Skip to main content
SpringerLink
Log in

Microbial communities associated with human decomposition and their potential use as postmortem clocks

  • Review Article
  • Published:
International Journal of Legal Medicine Aims and scope Submit manuscript

Abstract

Most forensic research that is used to better understand how to estimate the postmortem interval (PMI) entails the study of the physiochemical characteristics of decomposition and the effects that environmental factors have on the decomposition process. Forensic entomology exploits the life cycles of arthropods like Diptera (blow flies or flesh flies) and Coleoptera (beetles) deposited on the decaying carcass to determine PMI. Forensic taphonomy, from the Greek word taphos meaning burial, studies the creation of the fossils of decomposed cadavers to ascertain information as to the nature and time of death. Compared to other areas of taphonomy, there have been relatively few forensic science studies that have investigated the impact of human decomposition on the microbial changes occurring on or in a corpse or in the soil communities underneath a body. Such research may facilitate the critical determination of PMI. Therefore, the scope of this review is to provide a concise summary of the current progress in the newly emerging field of microbial diversity and the next-generation metagenomic sequencing approaches for assessing these communities in humans and in the soil beneath decomposing human.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Pechal J et al (2013) Microbial community functional change during vertebrate carrion decomposition. PLoS One 8:e79035

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  2. Hyde E et al (2013) The living dead: bacterial community structure of a cadaver at the onset and end of bloat stage of decomposition. PLoS ONE 8:e77733

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  3. Metcalf J et al (2013) A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. eLife 2:e01104

    Article  PubMed Central  PubMed  Google Scholar 

  4. Pechal J et al (2013) The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing. Int J Legal Med 128:193–205

    Article  PubMed  Google Scholar 

  5. Carter D, Yellowlees D, Tibbett M (2008) Temperature affects microbial decomposition of cadavers (Rattus rattus) in contrasting soils. Appl Soil Ecol 40:129–137

    Article  Google Scholar 

  6. Benninger L, Carter D, Forbes S (2008) The biochemical alterations of soil beneath a decomposing carcass. Forensic Sci Int 180:70–75

    Article  CAS  PubMed  Google Scholar 

  7. Carter D, Yellowlees D, Tibbett M (2007) Cadaver decomposition in terrestrial ecosystems. Naturwissenschaften 94:12–24

    Article  CAS  PubMed  Google Scholar 

  8. Forbes S, Stuart B, Dadour I, Dent B (2004) A preliminary investigation of the stages of adipocere formation. J Forensic Sci 49:1–9

    Article  Google Scholar 

  9. The Human Microbiome Consortium (2012) Structure, function and diversity of human microbiome in an adult reference population. Nature 486:207–214

    Article  Google Scholar 

  10. Gilbert JA et al (2010) Meeting report. The terabase metagenomics workshop and the vision of an earth microbiome project. Stand Genomic Sci 3:249–253

    Article  PubMed Central  PubMed  Google Scholar 

  11. Payne J (1965) A summer carrion study of the baby pig Sus scrofa Linnaeus. Ecology 46:592–602

    Article  Google Scholar 

  12. Tomberlin J et al (2011) A roadmap for bridging basic and applied research in forensic entomology. Annu Rev Entomol 56:401–421

    Article  CAS  PubMed  Google Scholar 

  13. Matuszewski S, Bajerlein D, Konwerski S, Szpila K (2010) Insect succession and carrion decomposition in selected forests of Central Europe. Part 1: pattern and rate of decomposition. Forensic Sci Int 194:85–93

    Article  PubMed  Google Scholar 

  14. Centeno N, Maldonado M, Oliva A (2002) Seasonal patterns of arthropods occuring on sheltered and unsheltered pig carcasses in Buenos Aires Province (Argentina). Forensic Sci Int 126:63–70

    Article  CAS  PubMed  Google Scholar 

  15. Hewadikaram K, Goff M (1991) Effect of carcass size on rate of decomposition and arthropod succession patterns. Am J Forensic Med Pathol 12:235–240

    Article  CAS  PubMed  Google Scholar 

  16. Scholenly K, Reid W (1987) Dynamics of heterotrophic succession in carrion arthropod assemblages: discrete series of a continuum of change? Oceologia (Berlin) 73:192–202

    Article  Google Scholar 

  17. Houck M, Siegel J (2006) Soil and glass. In: Fundamentals of forensic science. Elsevier, Amsterdam, pp 409–430

  18. Baldrian P et al (2012) Active and total microbial communities in forest soil are largely differenct and highly stratified during decomposition. ISME J 6:248–258

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  19. Roesch L et al (2007) Pyrosequencing enumerates and contrasts soil microbial diversity. ISME J 1:283–290

    PubMed Central  CAS  PubMed  Google Scholar 

  20. Vaninsberghe D, Hartmann M, Stewart G, Mohn W (2013) Isolation of a substantial proportion of forest soil bacterial communities detected via pyrotag sequencing. Appl Environ Microbiol 79:2096–2098

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  21. Peterson J et al (2009) The NIH human microbiome project. Genome Res 19:2317–2323

    Article  PubMed Central  PubMed  Google Scholar 

  22. Seo S et al (2013) Improvement of short tandem repeat analysis of samples highly contaminated by humic acid. J Forensic Legal Med 20:922–928

    Article  Google Scholar 

  23. Antony-Babu A et al (2013) An improved method compatible with metagenomic analyses to extract genomic DNA form soil in Tuber melanosporum orchards. J Appl Microbiol 115:163–170

    Article  CAS  PubMed  Google Scholar 

  24. Knauth S, Schmidt H, Tippkotter R (2012) Comparison of commercial kits for the extraction of DNA from paddy soils. Lett Appl Microbiol 56:222–228

    Article  Google Scholar 

  25. Sagova-Mareckova M et al (2008) Innovative methods for soil DNA purification tested in soils with widely differing characteristics. Appl Environ Microbiol 74:2902–2907

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Griffiths R, Whiteley A, O’Donnell A, Bailey M (2000) Rapid method of coextraction of DNA and RNA from natural environments for analysis of ribosomal DNA- and rRNA-based microbial community composition. Appl Environ Microbiol 66:5488–5491

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  27. Moreira D (1998) Efficient removal of PCR inhibitors using agarose-embedded DNA preparations. Nucleic Acid Res 26:3309–3310

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  28. Monroe C, Grier C, Kemp B (2013) Evaluating the efficacy of various thermo-stable polymerases against co-extracted PCR inhibitors in ancient DNA samples. Forensic Sci Int 228:142–153

    Article  CAS  PubMed  Google Scholar 

  29. Kermekchiev M, Kirilova L, Vail E, Barnes W (2009) Mutants of Taq DNA polymerases resistant to PCR inhibitors allow DNA amplification from whole blood and crude soil samples. Nucleic Acids Res 37:e40

    Article  PubMed Central  PubMed  Google Scholar 

  30. Paulin M et al (2013) Improving Griffith’s protocol for co-extraction of microbial DNA and RNA in adsorptive soils. Soil Biol Biochem 63:37–49

    Article  CAS  Google Scholar 

  31. Janda J, Abbott S (2007) 16S rRNA gene secquencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 45:2761–2764

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  32. Wooley J, Godzik A, Friedberg I (2010) A primer on metagenomics. PLoS Comput Biol 6:e1000667

    Article  PubMed Central  PubMed  Google Scholar 

  33. Lane D et al (1985) Rapid determination o f16S ribosomal RNA sequences for phylogenetic analyses. PNAS 82:6955–6959

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  34. Schloss P, Gevers S, Westcott S (2011) Reducing the effects of PCR amplicfication and sequencing artifacts on 16S rRNA-based studies. PLoS ONE 6:e27310

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  35. Haas B et al (2011) Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 21:494–504

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  36. Chakravorty S et al (2007) A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods 69:330–339

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  37. El-Metwally S, Hamza T, Zakaria M, Helmy M (2013) Next-generation sequence assembly: four stages for data processing and computational challenges. PLoS Comput Biol 9:e1003345

    Article  PubMed Central  PubMed  Google Scholar 

  38. Margulies M et al (2005) Genome sequencing in microfabricated high-density picoliter reactors. Nature 437:376–380

    PubMed Central  CAS  PubMed  Google Scholar 

  39. Kosugi S et al (2013) Coval: improving alignment quality and variant calling accuracy for next-generation sequencing data. PLoS ONE 8:e75402

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  40. Drancourt M et al (2000) 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates. J Clin Microbiol 38:3623–3630

    PubMed Central  CAS  PubMed  Google Scholar 

  41. Cline J, Braman J, Hogrefe H (1996) PCR fidelity of Pfu DNA polymerase and other thermostable DNA polymerases. Nucleic Acids Res 24:3546–3551

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  42. Kunkel T (1992) DNA replication fidelity. J Biol Chem 267:18251–18254

    CAS  PubMed  Google Scholar 

  43. Teeling H, Glockner F (2012) Current opportunities and challenges in microbial metagenome analysis—a bioinformatic perspective. Brief Bioinform 13:728–742

    Article  PubMed Central  PubMed  Google Scholar 

  44. Turnbaugh P et al (2007) The human microbiome project. Nature 449:804–810

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  45. Qin J et al (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464:59–65

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  46. Carter D, Yellowlees D, Tibbett M (2010) Moisture can be the dominant environmental parameter governing cadaver decomposition in soil. Forensic Sci Int 200:60–66

    Article  PubMed  Google Scholar 

  47. Delmont T et al (2011) Metagenomic comparison of direct and indirect soil DNA extraction approaches. J Microbiol Methods 86:397–400

    Article  CAS  PubMed  Google Scholar 

  48. Caporaso J et al (2012) Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms. ISME J 6:1621–1624

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  49. Vass A et al (1992) Time since death determinations of human cadavers using soil solution. J Forensic Sci 37:1236–1253

    CAS  PubMed  Google Scholar 

  50. Vass A (2001) Beyond the grave—understanding human decomposition. Microbiol Today 28:190–192

    Google Scholar 

  51. Gunn A, Pitt S (2012) Microbes as forensic indicators. Trop Biomed 29:311–330

    Google Scholar 

  52. Fiedler S, Graw M (2003) Decomposition of buried corpses, with special reference to the formation of adipocere. Naturwissenschaften 90:291–300

    Article  CAS  PubMed  Google Scholar 

  53. Teo C, Pawita AKO, Atiah Ayunni A, Noor Hazfalinda H (2013) Post mortem changes in relation to different types of clothing. Malyasian J Pathol 35:77–85

    CAS  Google Scholar 

  54. Hawksworth D, Wiltshire P (2011) Forensic mycology: the use of fungi in criminal investigations. Forensic Sci Int 206:1–11

    Article  PubMed  Google Scholar 

  55. Tabaac B et al (2013) Bacteria detected on surfaces of formalin fixed anatomy cadavers. Ital J Anat Embryol 118:1–5

    PubMed  Google Scholar 

  56. Ritchie N, Schutter M, Dick R, Myrold D (2000) Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil. Appl Environ Mircrobiol 66:1668–1675

    Article  CAS  Google Scholar 

  57. Hill G et al (2000) Methods for assessing the composition and diversity of soil microbial communities. Appl Soil Ecol 15:25–36

    Article  Google Scholar 

  58. Buyer J, Sasser M (2012) High throughput phospholipid fatty acid analysis of soils. Appl Soil Ecol 61:127–130

    Article  Google Scholar 

  59. Moreno L et al (2011) The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition. J Microbiol Methods 84:388–393

    Article  CAS  PubMed  Google Scholar 

  60. Heath L, Saunders B (2006) Assessing the potential of bacterial DNA profiling for forensic soil comparisons. J Forensic Sci 51:1062–1068

    Article  CAS  PubMed  Google Scholar 

  61. Moreno L et al (2006) Microbial metagenome profiling using amplicon length heterogeneity-polymerase chain reaction proves more effective than elemental analysis in discriminating soil specimens. J Forensic Sci 51:1315–1322

    Article  CAS  PubMed  Google Scholar 

  62. Osborne C, Rees G, Bernstein Y, Janssen P (2006) New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities. Appl Environ Microbiol 72:1270–1278

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  63. Dunbar J, Ticknor L, Kuske C (2001) Phylogenetic specificity and reproducibility and new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microbiol 67:190–197

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  64. Martiny J et al (2006) Microbial biogeography; putting microorganisms on the map. Nat Rev Microbiol 4:102–112

    Article  CAS  PubMed  Google Scholar 

  65. Muyzer G, DeWaal E, Uitterlinden A (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59:695–700

    PubMed Central  CAS  PubMed  Google Scholar 

  66. Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3:470–478

    Article  CAS  PubMed  Google Scholar 

  67. Tringe S, Rubin E (2005) Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 6:805–814

    Article  CAS  PubMed  Google Scholar 

  68. Quail M et al (2012) A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers. BMC Genomics 13:341

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  69. Mizrahi-Man O, Davenport E, Gilad Y (2013) Taxonomic classification of bacterial 16S rRNA genes using short sequencing reads: evaluation of effective study designs. PLoS ONE 8:e53608

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  70. Liu L et al (2012) Comparison of next-generation sequencing systems. J Biomed Biotechnol. doi:10.1155/2012/251364

    Google Scholar 

  71. Chandra J, Sabharwal K (1968) Determination of time since death from a study of various postmortem changes. J Indian Med Assoc 51:336–341

    CAS  PubMed  Google Scholar 

  72. Campobasso C, DiVella G, Introna F (2001) Factors affecting decomposition and Diptera colonization. Forensic Sci Int 120:18–27

    Article  CAS  PubMed  Google Scholar 

  73. Woese C (2000) Interpreting the universal phylogenetic tree. PNAS 97:8392–8396

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, 36104, USA

    Sheree J. Finley & Gulnaz T. Javan

  2. Department of Entomology and Department of Osteopathic Medicine, Michigan State University, East Lansing, MI, 48824, USA

    M. Eric Benbow

Authors
  1. Sheree J. Finley
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. M. Eric Benbow
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gulnaz T. Javan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Gulnaz T. Javan.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Finley, S.J., Benbow, M.E. & Javan, G.T. Microbial communities associated with human decomposition and their potential use as postmortem clocks. Int J Legal Med 129, 623–632 (2015). https://doi.org/10.1007/s00414-014-1059-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00414-014-1059-0

Keywords

Search

Navigation