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VOLUME 16 , ISSUE 7 ( July, 2015 ) > List of Articles


Oral Paleomicrobiology: Study of Ancient Oral Microbiome

Kusai Baroudi, Rushabh Dagli, Namrata Dagli, Bassel Tarakji

Citation Information : Baroudi K, Dagli R, Dagli N, Tarakji B. Oral Paleomicrobiology: Study of Ancient Oral Microbiome. J Contemp Dent Pract 2015; 16 (7):588-594.

DOI: 10.5005/jp-journals-10024-1726

Published Online: 01-01-2016

Copyright Statement:  Copyright © 2015; The Author(s).



Paleomicrobiology is a special branch of micropaleontology concerned with the study of bacterial fossils. We have used the term ‘oral paleomicrobiology’, as in this review we have focused on the ancient oral microflora. Recently, dental calculus and dental pulp have been identified as rich sources of ancient microbial DNA. Study of this ancient genetic material opens a new door to the ancient world. This review gives an overview of history of ancient DNA research, various techniques of analyzing ancient DNA in dental calculus and dental pulp, and the implications of the oral paleomicrobiology.

Materials and methods

A comprehensive literature search was performed in the following databases—pubmed, medline and google scholar for studies published before 10 April, 2015. The following keywords were used—‘ancient DNA’, ‘ancient oral flora, ‘oral paleomicrobiology’ and ‘oral microbiome’, ‘16S rRNA sequencing’. To obtain additional data, a manual search was performed using the reference lists of selected articles.


As a result of literature search, 27 articles were found in pubmed, 12 in google scholar and one in medline. Eight more articles were selected from the reference list of selected articles.


The combination of microbiology and paleontology has brought a revolution in the study of human evolution and microbial communities. The naturally well-preserved samples of microbial DNA from dental pulp and microbial colonies trapped in dental calculus are a potential source of microbial genetic material, which will prove invaluable in resolving mysteries of the past. This may be a beginning of a new era of oral paleomicrobiology, which will contribute in our studies about prevention of disease by establishing symbiosis between human beings and their microbiome.

How to cite this article

Dagli N, Dagli R, Baroudi K, Tarakji B. Oral Paleomicrobiology: Study of Ancient Oral Microbiome. J Contemp Dent Pract 2015;16(7):588-594.

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  1. Fossil bacteria: Paleomicrobiology and detection of fossil age. Available at:
  2. A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome. Philos Trans R Soc Lond B Biol Sci 2015;370(1660):20130376.
  3. DNA sequences from the quagga, an extinct member of the horse family. Nature 1984;312:282-284.
  4. Molecular cloning of ancient Egyptian mummy DNA. Nature 1985;314:644-645.
  5. Neandertal DNA sequences and the origin of modern humans. Cell 1997;90(1):19-30.
  6. Complete mitochondrial genome and phylogeny of pleistocene mammoth Mammuthus primigenius. PLoS Biol 2006;4(3):e73.
  7. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 2010;463(7282):757-762.
  8. A draft sequence of the Neandertal genome. Science 2010 7;328(5979):710-722.
  9. Paleomicrobiological study in dental calculus: Streptococcus mutans. Scanning Microsc 1996;10(4):1005-1013.
  10. Ancient bacterial DNA (aDNA) in dental calculus from archaeological human remains. J Archaeol Sci 2011;38(8):1827-1831.
  11. Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and industrial revolutions. Nat Genet 2013;45:450-455.
  12. Pathogens and host immunity in the ancient human oral cavity. Nat Genet 2014;46(4):336-344.
  13. Bartonella quintana in a 4000-year-old human tooth. J Infect Dis 2005;191(4):607-611.
  14. Regulation of pulpal blood flow. J Dent Res 1985;64:590-596.
  15. Emerging and Endemic Pathogens: advances in Surveillance, Detection and Identification (NATO Science for Peace and Security Series A: Chemistry and Biology). Gerard Aboudharam, Michel Drancourt, Didier Raoult. Applications of Paleomicrobiology to the Understanding of Emerging and Re-emerging Infectious Diseases. Springer 2010;91(8).
  16. Old dental pulp points to plague. Science 1998;282:619.
  17. Paleomicrobiology: past human infections. Berlin: Springer; 2008. Chapter 10, Typhoid fever epidemic in ancient Athens.
  18. Stability of bacterial DNA in relation to microbial detection in teeth. 2013. p. 35. Available at:
  19. Preservation of bacterial DNA by human dentin. J Endod 2014;40(2):241-245.
  20. Elsevier DNA binding to hydroxyapatite: A potential mechanism for preservation of microbial DNA. J Endod 2014;39(2):211-216.
  21. DNA From human ancient bacteria: a novel source of genetic evidence from archaeological dental calculus. Archaeometry 2013;55(4):767-778.
  22. Starch granules, dental calculus and new perspectives on ancient diet. J Archaeol Sci 2009;36(2):248-255.
  23. Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium). Proc Natl Acad Sci USA 2011;108(2):486-491.
  24. Dental calculus: Its relevance to ancient diet and oral ecology. Teeth Anthropol BAR Int Ser 1986;291:55-81.
  25. Paleopathology at the Origins of Agriculture. Orlando, FL: Academic Press; 1984. Paleopathology in Peruvian and Chilean populations; p. 515-529.
  26. Paleopathology at the Origins of Agriculture. Orlando, FL: Academic Press; 1984. Skeletal evidence for prehistoric subsistence adaptation in the central Ohio river valley; p. 307-345.
  27. Paleopathology at the origins of agriculture. Orlando, FL: Academic Press; 1984. Growth, nutrition and pathology in changing paleodemographic settings in South Asia; p. 169-192.
  28. A method for evaluating the amount of dental calculus on teeth from archaeological sites. J Archaeol Sci 1987;14(4):343-351.
  29. Standards for data collection from human skeletal remains. Arkansas Archeological Survey Research Series. Fayetteville, Arkansas, Wahington: Arkansas Archeological Survey; 1994. p. 206.
  30. et al. PCR Protocols: A Guide to Methods and Application. California: Academic press; 1990. Amplification of genomic DNA; p.13-20.
  31. Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. Proc Natl Acad Sci USA 1989;86(6):1939-1943.
  32. Gene conservation in Bacillus species. I. Conserved genetic and nucleic acid base sequence homologies. Proc Natl Acad Sci USA 1965;54(2):491-498.
  33. Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases. Clin Microbiol Rev 2004;17(4):840-862.
  34. Broad range DNA probes for detecting and amplifying eubacterial nucleic acids. FEMS Microbiol Lett 1989;48(1):19-24.
  35. Metagenomics: Application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004;68(4):669-685.
  36. The human microbiome: Our second genome. Annu Rev Genomics Hum Genet 2012;13:151-170.
  37. Mitochondrial DNA and human evolution. Annu Rev of Genomics Hum Genet 2005;6:165-183.
  38. Global analysis of saliva as a source of bacterial genes for insights into human population structure and migration studies. BMC Evol Biol 2014;14:190.
  39. Screening ancient tuberculosis with qPCR: challenges and opportunities. Philos Trans R Soc Lond B Biol Sci 2015;370(1660):20130622.
  40. Parallel detection of ancient pathogens via array-based DNA capture. Philos Trans R Soc Lond B Biol Sci 2015;370(1660):20130375.
  41. The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity. PLoS Genet 2009;5(12):e1000785.
  42. Study of inter- and intra-individual variations in the salivary microbiota. BMC Genomics 2010;11:523.
  43. Biofilm in endodontics: a review. J Int Soc Prevent Communit Dent 2015;5:1-12.
  44. Paleomicrobiology. Berlin Heidelberg: Springer-Verlag; 2008.
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