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Podar NA, Carrell AA, Cassidy KA, Klingeman DM, Yang Z, Stahler EA, Smith DW, Stahler DR, Podar M. From wolves to humans: oral microbiome resistance to transfer across mammalian hosts. mBio 2024; 15:e0334223. [PMID: 38299854 PMCID: PMC10936156 DOI: 10.1128/mbio.03342-23] [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: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024] Open
Abstract
The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.
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Affiliation(s)
- Nicholas A. Podar
- School of Engineering, Vanderbilt University, Nashville, Tennessee, USA
| | - Alyssa A. Carrell
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kira A. Cassidy
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Dawn M. Klingeman
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Zamin Yang
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Erin A. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Douglas W. Smith
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Daniel R. Stahler
- Yellowstone Center for Resources, National Park Service, Yellowstone National Park, Wyoming, USA
| | - Mircea Podar
- Biosciences Department, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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2
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Pascual-Garrido A, Carvalho S, Almeida-Warren K. Primate archaeology 3.0. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2024; 183:e24835. [PMID: 37671610 DOI: 10.1002/ajpa.24835] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 09/07/2023]
Abstract
The new field of primate archaeology investigates the technological behavior and material record of nonhuman primates, providing valuable comparative data on our understanding of human technological evolution. Yet, paralleling hominin archaeology, the field is largely biased toward the analysis of lithic artifacts. While valuable comparative data have been gained through an examination of extant nonhuman primate tool use and its archaeological record, focusing on this one single aspect provides limited insights. It is therefore necessary to explore to what extent other non-technological activities, such as non-tool aided feeding, traveling, social behaviors or ritual displays, leave traces that could be detected in the archaeological record. Here we propose four new areas of investigation which we believe have been largely overlooked by primate archaeology and that are crucial to uncovering the full archaeological potential of the primate behavioral repertoire, including that of our own: (1) Plant technology; (2) Archaeology beyond technology; (3) Landscape archaeology; and (4) Primate cultural heritage. We discuss each theme in the context of the latest developments and challenges, as well as propose future directions. Developing a more "inclusive" primate archaeology will not only benefit the study of primate evolution in its own right but will aid conservation efforts by increasing our understanding of changes in primate-environment interactions over time.
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Affiliation(s)
- Alejandra Pascual-Garrido
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, University of Oxford, Oxford, UK
| | - Susana Carvalho
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, University of Oxford, Oxford, UK
- Interdisciplinary Centre for Archaeology and the Evolution of Human Behaviour, University of Algarve, Faro, Portugal
- Gorongosa National Park, Sofala, Mozambique
| | - Katarina Almeida-Warren
- Primate Models for Behavioural Evolution Lab, Institute of Human Sciences, University of Oxford, Oxford, UK
- Interdisciplinary Centre for Archaeology and the Evolution of Human Behaviour, University of Algarve, Faro, Portugal
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3
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Albrecht A, Behringer V, Zierau O, Hannig C. Dental findings in wild great apes from macerated skull analysis. Am J Primatol 2024; 86:e23581. [PMID: 38041590 DOI: 10.1002/ajp.23581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 12/03/2023]
Abstract
Oral health is a crucial aspect of overall well-being in both humans and nonhuman primates. Understanding the oral pathologies and dental conditions in apes can provide valuable insights into their evolutionary history, dietary habits, and overall health. The present study evaluates dental findings in wild great apes from museum specimens to gain insights into the influence of natural nutrition on dental health. Complete macerated skulls of wild, adult great apes from the collection of the Museum of Natural History, Berlin, Germany, were examined. We analyzed skulls of 53 gorillas (Gorilla gorilla), 63 chimpanzees (Pan troglodytes), and 41 orangutans (Pongo spp.). For each skull, we recorded wear of dental hard tissues (Lussi and Ganss index), carious lesions, and periodontal bone loss. Incisal and occlusal dental hard tissue defects were found in all skulls, as well as considerable external staining. In all species, incisors and canines showed the greatest loss of tissue, followed by molars. The wear of molars decreased from the first to the third molars, premolars showed the least pronounced defects. Some individuals had apical osteolytic defects along with severe dental hard tissue loss with pulp involvement or after dental trauma, respectively (n = 5). Our study did not observe any carious lesions among the examined great ape skulls. However, we did find evidence for localized or generalized periodontal bone loss in a subset of the specimens (n = 3 chimpanzees, n = 7 orangutans). The natural diet and foraging behavior of great apes induces abrasion and attrition of dental hard tissue but does not yield carious lesions. The occurrence of periodontitis in individual apes indicates that the natural circumstances can induce periodontal bone loss even in the wild, despite physiological nutrition.
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Affiliation(s)
- Anja Albrecht
- Policlinic of Operative Dentistry, Periodontology, and Pediatric Dentistry Dresden, Faculty of Medicine 'Carl Gustav Carus', Technische Universität Dresden, Dresden, Germany
| | - Verena Behringer
- Endocrinology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Oliver Zierau
- Environmental Monitoring & Endocrinology, Faculty of Biology, Technische Universität Dresden, Dresden, Germany
| | - Christian Hannig
- Policlinic of Operative Dentistry, Periodontology, and Pediatric Dentistry Dresden, Faculty of Medicine 'Carl Gustav Carus', Technische Universität Dresden, Dresden, Germany
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Honap TP, Monroe CR, Johnson SJ, Jacobson DK, Abin CA, Austin RM, Sandberg P, Levine M, Sankaranarayanan K, Lewis CM. Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:542-556. [PMID: 37002784 DOI: 10.1002/ajpa.24735] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
OBJECTIVES Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. MATERIALS AND METHODS Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. RESULTS Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains. DISCUSSION We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.
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Affiliation(s)
- Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cara R Monroe
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Center for the Ethics of Indigenous Genomics Research (CEIGR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Sarah J Johnson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Christopher A Abin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Rita M Austin
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Paul Sandberg
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Marc Levine
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
- Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072, Norman, Oklahoma, USA
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, 73019, Norman, Oklahoma, USA
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072, Norman, Oklahoma, USA
- Department of Anthropology, University of Oklahoma, 73019, Norman, Oklahoma, USA
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Ozga AT, Ottoni C. Dental calculus as a proxy for animal microbiomes. QUATERNARY INTERNATIONAL : THE JOURNAL OF THE INTERNATIONAL UNION FOR QUATERNARY RESEARCH 2023; 653-654:47-52. [PMID: 37559969 PMCID: PMC7614904 DOI: 10.1016/j.quaint.2021.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/11/2023]
Abstract
The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.
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Affiliation(s)
- Andrew T. Ozga
- Nova Southeastern University, Halmos College of Arts and Sciences, Fort Lauderdale, FL, 33314, USA
| | - Claudio Ottoni
- DANTE - Diet and ANcient TEchnology Laboratory, Department of Oral and Maxillo-Facial Sciences, “Sapienza” University of Rome, 00161, Rome, Italy
- Centre of Molecular Anthropology for Ancient DNA Studies; Department of Biology, University of Rome “Tor Vergata”, Rome, Italy
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Gao Y, Kang K, Luo B, Sun X, Lan F, He J, Wu Y. Graphene oxide and mineralized collagen-functionalized dental implant abutment with effective soft tissue seal and romotely repeatable photodisinfection. Regen Biomater 2022; 9:rbac024. [PMID: 35529047 PMCID: PMC9071057 DOI: 10.1093/rb/rbac024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/21/2022] [Accepted: 04/10/2022] [Indexed: 11/13/2022] Open
Abstract
Grasping the boundary of antibacterial function may be better for the sealing of soft tissue around dental implant abutment. Inspired by ‘overdone is worse than undone’, we prepared a sandwich-structured dental implant coating on the percutaneous part using graphene oxide (GO) wrapped under mineralized collagen. Our unique coating structure ensured the high photothermal conversion capability and good photothermal stability of GO. The prepared coating not only achieved suitable inhibition on colonizing bacteria growth of Streptococcus sanguinis, Fusobacterium nucleatum and Porphyromonas gingivalis but also disrupted the wall/membrane permeability of free bacteria. Further enhancements on the antibacterial property were generally observed through the additional incorporation of dimethylaminododecyl methacrylate. Additionally, the coating with sandwich structure significantly enhanced the adhesion, cytoskeleton organization and proliferation of human gingival fibroblasts, which was effective to improve soft tissue sealing. Furthermore, cell viability was preserved when cells and bacteria were cultivated in the same environment by a coculture assay. This was attributed to the sandwich structure and mineralized collagen as the outmost layer, which would protect tissue cells from photothermal therapy and GO, as well as accelerate the recovery of cell activity. Overall, the coating design would provide a useful alternative method for dental implant abutment surface modification and functionalization.
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Affiliation(s)
- Yichun Gao
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Ke Kang
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Xiaoqing Sun
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Jing He
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu, 610064, P. R. China
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7
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Ottoni C, Borić D, Cheronet O, Sparacello V, Dori I, Coppa A, Antonović D, Vujević D, Price TD, Pinhasi R, Cristiani E. Tracking the transition to agriculture in Southern Europe through ancient DNA analysis of dental calculus. Proc Natl Acad Sci U S A 2021; 118:e2102116118. [PMID: 34312252 PMCID: PMC8364157 DOI: 10.1073/pnas.2102116118] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Archaeological dental calculus, or mineralized plaque, is a key tool to track the evolution of oral microbiota across time in response to processes that impacted our culture and biology, such as the rise of farming during the Neolithic. However, the extent to which the human oral flora changed from prehistory until present has remained elusive due to the scarcity of data on the microbiomes of prehistoric humans. Here, we present our reconstruction of oral microbiomes via shotgun metagenomics of dental calculus in 44 ancient foragers and farmers from two regions playing a pivotal role in the spread of farming across Europe-the Balkans and the Italian Peninsula. We show that the introduction of farming in Southern Europe did not alter significantly the oral microbiomes of local forager groups, and it was in particular associated with a higher abundance of the species Olsenella sp. oral taxon 807. The human oral environment in prehistory was dominated by a microbial species, Anaerolineaceae bacterium oral taxon 439, that diversified geographically. A Near Eastern lineage of this bacterial commensal dispersed with Neolithic farmers and replaced the variant present in the local foragers. Our findings also illustrate that major taxonomic shifts in human oral microbiome composition occurred after the Neolithic and that the functional profile of modern humans evolved in recent times to develop peculiar mechanisms of antibiotic resistance that were previously absent.
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Affiliation(s)
- Claudio Ottoni
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Vitale Sparacello
- Department of Environmental and Life Sciences, University of Cagliari, 09042 Monserrato, Italy
| | - Irene Dori
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le province di Verona, Rovigo e Vicenza, 37121 Verona, Italy
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University of Rome, 00185 Rome, Italy
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
- Department of Genetics, Harvard Medical School, Harvard University, Cambridge, MA 02138
| | | | - Dario Vujević
- Department of Archaeology, University of Zadar, 23000 Zadar, Croatia
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Emanuela Cristiani
- DANTE - Diet and Ancient Technology Laboratory, Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy;
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8
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Sawaswong V, Praianantathavorn K, Chanchaem P, Khamwut A, Kemthong T, Hamada Y, Malaivijitnond S, Payungporn S. Comparative analysis of oral-gut microbiota between captive and wild long-tailed macaque in Thailand. Sci Rep 2021; 11:14280. [PMID: 34253790 PMCID: PMC8275770 DOI: 10.1038/s41598-021-93779-4] [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: 03/16/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Long-tailed macaques (Macaca fascicularis), distributed in Southeast Asia, are generally used in biomedical research. At present, the expansion of human communities overlapping of macaques’ natural habitat causes human-macaque conflicts. To mitigate this problem in Thailand, the National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU), was granted the permit to catch the surplus wild-born macaques and transfer them to the center. Based on the fact that the diets provided and the captive environments were different, their oral-gut microbiota should be altered. Thus, we investigated and compared the oral and fecal microbiome between wild-born macaques that lived in the natural habitats and those transferred to and reared in the NPRCT-CU for 1 year. The results from 16S rRNA high-throughput sequencing showed that the captive macaques had distinct oral-gut microbiota profiles and lower bacterial richness compared to those in wild macaques. The gut of wild macaques was dominated by Firmicutes which is probably associated with lipid absorption and storage. These results implicated the effects of captivity conditions on the microbiome that might contribute to crucial metabolic functions. Our study should be applied to the animal health care program, with respect to microbial functions, for non-human primates.
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Affiliation(s)
- Vorthon Sawaswong
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand.,Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | | | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Ariya Khamwut
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Taratorn Kemthong
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand
| | - Yuzuru Hamada
- Evolutionary Morphology Section, Primate Research Institute, Kyoto University, Aichi, Japan
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi, 18110, Thailand. .,Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Chulalongkorn University, Bangkok, 10330, Thailand. .,Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
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9
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Weyrich LS. The evolutionary history of the human oral microbiota and its implications for modern health. Periodontol 2000 2020; 85:90-100. [PMID: 33226710 DOI: 10.1111/prd.12353] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Numerous biological and cultural factors influence the microbial communities (microbiota) that inhabit the human mouth, including diet, environment, hygiene, physiology, health status, genetics, and lifestyle. As oral microbiota can underpin oral and systemic diseases, tracing the evolutionary history of oral microbiota and the factors that shape its origins will unlock information to mitigate disease today. Despite this, the origins of many oral microbes remain unknown, and the key factors in the past that shaped our oral microbiota are only now emerging. High throughput DNA sequencing of oral microbiota using ancient DNA and comparative anthropological methodologies has been employed to investigate oral microbiota origins, revealing a complex, rich history. Here, I review the current literature on the factors that shaped and guided oral microbiota evolution, both in Europe and globally. In Europe, oral microbiota evolution was shaped by interactions with Neandertals, the adaptation of farming, widespread integration of industrialization, and postindustrial lifestyles that emerged after World War II. Globally, evidence for a multitude of different oral microbiota histories is emerging, likely supporting dissimilarities in modern oral health across discrete human populations. I highlight how these evolutionary changes are linked to the development of modern oral diseases and discuss the remaining factors that need to be addressed to improve this embryonic field of research. I argue that understanding the evolutionary history of our oral microbiota is necessary to identify new treatment and prevention options to improve oral and systemic health in the future.
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Affiliation(s)
- Laura S Weyrich
- Department of Anthropology and the Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, USA.,School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
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10
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Brealey JC, Leitão HG, van der Valk T, Xu W, Bougiouri K, Dalén L, Guschanski K. Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome. Mol Biol Evol 2020; 37:3003-3022. [PMID: 32467975 PMCID: PMC7530607 DOI: 10.1093/molbev/msaa135] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Dental calculus, the calcified form of the mammalian oral microbial plaque biofilm, is a rich source of oral microbiome, host, and dietary biomolecules and is well preserved in museum and archaeological specimens. Despite its wide presence in mammals, to date, dental calculus has primarily been used to study primate microbiome evolution. We establish dental calculus as a valuable tool for the study of nonhuman host microbiome evolution, by using shotgun metagenomics to characterize the taxonomic and functional composition of the oral microbiome in species as diverse as gorillas, bears, and reindeer. We detect oral pathogens in individuals with evidence of oral disease, assemble near-complete bacterial genomes from historical specimens, characterize antibiotic resistance genes, reconstruct components of the host diet, and recover host genetic profiles. Our work demonstrates that metagenomic analyses of dental calculus can be performed on a diverse range of mammalian species, which will allow the study of oral microbiome and pathogen evolution from a comparative perspective. As dental calculus is readily preserved through time, it can also facilitate the quantification of the impact of anthropogenic changes on wildlife and the environment.
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Affiliation(s)
- Jaelle C Brealey
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Henrique G Leitão
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Tom van der Valk
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Wenbo Xu
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Katia Bougiouri
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Katerina Guschanski
- Department of Ecology and Genetics, Animal Ecology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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11
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Ottoni C, Guellil M, Ozga AT, Stone AC, Kersten O, Bramanti B, Porcier S, Van Neer W. Metagenomic analysis of dental calculus in ancient Egyptian baboons. Sci Rep 2019; 9:19637. [PMID: 31873124 PMCID: PMC6927955 DOI: 10.1038/s41598-019-56074-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/06/2019] [Indexed: 02/07/2023] Open
Abstract
Dental calculus, or mineralized plaque, represents a record of ancient biomolecules and food residues. Recently, ancient metagenomics made it possible to unlock the wealth of microbial and dietary information of dental calculus to reconstruct oral microbiomes and lifestyle of humans from the past. Although most studies have so far focused on ancient humans, dental calculus is known to form in a wide range of animals, potentially informing on how human-animal interactions changed the animals' oral ecology. Here, we characterise the oral microbiome of six ancient Egyptian baboons held in captivity during the late Pharaonic era (9th-6th centuries BC) and of two historical baboons from a zoo via shotgun metagenomics. We demonstrate that these captive baboons possessed a distinctive oral microbiome when compared to ancient and modern humans, Neanderthals and a wild chimpanzee. These results may reflect the omnivorous dietary behaviour of baboons, even though health, food provisioning and other factors associated with human management, may have changed the baboons' oral microbiome. We anticipate our study to be a starting point for more extensive studies on ancient animal oral microbiomes to examine the extent to which domestication and human management in the past affected the diet, health and lifestyle of target animals.
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Affiliation(s)
- Claudio Ottoni
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway.
- Department of Oral and Maxillofacial Sciences, Diet and Ancient Technology Laboratory (DANTE), Sapienza University, Rome, Italy.
| | - Meriam Guellil
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
- University of Tartu, Institute of Genomics, Estonian Biocentre, 51010, Tartu, Estonia
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
- Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
| | - Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, N-0316, Oslo, Norway
- Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy, and Prevention, University of Ferrara, 35-441221, Ferrara, Italy
| | - Stéphanie Porcier
- Laboratoire CNRS ASM ≪ Archéologie des Sociétés Méditerranéennes (UMR 5140), Université Paul-Valéry, LabEx Archimede, F-34199, Montpellier, France
| | - Wim Van Neer
- Royal Belgian Institute of Natural Sciences, B-1000, Brussels, Belgium.
- KU Leuven-University of Leuven, Department of Biology, Laboratory of Biodiversity and Evolutionary Genomics, Center of Archaeological Sciences, B-3000, Leuven, Belgium.
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