Thanatomicrobiome and artificial intelligence: forensic microbiology today
DOI:
https://doi.org/10.24265/horizmed.2025.v25n3.15Keywords:
Forensic Microbiology , Postmortem Changes , Artificial Intelligence , Deep Learning, CadaverAbstract
Forensic microbiology enables, among other applications, the estimation of the post-mortem interval (PMI), the identification of individuals, and the location of crime scenes through microbiome analysis and the geolocation of biological remains. Artificial intelligence (AI), together with new sequencing techniques, has revolutionized this field, markedly improving the accuracy and speed of forensic analyses. In this study, a systematic review was conducted following PRISMA guidelines. Databases such as PubMed, Scopus, Web of Science, and Google Scholar were searched using keywords related to forensic microbiology, IA, and PMI. Inclusion criteria included studies published in English or Spanish, regardless of the publication date. Exclusion criteria included duplicate studies or those that did not address the thanatomicrobiome analysis using AI tools. After the search and selection process, 20 articles published between 2016 and 2024 were analyzed. The f indings show that some machine learning models, such as Random Forest (RF) and Convolutional Neural Networks (CNN), provide relatively accurate estimates of the PMI. Recent studies focusing on the thanatomicrobiome are emerging as a promising tool in the forensic field, as this microbiome is unique and individualizing. These characteristics render it useful in the various stages of human identification and geolocation in criminal investigations. However, the review underscores the need for studies with larger sample sizes and for exploring the role of microorganisms beyond bacteria, in order to broaden and enhance the research landscape in this emerging field.
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References
Javan GT, Finley SJ. What is the “Thanatomicrobiome” and what is its relevance to forensic investigations? In: Forensic Ecogenomics. Alabama: Elsevier; 2012; 133-43. Disponible en: https://doi.org/10.1016/B978-0-12-809360-3.00006-0
He Q, Niu X, Qi RQ, Liu M. Advances in microbial metagenomics and artificial intelligence analysis in forensic identification. Front Microbiol. 2022;13:1046733. Disponible en: https://doi.org/10.3389/fmicb.2022.1046733
Clarke TH, Gomez A, Singh H, Nelson KE, Brinkac LM. Integrating the microbiome as a resource in the forensics toolkit. Forensic Sci Int Genet. 2017;30:141–7. Disponible en: https://doi.org/10.1016/j.fsigen.2017.06.008
Mishra A, Khan S, Das A, Das BC. Evolution of diagnostic and forensic microbiology in the era of artificial intelligence. Cureus. 2023;15(9):e45738. Disponible en: https://doi. org/10.7759/cureus.45738
Díez López C, Vidaki A, Kayser M. Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions. Forensic Sci Int Genet. 2022;56:102627. Disponible en: https://doi.org/10.1016/j.fsigen.2021.102627
Oliveira M, Amorim A. Microbial forensics: new breakthroughs and future prospects. Appl Microbiol Biotechnol. 2018;102(24):10377–91. Disponible en: https://doi.org/10.1007/s00253-018-9414-6
Yuan H, Wang Z, Wang Z, Zhang F, Guan D, Zhao R. Trends in forensic microbiology: From classical methods to deep learning. Front Microbiol. 2023;14:1163741. Disponible en: https://doi.org/10.3389/fmicb.2023.1163741
Huys G, Coopman V, Van Varenbergh D, Cordonnier J. Selective culturing and genus-specific PCR detection for identification of Aeromonas in tissue samples to assist the medico-legal diagnosis of death by drowning. Forensic Sci Int. 2012;221(1–3):11–5. Disponible en: https://doi. org/10.1016/j.forsciint.2012.03.017
Robinson JM, Pasternak Z, Mason CE, Elhaik E. Forensic applications of microbiomics: A review. Front Microbiol. 2020;11:608101. Disponible en: https://doi.org/10.3389/ fmicb.2020.608101
Sguazzi G, Mickleburgh HL, Ghignone S, Voyron S, Renò F, Migliario M, et al. Microbial DNA in human nucleic acid extracts: Recoverability of the microbiome in DNA extracts stored frozen long-term and its potential and ethical implications for forensic investigation. Forensic Sci Int Genet. 2022;59:102686. Disponible en: https:// doi.org/10.1016/j.fsigen.2022.102686
Zapico SC, Adserias-Garriga J. Postmortem interval estimation: new approaches by the analysis of human tissues and microbial communities’ changes. Forensic Sci. 2022;2(1):163–74. Disponible en: https://doi. org/10.3390/forensicsci2010013
Pasciullo S, Brenner LJ, Gagorik CN, Schamel JT, Baker S, Tran E, et al. The gut microbiomes of Channel Island foxes and island spotted skunks exhibit fine-scale differentiation across host species and island populations. Ecol Evol. 2024;14(2):e11017. Disponible en: https://doi. org/10.1002/ece3.11017
Fierer N, Lauber CL, Zhou N, McDonald D, Costello EK, Knight R. Forensic identification using skin bacterial communities. Proc Natl Acad Sci U S A. 2010;107(14):6477–81. Disponible en: https://doi.org/10.1073/pnas.1000162107
Leake SL, Pagni M, Falquet L, Taroni F, Greub G. The salivary microbiome for differentiating individuals: proof of principle. Microbes Infect. 2016;18(6):399–405. Disponible en: https://doi.org/10.1016/j.micinf.2016.03.011
Williams DW, Gibson G. Individualization of pubic hair bacterial communities and the effects of storage time and temperature. Forensic Sci Int Genet. 2017;26:12–20. Disponible en: https://doi.org/10.1016/j.fsigen.2016.09.006
Martínez Aragonés ÁA, Martínez-Manzanares E, Tapia-Paniagua ST. Early post mortem interval estimation in a mouse model using molecular analyses of the gut thanatomicrobiome. Spanish J Leg Med. 2022;48(3):107–14. Disponible en: https://doi.org/10.1016/j.remle.2022.02.002
Neckovic A, van Oorschot RAH, Szkuta B, Durdle A. Investigation of direct and indirect transfer of microbiomes between individuals. Forensic Sci Int Genet. 2020;45:102212. Disponible en: https://doi. org/10.1016/j.fsigen.2019.102212
Wang Z, Zhang F, Wang L, Yuan H, Guan D, Zhao R. Advances in artificial intelligence-based microbiome for PMI estimation. Front Microbiol. 2022;13. Disponible en: https://doi.org/10.3389/fmicb.2022.1034051
Guo J, Fu X, Liao H, Hu Z, Long L, Yan W, et al. Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing. Sci Rep. 2016;6(1):24197. Disponible en: https://doi.org/10.1038/srep24197
Roy D, Tomo S, Purohit P, Setia P. Microbiome in death and beyond: current vistas and future trends. Front Ecol Evol. 2021;9:630397. Disponible en: https://doi.org/10.3389/ fevo.2021.630397
Dong K, Xin Y, Cao F, Huang Z, Sun J, Peng M, et al. Succession of oral microbiota community as a tool to estimate postmortem interval. Sci Rep. 2019;9(1):1–9. Disponible en: http://dx.doi.org/10.1038/s41598-019-49338-z
Sessa F, Pomara C, Esposito M, Grassi P, Cocimano G, Salerno M. Indirect DNA transfer and forensic implications: a literature review. Genes (Basel). 2023;14(12):2153. Disponible en: https://doi.org/10.3390/genes14122153
de la Torre E, Ustariz F. Avances en identificación genética y análisis de perfiles de ADN en biología forense. Anat Digit. 2024;7(2):222–39. Disponible en: https://doi. org/10.33262/anatomiadigital.v7i2.2.3173
Caenazzo L, Tozzo P. Microbiome forensic biobanking: a step toward microbial profiling for forensic human identification. Healthcare (Basel). 2021;9(10):1371. Disponible en: https://doi.org/10.3390/healthcare9101371
Page M, McKenzie J, Bossuyt P, Boutron I, Hoffmann T, Mulrow C, et al. The PRISMA 2020 statement: An updated guideline for reporting systematic reviews. BMJ. 2021;372(71). Disponible en: https://doi.org/10.1136/bmj.n71
Haddaway NR, Page MJ, Pritchard CC, McGuinness LA. PRISMA2020: An R package and Shiny app for producing PRISMA 2020-compliant flow diagrams, with interactivity for optimised digital transparency and Open Synthesis. Campbell Syst Rev. 2022;18(2):e1230. Disponible en: https://doi.org/10.1002/cl2.1230
Johnson H, Trinidad D, Guzman S, Khan Z, Parziale J, DeBruyn J, et al. A machine learning approach for using the postmortem skin microbiome to estimate the postmortem interval. PLoS One. 2016;11(12):1–23. Disponible en: https://doi.org/10.1371/journal.pone.0167370
Metcalf J, Xu Z, Bouslimani A, Dorrestein P, Carter D, Knight R. Microbiome tools for forensic science. Trends Biotechnol. 2017;35(9):814–23. Disponible en: https:// doi.org/10.1016/j.tibtech.2017.03.006
Metcalf JL. Estimating the postmortem interval using microbes: Knowledge gaps and a path to technology adoption. Forensic Sci Int Genet. 2019;38:211–218. Disponible en: https://doi.org/10.1016/j.fsigen.2018.11.004
Zhang Y, Pechal J, Schmidt C, Jordan H, Wang W, Benbow M, et al. Machine learning performance in a microbial molecular autopsy context: A cross-sectional postmortem human population study. PLoS One. 2019;14(4):e0213829. Disponible en: https://doi.org/10.1371/journal.pone.0213829
Liu R, Gu Y, Shen M, Li H, Zhang K, Wang Q, et al. Predicting postmortem interval based on microbial community sequences and machine learning algorithms. Environ Microbiol. 2020;22(6):2273–91. Disponible en: https://doi.org/10.1111/1462-2920.15000
Kaszubinski S, Pechal J, Schmidt C, Jordan H, Benbow M, Meek M. Evaluating bioinformatic pipeline performance for forensic microbiome analysis*,†,‡. J Forensic Sci. 2020;65(2):513–525. Disponible en: https://doi. org/10.1111/1556-4029.14213
Aragonés Á, Tapia-Paniagua S. Review of cadaveric dating methods and new perspectives from the necrobiome. Spanish J Leg Med. 2022;48(1):30–35. Disponible en: https://doi.org/10.1016/j.remle.2021.05.001
Sharma R, Diksha, Bhute A, Bastia B. Application of artificial intelligence and machine learning technology for the prediction of postmortem interval: A systematic review of preclinical and clinical studies. Forensic Sci Int. 2022;340:111473. Disponible en: https://doi. org/10.1016/j.forsciint.2022.111473
Cui C, Song Y, Mao D, Cao Y, Qiu B, Gui P, et al. Predicting the postmortem interval based on gravesoil microbiome data and a random forest model. Microorganisms. 2022;11(1):56. Disponible en: https://doi.org/10.3390/ microorganisms11010056
Cláudia-Ferreira A, Barbosa D, Saegeman V, FernándezRodríguez A, Dinis-Oliveira R, Freitas A. The future Is now: unraveling the expanding potential of human (necro) microbiome in forensic investigations. Microorganisms. 2023;11(10). Disponible en: https://doi.org/10.3390/ microorganisms11102509
Li N, Liang X, Zhou S dong, Dang L hong, Li J, An G shuai, et al. Exploring postmortem succession of rat intestinal microbiome for PMI based on machine learning algorithms and potential use for humans. Forensic Sci Int Genet. 2023;66:1–11. Disponible en: https://doi.org/10.1016/j. fsigen.2023.102904
Mason AR, McKee-Zech HS, Steadman DW, DeBruyn JM. Environmental predictors impact microbial-based postmortem interval (PMI) estimation models within human decomposition soils. PLoS One. 2024;19(10):e0311906. Disponible en: pone.0311906 http://dx.doi.org/10.1371/journal.
Yang MQ, Wang ZJ, Zhai CB, Chen LQ. Research progress on the application of 16S rRNA gene sequencing and machine learning in forensic microbiome individual identification. Front Microbiol. 2024;15:1–7. Disponible en: https://doi. org/10.3389/fmicb.2024.1360457
Hu S, Zhang X, Yang F, Nie H, Lu X, Guo Y, et al. Multimodal approaches based on microbial data for accurate postmortem interval estimation. Microorganisms. 2024;12(11):2193. Disponible en: org/10.3390/microorganisms12112193 https://doi.
Wu Z, Guo Y, Hayakawa M, Yang W, Lu Y, Ma J, et al. Artificial intelligence-driven microbiome data analysis for estimation of postmortem interval and crime location. Front Microbiol. 2024;15:1334703. Disponible en: https:// doi.org/10.3389/fmicb.2024.1334703
Martino C, Dilmore AH, Burcham ZM, Metcalf JL, Jeste D, Knight R. Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol. 2022;20(12):707–20. Disponible en: https://doi.org/10.1038/s41579-022-00768-z
Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D. ConStrains identifies microbial strains in metagenomic datasets. Nat Biotechnol. 2015;33(10):1045–52. Disponible en: https://doi.org/10.1038/nbt.3319
Regueira-Iglesias A, Balsa-Castro C, Blanco-Pintos T, Tomás I. Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis. Mol Oral Microbiol. 2023;38(5):347–99. Disponible en: https://doi.org/10.1111/omi.12434
Schmedes SE, Woerner AE, Budowle B. Forensic human identification using skin microbiomes. Appl Environ Microbiol. 2017;83(22):e01672-17. Disponible en: https:// doi.org/10.1128/AEM.01672-17
Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, et al. Forensic microbiology: when, where and how Microorganisms 2024;12(5). Disponible en: https://doi. org/10.3390/microorganisms12050988
Procopio N, Lovisolo F, Sguazzi G, Ghignone S, Voyron S, Migliario M, et al. “Touch microbiome” as a potential tool for forensic investigation: a pilot study. J Forensic Leg Med. 2021;82:102223. Disponible en: https://doi. org/10.1016/j.jflm.2021.102223
Simon LM, Flocco C, Burkart F, Methner A, Henke D, Rauer L, et al. Microbial fingerprints reveal interaction between museum objects, curators, and visitors. iScience. 2023;26(9):107578. Disponible en: https://doi. org/10.1016/j.isci.2023.107578
Cho HW, Eom YB. Forensic analysis of human microbiome in skin and body fluids based on geographic location. Front Cell Infect Microbiol. 2021;11:695191. Disponible en: https://doi.org/10.3389/fcimb.2021.695191
Liang X, Han X, Liu C, Du W, Zhong P, Huang L, et al. Integrating the salivary microbiome in the forensic toolkit by 16S rRNA gene: potential application in body fluid identification and biogeographic inference. Int J Legal Med. 2022;136(4):975–85. Disponible en: https://doi. org/10.1007/s00414-022-02831-z
Nagasawa S, Motani-Saitoh H, Inoue H, Iwase H. Geographic diversity of Helicobacter pylori in cadavers: forensic estimation of geographical origin. Forensic Sci Int. 2013;229(1–3):7–12. Disponible en: https://doi. org/10.1016/j.forsciint.2013.02.028
Haarkötter C, Saiz M, Gálvez X, Medina-Lozano MI, Álvarez JC, Lorente JA. Usefulness of microbiome for forensic geolocation: a review. Life (Basel). 2021;11(12):1322. Disponible en: https://doi.org/10.3390/life11121322
Knights D, Kuczynski J, Charlson ES, Zaneveld J, Mozer MC, Collman RG, et al. Bayesian community-wide cultureindependent microbial source tracking. Nat Methods. 2011;8(9):761–3. Disponible en: https://doi.org/10.1038/ nmeth.1650
Mathai PP, Staley C, Sadowsky MJ. Sequence-enabled community-based microbial source tracking in surface waters using machine learning classification: A review. J Microbiol Methods. 2020;177:106050. Disponible en: https://doi.org/10.1016/j.mimet.2020.106050
Metcalf JL, Xu ZZ, Weiss S, Lax S, Van Treuren W, Hyde ER, et al. Microbial community assembly and metabolic function during mammalian corpse decomposition. Science. 2016;351(6269):158–62. Disponible en: https:// doi.org/10.1126/science.aad2646
Jie CAO, Li WJ, Wang YF, An GS, Lu XJ, DU Q xiang, et al. Estimating postmortem interval using intestinal microbiota diversity based on 16S rRNA high-throughput sequencing technology. J Forensic Med. 2021;37(5):6216. Disponible en: https://doi.org/10.12116/j.issn.10045619.2020.400708
Giles SB, Harrison K, Errickson D, Márquez-Grant N. The effect of seasonality on the application of accumulated degree-days to estimate the early post-mortem interval. Forensic Sci Int. 2020;315:110419. Disponible en: https:// doi.org/10.1016/j.forsciint.2020.110419
Carter DO, Yellowlees D, Tibbett M. Moisture can be the dominant environmental parameter governing cadaver decomposition in soil. Forensic Sci Int. 2010;200(13):60–6. Disponible forsciint.2010.03.031 en: https://doi.org/10.1016/j.
Tolbert M, Finley SJ, Visonà SD, Soni S, Osculati A, Javan GT. The thanatotranscriptome: Gene expression of male reproductive organs after death. Gene. 2018;675:191–6. Disponible en: https://doi.org/10.1016/j.gene.2018.06.090
Zou Y, Zhuang C, Fang Q, Li F. Big data and artificial intelligence: new insight into the estimation of postmortem interval. Fa Yi Xue Za Zhi. 2020;36(1):86–90. Disponible en: https://doi.org/10.12116/j.issn.1004-5619.2020.01.017
Singh H, Clarke T, Brinkac L, Greco C, Nelson KE. Forensic microbiome database: a tool for forensic geolocation metaanalysis using publicly available 16S rRNA microbiome sequencing. Front Microbiol. 2021;12:644861. Disponible en: https://doi.org/10.3389/fmicb.2021.644861
Aditya S, Sharma AK, Bhattacharyya CN, Chaudhuri K. Generating STR profile from “Touch DNA”. J Forensic Leg Med. 2011;18(7):295–8. Disponible en: https://doi. org/10.1016/j.jflm.2011.05.007
D’angiolella G, Tozzo P, Gino S, Caenazzo L. Trick or treating in forensics—the challenge of the saliva microbiome: a narrative review. Microorganisms. 2020;8(10):1501. Disponible en: https://doi.org/10.3390/ microorganisms8101501
Wang S, Song F, Gu H, Shu Z, Wei X, Zhang K, et al. Assess the diversity of gut microbiota among healthy adults for forensic application. Microb Cell Fact. 2022;21(1):46. Disponible en: https://doi.org/10.1186/s12934-022-01769-6
Watts GS, Youens-Clark K, Slepian MJ, Wolk DM, Oshiro MM, Metzger GS, et al. 16S rRNA gene sequencing on a benchtop sequencer: accuracy for identification of clinically important bacteria. J Appl Microbiol. 2017;123(6):158496. Disponible en: https://doi.org/10.1111/jam.13590
Johnson JS, Spakowicz DJ, Hong BY, Petersen LM, Demkowicz P, Chen L, et al. Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis. Nat Commun. 2019;10(1):5029. Disponible en: https://doi.org/10.1038/s41467-019-13036-1
Chakravorty S, Helb D, Burday M, Connell N, Alland D. A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. J Microbiol Methods. 2007;69(2):330–9. Disponible en: https://doi. org/10.1016/j.mimet.2007.02.005
Franzosa EA, Huang K, Meadow JF, Gevers D, Lemon KP, Bohannan BJM, et al. Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci. 2015;112(22):E2930–8. Disponible en: https://doi. org/10.1073/pnas.1423854112
Schloissnig S, Arumugam M, Sunagawa S, Mitreva M, Tap J, Zhu A, et al. Genomic variation landscape of the human gut microbiome. Nature. 2013;493(7430):45–50. Disponible en: https://doi.org/10.1038/nature11711
Young JM, Linacre A. Massively parallel sequencing is unlocking the potential of environmental trace evidence. Forensic Sci Int Genet. 2021;50:102393. Disponible en: https://doi.org/10.1016/j.fsigen.2020.102393
Allwood JS, Fierer N, Dunn RR. The future of environmental DNA in forensic science. Appl Environ Microbiol. 2020;86(2):e01504-19. Disponible en: https:// doi.org/10.1128/AEM.01504-19

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