Estimation of time since death with the postmortem microbiome: a modern view and approaches to solving the problem

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The aim of the review is to summarize and update the data of modern studies devoted to determining the post-mortem interval (PMI) with the use of microorganisms, as well as disclosing prospects for further study in the presented direction. Estimating the time elapsed since death based on the postmortem microbiome has great potential for accurate determination of PMI, but all methods currently used have their limitations. The dynamics of changes in microbial communities due to the influence of many external and internal factors significantly complicates the process of interpreting the results. The change of microbial communities in the human corpse has shown promising results for the assessment of PMI, but to date there is no evidence of the repeatability of such a continuity in various geographic and ecological conditions. The question of conducting new, large-scale studies, taking in all the factors that could affect the posthumous microbiome, is becoming urgent.

Keywords:

post-mortem interval estimation

postmortem microbiome

microorganisms

personality factors

Authors:

Khalikov A.A.

Bashkir State Medical University

ORCID: 0000-0003-1045-5677

Kildyushov E.M.

N.I. Pirogov Russian National Research Medical University

ORCID: 0000-0001-7571-0312

Kuznetsov K.O.

N.I. Pirogov Russian National Research Medical University

ORCID: 0000-0002-2405-1801

Rahmatullina G.R.

Volga-Ural Bureau of Forensic Medicine

Received:

18.03.2021

Accepted:

15.04.2021

List of references:

Indiaminov SI, Zhumanov ZE, Blinova SA. Problems of establishing the prescription of death. Sudebno-meditsinskaya ekspertiza. 2020;63(6):45-50. (In Russ.). https://doi.org/10.17116/sudmed20206306145
Kildyushov EM, Ermakova YuV, Tumanov EV, Kuznecova GS. Estimation of time since deathin the late postmortem period in forensic medicine (literature review). Sudebnaya meditsina. 2018;4(1):34-38. (In Russ.). https://doi.org/10.19048/2411-8729-2018-4-1-34-38
Khalikov AA, Kanzafarova GA, Pozdeev AR, Kuznetsov KO. Study of the optical density of the pericardial fluid of corpses in different types of thanatogenesis. Sovremennye problemy nauki i obrazovaniya. 2021.(2). (In Russ.). https://doi.org/10.17513/spno.30656
Javan GT, Finley SJ, Smith T, Miller J, Wilkinson JE. Cadaver Thanatomicrobiome Signatures: The Ubiquitous Nature of Clostridium Species in Human Decomposition. Front Microbiol. 2017;30(8):2096. https://doi.org/10.3389/fmicb.2017.02096
Metcalf JL, Xu ZZ, Bouslimani A, Dorrestein P, Carter DO, Knight R. Microbiome Tools for Forensic Science. Trends Biotechnol. 2017;35(9):814-823. https://doi.org/10.1016/j.tibtech.2017.03.006
Oliveira M, Amorim A. Microbial forensics: new breakthroughs and future prospects. Appl Microbiol Biotechnol. 2018;102(24):10377-10391. https://doi.org/10.1007/s00253-018-9414-6
Javan GT, Finley SJ, Can I, Wilkinson JE, Hanson JD, Tarone AM. Human Thanatomicrobiome Succession and Time Since Death. Sci Rep. 2016;6:29598. https://doi.org/10.1038/srep29598
Carter DO, Tomberlin JK, Benbow EM, Metcalf JL. Forensic Microbiology. New York City: John Wiley & Sons. 2017.
DeBruyn JM, Hauther KA. Postmortem succession of gut microbial communities in deceased human subjects. PeerJ. 2017;5:e3437. https://doi.org/10.7717/peerj.3437
Metcalf JL, Wegener Parfrey L, Gonzalez A, Lauber CL, Knights D, Ackermann G, Humphrey GC, Gebert MJ, Van Treuren W, Berg-Lyons D, Keepers K, Guo Y, Bullard J, Fierer N, Carter DO, Knight R. A microbial clock provides an accurate estimate of the postmortem interval in a mouse model system. Elife. 2013;2:e01104. https://doi.org/10.7554/eLife.01104
Pechal JL, Crippen TL, Benbow ME, Tarone AM, Dowd S, Tomberlin JK. The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing. Int J Legal Med. 2014;128(1):193-205. https://doi.org/10.1007/s00414-013-0872-1
Pechal JL, Crippen TL, Tarone AM, Lewis AJ, Tomberlin JK, Benbow ME. Microbial community functional change during vertebrate carrion decomposition. PLoS One. 2013;8(11):e79035. https://doi.org/10.1371/journal.pone.0079035
Carter DO, Metcalf JL, Bibat A, Knight R. Seasonal variation of postmortem microbial communities. Forensic Sci Med Pathol. 2015;11(2):202-207. https://doi.org/10.1007/s12024-015-9667-7
Cobaugh KL, Schaeffer SM, DeBruyn JM. Functional and Structural Succession of Soil Microbial Communities below Decomposing Human Cadavers. PLoS One. 2015;10(6):e0130201. https://doi.org/10.1371/journal.pone.0130201
Finley SJ, Pechal JL, Benbow ME, Robertson BK, Javan GT. Microbial Signatures of Cadaver Gravesoil During Decomposition. Microb Ecol. 2016;71(3):524-529. https://doi.org/10.1007/s00248-015-0725-1
Hauther KA, Cobaugh KL, Jantz LM, Sparer TE, DeBruyn JM. Estimating Time Since Death from Postmortem Human Gut Microbial Communities. J Forensic Sci. 2015;60(5):1234-1240. https://doi.org/10.1111/1556-4029.12828
Prihod’ko AN, Lavrukova OS, Lyabzina SN, Sidorova NA, Popov VL. The use of the microbial and entomological data for the diagnostics of prescription of death coming. Sudebno-meditsinskaya ekspertiza. 2018;61(6):52-56. (In Russ.). https://doi.org/10.17116/sudmed20186106152
Sidorova NA, Popov VL, Lavrukova OS Prospects for molecular-genetic support of research on proteolytics in the necrobiome composition. Sudebno-meditsinskaya ekspertiza. 2021;64(2):32-36. (In Russ.). https://doi.org/10.17116/sudmed20216402132
Johnson HR, Trinidad DD, Guzman S, Khan Z, Parziale JV, DeBruyn JM, Lents NH. A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval. PLoS One. 2016;11(12):e0167370. https://doi.org/10.1371/journal.pone.0167370
Lax S, Hampton-Marcell JT, Gibbons SM, Colares GB, Smith D, Eisen JA, Gilbert JA. Forensic analysis of the microbiome of phones and shoes. Microbiome. 2015;3:21. https://doi.org/10.1186/s40168-015-0082-9
Meadow JF, Altrichter AE, Kembel SW, Moriyama M, O’Connor TK, Womack AM, Brown GZ, Green JL, Bohannan BJ. Bacterial communities on classroom surfaces vary with human contact. Microbiome. 2014;2(1):7. https://doi.org/10.1186/2049-2618-2-7
Pechal JL, Schmidt CJ, Jordan HR, Benbow ME. A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition. Sci Rep. 2018;8:5724. https://doi.org/10.1038/s41598-018-23989-w
Kodama WA, Xu Z, Metcalf JL, Song SJ, Harrison N, Knight R, Carter DO, Happy CB. Trace evidence potential in postmortem skin microbiomes: from death scene to morgue. J Forensic Sciences. 2019;64(3):791-798. https://doi.org/10.1111/1556-4029.13949
Lauber CL, Metcalf JL, Keepers K, Ackermann G, Carter DO, Knight R. Vertebrate decomposition is accelerated by soil microbes. Appl Environ Microbiol. 2014;80(16):4920-4929. https://doi.org/10.1128/AEM.00957-14
Lutz H, Vangelatos A, Gottel N, Speed E, Osculati A, Visona S, Finley SJ, Tuomisto S, Karhunen P, Gilbert JA, Javan GT. Manner of death and demographic effects on microbial community composition in organs of the human cadaver. BioRxiv. 2019. [Preprint]. https://doi.org/10.1101/752576
Carter DO, Yellowlees D, Tibbett M. Temperature affects microbial decomposition of cadavers (Rattus rattus) in contrasting soils. Appl Soil Ecol. 2008;40:129-137. https://doi.org/10.1016/j.apsoil.2008.03.010
Donaldson AE, Lamont IL. Biochemistry changes that occurafter death: potential markers for determining post-mortem interval. PLoS One. 2013;8:e82011. https://doi.org/10.1371/journal.pone.0082011
Gill JR, Landi K. Putrefactive rigor: apparent rigor mortis due to gas distension. Am J Forensic Med Pathol. 2011;32:242-244. https://doi.org/10.1097/PAF.0b013e3181dd17b9
Barton W, O’Sullivan O, Cotter PD. Metabolic phenotyping of the human microbiome. F1000Res. 2019;8:1956. https://doi.org/10.12688/f1000research.19481.1
Sharma A, Kawarabayasi Y, Satyanarayana T. Acidophilic bacteria and archaea: acid stable biocatalysts and their potential applications. Extremophiles. 2012;16:1-19. https://doi.org/10.1007/s00792-011-0402-3
Haslam TCF, Tibbett M. Soils of contrasting pH affect the decomposition of buried mammalian (Ovis aries) skeletal muscle tissue. J Forensic Sci. 2009;54:900-904. https://doi.org/10.1111/j.1556-4029.2009.01070.x
Muhamed AMC, Atkins K, Stannard SR, Mündel T, Thompson MW The effects of a systematic increase in relative humidity on thermoregulatory and circulatory responses during prolonged running exercise in the heat. Temperature. 2016;3:455-464. https://doi.org/10.1080/23328940.2016.1182669
Jordan HR, Tomberlin JK Abiotic and biotic factors regulating inter-kingdom engagement between insects and microbe activity on vertebrate remains. Insects. 2017;8:54. https://doi.org/10.3390/insects8020054
Langdon A, Crook N, Dantas G The effects of antibiotics on themicrobiome throughout development and alternative approaches for therapeutic modulation. Genom Med. 2016;8:39. https://doi.org/10.1186/s13073-016-0294-z
Nogueira T, David PHC, Pothier J. Antibiotics as both friends and foes of the human gut microbiome: the microbial community approach. Drug Dev Res. 2019;80:86-97. https://doi.org/10.1002/ddr.21466
Vila AV, Collij V, Sanna S, Sinha T, Imhann F, Bourgonje AR, Mujagic Z, Jonkers DMAE, Masclee AAM, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Weersma RK. Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Nat Commun. 2020;11:362. https://doi.org/10.1038/s41467-019-14177-z
Maier L, Pruteanu M, Kuhn M, Zeller G, Telzerow A, Anderson EE, Brochado AR, Fernandez KC, Dose H, Mori H, Patil KR, Bork P, Typas A. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature. 2018;555:623-628. https://doi.org/10.1038/nature25979
Brackett E. Thanatomicrobiome signatures in drug overdose cases. Thesis presented to the Honors College of Middle Tennessee State University. Knoxville. 2018. https://jewlscholar.mtsu.edu/bitstream/handle/mtsu/5596/BRACKETT%20Final%20Thesis.pdf?sequence=1&isAllowed=y
Hau TC, Hamzah NH, Lian HH, Hamzah SPAA. Decomposition process and post mortem changes: review. Sains Malaysiana. 2014;43:1873-1882.
Bell CR, Wilkinson JE, Robertson BK, Javan GT. Sex-related differences in the thanatomicrobiome in postmortem heart samples using bacterial gene regions V1-2 and V4. Lett Appl Microbiol. 2018;67:144-153. https://doi.org/10.1111/lam.13005

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