Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies

BMC Evolutionary Biology

Volumn 14, Issue 1, 2014, Pages

  Henne, Karsten ^a   Li, Jing ^b,c   Stoneking, Mark ^b   Kessler, Olga ^a   Schilling, Hildegard ^a   Sonanini, Anne ^a   Conrads, Georg ^a   Horz, Hans Peter ^a  

^a UNIVERSITY HOSPITAL RWTH AACHEN   (Germany)

^b MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

^c Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

Author keywords

Glucosyltransferase; Human migration pattern; Oral Microbiome

Indexed keywords

BACTERIOLOGY; BACTERIUM; GENE; GENETIC MARKER; GENETIC VARIATION; GLOBAL PERSPECTIVE; MIGRATION; POPULATION STRUCTURE; SALIVA;

BACTERIA (MICROORGANISMS);

BACTERIAL DNA; GENETIC MARKER;

BACTERIAL GENE; BACTERIUM; CLASSIFICATION; GENETIC MARKER; GENETICS; GEOGRAPHY; HUMAN; ISOLATION AND PURIFICATION; MICROBIOLOGY; MIGRATION; SALIVA;

BACTERIA; DNA, BACTERIAL; GENES, BACTERIAL; GENETIC MARKERS; GEOGRAPHY; HUMAN MIGRATION; HUMANS; SALIVA;

EID: 84908507442     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/s12862-014-0190-3     Document Type: Article

References (59)

1. Population dynamics of Streptococcus mitis in its natural habitat. J Hohwy, J Reinholdt, M Kilian, Infect Immun 2001 69 6055 6063 10.1128/IAI.69.10.6055-6063.2001 11553543
2. Population diversity and dynamics of Streptococcus mitis, Streptococcus oralis, and Streptococcus infantis in the upper respiratory tracts of adults, determined by a nonculture strategy. M Bek-Thomsen, H Tettelin, I Hance, KE Nelson, M Kilian, Infect Immun 2008 76 1889 1896 10.1128/IAI.01511-07 18316382
3. An African origin for the intimate association between humans and Helicobacter pylori. B Linz, F Balloux, Y Moodley, A Manica, H Liu, P Roumagnac, D Falush, C Stamer, F Prugnolle, SW van der Merwe, Y Yamaoka, DY Graham, E Perez-Trallero, T Wadstrom, S Suerbaum, M Achtman, Nature 2007 445 915 918 10.1038/nature05562 17287725
4. Traces of human migrations in Helicobacter pylori populations. D Falush, T Wirth, B Linz, JK Pritchard, M Stephens, M Kidd, MJ Blaser, DY Graham, S Vacher, GI Perez-Perez, Y Yamaoka, F Megraud, K Otto, U Reichard, E Katzowitsch, X Wang, M Achtman, S Suerbaum, Science 2003 299 1582 1585 10.1126/science.1080857 12624269
5. The peopling of the Pacific from a bacterial perspective. Y Moodley, B Linz, Y Yamaoka, HM Windsor, S Breurec, JY Wu, A Maady, S Bernhoft, JM Thiberge, S Phuanukoonnon, G Jobb, P Siba, DY Graham, BJ Marshall, M Achtman, Science 2009 323 527 530 10.1126/science.1166083 19164753
6. Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. T Melton, R Peterson, AJ Redd, N Saha, AS Sofro, J Martinson, M Stoneking, Am J Hum Genet 1995 57 403 414 10.1002/ajmg.1320570308 7668267
7. Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations. JA Trejaut, T Kivisild, JH Loo, CL Lee, CL He, CJ Hsu, ZY Lee, M Lin, PLoS Biol 2005 3 247 10.1371/journal.pbio.0030247 15984912
8. Polynesian origins. Slow boat to Melanesia? SJ Oppenheimer, M Richards, Nature 2001 410 166 167 10.1038/35065520 11242066
9. mtDNA suggests Polynesian origins in Eastern Indonesia. M Richards, S Oppenheimer, B Sykes, Am J Hum Genet 1998 63 1234 1236 10.1086/302043 9758601
10. Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: lessons from Ladakh. T Wirth, X Wang, B Linz, RP Novick, JK Lum, M Blaser, G Morelli, D Falush, M Achtman, Proc Natl Acad Sci U S A 2004 101 4746 4751 10.1073/pnas.0306629101 15051885
11. Helicobacter pylori evolution and phenotypic diversification in a changing host. S Suerbaum, C Josenhans, Nat Rev Microbiol 2007 5 441 452 10.1038/nrmicro1658 17505524
12. What are the consequences of the disappearing human microbiota? MJ Blaser, S Falkow, Nat Rev Microbiol 2009 7 887 894 10.1038/nrmicro2245 19898491
13. Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. N Segata, SK Haake, P Mannon, KP Lemon, L Waldron, D Gevers, C Huttenhower, J Izard, Genome Biol 2012 13 42 10.1186/gb-2012-13-6-r42 22698087
14. Pathogens and host immunity in the ancient human oral cavity. C Warinner, JF Rodrigues, R Vyas, C Trachsel, N Shved, J Grossmann, A Radini, Y Hancock, RY Tito, S Fiddyment, C Speller, J Hendy, S Charlton, HU Luder, DC Salazar-Garcia, E Eppler, R Seiler, LH Hansen, JA Castruita, S Barkow-Oesterreicher, Y Teoh, CD Kelstrup, JV Olsen, P Nanni, T Kawai, E Willerslev, C von Mering, CM Lewis, MJ Collins, MT Gilbert, et al. Nat Genet 2014 46 336 344 10.1038/ng.2906 24562188
15. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. CJ Adler, K Dobney, LS Weyrich, J Kaidonis, AW Walker, W Haak, CJ Bradshaw, G Townsend, A Soltysiak, KW Alt, J Parkhill, A Cooper, Nat Genet 2013 45 450 455 10.1038/ng.2536 23416520
16. Evaluation of saliva as a source of human DNA for population and association studies. D Quinque, R Kittler, M Kayser, M Stoneking, I Nasidze, Anal Biochem 2006 353 272 277 10.1016/j.ab.2006.03.021 16620753
17. Similarity of bacterial populations in saliva from African-American mother-child dyads. Y Li, AI Ismail, Y Ge, M Tellez, W Sohn, J Clin Microbiol 2007 45 3082 3085 10.1128/JCM.00771-07 17634300
18. The fidelity of initial acquisition of mutans streptococci by infants from their mothers. Y Li, PW Caufield, J Dent Res 1995 74 681 685 10.1177/00220345950740020901 7722065
19. Transmission of periodontal bacteria and models of infection. AJ Van Winkelhoff, K Boutaga, J Clin Periodontol 2005 32 Suppl 6 16 27 10.1111/j.1600-051X.2005.00805.x 16128826
20. Tracking human migration patterns through the oral bacterial flora. PW Caufield, Clin Microbiol Infect 2009 15 Suppl 1 37 39 10.1111/j.1469-0691.2008.02680.x 19220352
21. Plasmid-containing strains of Streptococcus mutans cluster within family and racial cohorts: implications for natural transmission. PW Caufield, K Ratanapridakul, DN Allen, GR Cutter, Infect Immun 1988 56 3216 3220 3182079
22. Clonal persistence of oral Fusobacterium nucleatum in infancy. G Haraldsson, WP Holbrook, E Kononen, J Dent Res 2004 83 500 504 10.1177/154405910408300613 15153460
23. Highly toxic clone of Actinobacillus actinomycetemcomitans in geographically widespread cases of juvenile periodontitis in adolescents of African origin. D Haubek, K Poulsen, J Westergaard, G Dahlen, M Kilian, J Clin Microbiol 1996 34 1576 1578 8735124
24. Global genetic structure and molecular epidemiology of encapsulated Haemophilus influenzae. JM Musser, JS Kroll, DM Granoff, ER Moxon, BR Brodeur, J Campos, H Dabernat, W Frederiksen, J Hamel, G Hammond, EA Arne Høiby, KE Jonsdottir, M Kabeer, I Kallings, WN Khan, M Kilian, K Knowles, HJ Koornhof, B Law, KI Li, J Montgomery, PE Pattison, JC Piffaretti, AK Takala, ML Thong, RA Wall, JI Ward, RK Selander, Rev Infect Dis 1990 12 75 111 10.1093/clinids/12.1.75 1967849
25. Global diversity in the human salivary microbiome. I Nasidze, J Li, D Quinque, K Tang, M Stoneking, Genome Res 2009 19 636 643 10.1101/gr.084616.108 19251737
26. Multi-locus sequence typing: a tool for global epidemiology. R Urwin, MC Maiden, Trends Microbiol 2003 11 479 487 10.1016/j.tim.2003.08.006 14557031
27. Population structure of Streptococcus oralis. T Do, KA Jolley, MC Maiden, SC Gilbert, D Clark, WG Wade, D Beighton, Microbiology 2009 155 2593 2602 10.1099/mic.0.027284-0 19423627
28. Use of the housekeeping genes, gdh (zwf) and gki, in multilocus sequence typing to differentiate Streptococcus pneumoniae from Streptococcus mitis and Streptococcus oralis. M Ip, F Chi, SS Chau, M Hui, J Tang, PK Chan, Diagn Microbiol Infect Dis 2006 56 321 324 10.1016/j.diagmicrobio.2006.04.013 16765553
29. Glucansucrases: mechanism of action and structure-function relationships. V Monchois, RM Willemot, P Monsan, FEMS Microbiol Rev 1999 23 131 151 10234842
30. Maternal oral origin of Fusobacterium nucleatum in adverse pregnancy outcomes as determined using the 16S-23S rRNA gene intergenic transcribed spacer region. C Gonzales-Marin, DA Spratt, RP Allaker, J Med Microbiol 2013 62 133 144 10.1099/jmm.0.049452-0 23002071
31. 16S-23S rDNA internal transcribed spacer sequences for analysis of the phylogenetic relationships among species of the genus Fusobacterium. G Conrads, MC Claros, DM Citron, KL Tyrrell, V Merriam, EJ Goldstein, Int J Syst Evol Microbiol 2002 52 493 499 11931161
32. Use of housekeeping gene sequencing for species identification of viridans streptococci. P Kiratisin, L Li, PR Murray, SH Fischer, Diagn Microbiol Infect Dis 2005 51 297 301 10.1016/j.diagmicrobio.2004.12.001 15808322
33. Ribosomal ITS sequences and plant phylogenetic inference. I Alvarez, JF Wendel, Mol Phylogenet Evol 2003 29 417 434 10.1016/S1055-7903(03)00208-2 14615184
34. Phylogenetic analysis of glucosyltransferases and implications for the coevolution of mutans streptococci with their mammalian hosts. S Argimon, AV Alekseyenko, R DeSalle, PW Caufield, PLoS One 2013 8 56305 10.1371/journal.pone.0056305 23457545
35. PCR detection and identification of oral streptococci in saliva samples using gtf genes. T Hoshino, M Kawaguchi, N Shimizu, N Hoshino, T Ooshima, T Fujiwara, Diagn Microbiol Infect Dis 2004 48 195 199 10.1016/j.diagmicrobio.2003.10.002 15023429
36. Purification, characterization, and molecular analysis of the gene encoding glucosyltransferase from Streptococcus oralis. T Fujiwara, T Hoshino, T Ooshima, S Sobue, S Hamada, Infect Immun 2000 68 2475 2483 10.1128/IAI.68.5.2475-2483.2000 10768934
37. ARB: a software environment for sequence data. W Ludwig, O Strunk, R Westram, L Richter, H Meier, A Yadhukumar Buchner, T Lai, S Steppi, G Jobb, W Forster, I Brettske, S Gerber, AW Ginhart, O Gross, S Grumann, S Hermann, R Jost, A Konig, T Liss, R Lussmann, M May, B Nonhoff, B Reichel, R Strehlow, A Stamatakis, N Stuckmann, A Vilbig, M Lenke, T Ludwig, Nucleic Acids Res 2004 32 1363 1371 10.1093/nar/gkh293 14985472
38. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. C Quast, E Pruesse, P Yilmaz, J Gerken, T Schweer, P Yarza, J Peplies, FO Glockner, Nucleic Acids Res 2013 41 590 D596 10.1093/nar/gks1219 23193283
39. Recent developments in the MAFFT multiple sequence alignment program. K Katoh, H Toh, Brief Bioinform 2008 9 286 298 10.1093/bib/bbn013 18372315
40. Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. PD Schloss, SL Westcott, T Ryabin, JR Hall, M Hartmann, EB Hollister, RA Lesniewski, BB Oakley, DH Parks, CJ Robinson, JW Sahl, B Stres, GG Thallinger, DJ Van Horn, CF Weber, Appl Environ Microbiol 2009 75 7537 7541 10.1128/AEM.01541-09 19801464
41. Estimating the population size for capture-recapture data with unequal catchability. A Chao, Biometrics 1987 43 783 791 10.2307/2531532 3427163
42. Arlequin (version 3.0): an integrated software package for population genetics data analysis. L Excoffier, G Laval, S Schneider, Evol Bioinform Online 2005 1 47 50
43. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. K Tamura, D Peterson, N Peterson, G Stecher, M Nei, S Kumar, Mol Biol Evol 2011 28 2731 2739 10.1093/molbev/msr121 21546353
44. UniFrac-an online tool for comparing microbial community diversity in a phylogenetic context. C Lozupone, M Hamady, R Knight, BMC Bioinformatics 2006 7 371 10.1186/1471-2105-7-371 16893466
45. Median-joining networks for inferring intraspecific phylogenies. HJ Bandelt, P Forster, A Rohl, Mol Biol Evol 1999 16 37 48 10.1093/oxfordjournals.molbev.a026036 10331250
46. Utility of JC polyomavirus in tracing the pattern of human migrations dating to prehistoric times. A Pavesi, J Gen Virol 2005 86 1315 1326 10.1099/vir.0.80650-0 15831942
47. A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets. O Koren, D Knights, A Gonzalez, L Waldron, N Segata, R Knight, C Huttenhower, RE Ley, PLoS Comput Biol 2013 9 1002863 10.1371/journal.pcbi.1002863 23326225
48. Metagenomic analysis of the human distal gut microbiome. SR Gill, M Pop, RT Deboy, PB Eckburg, PJ Turnbaugh, BS Samuel, JI Gordon, DA Relman, CM Fraser-Liggett, KE Nelson, Science 2006 312 1355 1359 10.1126/science.1124234 16741115
49. The human microbiome project. PJ Turnbaugh, RE Ley, M Hamady, CM Fraser-Liggett, R Knight, JI Gordon, Nature 2007 449 804 810 10.1038/nature06244 17943116
50. Genomic variation landscape of the human gut microbiome. S Schloissnig, M Arumugam, S Sunagawa, M Mitreva, J Tap, A Zhu, A Waller, DR Mende, JR Kultima, J Martin, K Kota, SR Sunyaev, GM Weinstock, P Bork, Nature 2013 493 45 50 10.1038/nature11711 23222524
51. Anthropology of microbes. A Benezra, J DeStefano, JI Gordon, Proc Natl Acad Sci U S A 2012 109 6378 6381 10.1073/pnas.1200515109 22460792
52. The uses of race and ethnicity in human microbiome research. JD Fortenberry, Trends Microbiol 2013 21 165 166 10.1016/j.tim.2013.01.001 23566633
53. Going east: new genetic and archaeological perspectives on the modern human colonization of Eurasia. P Mellars, Science 2006 313 796 800 10.1126/science.1128402 16902130
54. Early Old World migrations of Homo sapiens: human biology. M Stoneking, K Harvarti, The Encyclopedia of Global Human Migration Blackwell, New York, Ness I, 2013
55. Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. C Romualdi, D Balding, IS Nasidze, G Risch, M Robichaux, ST Sherry, M Stoneking, MA Batzer, G Barbujani, Genome Res 2002 12 602 612 10.1101/gr.214902 11932244
56. Adsorption of glucosyltransferase to saliva coated hydroxyapatite. Possible mechanism for sucrose dependent bacterial colonization of teeth. G Rolla, JE Ciardi, SA Schultz, Scand J Dent Res 1983 91 112 117 6304864
57. Biology of Streptococcus mutans-derived glucosyltransferases: role in extracellular matrix formation of cariogenic biofilms. WH Bowen, H Koo, Caries Res 2011 45 69 86 10.1159/000324598 21346355
58. Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia. S Breurec, B Guillard, S Hem, S Brisse, FB Dieye, M Huerre, C Oung, J Raymond, TS Tan, JM Thiberge, S Vong, D Monchy, B Linz, PLoS One 2011 6 22058 10.1371/journal.pone.0022058 21818291
59. The oral metagenome in health and disease. P Belda-Ferre, LD Alcaraz, R Cabrera-Rubio, H Romero, A Simon-Soro, M Pignatelli, A Mira, Isme J 2012 6 46 56 10.1038/ismej.2011.85 21716308