Advertisement

Unique Individualistic Microflora: The Future of DNA Fingerprinting Technique

  • Pankaj Shrivastava
  • Hirak R. Dash
  • Sonia Kakkar
  • Mahendra K. Gupta
  • Toshi Jain
Chapter

Abstract

Microbial forensics is a newly emerging discipline in forensic science, which is the amalgam of both classical and advanced microbiology. Microbial phylogenetics and bioinformatics also play an important role in microbial forensic analysis. The omnipresence of bacteria and its uniqueness to a particular individual makes microbial genome analysis a potential tool for personal identification in addition to human genome analysis. Most of the studies on microbial forensics are based upon bioweapons; however, use of bacterial community for individualization and their possible role in body fluid degradation resulting into failure of even the most sensitive DNA fingerprinting technique is also of major concern and needs to be explored. From microbial forensics point of view, in addition to the conventional practices such as 16S rRNA and other housekeeping gene sequencing, metagenomic analysis by using high-throughput sequencing and polyphasic taxonomic approach can be employed for a better output in criminal investigation. This review unveils the current status of microbial forensics and takes the account of future requisites that should be inculcated in the present technology to probe forensic microbiology in criminal casework more efficaciously.

Keywords

Forensic Microbiology Biocrimes Human identification NGS 

References

  1. 1.
    Aas JA, Paster BJ, Stokes LN, Olsen I, Dewhirst FE (2005) Defining the normal bacterial flora of the oral cavity. J Clin Microbiol 43:5721–5732CrossRefGoogle Scholar
  2. 2.
    Aggarwal P, Chopra AK, Gupte S, Sandhu SS (2011) Microbial forensic-an upcoming investigative discipline. J Indian Acad Forensic Med 33:163–165Google Scholar
  3. 3.
    Alexandre A, Laranjo M, Young JPW, Oliveira S (2008) dnaJ is a useful phylogenetic marker for alphaproteobacteria. Int J Syst Evol Microbiol 58:2839–2849CrossRefGoogle Scholar
  4. 4.
    Ali MM, Shorky DA, Zaghlout HS, Rashed LA, Nanda MG (2013) PCR application in identification of saliva samples exposed to different conditions (streptococci detection based). Pak J Biol Sci 16:575–579CrossRefGoogle Scholar
  5. 5.
    Aly R, Shirley C, Cunico B, Aibach HI (1978) Effects of prolonged occlusion on the microbial flora, pH, carbon dioxide and transepidermal water loss in human skin. J Invest Dermatol 71:378–381CrossRefGoogle Scholar
  6. 6.
    Amann RI, Ludwig W, Schleifer KH, Amann RI, Ludwig W, Schleifer KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169PubMedPubMedCentralGoogle Scholar
  7. 7.
    Bakhtiar SM, LeBlanc JG, Salvucci E, Ali A, Martin R, Langella P (2013) Implications of the human microbiome in inflammatory bowel diseases. FEMS Microbiol Lett 342:10–17CrossRefGoogle Scholar
  8. 8.
    Braggemann H, Henne A, Hoster F, Liesegang H, Wiezer A, Strittmatter A (2004) The complete genome sequence of Propionibacterium acnes a commensal of human skin. Science 305:671–673CrossRefGoogle Scholar
  9. 9.
    Brenig B, Beck J, Schutz E (2010) Shotgun metagenomics of biological stains using ultra-deep DNA sequencing. Forensic Sci Int Genet 4:228–231CrossRefGoogle Scholar
  10. 10.
    Brenner S, Williams SR, Vermaas EH, Storck T, Moon K, McCollum C (2000) In vitro cloning of complex mixtures of DNA on microbeads: physical separation of differentially expressed cDNAs. Proc Natl Acad Sci USA 97:1665–1670CrossRefGoogle Scholar
  11. 11.
    Brooke JS, Annand JW, Hammer A, Dembkowski K, Shulman ST (2009) Investigation of bacterial pathogens on 70 frequently used environmental surfaces in a large urban U.S. university. J Environ Health 71:17–22PubMedGoogle Scholar
  12. 12.
    Brüls T, Weissenbach J (2011) The human metagenome: our other genome. Hum Mol Genet 20(R2):R142–R128.  https://doi.org/10.1093/hmg/ddr353CrossRefPubMedGoogle Scholar
  13. 13.
    Budowle B, Chakraborty R (2004) Genetic considerations for interpreting molecular microbial forensic evidence. Int Congress Ser 1261:56–58CrossRefGoogle Scholar
  14. 14.
    Budowle B, Schutzer SE, Einseln A, Kelly LC, Walash AC, Smith JA (2003) Public health, building microbial forensic as a response to bioterrorism. Science 301:1852–1853CrossRefGoogle Scholar
  15. 15.
    Budowle B, Schmedes S, Murch RS (2013) The microbial forensics pathway for use of massively-parallel sequencing technologies in the science and applications of microbial genomics. The National Academies Press, Washington, DC, pp 117–133Google Scholar
  16. 16.
    Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, Corbett CR, Fletcher J (2014) Validation of high throughput sequencing and microbial forensic applications. Investig Genet 5:9.  https://doi.org/10.1186/2041-2223-5-9 eCollection 2014CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Burney I (2013) Our environment in miniature: dust and the early twentieth-century forensic imagination. Representations (Berkeley) 121:31–59CrossRefGoogle Scholar
  18. 18.
    Butler JC, Cohen ML, Friedman CR, Scripp RM, Watz CG (2008) Collaboration between public health and law enforcement: new paradigms and partnerships for bioterrorism planning and response. Emerg Infect Dis 8:1152–1156CrossRefGoogle Scholar
  19. 19.
    Chiller K, Selkin BA, Murakawa GJ (2001) Skin microflora and bacterial infections of the skin. J Investig Dermatol SYP Proc 6:170–174CrossRefGoogle Scholar
  20. 20.
    Cohn BA (1994) In search of human skin pheromones. Arch Dermatol 130:1048–1051CrossRefGoogle Scholar
  21. 21.
    Costello EK, Lauber CL, Hamad M, Fiere N, Gordo JI, Knight R (2009) Bacterial community variation in human body habitats across space and time. Science 326:1694–1697CrossRefGoogle Scholar
  22. 22.
    Cummings CA, Bormann Chung CA, Fang R, Barker M, Brzoska P, Williamson PC (2010) Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing. Investig Genet 1:5CrossRefGoogle Scholar
  23. 23.
    Das S, Dash HR, Mangwani N, Chakraborty J, Kumari S (2014) Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Met 103:80–100CrossRefGoogle Scholar
  24. 24.
    Dominguez-Bello MG, Costello EK, Contrera M, Magri M, Hidalgo G, Fierer N, Knight R (2010) Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns. Proc Natl Acad Sci USA 107:11971–11975CrossRefGoogle Scholar
  25. 25.
    Eliaz PM (2006) The skin barrier formation and recovery in skin disorders. J Clin Invest 116:1150–1158CrossRefGoogle Scholar
  26. 26.
    Eloe-Fadrosh EA, Rasko DA (2013) The human microbiome: from symbiosis to pathogenesis. Ann Rev Med 64:145–163CrossRefGoogle Scholar
  27. 27.
    Enserink M, Ferber D (2003) Microbial forensic: reports spells out how to fight bio crimes. Science 299:1164–1165CrossRefGoogle Scholar
  28. 28.
    Fierer N, Hamady M, Lauber CL, Knight R (2008) The influence of sex, handedness and washing on the diversity of hand surface bacteria. Proc Natl Acad Sci USA 105:17994–17999CrossRefGoogle Scholar
  29. 29.
    Fierer N, Lauber CL, Zhou N, Donald DM, Costello EK, Knight R (2010) Forensic identification using skin bacterial communities. PNAS 107:6477–6481CrossRefGoogle Scholar
  30. 30.
    Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR (1995) Whole genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496–512CrossRefGoogle Scholar
  31. 31.
    Gao Z, Tseng CH, Pei Z, Blaser MJ (2007) Molecular analysis of human forearm superficial skin bacterial biota. Proc Natl Acad Sci USA 104:2927–2932CrossRefGoogle Scholar
  32. 32.
    Giovannoni SJ, Britschgi TB, Moyer CL, Field KG (1990) Genetic diversity in Sargasso Sea bacterioplankton. Nature 345:60–63CrossRefGoogle Scholar
  33. 33.
    Goh MS, Gorton TS, Forsyth MH, Troy KE, Geary SJ (1998) Molecular and biochemical analysis of a 105 kDa Mycoplasma gallisepticum cytadhesin (GapA). Microbiol 144:2971–2978CrossRefGoogle Scholar
  34. 34.
    Gribbon EM, Cunliffe WJ, Holand KT (1993) Interaction of Propionibacterium acnes with skin lipids in vitro. J Gen Microbiol 139:1745–1751CrossRefGoogle Scholar
  35. 35.
    Grice EA, Serge JA (2011) The skin microbiome. Nat Rev Microbiol 9:244–253CrossRefGoogle Scholar
  36. 36.
    Grice EA, Kong HH, Conlan S, Deming CB, Davis J, Young CA (2009) Topographical and temporal diversity of the human skin microbiome. Science 324:1190–1192CrossRefGoogle Scholar
  37. 37.
    Hill KK, Ticknor LO, Okinaka RT, Asay M, Blair H, Bliss KA (2004) Fluorescent amplified fragment length polymorphism analysis of Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis isolates. Appl Environ Microbiol 70:1068–1080CrossRefGoogle Scholar
  38. 38.
    Horswell J, Cordiner SJ, Maas EW, Martin TM, Sutherland KBW, Speir TW (2002) Forensic comparison of soils by bacterial community DNA profiling. J Forensic Sci 47:350–353CrossRefGoogle Scholar
  39. 39.
    Hugenholtz P, Goebel BM, Pace NR (1998) Impact of culture independent studies on the emerging phylogenetic view of bacterial diversity. J Bacteriol 180:4765–4774PubMedPubMedCentralGoogle Scholar
  40. 40.
    Jain R, Rivera MC, Lake JA (1999) Horizontal gene transfer among genomes: the complexity hypothesis. Proc Natl Acad Sci USA 96:3801–3806CrossRefGoogle Scholar
  41. 41.
    Jain R, Rivera MC, Moore JE, Lake JA (2002) Horizontal gene transfer in microbial genome evolution. Theor Popul Biol 61:489–495CrossRefGoogle Scholar
  42. 42.
    Jain S, Kumar A, Gupta P, Prasad R (2005) Microbial forensic: a new forensic discipline. JIAFM 27:112–116Google Scholar
  43. 43.
    Janda JM, Abott S (2007) 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: Pluses, Perils and Pitfalls. J Clin Microbiol 45:2761–2764CrossRefGoogle Scholar
  44. 44.
    Jarvis WR (1994) Handwashing- the Semmelweis lesson forgotten? Lancet 344:1311–1312CrossRefGoogle Scholar
  45. 45.
    Keane FE, Ison CA, Taylor-Robinson D (1997) A longitudinal study of the vaginal flora over a menstrual cycle. Int J STD AIDS 8:489–494CrossRefGoogle Scholar
  46. 46.
    Kitahara K, Miyazaki K (2013) Revisiting bacterial phylogeny: natural and experimental evidence for horizontal gene transfer of 16S rRNA. Mob Genet Elem 3(1):e24210CrossRefGoogle Scholar
  47. 47.
    Korting HC, Hubner K, Greiner K, Hamm G, Braun- Falco O (1990) Differences in the skin surface pH and bacterial microflora due to long term application of synthetic detergent preparations of pH 5.5 and pH 7.0. Result of a crossover trial in healthy volunteers. Acta Derm Venereol 70:429–431PubMedGoogle Scholar
  48. 48.
    Kotewicz ML, Brown EW, LeClerc JE, Cebula TA (2003) Genomic variability among enteric pathogens: the case of the mutSrpoS intergenic region. Trends Microbiol 11:2–6CrossRefGoogle Scholar
  49. 49.
    Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Sougnez C (2001) Initial sequencing and analysis of the human genome. Nature 409:860–921CrossRefGoogle Scholar
  50. 50.
    Le Clerc JE, Li B, Payne WL, Cebula TA (1996) High mutation frequencies among Escherichia coli and Salmonella pathogens. Science 274:1208–1211CrossRefGoogle Scholar
  51. 51.
    Leeming JP, Holland KT, Cunliffe WJ (1984) The microbial ecology of pilosebaceous units isolated from human skin. J Gen Microbiol 130:803–807PubMedGoogle Scholar
  52. 52.
    Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380CrossRefGoogle Scholar
  53. 53.
    Marples M (1965) The ecology of human skin. Bannerstone House, SpringfieldGoogle Scholar
  54. 54.
    Marshall JC (1999) Gastrointestinal flora and its alterations in critical illness. Curr Opin Clin Nutr Metab Care 2:405–411CrossRefGoogle Scholar
  55. 55.
    Martin HL Jr, Richardson BA, Nyange PM, Lavreys L, Hillier SL, Chohan B (1999) Vaginal lactobacilli, microbial flora, and risk of human immunodeficiency virus type 1 and sexually transmitted disease acquisition. J Infect Dis 180:1863–1868CrossRefGoogle Scholar
  56. 56.
    Martín R, Miquel S, Ulmer J, Kechaou N, Langella P, Bermúdez-Humarán LG (2013) Role of commensal and probiotic bacteria in human health: a focus on inflammatory bowel disease. Microb Cell Fact 12:71.  https://doi.org/10.1186/1475-2859-12-71CrossRefPubMedPubMedCentralGoogle Scholar
  57. 57.
    Metzker ML (2010) Sequencing technologies-the next generation. Nat Rev Genet 11:31–46CrossRefGoogle Scholar
  58. 58.
    Morse SA, Khan AS (2005) Epidemiologic investigation for public health, biodefense, and forensic microbiology. In: Breeze RG, Budowle B, Schutzer SE (eds) Microbial forensics. Academic, Amsterdam, pp 157–171CrossRefGoogle Scholar
  59. 59.
    Munson MA, Pitt Ford T, Chong B, Weightman AJ, Wade WG (2002) Molecular and cultural analysis of the microflora associated with endodontic infections. J Dent Res 81:761–766CrossRefGoogle Scholar
  60. 60.
    Muthiani YM, Matiru VN, Bii C (2010) Potential skin pathogens on second hand clothes and the effectiveness of disinfection methods, Nairobi, Kenya. In: Proceedings of 2010 JKUAT Scientific Technological and Industrialization ConferenceGoogle Scholar
  61. 61.
    Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K, Cleenwerck I, Vancanneyt M, Swings J (2007) Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 57(12):2777–2789CrossRefGoogle Scholar
  62. 62.
    Nelly AN, Orloff M (2001) Survival of some medically important Fungi on hospital fabrics and plastics. J Clin Microbiol 39:3360–3361CrossRefGoogle Scholar
  63. 63.
    Pace NR (1997) A molecular view of microbial diversity and the biosphere. Science 276:734–740CrossRefGoogle Scholar
  64. 64.
    Pennisi E (2004) Researchers trade insights about gene swapping. Science 305:334–335CrossRefGoogle Scholar
  65. 65.
    Peterson J, Garges S, Giovanni M, McInnes P, Wang L, Schloss JA (2009) NIH HMP Working Group. The NIH human microbiome project. Genome Res 19:2317–2323CrossRefGoogle Scholar
  66. 66.
    Pittet D, Allegranzi B, Boyce J (2009) The World Health Organization guidelines on hand hygiene in health care and their consensus recommendations. Infect Contrl Hosp Epidemiol 30:611–622CrossRefGoogle Scholar
  67. 67.
    Poretsky R, Rodriguez-R LM, Luo C, Tsementzi D, Konstantinidis KT (2014) Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics. PLoS One 9(4):e93827CrossRefGoogle Scholar
  68. 68.
    Priestley CJ, Jones BM, Dhar J, Goodwin L (1997) What is normal vaginal flora? Genitourin Med 73:23–28CrossRefGoogle Scholar
  69. 69.
    Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R (2008) A large genome center’s improvements to the Illumina sequencing system. Nat Methods 5:1005–1010CrossRefGoogle Scholar
  70. 70.
    Radnedge L, Agron PG, Hill KK, Jackson PJ, Ticknor LO, Keim P (2003) Genome differences that distinguish Bacillus anthracis from Bacillus cereus and Bacillus thuringiensis. Appl Environ Microbiol 69:2755–2764CrossRefGoogle Scholar
  71. 71.
    Rappe MS, Giovannoni SJ (2003) The uncultured microbial majority. Ann Rev Microbiol 57:369–394CrossRefGoogle Scholar
  72. 72.
    Roth RR, James WD (1988) Microbial ecology of the skin. Ann Rev Microbiol 42:441–464CrossRefGoogle Scholar
  73. 73.
    Salminen S, Isolauri E, Onnela T (1995) Gut flora in normal and disordered states. Chemotherapy 41:5–15CrossRefGoogle Scholar
  74. 74.
    Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467CrossRefGoogle Scholar
  75. 75.
    Sarkany I, Gaylarde CC (1968) Bacterial colonization of the skin of a newborn. J Pathol Bacteriol 95:115–122CrossRefGoogle Scholar
  76. 76.
    Schleifer KH (2004) Microbial diversity: facts, problems, prospects. Syst Appl Microbiol 27:3–9CrossRefGoogle Scholar
  77. 77.
    Schofield MJ, Hsieh P (2003) DNA mismatch repair: molecular mechanisms and biological function. Ann Rev Microbiol 57:579–608CrossRefGoogle Scholar
  78. 78.
    Schouls LM, Schot CS, Jacobs JA (2003) Horizontal transfer of segments of the 16S rRNA genes between species of the Streptococcus anginosus group. J Bacteriol 185:7241–7246CrossRefGoogle Scholar
  79. 79.
    Sebastian T, Willem VW, Hubert PE, Alex VB, Kayser M (2010) Microbial DNA fingerprinting of human fingerprints: dynamic colonization of fingertip microflora challenges human host inference for forensic purposes. Int J Legal Med 124:477–481CrossRefGoogle Scholar
  80. 80.
    Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26:1135–1145CrossRefGoogle Scholar
  81. 81.
    Shrivastava P, Jain T, Gupta MK (2015) Microbial forensics in legal medicine. SAS J Med 1:33–40Google Scholar
  82. 82.
    Smith SM, Eng RHK, Padberg FT (1996) Survival of nosocomial pathogenic bacteria at ambient temperature. J Med 27:293–302PubMedGoogle Scholar
  83. 83.
    Sniegowski PD, Gerrish PJ, Lenski RE (1997) Evolution of high mutation rates in experimental populations of E. coli. Nature 387:703–705CrossRefGoogle Scholar
  84. 84.
    Staley JT, Konopka A (1985) Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Ann Rev Microbiol 39:321–346CrossRefGoogle Scholar
  85. 85.
    Takashima M, Shirai F, Sageshma M, Ikeda OY, Dohi Y (2004) Distinctive bacteria binding property of cloth materials. Am J Infect Contrl 32:27–30CrossRefGoogle Scholar
  86. 86.
    Treadwell TE, Koo D, Kuker K, Kahn AS (2003) Epidemiologic clues to bioterrorism. Public Health Rep 118:92–98CrossRefGoogle Scholar
  87. 87.
    Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI (2007) The human microbiome project. Nature 449:804–810CrossRefGoogle Scholar
  88. 88.
    Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE (2009) A core gut microbiome in obese and lean twins. Nature 457:480–484.  https://doi.org/10.1038/nature07540CrossRefGoogle Scholar
  89. 89.
    Ursell LK, Metcalf JL, Parfrey LW, Knight R (2012) Defining the human microbiome. Nutr Rev Suppl 70(Suppl 1):S38–S44.  https://doi.org/10.1111/j.1753-4887.2012.00493.xCrossRefGoogle Scholar
  90. 90.
    Venter JC, Adam MD, Myers EW, Li PW, Mural RJ, Zinder N (2001) The sequence of human. Genome Sci 291:1304–1351Google Scholar
  91. 91.
    Weinstock GM (2012) Genomic approaches to studying the human microbiota. Nature 489:250–256CrossRefGoogle Scholar
  92. 92.
    Wetterstrand, K.S. (2013) DNA sequencing costs: data from the NHGRI Large-Scale Genome Sequencing Program. Available at: https://www.genome.gov/sequencingcosts/
  93. 93.
    Woo PC, Lau SK, Teng JL, Tse H, Yuen KY (2008) Then and now: use of 16S rDNA gene sequencing for bacterial identification and discovery of novel bacteria in clinical microbiology laboratories. Clin Microbiol Infect 14:908–934CrossRefGoogle Scholar
  94. 94.
    Zhou X, Bent SJ, Schneider MG, Davis CC, Islam MR, Forney LJ (2004) Characterization of vaginal microbial communities in adult healthy women using cultivation-independent methods. Microbiol 150:2565–2573CrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Pankaj Shrivastava
    • 1
  • Hirak R. Dash
    • 1
  • Sonia Kakkar
    • 2
  • Mahendra K. Gupta
    • 3
  • Toshi Jain
    • 3
  1. 1.DNA Fingerprinting Unit, State Forensic Science LaboratorySagarIndia
  2. 2.Department of Forensic MedicinePGIMERChandigarhIndia
  3. 3.School of Studies in MicrobiologyJiwaji UniversityGwaliorIndia

Personalised recommendations