Dna from human ancient bacteria: A novel source of genetic evidence from archaeological dental calculus

Archaeometry

Volumn 55, Issue 4, 2013, Pages 767-778

  De La Fuente, C ^a,b   Flores, S ^b   Moraga, M ^a,b  

^a UNIVERSITY OF CHILE   (Chile)

^b UNIVERSITY OF CHILE   (Chile)

Author keywords

Ancient Bacterial Dna; Co Evolution; Micro Evolution; Oral Microbiome

Indexed keywords

BACTERIUM; BIOME; DNA; GENOMICS; MICROORGANISM; POLYMERASE CHAIN REACTION;

BACTERIA (MICROORGANISMS);

EID: 84879418536     PISSN: 0003813X     EISSN: 14754754     Source Type: Journal    
DOI: 10.1111/j.1475-4754.2012.00707.x     Document Type: Article

References (62)

1. Achilli, A., Perego, U. A., Bravi, C. M., Coble, M. D., Kong, Q. P., Woodward, S. R., Salas, A., Torroni, A., and Bandelt, H. J., 2008, The phylogeny of the four pan-American MtDNA haplogroups: implications for evolutionary and disease studies, PLoS ONE, 3, e1764.
2. Agostini, H. T., Yanagihara, R., Davis, V., Ryschkewitsch, C. F., and Stoner, G. L., 1997, Asian genotypes of JC virus in Native Americans and in a Pacific Island population: markers of viral evolution and human migration, Proceedings of the National Academy of Sciences, USA, 94(26), 14 542-6.
3. Ashford, R. W., 2000, Parasites as indicators of human biology and evolution, Journal of Medical Microbiology, 49(9), 771-2.
4. Avila, M., Ojcius, D. M., and Yilmaz, Ö., 2009, The oral microbiota: living with a permanent guest, DNA and Cell Biology, 28, 405-11.
5. Bodner, M., Perego, U. A., Huber, G., Fendt, L., Röck, A. W., Zimmermann, B., Olivieri, A., Gómez-Carballa, A., Lancioni, H., Angerhofer, N., Bobillo, M. C., Corach, D., Woodward, S. R., Salas, A., Achilli, A., Torroni, A., Bandelt, H. J., and Parson, W., 2012, Rapid coastal spread of First Americans: novel insights from South America's Southern Cone mitochondrial genomes, Genome Research, 22(5), 811-20.
6. Castillo-Rojas, G., Cerbón, M. A., and López-Vidal, Y., 2008, Presence of Helicobacter pylori in a Mexican pre-Columbian mummy, BMC Microbiology, 8, 119.
7. Caufield, P. W., 2009, Tracking human migration patterns through the oral bacterial flora, Clinical Microbiology and Infection, 15, 37-9.
8. Chan, S. Y., Ho, L., Ong, C. K., Chow, V., Drescher, B., Dürst, M., ter Meulen, J., Villa, L., Luande, J., Mgaya, H. N., and Bernard, H. U., 1992, Molecular variants of human papillomavirus type 16 from four continents suggest ancient pandemic spread of the virus and its coevolution with humankind, Journal of Virology, 66(4), 2057-66.
9. Duncan, M. J., 2003, Genomics of oral bacteria, Critical Reviews in Oral Biology and Medicine, 14, 175-87.
10. Filoche, S., Wong, L., and Sissons, C., 2010, Oral biofilms: emerging concepts in microbial ecology, Journal of Dental Research, 89, 8-18.
11. Franco, N. V., 2008, La estructura tecnológica regional y la comprensión de la movilidad humana: tendencias para la cuenca del río Santa Cruz, in Arqueología del extremo sur del continente americano: resultados de nuevos proyectos (eds. L. A. Borrero and N. V. Franco ), 119-54, Ed. Instituto Multidisciplinario de Historia y Ciencias Humanas (CONICET), Buenos Aires.
12. Gilbert, M. T., Hansen, A. J., Willerslev, E., Rudbeck, L., Barnes, I., Lynnerup, N., and Cooper, A., 2003, Characterization of genetic miscoding lesions caused by postmortem damage, American Journal of Human Genetics, 72, 48-61.
13. Han, Y. W., Ikegami, A., Rajanna, C., Kawsar, H. I., Zhou, Y., Li, M., Sojar, H. T., Genco, R. J., Kuramitsu, H. K., and Deng, C. X., 2005, Identification and characterization of a novel adhesin unique to oral fusobacteria, Journal of Bacteriology, 187(15), 5330-40.
14. Handfield, M., Baker, H. V., and Lamont, R. J., 2008, Beyond good and evil in the oral cavity: insight into host-microbe relationships derived from transcriptional profiling of gingival cells, Journal of Dental Research, 87, 203-23.
15. Hojo, K., Nagaoka, S., Ohshima, T., and Maeda, N., 2009, Bacterial interactions in dental biofilm development, Journal of Dental Research, 88, 982-90.
16. Holmes, E. C., 2004, The phylogeography of human viruses, Molecular Ecology, 13, 745-56.
17. Hunter, S. J., Easton, S., Booth, V., Henderson, B., Wade, W. G., and Ward, J. M., 2011, Selective removal of human DNA from metagenomic DNA samples extracted from dental plaque, Journal of Basic Microbiology, 51, 1-5.
18. Kawano, S., Tsukamoto, T., Ohtaguro, H., Tsutsumi, H., Takahashi, T., Miura, I., Mukoyama, R., Aboshi, H., and Komuro, T., 1995, Sex determination from dental calculus by polymerase chain reaction (PCR), Nihon Hoigaku Zasshi, 49(3), 193-8.
19. Kemp, B. M., Monroe, C., and Glenn Smith, D., 2006, Repeat silica extraction: a simple technique for the removal of PCR inhibitors from DNA extracts, Journal of Archaeological Science, 33, 1680-9.
20. Kim, H., Lee, D., Chang, Y., Kim, M. J., Koh, S., Kim, J., Seong, J., Song, S. K., Shin, H. S., Son, J., Jung, M. Y., Park, S., Yoo, S. Y., Cho, K. W., Kim, D., Moon, S., Kim, D., Choi, Y., Kim, B., Jang, H., Kim, C. S., Kim, C., Choe, S., and Kook, J., 2010, Application of rpoB and zinc protease gene for use in molecular discrimination of Fusobacterium nucleatum subspecies, Journal of Clinical Microbiology, 48, 545-53.
21. Kimura, M., 1980, A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, 16, 111-20.
22. Kitchen, A., Miyamoto, M. M., and Mulligan, C. J., 2008, Utility of DNA viruses for studying human host history: case study of JC virus, Molecular Phylogenetics and Evolution, 46, 673-82.
23. Kolenbrander, P. E., Andersen, R. N., Blehert, D. S., Egland, P. G., Foster, J. S., Palmer, R. J. Jr, and Colonizers, L., 2002, Communication among oral bacteria, Microbiology and Molecular Biology Reviews, 66, 486-505.
24. Legoupil, D., and Sellier, P., 2004, La sepultura de la Cueva Ayayema (Isla Madre de Dios, archipiélagos occidentales de Patagonia), Magallania, 32, 115-24.
25. L'Heureux, G. L., and Barberena, B., 2008, Evidencias bioarqueológicas en patagonia meridional: el sitio Orejas de Burro 1 (Pali Aike, provincia de Santa Cruz), Intersecciones en Antropología, 9, 11-24.
26. Li, J., Helmerhorst, E. J., Leone, C. W., Troxler, R. F., Yaskell, T., Haffajee, A. D., Socransky, S. S., and Oppenheim, F. G., 2004, Identification of early microbial colonizers in human dental biofilm, Journal of Applied Microbiology, 97, 1311-8.
27. Liébana Ureña, J., 1995, Microbiología oral, Interamericana-McGraw-Hill, Madrid.
28. Lieverse, A. R., 1999, Diet and the aetiology of dental calculus, International Journal of Osteoarchaeology, 9(1), 219-32.
29. Linossier, A., Aspillaga, E., and Gajardo, M., 1988, Hallazgo de bacterias comensales de la cavidad oral en tártaro dental de restos óseos de indígenas chonos, Revista Chilena de Antropología, 7(1), 123-8.
30. Linossier, A., Gajardo, M., and Olavarria, J., 1996, Paleomicrobiological study in dental calculus: Streptococcus mutans, Scanning Microscopy, 10(4), 1005-13.
31. Lo, A., Seers, C., Dashper, S., Butler, C., Walker, G., Walsh, K., Catmull, D., Hoffmann, B., Cleal, S., Lissel, P., Boyce, J., and Reynolds, E., 2010, FimR and FimS: biofilm formation and gene expression in Porphyromonas gingivalis, Journal of Bacteriology, 192(5), 1332-43.
32. Malhi, R. S., Kemp, B., Eshleman, J., Cybulski, J., Glenn Smith, D., Cousins, S., and Harry, H., 2007, Mitochondrial haplogroup M discovered in prehistoric North Americans, Journal of Archaeological Science, 34, 642-8.
33. Marsh, P. D., 2005, Dental plaque: biological significance of a biofilm and community life-style, Journal of Clinical Periodontology, 32, 7-15.
34. Matsumura, M., Izumi, T., Matsumoto, M., Tsuji, M., Fujiwara, T., and Ooshima, T., 2003, The role of glucan-binding proteins in the cariogenicity of Streptococcus mutans, Microbiolology and Immunology, 47(3), 213-15.
35. Miura, T., Fukunaga, T., Igarashi, T., Yamashita, M., Ido, E., Funahashi, S., Ishida, T., Washio, K., Ueda, S., Hashimoto, K., Yoshida, M., Osame, M., Singhal, B. S., Zaninovic, V., Cartier, L., Sonoda, S., Tajima, K., Ina, Y., Gojobori, T., and Hayami, M., 1994, Phylogenetics subtypes of human T-lymphotropic virus type I and their relations to the anthropological background, Proceedings of the National Academy of Sciences, USA, 91(3), 1124-7.
36. Morou-Bermudez, E., and Burne, R. A., 1999, Genetic and physiologic characterization of urease of Actinomyces naeslundii, Infection and Immunity, 67(2), 504-12.
37. Nasidze, I., Li, J., Quinque, D., Tang, K., and Stoneking, M., 2009, Global diversity in the human salivary microbiome, Genome Research, 19, 636-43.
38. Nieberding, C. M., and Olivieri, I., 2007, Parasites: proxies for host genealogy and ecology? Trends in Ecology and Evolution, 22, 156-65.
39. Núñez, L., 1982, Temprana emergencia de sedentarismo en el desierto chileno: Proyecto Caserones, Chungara, 9, 80-122.
40. Ocampo, C., and Aspillaga, E., 1984, Breves notas sobre una prospección arqueológica en los archipiélagos de las Guaitecas y de los Chonos, Revista Chilena de Antropología, 4, 155-6.
41. Pap, I., Tillier A., Arensburg, B., Weiner, S., and Chech, M., 1995, First scanning electron microscope analysis of dental calculus from European Neanderthals: Subalyuk (Middle Paleolithic, Hungary), Bulletins et mémoires de la Société d'anthropologie de Paris, 7, 69-72.
42. Pavesi, A., 2001, Origin and evolution of GBV-C/hepatitis G virus and relationship with ancient human migrations, Journal of Molecular Evolution, 53(2), 104-13.
43. Pavesi, A., 2005, Utility of JC polyomavirus in tracing the pattern of human migrations dating to prehistoric times, Journal of General Virology, 86, 1315-26.
44. Poinar, H. N., and Stankiewicz, B. A., 1999, Protein preservation and DNA retrieval from ancient tissues, Proceedings of the National Academy of Sciences, USA, 96(15), 8426-31.
45. Preus, H., Marvik, O., Selvig, K., and Bennike, P., 2011, Ancient bacterial DNA (aDNA) in dental calculus from archaeological human remains, Journal of Archaeological Science, 38, 1827-31.
46. Rozen, S., and Skaletsky, H. J., 2000, Primer3 on the WWW for general users and for biologist programmers, in Bioinformatics methods and protocols: methods in molecular biology (eds. S. Krawetz and S. Misener ), 365-86, Humana Press, Totowa, NJ.
47. Saitou, N., and Nei, M., 1987, The neighbor-joining method: a new method for reconstructing phylogenetic trees, Molecular Biology and Evolution, 4, 406-25.
48. Schiappacasse, V., Castro, V., and Niemeyer, H., 1989, Los Desarrollos Regionales en el Norte Grande, in Culturas de Chile. Prehistoria: desde sus orígenes hasta los albores de la conquista (eds. J. Hidalgo, V. Schiappacasse, H. Niemeyer, C. Aldunate and I. Solimano ), 181-220, Andrés Bello, Santiago.
49. Suerbaum, S., and Josenhans, C., 2007, Helicobacter pylori evolution and phenotypic diversification in a changing host, Nature Reviews: Microbiology, 5(6), 441-52.
50. Sugimoto, C., Kitamura, T., Guo, J., Al-Ahdal, M. N., Shchelkunov, S. N., Otova, B., Ondrejka, P., Chollet, J. Y., El-Safi, S., Ettayebi, M., Grésenguet, G., Kocagöz, T., Chaiyarasamee, S., Thant, K. Z., Thein, S., Moe, K., Kobayashi, N., Taguchi, F., and Yogo, Y., 1997, Typing of urinary JC virus DNA offers a novel means of tracing human migrations, Proceedings of the National Academy of Sciences, USA, 19(94), 9191-6.
51. Tamm, E., Kivisild, T., Reidla, M., Metspalu, M., Glenn Smith, D., Mulligan, C. J., Bravi, C. M., Rickards, O., Martinez-Labarga, C., and Khusnutdinova, E. K., 2007, Beringian standstill and spread of Native American founders, PLoS ONE, 2, 1-6.
52. Tamura, K., Dudley, J., Nei, M., and Kumar, S., 2007, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0, Molecular Biology and Evolution, 24, 1596-9.
53. Templeton, A. R., 2007, Shared history of human and gut bacteria. Evolutionary togetherness: coupled evolution of human and pathogen, Heredity, 98(6), 337-8.
54. Torroni, A., Achilli, A., Macaulay, V., Richards, M., and Bandelt, H. J., 2006, Harvesting the fruit of the human mtDNA tree, Trends in Genetics, 22(6), 339-45.
55. True, D., 1980, Archaeological investigations in northern Chile: Caserones, in Prehistoric trails of Atacama: archaeology of northern Chile (eds. C. Meighan and D. True ), 139-78, Monumenta Archaeologica 7, University of California Press, Los Angeles.
56. Uribe, M., Adán, L., and Agüero, C., 2004, Arqueología de los períodos Intermedio Tardío y Tardío de San Pedro de Atacama y su relación con la cuenca del río Loa, Chungara, 36, Volumen Especial, 943-56.
57. Vandermeersch, B., Arensburg, B., Tillier A., Rak, Y., Weiner, S., Spiers, M., and Aspillaga, E., 1994, Middle Palaeolithic dental bacteria from Kebara, Israel, Compte Rendus de l'Academie des Sciences, Paris, serie II, 319, 727-31.
58. Willerslev, E., and Cooper, A., 2004, Ancient DNA, Proceedings of the Royal Society B: Biological Sciences, 272, 3-16.
59. Wirth, T., Meyer, A., and Achtman, M., 2005, Deciphering host migrations and origins by means of their microbes, Molecular Ecology, 14, 3289-306.
60. Xie, G., Chain, P., Lo, C., Liu, K., Gans, J., Merritt, J., and Qi, F., 2010, Community and gene composition of a human dental plaque microbiota obtained by metagenomic sequencing, Molecular Oral Microbiology, 25, 391-405.
61. Yamaoka, Y., 2009, Helicobacter pylori typing as a tool for tracking human migration, Clinical Microbiology and Infection, 15, 829-34.
62. Zlatar, V., 1984, Cementerio prehispánico Pica-8, Universidad de Antofagasta, Antofagasta.