1
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Trumble BC, Schwartz M, Ozga AT, Schwartz GT, Stojanowski CM, Jenkins CL, Kraft TS, Garcia AR, Cummings DK, Hooper PL, Eid Rodriguez D, Buetow K, Beheim B, Irimia A, Thomas GS, Thompson RC, Gatz M, Stieglitz J, Finch CE, Gurven M, Kaplan H. Poor Oral Health Is Associated With Inflammation, Aortic Valve Calcification, and Brain Volume Among Forager-Farmers. J Gerontol A Biol Sci Med Sci 2024; 79:glae013. [PMID: 38291985 PMCID: PMC11044433 DOI: 10.1093/gerona/glae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Indexed: 02/01/2024] Open
Abstract
Poor oral health is associated with cardiovascular disease and dementia. Potential pathways include sepsis from oral bacteria, systemic inflammation, and nutritional deficiencies. However, in post-industrialized populations, links between oral health and chronic disease may be confounded because the lower socioeconomic exposome (poor diet, pollution, and low physical activity) often entails insufficient dental care. We assessed tooth loss, caries, and damaged teeth, in relation to cardiovascular and brain aging among the Tsimane, a subsistence population living a relatively traditional forager-horticulturalist lifestyle with poor dental health, but minimal cardiovascular disease and dementia. Dental health was assessed by a physician in 739 participants aged 40-92 years with cardiac and brain health measured by chest computed tomography (CT; n = 728) and brain CT (n = 605). A subset of 356 individuals aged 60+ were also assessed for dementia and mild cognitive impairment (n = 33 impaired). Tooth loss was highly prevalent, with 2.2 teeth lost per decade and a 2-fold greater loss in women. The number of teeth with exposed pulp was associated with higher inflammation, as measured by cytokine levels and white blood cell counts, and lower body mass index. Coronary artery calcium and thoracic aortic calcium were not associated with tooth loss or damaged teeth. However, aortic valve calcification and brain tissue loss were higher in those who had more teeth with exposed pulp. Overall, these results suggest that dental health is associated with indicators of chronic diseases in the absence of typical confounds, even in a population with low cardiovascular and dementia risk factors.
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Affiliation(s)
- Benjamin C Trumble
- School of Human Evolution and Social Change, Center for Evolution and Medicine, Institute of Human Origins, Arizona State University, Tempe, Arizona, USA
| | - Matthew Schwartz
- School of Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Andrew T Ozga
- Department of Biological Sciences, Halmos College of Arts and Sciences, Fort Lauderdale, Florida, USA
| | - Gary T Schwartz
- School of Human Evolution and Social Change, Center for Evolution and Medicine, Institute of Human Origins, Arizona State University, Tempe, Arizona, USA
| | - Christopher M Stojanowski
- School of Human Evolution and Social Change, Center for Evolution and Medicine, Institute of Human Origins, Arizona State University, Tempe, Arizona, USA
| | - Carrie L Jenkins
- School of Human Evolution and Social Change, Center for Evolution and Medicine, Institute of Human Origins, Arizona State University, Tempe, Arizona, USA
| | - Thomas S Kraft
- Department of Anthropology, University of Utah, Salt Lake City, Utah, USA
| | - Angela R Garcia
- School of Human Evolution and Social Change, Center for Evolution and Medicine, Institute of Human Origins, Arizona State University, Tempe, Arizona, USA
| | - Daniel K Cummings
- Economic Science Institute, Chapman University, Orange, California, USA
| | - Paul L Hooper
- Economic Science Institute, Chapman University, Orange, California, USA
| | | | - Kenneth Buetow
- School of Human Evolution and Social Change, Center for Evolution and Medicine, Institute of Human Origins, Arizona State University, Tempe, Arizona, USA
| | - Bret Beheim
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Andrei Irimia
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Gregory S Thomas
- Heart & Vascular Institute, MemorialCare Health System, Fountain Valley, CA and University of California Irvine, Orange, California, USA
| | - Randall C Thompson
- Department of Cardiology, Saint Luke’s Mid America Heart Institute, Kansas City, Missouri, USA
| | - Margaret Gatz
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Jonathan Stieglitz
- Insititue for Advanced Study, Toulouse School of Economics, Toulouse, France
| | - Caleb E Finch
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, California, USA
| | - Michael Gurven
- Integrative Anthropological Sciences, University of California Santa Barbara, Santa Barbara, California, USA
| | - Hillard Kaplan
- Economic Science Institute, Chapman University, Orange, California, USA
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2
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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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3
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Fagernäs Z, Salazar-García DC, Haber Uriarte M, Avilés Fernández A, Henry AG, Lomba Maurandi J, Ozga AT, Velsko IM, Warinner C. Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation. FEMS Microbes 2022; 3:xtac006. [PMID: 37332506 PMCID: PMC10117714 DOI: 10.1093/femsmc/xtac006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 10/22/2023] Open
Abstract
The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.
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Affiliation(s)
- Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, 46010, Spain
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, 01006, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, 7701, South Africa
| | - María Haber Uriarte
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Azucena Avilés Fernández
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Amanda G Henry
- Faculty of Archaeology, Leiden University, Leiden, 2332 CC, The Netherlands
| | - Joaquín Lomba Maurandi
- Departamento de Prehistoria, Arqueología, Historia Antigua, Historia Medieval y Ciencias y Técnicas Historiográficas, Universidad de Murcia, Murcia, 30001, Spain
| | - Andrew T Ozga
- Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Irina M Velsko
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- Department of Anthropology, Harvard University, Cambridge, MA, 02138, USA
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4
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Jacobson DK, Honap TP, Ozga AT, Meda N, Kagoné TS, Carabin H, Spicer P, Tito RY, Obregon-Tito AJ, Reyes LM, Troncoso-Corzo L, Guija-Poma E, Sankaranarayanan K, Lewis CM. Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle. Sci Rep 2021; 11:1724. [PMID: 33462272 PMCID: PMC7813856 DOI: 10.1038/s41598-021-81257-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2-5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.
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Affiliation(s)
- David K Jacobson
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, 73019, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA
| | - Tanvi P Honap
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, 73019, USA.,Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA
| | - Andrew T Ozga
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | | | | | - Hélène Carabin
- Department of Biostatistics and Epidemiology, College of Public Health, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Département de Pathologie et Microbiologie, Faculté de médecine vétérinaire, Université de Montréal, Saint-Hyacinthe, QC, J2S 2M2, Canada.,Département de médecine sociale et préventive, École de santé publique de l'université de Montréal, Montréal, QC, H3N 1X9, Canada.,Centre de Recherche en Santé Publique (CReSP) de l'université de Montréal et du CIUSS du Centre Sud de Montréal, Montréal, QC, H3N 1X9, Canada
| | - Paul Spicer
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.,Center for Applied Social Research, University of Oklahoma, Norman, OK, 73019, USA
| | - Raul Y Tito
- Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA
| | | | - Luis Marin Reyes
- Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Perú
| | | | - Emilio Guija-Poma
- Centro de Investigación de Bioquímica y Nutrición, Facultad de Medicina Humana, Universidad de San Martín de Porres, Lima, Perú
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, 73019, USA.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 David L. Boren Blvd, Norman, OK, 73019, USA. .,Department of Anthropology, University of Oklahoma, Norman, OK, 73019, USA.
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5
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Perri AR, Mitchell KJ, Mouton A, Álvarez-Carretero S, Hulme-Beaman A, Haile J, Jamieson A, Meachen J, Lin AT, Schubert BW, Ameen C, Antipina EE, Bover P, Brace S, Carmagnini A, Carøe C, Samaniego Castruita JA, Chatters JC, Dobney K, Dos Reis M, Evin A, Gaubert P, Gopalakrishnan S, Gower G, Heiniger H, Helgen KM, Kapp J, Kosintsev PA, Linderholm A, Ozga AT, Presslee S, Salis AT, Saremi NF, Shew C, Skerry K, Taranenko DE, Thompson M, Sablin MV, Kuzmin YV, Collins MJ, Sinding MHS, Gilbert MTP, Stone AC, Shapiro B, Van Valkenburgh B, Wayne RK, Larson G, Cooper A, Frantz LAF. Dire wolves were the last of an ancient New World canid lineage. Nature 2021; 591:87-91. [PMID: 33442059 DOI: 10.1038/s41586-020-03082-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 11/09/2022]
Abstract
Dire wolves are considered to be one of the most common and widespread large carnivores in Pleistocene America1, yet relatively little is known about their evolution or extinction. Here, to reconstruct the evolutionary history of dire wolves, we sequenced five genomes from sub-fossil remains dating from 13,000 to more than 50,000 years ago. Our results indicate that although they were similar morphologically to the extant grey wolf, dire wolves were a highly divergent lineage that split from living canids around 5.7 million years ago. In contrast to numerous examples of hybridization across Canidae2,3, there is no evidence for gene flow between dire wolves and either North American grey wolves or coyotes. This suggests that dire wolves evolved in isolation from the Pleistocene ancestors of these species. Our results also support an early New World origin of dire wolves, while the ancestors of grey wolves, coyotes and dholes evolved in Eurasia and colonized North America only relatively recently.
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Affiliation(s)
- Angela R Perri
- Department of Archaeology, Durham University, Durham, UK.
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia.
| | - Alice Mouton
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | | | - Ardern Hulme-Beaman
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
| | - James Haile
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alexandra Jamieson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Julie Meachen
- Department of Anatomy, Des Moines University, Des Moines, IA, USA
| | - Audrey T Lin
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Zoology, University of Oxford, Oxford, UK.,Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Blaine W Schubert
- Center of Excellence in Paleontology & Department of Geosciences, East Tennessee State University, Johnson City, TN, USA
| | - Carly Ameen
- Department of Archaeology, University of Exeter, Exeter, UK
| | | | - Pere Bover
- ARAID Foundation, Instituto Universitario de Investigación en Ciencias Ambientales (IUCA) - Aragosaurus Group, Universidad de Zaragoza, Zaragoza, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Christian Carøe
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Keith Dobney
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool, UK.,Department of Archaeology, University of Sydney, Sydney, New South Wales, Australia.,Department of Archaeology, University of Aberdeen, Aberdeen, UK.,Department of Archaeology, Simon Fraser University, Burnaby, Canada
| | - Mario Dos Reis
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Allowen Evin
- Institut des Sciences de l'Evolution - Montpellier, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France
| | - Philippe Gaubert
- Laboratoire Evolution & Diversité Biologique, UPS/CNRS/IRD, Université Paul Sabatier, Toulouse, France
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Graham Gower
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Holly Heiniger
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Josh Kapp
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Pavel A Kosintsev
- Institute of Plant and Animal Ecology, Urals Branch of the Russian Academy of Sciences, Yekaterinburg, Russia.,Ural Federal University, Yekaterinburg, Russia
| | - Anna Linderholm
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK.,Department of Anthropology, Texas A&M University, College Station, TX, USA
| | - Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | - Alexander T Salis
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Nedda F Saremi
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Colin Shew
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Katherine Skerry
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Dmitry E Taranenko
- Institute of Systematics and Ecology of Animals, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Mary Thompson
- Idaho Museum of Natural History, Idaho State University, Pocatello, ID, USA
| | - Mikhail V Sablin
- Zoological Institute of the Russian Academy of Sciences, St Petersburg, Russia
| | - Yaroslav V Kuzmin
- Sobolev Institute of Geology and Mineralogy, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Tomsk State University, Tomsk, Russia
| | - Matthew J Collins
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Mikkel-Holger S Sinding
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Greenland Institute of Natural Resources, Nuuk, Greenland
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,NTNU University Museum, Trondheim, Norway
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA.,Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Blaire Van Valkenburgh
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Greger Larson
- The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, The University of Oxford, Oxford, UK
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK. .,Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany.
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6
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Ozga AT, Webster TH, Gilby IC, Wilson MA, Nockerts RS, Wilson ML, Pusey AE, Li Y, Hahn BH, Stone AC. Urine as a high-quality source of host genomic DNA from wild populations. Mol Ecol Resour 2021; 21:170-182. [PMID: 32985084 PMCID: PMC7746602 DOI: 10.1111/1755-0998.13260] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 12/28/2022]
Abstract
The ability to generate genomic data from wild animal populations has the potential to give unprecedented insight into the population history and dynamics of species in their natural habitats. However, for many species, it is impossible legally, ethically or logistically to obtain tissue samples of quality sufficient for genomic analyses. In this study we evaluate the success of multiple sources of genetic material (faeces, urine, dentin and dental calculus) and several capture methods (shotgun, whole-genome, exome) in generating genome-scale data in wild eastern chimpanzees (Pan troglodytes schweinfurthii) from Gombe National Park, Tanzania. We found that urine harbours significantly more host DNA than other sources, leading to broader and deeper coverage across the genome. Urine also exhibited a lower rate of allelic dropout. We found exome sequencing to be far more successful than both shotgun sequencing and whole-genome capture at generating usable data from low-quality samples such as faeces and dental calculus. These results highlight urine as a promising and untapped source of DNA that can be noninvasively collected from wild populations of many species.
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Affiliation(s)
- Andrew T. Ozga
- Department of Biological Sciences, Halmos College of Arts and Sciences, Nova Southeastern University
- Center for Evolution and Medicine, Arizona State University
| | - Timothy H. Webster
- Department of Anthropology, University of Utah
- School of Life Sciences, Arizona State University
| | - Ian C. Gilby
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
| | - Melissa A. Wilson
- Center for Evolution and Medicine, Arizona State University
- School of Life Sciences, Arizona State University
| | | | - Michael L. Wilson
- Department of Anthropology, University of Minnesota
- Department of Ecology, Evolution and Behavior, University of Minnesota
| | | | - Yingying Li
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Beatrice H. Hahn
- Departments of Medicine and Microbiology, Perelman School of Medicine, University of Pennsylvania
| | - Anne C. Stone
- Center for Evolution and Medicine, Arizona State University
- School of Human Evolution and Social Change, Arizona State University
- Institute of Human Origins, Arizona State University
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7
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Honap TP, Sankaranarayanan K, Schnorr SL, Ozga AT, Warinner C, Lewis CM. Biogeographic study of human gut-associated crAssphage suggests impacts from industrialization and recent expansion. PLoS One 2020; 15:e0226930. [PMID: 31940321 PMCID: PMC6961876 DOI: 10.1371/journal.pone.0226930] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 12/06/2019] [Indexed: 12/13/2022] Open
Abstract
CrAssphage (cross-assembly phage) is a bacteriophage that was first discovered in human gut metagenomic data. CrAssphage belongs to a diverse family of crAss-like bacteriophages thought to infect gut commensal bacteria belonging to Bacteroides species. However, not much is known about the biogeography of crAssphage and whether certain strains are associated with specific human populations. In this study, we screened publicly available human gut metagenomic data from 3,341 samples for the presence of crAssphage sensu stricto (NC_024711.1). We found that crAssphage prevalence is low in traditional, hunter-gatherer populations, such as the Hadza from Tanzania and Matses from Peru, as compared to industrialized, urban populations. Statistical comparisons showed no association of crAssphage prevalence with variables such as age, sex, body mass index, and health status of individuals. Phylogenetic analyses show that crAssphage strains reconstructed from the same individual over multiple time-points, cluster together. CrAssphage strains from individuals from the same study population do not always cluster together. Some evidence of clustering is seen at the level of broadly defined geographic regions, however, the relative positions of these clusters within the crAssphage phylogeny are not well-supported. We hypothesize that this lack of strong biogeographic structuring is suggestive of an expansion event within crAssphage. Using a Bayesian dating approach, we estimate that this expansion has occurred fairly recently. Overall, we determine that crAssphage presence is associated with an industrialized lifestyle and the absence of strong biogeographic structuring within global crAssphage strains is likely due to a recent population expansion within this bacteriophage.
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Affiliation(s)
- Tanvi P. Honap
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Stephanie L. Schnorr
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Andrew T. Ozga
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Christina Warinner
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Cecil M. Lewis
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, Oklahoma, United States of America
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
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8
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Ozga AT, Gilby I, Nockerts RS, Wilson ML, Pusey A, Stone AC. Oral microbiome diversity in chimpanzees from Gombe National Park. Sci Rep 2019; 9:17354. [PMID: 31758037 PMCID: PMC6874655 DOI: 10.1038/s41598-019-53802-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 10/28/2019] [Indexed: 12/27/2022] Open
Abstract
Historic calcified dental plaque (dental calculus) can provide a unique perspective into the health status of past human populations but currently no studies have focused on the oral microbial ecosystem of other primates, including our closest relatives, within the hominids. Here we use ancient DNA extraction methods, shotgun library preparation, and next generation Illumina sequencing to examine oral microbiota from 19 dental calculus samples recovered from wild chimpanzees (Pan troglodytes schweinfurthii) who died in Gombe National Park, Tanzania. The resulting sequences were trimmed for quality, analyzed using MALT, MEGAN, and alignment scripts, and integrated with previously published dental calculus microbiome data. We report significant differences in oral microbiome phyla between chimpanzees and anatomically modern humans (AMH), with chimpanzees possessing a greater abundance of Bacteroidetes and Fusobacteria, and AMH showing higher Firmicutes and Proteobacteria. Our results suggest that by using an enterotype clustering method, results cluster largely based on host species. These clusters are driven by Porphyromonas and Fusobacterium genera in chimpanzees and Haemophilus and Streptococcus in AMH. Additionally, we compare a nearly complete Porphyromonas gingivalis genome to previously published genomes recovered from human gingiva to gain perspective on evolutionary relationships across host species. Finally, using shotgun sequence data we assessed indicators of diet from DNA in calculus and suggest exercising caution when making assertions related to host lifestyle. These results showcase core differences between host species and stress the importance of continued sequencing of nonhuman primate microbiomes in order to fully understand the complexity of their oral ecologies.
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Affiliation(s)
- Andrew T Ozga
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA. .,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA. .,Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Fort Lauderdale, Florida, USA.
| | - Ian Gilby
- Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Rebecca S Nockerts
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Michael L Wilson
- Department of Anthropology, University of Minnesota, Minneapolis, Minnesota, USA.,Department of Ecology, Evolution, and Behavior, University of Minnesota, Minneapolis, Minnesota, USA
| | - Anne Pusey
- Department of Evolutionary Anthropology, Duke University, Durham, North Carolina, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,Institute of Human Origins, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
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10
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Aronsen GP, Fehren-Schmitz L, Krigbaum J, Kamenov GD, Conlogue GJ, Warinner C, Ozga AT, Sankaranarayanan K, Griego A, DeLuca DW, Eckels HT, Byczkiewicz RK, Grgurich T, Pelletier NA, Brownlee SA, Marichal A, Williamson K, Tonoike Y, Bellantoni NF. "The dead shall be raised": Multidisciplinary analysis of human skeletons reveals complexity in 19th century immigrant socioeconomic history and identity in New Haven, Connecticut. PLoS One 2019; 14:e0219279. [PMID: 31498793 PMCID: PMC6733446 DOI: 10.1371/journal.pone.0219279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/21/2019] [Indexed: 01/04/2023] Open
Abstract
In July 2011, renovations to Yale-New Haven Hospital inadvertently exposed the cemetery of Christ Church, New Haven, Connecticut’s first Catholic cemetery. While this cemetery was active between 1833 and 1851, both the church and its cemetery disappeared from public records, making the discovery serendipitous. Four relatively well-preserved adult skeletons were recovered with few artifacts. All four individuals show indicators of manual labor, health and disease stressors, and dental health issues. Two show indicators of trauma, with the possibility of judicial hanging in one individual. Musculoskeletal markings are consistent with physical stress, and two individuals have arthritic indicators of repetitive movement/specialized activities. Radiographic analyses show osteopenia, healed trauma, and other pathologies in several individuals. Dental calculus analysis did not identify any tuberculosis indicators, despite osteological markers. Isotopic analyses of teeth indicate that all four were likely recent immigrants to the Northeastern United States. Nuclear and mitochondrial DNA were recovered from three individuals, and these analyses identified ancestry, hair/eye color, and relatedness. Genetic and isotopic results upended our initial ancestry assessment based on burial context alone. These individuals provide biocultural evidence of New Haven’s Industrial Revolution and the plasticity of ethnic and religious identity in the immigrant experience. Their recovery and the multifaceted analyses described here illuminate a previously undescribed part of the city’s rich history. The collective expertise of biological, geochemical, archaeological, and historical researchers interprets socioeconomic and cultural identity better than any one could alone. Our combined efforts changed our initial assumptions of a poor urban Catholic cemetery’s membership, and provide a template for future discoveries and analyses.
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Affiliation(s)
- Gary P. Aronsen
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
| | - Lars Fehren-Schmitz
- Department of Historical Anthropology and Human Ecology, Johann-Friedrich-Blumenbach Institute for Zoology and Anthropology, Georg-August-University Göttingen, Göttingen, Germany
| | - John Krigbaum
- Department of Anthropology, University of Florida, Gainesville, Florida, United States of America
| | - George D. Kamenov
- Department of Geological Sciences, University of Florida, Gainesville, Florida, United States of America
| | - Gerald J. Conlogue
- Department of Diagnostic Imaging, Quinnipiac University, Hamden, Connecticut, United States of America
- Bioanthropology Research Institute, Quinnipiac University, Hamden, Connecticut, United States of America
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Andrew T. Ozga
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Krithivasan Sankaranarayanan
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Anthony Griego
- Independent Scholar, New Haven, Connecticut, United States of America
| | - Daniel W. DeLuca
- Independent Scholar, New Haven, Connecticut, United States of America
| | - Howard T. Eckels
- Independent Scholar, New Haven, Connecticut, United States of America
| | - Romuald K. Byczkiewicz
- Department of History, Central Connecticut State University, New Britain, Connecticut, United States of America
| | - Tania Grgurich
- Department of Diagnostic Imaging, Quinnipiac University, Hamden, Connecticut, United States of America
- Bioanthropology Research Institute, Quinnipiac University, Hamden, Connecticut, United States of America
| | - Natalie A. Pelletier
- Department of Diagnostic Imaging, Quinnipiac University, Hamden, Connecticut, United States of America
| | - Sarah A. Brownlee
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Ana Marichal
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Kylie Williamson
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Yukiko Tonoike
- Department of Anthropology, Yale University, New Haven, Connecticut, United States of America
| | - Nicholas F. Bellantoni
- Connecticut State Museum of Natural History, University of Connecticut, Storrs, Connecticut, United States of America
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11
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Ziesemer KA, Ramos-Madrigal J, Mann AE, Brandt BW, Sankaranarayanan K, Ozga AT, Hoogland M, Hofman CA, Salazar-García DC, Frohlich B, Milner GR, Stone AC, Aldenderfer M, Lewis CM, Hofman CL, Warinner C, Schroeder H. The efficacy of whole human genome capture on ancient dental calculus and dentin. Am J Phys Anthropol 2018; 168:496-509. [PMID: 30586168 PMCID: PMC6519167 DOI: 10.1002/ajpa.23763] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/09/2018] [Accepted: 11/10/2018] [Indexed: 12/28/2022]
Abstract
Objectives Dental calculus is among the richest known sources of ancient DNA in the archaeological record. Although most DNA within calculus is microbial, it has been shown to contain sufficient human DNA for the targeted retrieval of whole mitochondrial genomes. Here, we explore whether calculus is also a viable substrate for whole human genome recovery using targeted enrichment techniques. Materials and methods Total DNA extracted from 24 paired archaeological human dentin and calculus samples was subjected to whole human genome enrichment using in‐solution hybridization capture and high‐throughput sequencing. Results Total DNA from calculus exceeded that of dentin in all cases, and although the proportion of human DNA was generally lower in calculus, the absolute human DNA content of calculus and dentin was not significantly different. Whole genome enrichment resulted in up to four‐fold enrichment of the human endogenous DNA content for both dentin and dental calculus libraries, albeit with some loss in complexity. Recovering more on‐target reads for the same sequencing effort generally improved the quality of downstream analyses, such as sex and ancestry estimation. For nonhuman DNA, comparison of phylum‐level microbial community structure revealed few differences between precapture and postcapture libraries, indicating that off‐target sequences in human genome‐enriched calculus libraries may still be useful for oral microbiome reconstruction. Discussion While ancient human dental calculus does contain endogenous human DNA sequences, their relative proportion is low when compared with other skeletal tissues. Whole genome enrichment can help increase the proportion of recovered human reads, but in this instance enrichment efficiency was relatively low when compared with other forms of capture. We conclude that further optimization is necessary before the method can be routinely applied to archaeological samples.
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Affiliation(s)
| | | | - Allison E Mann
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, Amsterdam, The Netherlands
| | - Krithivasan Sankaranarayanan
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma.,Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma
| | - Andrew T Ozga
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute for Human Origins, Arizona State University, Tempe, Arizona.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Courtney A Hofman
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Domingo C Salazar-García
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Grupo de Investigación en Prehistoria IT-622-13 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain
| | | | - George R Milner
- Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona.,Institute for Human Origins, Arizona State University, Tempe, Arizona.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona
| | - Mark Aldenderfer
- Department of Anthropology and Heritage Studies, University of California, Merced, California
| | - Cecil M Lewis
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma
| | - Corinne L Hofman
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Christina Warinner
- Laboratories of Molecular Anthropology and Microbiome Research and Department of Anthropology, University of Oklahoma, Norman, Oklahoma.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hannes Schroeder
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.,Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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12
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Nieves-Colón MA, Ozga AT, Pestle WJ, Cucina A, Tiesler V, Stanton TW, Stone AC. Comparison of two ancient DNA extraction protocols for skeletal remains from tropical environments. Am J Phys Anthropol 2018; 166:824-836. [PMID: 29603124 DOI: 10.1002/ajpa.23472] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Revised: 12/15/2017] [Accepted: 03/13/2018] [Indexed: 12/22/2022]
Abstract
OBJECTIVES The tropics harbor a large part of the world's biodiversity and have a long history of human habitation. However, paleogenomics research in these climates has been constrained so far by poor ancient DNA yields. Here we compare the performance of two DNA extraction methods on ancient samples of teeth and petrous portions excavated from tropical and semi-tropical sites in Tanzania, Mexico, and Puerto Rico (N = 12). MATERIALS AND METHODS All samples were extracted twice, built into double-stranded sequencing libraries, and shotgun sequenced on the Illumina HiSeq 2500. The first extraction protocol, Method D, was previously designed for recovery of ultrashort DNA fragments from skeletal remains. The second, Method H, modifies the first by adding an initial EDTA wash and an extended digestion and decalcification step. RESULTS No significant difference was found in overall ancient DNA yields or post-mortem damage patterns recovered from samples extracted with either method, irrespective of tissue type. However, Method H samples had higher endogenous content and more mapped reads after quality-filtering, but also higher clonality. In contrast, samples extracted with Method D had shorter average DNA fragments. DISCUSSION Both methods successfully recovered endogenous ancient DNA. But, since surviving DNA in ancient or historic remains from tropical contexts is extremely fragmented, our results suggest that Method D is the optimal choice for working with samples from warm and humid environments. Additional optimization of extraction conditions and further testing of Method H with different types of samples may allow for improvement of this protocol in the future.
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Affiliation(s)
- Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287
| | - Andrew T Ozga
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287.,Institute of Human Origins, Arizona State University, Tempe, Arizona 85287.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287
| | - William J Pestle
- Department of Anthropology, University of Miami, Coral Gables, Florida 33124
| | - Andrea Cucina
- Facultad de Ciencias Antropológicas Universidad Autónoma de Yucatán, Mérida, Yucatán 97305, México
| | - Vera Tiesler
- Facultad de Ciencias Antropológicas Universidad Autónoma de Yucatán, Mérida, Yucatán 97305, México
| | - Travis W Stanton
- Department of Anthropology, University of California Riverside, Riverside, California 92521
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona 85287.,Institute of Human Origins, Arizona State University, Tempe, Arizona 85287.,Center for Evolution and Medicine, Arizona State University, Tempe, Arizona 85287.,Center for Bioarchaeological Research, Arizona State University, Tempe, Arizona 85287
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13
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Ozga AT, Sankaranarayanan K, Tito RY, Obregon-Tito AJ, Foster MW, Tallbull G, Spicer P, Warinner CG, Lewis CM. Oral microbiome diversity among Cheyenne and Arapaho individuals from Oklahoma. Am J Phys Anthropol 2016; 161:321-7. [DOI: 10.1002/ajpa.23033] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/20/2016] [Accepted: 06/05/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Andrew T. Ozga
- Department of Anthropology; University of Oklahoma; Norman Oklahoma 73019
| | | | - Raúl Y. Tito
- Department of Anthropology; University of Oklahoma; Norman Oklahoma 73019
| | | | | | - Gloria Tallbull
- Center for Applied Social Research, University of Oklahoma; Norman Oklahoma 73019
| | - Paul Spicer
- Department of Anthropology; University of Oklahoma; Norman Oklahoma 73019
- Center for Applied Social Research, University of Oklahoma; Norman Oklahoma 73019
| | | | - Cecil M. Lewis
- Department of Anthropology; University of Oklahoma; Norman Oklahoma 73019
- Center for Applied Social Research, University of Oklahoma; Norman Oklahoma 73019
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14
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Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar-García DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C. Erratum: Corrigendum: Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep 2016; 6:27163. [PMID: 27254246 PMCID: PMC4890581 DOI: 10.1038/srep27163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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15
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Ozga AT, Nieves‐Colón MA, Honap TP, Sankaranarayanan K, Hofman CA, Milner GR, Lewis CM, Stone AC, Warinner C. Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus. Am J Phys Anthropol 2016; 160:220-8. [PMID: 26989998 PMCID: PMC4866892 DOI: 10.1002/ajpa.22960] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 01/05/2016] [Accepted: 01/25/2016] [Indexed: 11/06/2022]
Abstract
OBJECTIVES Archaeological dental calculus is a rich source of host-associated biomolecules. Importantly, however, dental calculus is more accurately described as a calcified microbial biofilm than a host tissue. As such, concerns regarding destructive analysis of human remains may not apply as strongly to dental calculus, opening the possibility of obtaining human health and ancestry information from dental calculus in cases where destructive analysis of conventional skeletal remains is not permitted. Here we investigate the preservation of human mitochondrial DNA (mtDNA) in archaeological dental calculus and its potential for full mitochondrial genome (mitogenome) reconstruction in maternal lineage ancestry analysis. MATERIALS AND METHODS Extracted DNA from six individuals at the 700-year-old Norris Farms #36 cemetery in Illinois was enriched for mtDNA using in-solution capture techniques, followed by Illumina high-throughput sequencing. RESULTS Full mitogenomes (7-34×) were successfully reconstructed from dental calculus for all six individuals, including three individuals who had previously tested negative for DNA preservation in bone using conventional PCR techniques. Mitochondrial haplogroup assignments were consistent with previously published findings, and additional comparative analysis of paired dental calculus and dentine from two individuals yielded equivalent haplotype results. All dental calculus samples exhibited damage patterns consistent with ancient DNA, and mitochondrial sequences were estimated to be 92-100% endogenous. DNA polymerase choice was found to impact error rates in downstream sequence analysis, but these effects can be mitigated by greater sequencing depth. DISCUSSION Dental calculus is a viable alternative source of human DNA that can be used to reconstruct full mitogenomes from archaeological remains. Am J Phys Anthropol 160:220-228, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Andrew T. Ozga
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | | | - Tanvi P. Honap
- School of Life SciencesArizona State UniversityTempeAZ85287
| | | | | | - George R. Milner
- Department of AnthropologyPennsylvania State University, University ParkPA16802
| | - Cecil M. Lewis
- Department of AnthropologyUniversity of OklahomaNormanOK73019
| | - Anne C. Stone
- School of Human Evolution and Social ChangeArizona State UniversityTempeAZ85287
- Center for Bioarchaeological Research, Arizona State UniversityTempeAZ85287
- Institute of Human Origins, Arizona State UniversityTempeAZ85287
| | - Christina Warinner
- Department of AnthropologyUniversity of OklahomaNormanOK73019
- Institute of Evolutionary Medicine, University of Zurich8057 ZurichSwitzerland
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16
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Abstract
Determining the origins of those buried within undocumented cemeteries is of incredible importance to historical archaeologists and, in many cases, the nearby communities. In the case of Avondale Burial Place, a cemetery in Bibb County, Georgia, in use from 1820 to 1950, all written documentation of those interred within it has been lost. Osteological and archaeological evidence alone could not describe, with confidence, the ancestral origins of the 101 individuals buried there. In the present study, we used ancient DNA extraction methods in well-preserved skeletal fragments from 20 individuals buried in Avondale Burial Place to investigate the origins of the cemetery. Through examination of hypervariable region I (HVR1) in the mitochondrial genome (mtDNA), we determined haplotypes for all 20 of these individuals. Eighteen of these individuals belong to the L or U haplogroups, suggesting that Avondale Burial Place was most likely used primarily as a resting place for African Americans. After the surrounding Bibb County community expressed interest in investigating potential ancestral relationships to those within the cemetery, eight potential descendants provided saliva to obtain mtDNA HVR1 information. Three individuals from Avondale Burial Place matched three individuals with oral history ties to the cemetery. Using the online tool EMPOP, we calculated the likelihood of these exact matches occurring by chance alone (< 1%). The present findings exhibit the importance of genetic analysis of cemetery origins when archaeological and osteological data are inconclusive for estimating ancestry of anonymous historical individuals.
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Affiliation(s)
| | | | - Brian M Kemp
- Department of Anthropology and the School of Biological Sciences, Washington State University, Pullman, Washington
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17
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Sankaranarayanan K, Ozga AT, Warinner C, Tito RY, Obregon-Tito AJ, Xu J, Gaffney PM, Jervis LL, Cox D, Stephens L, Foster M, Tallbull G, Spicer P, Lewis CM. Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma. Curr Biol 2015; 25:3161-9. [PMID: 26671671 DOI: 10.1016/j.cub.2015.10.060] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 09/18/2015] [Accepted: 10/28/2015] [Indexed: 12/20/2022]
Abstract
Existing studies characterizing gut microbiome variation in the United States suffer from population ascertainment biases, with individuals of American Indian ancestry being among the most underrepresented. Here, we describe the first gut microbiome diversity study of an American Indian community. We partnered with the Cheyenne and Arapaho (C&A), federally recognized American Indian tribes in Oklahoma, and compared gut microbiome diversity and metabolic function of C&A participants to individuals of non-native ancestry in Oklahoma (NNIs). While the C&A and NNI participants share microbiome features common to industrialized populations, the C&A participants had taxonomic profiles characterized by a reduced abundance of the anti-inflammatory bacterial genus Faecalibacterium, along with a fecal metabolite profile similar to dysbiotic states described for metabolic disorders. American Indians are known to be at elevated risk for metabolic disorders. While many aspects of this health disparity remain poorly understood, our results support the need to further study the microbiome as a contributing factor. As the field of microbiome research transitions to therapeutic interventions, it raises concerns that the continued exclusion and lack of participation of American Indian communities in these studies will further exacerbate health disparities. To increase momentum in fostering these much needed partnerships, it is essential that the scientific community actively engage in and recruit these vulnerable populations in basic research through a strategy that promotes mutual trust and understanding, as outlined in this study.
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Affiliation(s)
- Krithivasan Sankaranarayanan
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | - Andrew T Ozga
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | - Raul Y Tito
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | - Alexandra J Obregon-Tito
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | - Jiawu Xu
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | | | - Lori L Jervis
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Center for Applied Social Research, University of Oklahoma, Norman, OK 73019, USA
| | - Derrell Cox
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA
| | - Lancer Stephens
- Oklahoma Shared Clinical and Translational Resources, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA; American Indian Diabetes Prevention Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA; Health Promotion Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73126, USA
| | | | - Gloria Tallbull
- Center for Applied Social Research, University of Oklahoma, Norman, OK 73019, USA
| | - Paul Spicer
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Center for Applied Social Research, University of Oklahoma, Norman, OK 73019, USA
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA; Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA; Center for Applied Social Research, University of Oklahoma, Norman, OK 73019, USA.
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18
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Ziesemer KA, Mann AE, Sankaranarayanan K, Schroeder H, Ozga AT, Brandt BW, Zaura E, Waters-Rist A, Hoogland M, Salazar-García DC, Aldenderfer M, Speller C, Hendy J, Weston DA, MacDonald SJ, Thomas GH, Collins MJ, Lewis CM, Hofman C, Warinner C. Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep 2015; 5:16498. [PMID: 26563586 PMCID: PMC4643231 DOI: 10.1038/srep16498] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 10/14/2015] [Indexed: 12/18/2022] Open
Abstract
To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli 341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon sequencing. Through comparisons of microbial taxonomic counts from paired amplicon (V3 U341F/534R) and shotgun sequencing datasets, we demonstrate that extensive length polymorphisms in the V3 region are a consistent and major cause of differential amplification leading to taxonomic bias in ancient microbiome reconstructions based on amplicon sequencing. We conclude that systematic amplification bias confounds attempts to accurately reconstruct microbiome taxonomic profiles from 16S rRNA V3 amplicon data generated using universal primers. Because in silico analysis indicates that alternative 16S rRNA hypervariable regions will present similar challenges, we advocate for the use of a shotgun metagenomics approach in ancient microbiome reconstructions.
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Affiliation(s)
- Kirsten A Ziesemer
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Allison E Mann
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | | | - Hannes Schroeder
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands.,Center for Geogenetics, University of Copenhagen, Denmark
| | - Andrew T Ozga
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Bernd W Brandt
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands
| | - Egija Zaura
- Department of Preventive Dentistry, Academic Center for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, the Netherlands
| | - Andrea Waters-Rist
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
| | - Domingo C Salazar-García
- Department of Anthropology, University of Cape Town, South Africa.,Departament de Prehistòria i Arqueologia, Universitat de València, Spain.,Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mark Aldenderfer
- School of Social Sciences, Humanities, and Arts, University of California, Merced, USA
| | | | - Jessica Hendy
- Department of Archaeology, University of York, York, UK
| | - Darlene A Weston
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands.,Department of Anthropology, University of British Columbia, Vancouver, Canada
| | | | | | | | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, Norman, OK, USA
| | - Corinne Hofman
- Faculty of Archaeology, Leiden University, Einsteinweg 2, 2333 CC, Leiden, the Netherlands
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19
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O'Neal L, Obregón-Tito AJ, Tito RY, Ozga AT, Polo SI, Lewis CM, Lawson PA. Clostridium amazonense sp. nov. an obliqately anaerobic bacterium isolated from a remote Amazonian community in Peru. Anaerobe 2015; 35:33-7. [PMID: 26123611 DOI: 10.1016/j.anaerobe.2015.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/18/2015] [Accepted: 06/23/2015] [Indexed: 10/23/2022]
Abstract
A strictly anaerobic Gram-stain positive, spore-forming, rod-shaped bacterium designated NE08V(T), was isolated from a fecal sample of an individual residing in a remote Amazonian community in Peru. Phylogenetic analysis based on the 16S rRNA gene sequence showed the organism belonged to the genus Clostridium and is most closely related to Clostridium vulturis (97.4% sequence similarity) and was further characterized using biochemical and chemotaxonomic methods. The major cellular fatty acids were anteiso C13:0 and C16:0 with a genomic DNA G + C content of 31.6 mol%. Fermentation products during growth with PYG were acetate and butyrate. Based on phylogenetic, phenotypic and chemotaxonomic information, strain NE08V was identified as representing a novel species of the genus Clostridium, for which the name Clostridium amazonense sp. nov. is proposed. The type strain is NE08V(T) (DSM 23598(T) = CCUG 59712(T)).
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Affiliation(s)
- Lindsey O'Neal
- Department of Microbiology and Plant Biology, University of Oklahoma, USA
| | | | - Raul Y Tito
- Department of Anthropology, University of Oklahoma, USA
| | - Andrew T Ozga
- Department of Anthropology, University of Oklahoma, USA
| | - Susan I Polo
- Department of Anthropology, University of Oklahoma, USA
| | - Cecil M Lewis
- Department of Anthropology, University of Oklahoma, USA
| | - Paul A Lawson
- Department of Microbiology and Plant Biology, University of Oklahoma, USA.
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20
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Obregon-Tito AJ, Tito RY, Metcalf J, Sankaranarayanan K, Clemente JC, Ursell LK, Zech Xu Z, Van Treuren W, Knight R, Gaffney PM, Spicer P, Lawson P, Marin-Reyes L, Trujillo-Villarroel O, Foster M, Guija-Poma E, Troncoso-Corzo L, Warinner C, Ozga AT, Lewis CM. Subsistence strategies in traditional societies distinguish gut microbiomes. Nat Commun 2015; 6:6505. [PMID: 25807110 PMCID: PMC4386023 DOI: 10.1038/ncomms7505] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 02/04/2015] [Indexed: 01/23/2023] Open
Abstract
Recent studies suggest that gut microbiomes of urban-industrialized societies are different from those of traditional peoples. Here we examine the relationship between lifeways and gut microbiota through taxonomic and functional potential characterization of faecal samples from hunter-gatherer and traditional agriculturalist communities in Peru and an urban-industrialized community from the US. We find that in addition to taxonomic and metabolic differences between urban and traditional lifestyles, hunter-gatherers form a distinct sub-group among traditional peoples. As observed in previous studies, we find that Treponema are characteristic of traditional gut microbiomes. Moreover, through genome reconstruction (2.2-2.5 MB, coverage depth × 26-513) and functional potential characterization, we discover these Treponema are diverse, fall outside of pathogenic clades and are similar to Treponema succinifaciens, a known carbohydrate metabolizer in swine. Gut Treponema are found in non-human primates and all traditional peoples studied to date, suggesting they are symbionts lost in urban-industrialized societies.
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Affiliation(s)
- Alexandra J. Obregon-Tito
- Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA
- Universidad Científica del Sur, Lima 18, Perú
- City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Raul Y. Tito
- Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA
- Universidad Científica del Sur, Lima 18, Perú
| | - Jessica Metcalf
- City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA
| | | | - Jose C. Clemente
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309, USA
| | - Luke K. Ursell
- City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Zhenjiang Zech Xu
- City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Will Van Treuren
- City of Hope, NCI-designated Comprehensive Cancer Center, Duarte, California 91010, USA
| | - Rob Knight
- Departments of Pediatrics and Computer Science & Engineering University of California San Diego, La Jolla, CA 92093, USA
| | - Patrick M. Gaffney
- Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma 73104, USA
| | - Paul Spicer
- Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA
| | - Paul Lawson
- Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA
| | | | | | - Morris Foster
- Old Dominion University, Norfolk, Virginia 23529, USA
| | | | | | - Christina Warinner
- Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA
| | - Andrew T. Ozga
- Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA
| | - Cecil M. Lewis
- Department of Anthropology, University of Oklahoma, Dale Hall Tower, 521 Norman, Oklahoma 73019, USA
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