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Chapter 6 : Paleomicrobiology Data: Authentification and Interpretation

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Paleomicrobiology Data: Authentification and Interpretation, Page 1 of 2

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Abstract:

Paleomicrobiology is a part of general microbiology that aims to describe microbial flora (including bacteria, archaea, viruses, parasites, and microscopic fungi) in older specimens; it includes the retrospective diagnosis of infectious and tropical diseases ( ). There is no precise numerical definition of an old specimen; we consider as paleomicrobiological specimens any specimen older than 100 years, while the study of more recent samples may be called meso-microbiology. Also, we will consider in this chapter only animal and human specimens, excluding inanimate environmental specimens. The initial works of paleopathology, which used molecular biology techniques based on PCR, highlighted the possibility of the contamination of old samples by contemporary human DNA, casting doubt on the validity of PCR-based work for the detection of human and microbial ancient DNA (aDNA). These doubts, arising in the field of human aDNA, were then relayed to the field of paleomicrobiology by colleagues not practicing microbiology and without microbiological knowledge, who simply derived doubts from their observations of old human DNA. In fact, microbial contamination of an ancient specimen can take place from the surrounding flora, which can be either ancient flora contemporary with the sample or flora from operators at the time of excavation and storage of the old material or during laboratory manipulations, which is modern contamination. Contamination can occur with whole organisms or biomolecules of interest, such as nucleic acids or proteins or mycolic acids ( Fig. 1 ). Indeed, several methods are now used for discovering microbes in ancient specimens beyond the now-conventional aDNA analyses ( ).

Citation: Drancourt M. 2017. Paleomicrobiology Data: Authentification and Interpretation, p 51-58. In Drancourt M, Raoult D (ed), Paleomicrobiology of Humans. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PoH-0017-2015
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Figures

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Figure 1

Sources and prevention of contamination of ancient specimens by microbes and microbial products in the common example of buried specimens. Red bars indicate a pathogen present in the specimen at the time of death; blue and green circles indicate environmental microbes naturally contaminating the specimen during taphonomic processes; blue stars and yellow triangles indicate microbial contamination from discoverers of the specimen and fomites.

Citation: Drancourt M. 2017. Paleomicrobiology Data: Authentification and Interpretation, p 51-58. In Drancourt M, Raoult D (ed), Paleomicrobiology of Humans. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PoH-0017-2015
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Figure 2

Distribution of read length after throughput pyrosequencing of DNA extracted from a 14th century coprolite (blue curve) and from 1720 plague dental pulp specimens (red curve).

Citation: Drancourt M. 2017. Paleomicrobiology Data: Authentification and Interpretation, p 51-58. In Drancourt M, Raoult D (ed), Paleomicrobiology of Humans. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PoH-0017-2015
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References

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1. Drancourt M,, Raoult D . 2005. Palaeomicrobiology: current issues and perspectives. Nat Rev Microbiol 3 : 2335.[PubMed] [CrossRef]
2. Huynh HT,, Verneau J,, Levasseur A,, Drancourt M,, Aboudharam G . 2015. Bacteria and archaea paleomicrobiology of the dental calculus: a review. Mol Oral Microbiol. doi:10.1111/omi.12118. [PubMed] [CrossRef]
3. Appelt S,, Francello L,, Le Bailly M,, Raoult D,, Drancourt M,, Desnues C . 2014. Viruses in a 14th-century coprolite. Appl Environ Microbiol 80 : 26482655.[PubMed] [CrossRef]
4. Appelt S,, Armougom F,, Le Bailly M,, Robert C,, Drancourt M . 2014. Polyphasic analysis of a middle ages coprolite microbiota, Belgium. PLoS One 9 : e88376. doi:10.1371/journal.pone.0088376. [PubMed] [CrossRef]
5. Raoult D,, Aboudharam G,, Crubézy E,, Larrouy G,, Ludes B,, Drancourt M . 2000. Molecular identification by “suicide PCR” of Yersinia pestis as the agent of medieval black death. Proc Natl Acad Sci U S A 97 : 1280012803.[PubMed] [CrossRef]
6. Wiechmann I,, Grupe G . 2005. Detection of Yersinia pestis DNA in two early medieval skeletal finds from Aschheim (Upper Bavaria, 6th century A.D.). Am J Phys Anthropol 126 : 4855.[PubMed] [CrossRef]
7. Fournier PE,, Raoult D . 2004. Suicide PCR on skin biopsy specimens for diagnosis of rickettsioses. J Clin Microbiol 42 : 34283434.[PubMed] [CrossRef]
8. Thèves C,, Senescau A,, Vanin S,, Keyser C,, Ricaut FX,, Alekseev AN,, Dabernat H,, Ludes B,, Fabre R,, Crubézy E . 2011. Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. PLoS One 6 : e21733. doi:10.1371/journal.pone.0021733. [PubMed] [CrossRef]
9. Ninove L,, Nougairede A,, Gazin C,, Thirion L,, Delogu I,, Zandotti C,, Charrel RN,, De Lamballerie X . 2011. RNA and DNA bacteriophages as molecular diagnosis controls in clinical virology: a comprehensive study of more than 45,000 routine PCR tests. PLoS One 6 : e16142. doi:10.1371/journal.pone.0016142. [PubMed] [CrossRef]
10. Dabney J,, Meyer M,, Pääbo S . 2013. Ancient DNA damage. Cold Spring Harb Perspect Biol 5 pii: a012567. [PubMed] [CrossRef]
11. Lindahl T . 1993. Recovery of antediluvian DNA. Nature 365 : 700. [PubMed] [CrossRef]
12. Poinar HN,, Höss M,, Bada JL,, Pääbo S . 1996. Amino acid racemization and the preservation of ancient DNA. Science 272 : 864866.[PubMed] [CrossRef]
13. Smith CI,, Chamberlain AT,, Riley MS,, Cooper A,, Stringer CB,, Collins MJ . 2001. Neanderthal DNA. Not just old but old and cold? Nature 410 : 771772.[PubMed] [CrossRef]
14. Gilbert MTP,, Willerslev E,, Hansen EA,, Barnes I,, Rudbeck L,, Lynnerup N,, Cooper A . 2003. Distribution patterns of postmortem damage in human mitochondrial DNA. Am J Hum Genet 72 : 3247.[PubMed] [CrossRef]
15. Allentoft ME,, Collins M,, Harker D,, Haile J,, Oskam CL,, Hale ML,, Campos PF,, Samaniego JA,, Gilbert MT,, Willerslev E,, Zhang G,, Scofield RP,, Holdaway RN,, Bunce M . 2012. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Biol Sci 279 : 47244733.[PubMed] [CrossRef]
16. Johnson SS,, Hebsgaard MB,, Christensen TR,, Mastepanov M,, Nielsen R,, Munch K,, Brand T,, Gilbert MT,, Zuber MT,, Bunce M,, Rønn R,, Gilichinsky D,, Froese D,, Willerslev E . 2007. Ancient bacteria show evidence of DNA repair. Proc Natl Acad Sci U S A 104 : 1440114405.[PubMed] [CrossRef]
17. Nguyen-Hieu T,, Aboudharam G,, Drancourt M . 2012. Heat degradation of eukaryotic and bacterial DNA: an experimental model for paleomicrobiology. BMC Res Notes 5 : 528. [PubMed] [CrossRef]
18. Prentice MB,, Gilbert T,, Cooper A . 2004. Was the Black Death caused by Yersinia pestis? Lancet Infect Dis 4 : 72. [PubMed] [CrossRef]
19. Gilbert MT,, Cuccui J,, White W,, Lynnerup N,, Titball RW,, Cooper A,, Prentice MB . 2004. Absence of Yersinia pestis specific DNA in human teeth from five European excavations of putative plague victims. Microbiology 150 : 341354.[PubMed] [CrossRef]
20. Drancourt M,, Aboudharam G,, Signoli M,, Dutour O,, Raoult D . 1998. Detection of 400-year-old Yersinia pestis DNA in human dental pulp: an approach to the diagnosis of ancient septicemia. Proc Natl Acad Sci U S A 95 : 1263712640.[PubMed] [CrossRef]
21. Bos KI,, Schuenemann VJ,, Golding GB,, Burbano HA,, Waglechner N,, Coombes BK,, McPhee JB,, DeWitte SN,, Meyer M,, Schmedes S,, Wood J,, Earn DJ,, Herring DA,, Bauer P,, Poinar HN,, Krause J . 2011. A draft genome of Yersinia pestis from victims of the Black Death. Nature 478 : 506510.[PubMed] [CrossRef]
22. Schuenemann VJ,, Bos K,, DeWitte S,, Schmedes S,, Jamieson J,, Mittnik A,, Forrest S,, Coombes BK,, Wood JW,, Earn DJ,, White W,, Krause J,, Poinar HN . 2011. Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death. Proc Natl Acad Sci U S A 10 : E746E752. doi:10.1073/pnas.1105107108. [CrossRef]
23. Hawass Z,, Gad YZ,, Ismail S,, Khairat R,, Fathalla D,, Hasan N,, Ahmed A,, Elleithy H,, Ball M,, Gaballah F,, Wasef S,, Fateen M,, Amer H,, Gostner P,, Selim A,, Zink A,, Pusch CM . 2010. Ancestry and pathology in King Tutankhamun’s family. JAMA 303 : 638647.[PubMed] [CrossRef]
24. Tran TN,, Aboudharam G,, Raoult D,, Drancourt M . 2011. Beyond ancient microbial DNA: nonnucleotidic biomolecules for paleomicrobiology. Biotechniques 50 : 370380.[PubMed] [CrossRef]
25. Lee OY,, Wu HH,, Besra GS,, Rothschild BM,, Spigelman M,, Hershkovitz I,, Bar-Gal GK,, Donoghue HD,, Minnikin DE . 2015. Lipid biomarkers provide evolutionary signposts for the oldest known cases of tuberculosis. Tuberculosis (Edinb) 95(Suppl 1): S127S132.[PubMed] [CrossRef]
26. Minnikin DE,, Lee OY,, Wu HH,, Besra GS,, Bhatt A,, Nataraj V,, Rothschild BM,, Spigelman M,, Donoghue HD . 2015. Ancient mycobacterial lipids: key reference biomarkers in charting the evolution of tuberculosis. Tuberculosis (Edinb) 95(Suppl 1): S133S139.[PubMed] [CrossRef]
27. Lee OY,, Wu HH,, Donoghue HD,, Spigelman M,, Greenblatt CL,, Bull ID,, Rothschild BM,, Martin LD,, Minnikin DE,, Besra GS . 2012. Mycobacterium tuberculosis complex lipid virulence factors preserved in the 17,000-year-old skeleton of an extinct bison, Bison antiquus . PLoS One 7 : e41923. doi:10.1371/journal.pone.0041923. [PubMed] [CrossRef]
28. Witas HW,, Donoghue HD,, Kubiak D,, Lewandowska M,, Gładykowska-Rzeczycka JJ . 2015. Molecular studies on ancient M. tuberculosis and M. leprae: methods of pathogen and host DNA analysis. Eur J Clin Microbiol Infect Dis 34 : 17331749.[PubMed] [CrossRef]
29. Bianucci R,, Rahalison L,, Massa ER,, Peluso A,, Ferroglio E,, Signoli M . 2008. Technical note: a rapid diagnostic test detects plague in ancient human remains: an example of the interaction between archeological and biological approaches (southeastern France, 16th-18th centuries). Am J Phys Anthropol 136 : 361367.[PubMed] [CrossRef]
30. Malou N,, Tran TN,, Nappez C,, Signoli M,, Le Forestier C,, Castex D,, Drancourt M,, Raoult D . 2012. Immuno-PCR—a new tool for paleomicrobiology: the plague paradigm. PLoS One 7 : e31744. doi:10.1371/journal.pone.0031744. [PubMed] [CrossRef]
31. Huynh HT,, Gotthard G,, Terras J,, Aboudharam G,, Drancourt M,, Chabrière E . 2015. Surface plasmon resonance imaging of pathogens: the Yersinia pestis paradigm. BMC Res Notes 8 : 259. [PubMed] [CrossRef]
32. Rasmussen S,, Allentoft ME,, Nielsen K,, Orlando L,, Sikora M,, Sjögren KG,, Pedersen AG,, Schubert M,, Van Dam A,, Kapel CM,, Nielsen HB,, Brunak S,, Avetisyan P,, Epimakhov A,, Khalyapin MV,, Gnuni A,, Kriiska A,, Lasak I,, Metspalu M,, Moiseyev V,, Gromov A,, Pokutta D,, Saag L,, Varul L,, Yepiskoposyan L,, Sicheritz-Pontén T,, Foley RA,, Lahr MM,, Nielsen R,, Kristiansen K,, Willerslev E . 2015. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 163 : 571582.[PubMed] [CrossRef]
33. Willerslev E,, Cooper A . 2005. Ancient DNA. Proc Biol Sci 272 : 316.[PubMed] [CrossRef]
34. Audic S,, Béraud-Colomb E . 1997. Ancient DNA is thirteen years old. Nat Biotechnol 15 : 855858.[PubMed] [CrossRef]

Tables

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TABLE 1

A list of criteria for the authentication of microbes in ancient specimens appears below

Citation: Drancourt M. 2017. Paleomicrobiology Data: Authentification and Interpretation, p 51-58. In Drancourt M, Raoult D (ed), Paleomicrobiology of Humans. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PoH-0017-2015

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