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Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era |
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| Authors: | Tanvi P Honap Cara R Monroe Sarah J Johnson David K Jacobson Christopher A Abin Rita M Austin Paul Sandberg Marc Levine Krithivasan Sankaranarayanan Cecil M Lewis Jr |
| Institution: | 1. Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072 Norman, Oklahoma, USA;2. 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 Contribution: Conceptualization (equal), Formal analysis (supporting), Funding acquisition (supporting), ?Investigation (lead), Project administration (equal), Supervision (supporting), Writing - original draft (supporting), Writing - review & editing (supporting);3. 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 Contribution: Data curation (supporting), Formal analysis (equal), Visualization (equal), Writing - review & editing (supporting);4. 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 Contribution: Formal analysis (supporting), Writing - review & editing (supporting);5. Laboratories of Molecular Anthropology and Microbiome Research (LMAMR), University of Oklahoma, 73072 Norman, Oklahoma, USA Contribution: ?Investigation (supporting);6. 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 Contribution: ?Investigation (supporting), Writing - review & editing (supporting);7. Department of Anthropology, University of Oklahoma, 73019 Norman, Oklahoma, USA Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072 Norman, Oklahoma, USA Contribution: ?Investigation (supporting);8. Department of Anthropology, University of Oklahoma, 73019 Norman, Oklahoma, USA Sam Noble Oklahoma Museum of Natural History, University of Oklahoma, 73072 Norman, Oklahoma, USA Contribution: Conceptualization (equal), Funding acquisition (supporting), Project administration (equal), Writing - original draft (supporting), Writing - review & editing (supporting);9. 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 Contribution: Data curation (supporting), Formal analysis (equal), Supervision (supporting), Visualization (equal), Writing - review & editing (supporting) |
| Abstract: | ObjectivesLimited 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 MethodsSkeletal 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.ResultsPaleopathological 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.DiscussionWe 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. |
| Keywords: | ancient DNA dental calculus oral microbiome oral pathogens |