methods and software tools dedicated to the analysis of data from metaproteomics and metaproteogenomics experiments. In particular, it focuses on the creation of tailored protein sequence databases, on the optimal use of database search algorithms including methods of error rate estimation, and finally on taxonomic and functional annotation of peptide and protein identifications. Expert opinion: Recently, various promising strategies and software tools have been proposed for handling typical data analysis issues in metaproteomics. However, severe challenges remain that are highlighted and discussed in this article; these include: (i) robust false-positive assessment of peptide and protein identifications, (ii) complex protein inference against a background of highly redundant data, (iii) taxonomic and functional post-processing of identification data, and finally, (iv) the assessment and provision of metrics and tools for quantitative analysis.
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Affiliation(s)
- Henning Schiebenhoefer
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Tim Van Den Bossche
- b VIB - UGent Center for Medical Biotechnology, VIB , Ghent , Belgium.,c Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
| | - Stephan Fuchs
- d FG13 Division of Nosocomial Pathogens and Antibiotic Resistances , Robert Koch Institute , Wernigerode , Germany
| | - Bernhard Y Renard
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Thilo Muth
- a Bioinformatics Unit (MF1), Department for Methods Development and Research Infrastructure , Robert Koch Institute , Berlin , Germany
| | - Lennart Martens
- b VIB - UGent Center for Medical Biotechnology, VIB , Ghent , Belgium.,c Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences , Ghent University , Ghent , Belgium
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Abstract
The microbiome is emerging as a prominent factor affecting human health, and its dysbiosis is associated with various diseases. Compositional profiling of microbiome is increasingly being supplemented with functional characterization. Metaproteomics is intrinsically focused on functional changes and therefore will be an important tool in those studies of the human microbiome. In the past decade, development of new experimental and bioinformatic approaches for metaproteomics has enabled large-scale human metaproteomic studies. However, challenges still exist, and there remains a lack of standardizations and guidelines for properly performing metaproteomic studies on human microbiome. Herein, we provide a perspective of recent developments, the challenges faced, and the future directions of metaproteomics and its applications. In addition, we propose a set of guidelines/recommendations for performing and reporting the results from metaproteomic experiments for the study of human microbiomes. We anticipate that these guidelines will be optimized further as more metaproteomic questions are raised and addressed, and metaproteomic applications are published, so that they are eventually recognized and applied in the field.
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Affiliation(s)
- Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine , University of Ottawa , Ottawa , Ontario K1H 8M5 , Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine , University of Ottawa , Ottawa , Ontario K1H 8M5 , Canada
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43
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Doll S, Gnad F, Mann M. The Case for Proteomics and Phospho-Proteomics in Personalized Cancer Medicine. Proteomics Clin Appl 2019; 13:e1800113. [PMID: 30790462 PMCID: PMC6519247 DOI: 10.1002/prca.201800113] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 02/01/2019] [Indexed: 02/06/2023]
Abstract
The concept of personalized medicine is predominantly been pursued through genomic and transcriptomic technologies, leading to the identification of multiple mutations in a large variety of cancers. However, it has proven challenging to distinguish driver and passenger mutations and to deal with tumor heterogeneity and resistant clonal populations. More generally, these heterogeneous mutation patterns do not in themselves predict the tumor phenotype. Analysis of the expressed proteins in a tumor and their modification states reveals if and how these mutations are translated to the functional level. It is already known that proteomic changes including posttranslational modifications are crucial drivers of oncogenesis, but proteomics technology has only recently become comparable in depth and accuracy to RNAseq. These advances also allow the rapid and highly sensitive analysis of formalin-fixed and paraffin-embedded biobank tissues, on both the proteome and phosphoproteome levels. In this perspective, pioneering mass spectrometry-based proteomic studies are highlighted that pave the way toward clinical implementation. It is argued that proteomics and phosphoproteomics could provide the missing link to make omics analysis actionable in the clinic.
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Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Florian Gnad
- Department of Bioinformatics and Computational BiologyCell Signaling Technology Inc01923DanversMAUSA
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- NNF Center for Protein ResearchFaculty of Health SciencesUniversity of CopenhagenCopenhagenDenmark
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