Application of Microbiome in Forensics

Overview

Journal Genomics Proteomics Bioinformatics

Specialty Biology

Date 2022 Aug 28

PMID 36031058

Authors

Jun Zhang

Wenli Liu

Halimureti Simayijiang

Ping Hu

Jiangwei Yan

Affiliations

Soon will be listed here.

Abstract

Recent advances in next-generation sequencing technologies and improvements in bioinformatics have expanded the scope of microbiome analysis as a forensic tool. Microbiome research is concerned with the study of the compositional profile and diversity of microbial flora as well as the interactions between microbes, hosts, and the environment. It has opened up many new possibilities for forensic analysis. In this review, we discuss various applications of microbiome in forensics, including identification of individuals, geolocation inference, and post-mortem interval (PMI) estimation.

Citing Articles

Methodology for the analysis of biological impurities associated with peri-eucharistic phenomena.

Grzybowski T, Wrzosek M, Wolyniec W, Halon A, Chmielik E, Gorzkiewicz M Appl Microbiol Biotechnol. 2025; 109(1):58.

PMID: 40042646 PMC: 11882681. DOI: 10.1007/s00253-025-13439-9.

Gut microbial predictors of first-line immunotherapy efficacy in advanced NSCLC patients.

Grenda A, Iwan E, Kuznar-Kaminska B, Bomba A, Bielinska K, Krawczyk P Sci Rep. 2025; 15(1):6139.

PMID: 39979394 PMC: 11842579. DOI: 10.1038/s41598-025-89406-1.

Exploring the impact of xenobiotic drugs on forensic entomology for accurate post-mortem interval estimation.

Jain S, Parrott J, Javan G Front Insect Sci. 2025; 4:1411342.

PMID: 39935767 PMC: 11810894. DOI: 10.3389/finsc.2024.1411342.

Medico-Legal Applications of the Human Microbiome and Critical Issues Due to Environmental Transfer: A Review.

Ricchezze G, Buratti E, De Micco F, Cingolani M, Scendoni R Microorganisms. 2025; 12(12.

PMID: 39770627 PMC: 11677503. DOI: 10.3390/microorganisms12122424.

Forensic Microbiology: When, Where and How.

Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, DAleo F Microorganisms. 2024; 12(5).

PMID: 38792818 PMC: 11123702. DOI: 10.3390/microorganisms12050988.

References

Deschasaux M, Bouter K, Prodan A, Levin E, Groen A, Herrema H . Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography. Nat Med. 2018; 24(10):1526-1531. DOI: 10.1038/s41591-018-0160-1. View

Franzosa E, Huang K, Meadow J, Gevers D, Lemon K, Bohannan B . Identifying personal microbiomes using metagenomic codes. Proc Natl Acad Sci U S A. 2015; 112(22):E2930-8. PMC: 4460507. DOI: 10.1073/pnas.1423854112. View

Choi A, Shin K, Yang W, Lee H . Body fluid identification by integrated analysis of DNA methylation and body fluid-specific microbial DNA. Int J Legal Med. 2013; 128(1):33-41. DOI: 10.1007/s00414-013-0918-4. View

Wagner J, Coupland P, Browne H, Lawley T, Francis S, Parkhill J . Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification. BMC Microbiol. 2016; 16(1):274. PMC: 5109829. DOI: 10.1186/s12866-016-0891-4. View

Perez Perez G, Gao Z, Jourdain R, Ramirez J, Gany F, Clavaud C . Body Site Is a More Determinant Factor than Human Population Diversity in the Healthy Skin Microbiome. PLoS One. 2016; 11(4):e0151990. PMC: 4835103. DOI: 10.1371/journal.pone.0151990. View

. Structure, function and diversity of the healthy human microbiome. Nature. 2012; 486(7402):207-14. PMC: 3564958. DOI: 10.1038/nature11234. View

Toyomane K, Yokota R, Watanabe K, Akutsu T, Asahi A, Kubota S . Evaluation of CRISPR Diversity in the Human Skin Microbiome for Personal Identification. mSystems. 2021; 6(1). PMC: 7857535. DOI: 10.1128/mSystems.01255-20. View

Dobay A, Haas C, Fucile G, Downey N, Morrison H, Kratzer A . Microbiome-based body fluid identification of samples exposed to indoor conditions. Forensic Sci Int Genet. 2019; 40:105-113. DOI: 10.1016/j.fsigen.2019.02.010. View

Zhang J, Wang M, Qi X, Shi L, Zhang J, Zhang X . Predicting the postmortem interval of burial cadavers based on microbial community succession. Forensic Sci Int Genet. 2021; 52:102488. DOI: 10.1016/j.fsigen.2021.102488. View

10.

Schmedes S, Woerner A, Novroski N, Wendt F, King J, Stephens K . Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification. Forensic Sci Int Genet. 2017; 32:50-61. DOI: 10.1016/j.fsigen.2017.10.004. View

11.

Gilbert J, Jansson J, Knight R . The Earth Microbiome project: successes and aspirations. BMC Biol. 2014; 12:69. PMC: 4141107. DOI: 10.1186/s12915-014-0069-1. View

12.

Budowle B, Schmedes S, Wendt F . Increasing the reach of forensic genetics with massively parallel sequencing. Forensic Sci Med Pathol. 2017; 13(3):342-349. DOI: 10.1007/s12024-017-9882-5. View

13.

Kuleshov V, Jiang C, Zhou W, Jahanbani F, Batzoglou S, Snyder M . Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome. Nat Biotechnol. 2015; 34(1):64-9. PMC: 4884093. DOI: 10.1038/nbt.3416. View

14.

Prodan A, Tremaroli V, Brolin H, Zwinderman A, Nieuwdorp M, Levin E . Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing. PLoS One. 2020; 15(1):e0227434. PMC: 6964864. DOI: 10.1371/journal.pone.0227434. View

15.

Carter D, Metcalf J, Bibat A, Knight R . Seasonal variation of postmortem microbial communities. Forensic Sci Med Pathol. 2015; 11(2):202-7. PMC: 9636889. DOI: 10.1007/s12024-015-9667-7. View

16.

Cummings C, Bormann Chung C, Fang R, Barker M, Brzoska P, Williamson P . Accurate, rapid and high-throughput detection of strain-specific polymorphisms in Bacillus anthracis and Yersinia pestis by next-generation sequencing. Investig Genet. 2010; 1(1):5. PMC: 2988479. DOI: 10.1186/2041-2223-1-5. View

17.

Li D, Liu C, Luo R, Sadakane K, Lam T . MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015; 31(10):1674-6. DOI: 10.1093/bioinformatics/btv033. View

18.

Pechal J, Crippen T, Benbow M, Tarone A, Dowd S, Tomberlin J . The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing. Int J Legal Med. 2013; 128(1):193-205. DOI: 10.1007/s00414-013-0872-1. View

19.

Schloss P, Westcott S, Ryabin T, Hall J, Hartmann M, Hollister E . Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol. 2009; 75(23):7537-41. PMC: 2786419. DOI: 10.1128/AEM.01541-09. View

20.

Camacho D, Collins K, Powers R, Costello J, Collins J . Next-Generation Machine Learning for Biological Networks. Cell. 2018; 173(7):1581-1592. DOI: 10.1016/j.cell.2018.05.015. View