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Karadayı B, Karaismailoğlu B, Karadayı S, Arslan A, Gözen ED, Özbek T. The uselessness of using salivary microbiota in forensic identification purposes of a person with recent antibiotic use. Leg Med (Tokyo) 2024; 69:102338. [PMID: 37884410 DOI: 10.1016/j.legalmed.2023.102338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
The detection of microbial flora changes in saliva samples because of antibiotic use through advanced molecular genetic analysis is important for forensic and clinical applications. This study aims to reveal the variability in the microbial structure of human saliva after antibiotic use with metagenomic analysis techniques from a forensic point of view. Within the scope of the study, saliva samples were collected from patients who were under the effect of regional anesthesia to be administered a standardized course of antibiotic therapy that lasted for a week. The analysis was conducted on 56 saliva samples from 14 individuals over four different time intervals. Isolation of the 16S rRNA region and PCR analysis were performed prior to sequence analysis to determine the microbiome structure of the samples at phylum, genus, and species levels. As expected, changes were observed in bacterial species found in saliva samples after administration of antibiotics and this was linked to the specific type of antibiotics that were administered. This change was statistically significant for Firmicutes, Spirochetes, and Verrucomicrobiota. Furthermore, although the oral microbiome tends to return to its former state at the phylum and genus level within a 4-week period after the start of antibiotic use, it is observed that the change, especially in some bacterial species, still continues. The findings of this study show that because of the inability of stabilization at species-level in a period of 4 weeks from the start of antibiotic use, it is not suitable to assess saliva samples at species-level for forensic identification.
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Affiliation(s)
- Beytullah Karadayı
- Department of Forensic Medicine, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
| | - Bedri Karaismailoğlu
- Department of Orthopaedics and Traumatology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
| | - Sukriye Karadayı
- Department of Medical Laboratory Techniques, Altınbaş University, Istanbul, Turkey.
| | - Ali Arslan
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, Istanbul, Turkey.
| | - Emine Deniz Gözen
- Department of Otorhinolaryngology, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
| | - Tülin Özbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, Istanbul, Turkey.
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Worrapitirungsi W, Sathirapatya T, Sukawutthiya P, Vongpaisarnsin K, Varrathyarom P. Assessing the feasibility of free DNA for disaster victim identification and forensic applications. Sci Rep 2024; 14:5411. [PMID: 38443390 PMCID: PMC10914783 DOI: 10.1038/s41598-024-53040-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/27/2024] [Indexed: 03/07/2024] Open
Abstract
In tropical disaster victim identification (DVI) scenarios, challenging environmental conditions lead to accelerated DNA degradation in remains. To further enhance the utilization of leached DNA from tissue in the preservative solution (termed "free DNA") as an alternative source, we incorporated new results by assessing its integrity in postmortem and decomposing cadavers preserved in DNA/RNA Shield™ and modified TENT, with silica-based purification (QIAquick®) for faster processing. The psoas muscle tissues of one decomposed and ten cadavers were preserved in each solution at 25 °C and 35 °C for 3 months. Free DNA efficiency was compared with individual reference samples for reliable results in quantity, quality, and STR profiles. The findings revealed that DNA/RNA Shield™ effectively preserves free DNA integrity for extended storage, while modified TENT is more suitable for short-term storage due to higher degradation levels. Moreover, the use of free DNA samples with massive parallel sequencing displays potential for forensic DNA analysis. Successful amplification of the mtDNA control region enables variant calling and heteroplasmy analysis while also serving as quality control using ACTB and enabling differentiation within the 16S rRNA region for microbiome analysis. The simplicity of handling free DNA for PCR-based forensic analysis adds to its potential for various applications, including DVI and field-based analysis of biological evidence.
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Affiliation(s)
- Wikanda Worrapitirungsi
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tikumphorn Sathirapatya
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
| | - Pagparpat Varrathyarom
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
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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; 15:1360457. [PMID: 38371926 PMCID: PMC10869621 DOI: 10.3389/fmicb.2024.1360457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
Forensic microbiome research is a field with a wide range of applications and a number of protocols have been developed for its use in this area of research. As individuals host radically different microbiota, the human microbiome is expected to become a new biomarker for forensic identification. To achieve an effective use of this procedure an understanding of factors which can alter the human microbiome and determinations of stable and changing elements will be critical in selecting appropriate targets for investigation. The 16S rRNA gene, which is notable for its conservation and specificity, represents a potentially ideal marker for forensic microbiome identification. Gene sequencing involving 16S rRNA is currently the method of choice for use in investigating microbiomes. While the sequencing involved with microbiome determinations can generate large multi-dimensional datasets that can be difficult to analyze and interpret, machine learning methods can be useful in surmounting this analytical challenge. In this review, we describe the research methods and related sequencing technologies currently available for application of 16S rRNA gene sequencing and machine learning in the field of forensic identification. In addition, we assess the potential value of 16S rRNA and machine learning in forensic microbiome science.
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Affiliation(s)
- Mai-Qing Yang
- Department of Pathology, Weifang People's Hospital (First Affiliated Hospital of Shandong Second Medical University), Weifang, China
| | - Zheng-Jiang Wang
- Department of Pathology, Weifang People's Hospital (First Affiliated Hospital of Shandong Second Medical University), Weifang, China
| | - Chun-Bo Zhai
- Department of Second Ward of Thoracic Surgery, Weifang People's Hospital (First Affiliated Hospital of Shandong Second Medical University), Weifang, China
| | - Li-Qian Chen
- Department of Pathology, Weifang People's Hospital (First Affiliated Hospital of Shandong Second Medical University), Weifang, China
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Wu Z, Guo Y, Hayakawa M, Yang W, Lu Y, Ma J, Li L, Li C, Liu Y, Niu J. Artificial intelligence-driven microbiome data analysis for estimation of postmortem interval and crime location. Front Microbiol 2024; 15:1334703. [PMID: 38314433 PMCID: PMC10834752 DOI: 10.3389/fmicb.2024.1334703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Microbial communities, demonstrating dynamic changes in cadavers and the surroundings, provide invaluable insights for forensic investigations. Conventional methodologies for microbiome sequencing data analysis face obstacles due to subjectivity and inefficiency. Artificial Intelligence (AI) presents an efficient and accurate tool, with the ability to autonomously process and analyze high-throughput data, and assimilate multi-omics data, encompassing metagenomics, transcriptomics, and proteomics. This facilitates accurate and efficient estimation of the postmortem interval (PMI), detection of crime location, and elucidation of microbial functionalities. This review presents an overview of microorganisms from cadavers and crime scenes, emphasizes the importance of microbiome, and summarizes the application of AI in high-throughput microbiome data processing in forensic microbiology.
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Affiliation(s)
- Ze Wu
- Department of Dermatology, General Hospital of Northern Theater Command, Shenyang, China
| | - Yaoxing Guo
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, Shenyang, China
- National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Miren Hayakawa
- Beijing Anzhen Hospital, Capital Medical University, Beijing, China
| | - Wei Yang
- Department of Dermatology, General Hospital of Northern Theater Command, Shenyang, China
| | - Yansong Lu
- Department of Dermatology, General Hospital of Northern Theater Command, Shenyang, China
| | - Jingyi Ma
- Department of Dermatology, General Hospital of Northern Theater Command, Shenyang, China
| | - Linghui Li
- Department of Dermatology, General Hospital of Northern Theater Command, Shenyang, China
| | - Chuntao Li
- Department of Dermatology, General Hospital of Northern Theater Command, Shenyang, China
| | - Yingchun Liu
- Department of Dermatology, General Hospital of Northern Theater Command, Shenyang, China
| | - Jun Niu
- Department of Dermatology, General Hospital of Northern Theater Command, Shenyang, China
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Kasprzyk I. Forensic botany: who?, how?, where?, when? Sci Justice 2023; 63:258-275. [PMID: 36870705 DOI: 10.1016/j.scijus.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/19/2023]
Abstract
Plants are a good source of biological forensic evidence; this is due to their ubiquity, their ability to collect reference material, and their sensitivity to environmental changes. However, in many countries, botanical evidence is recognised as being scientifically. Botanical evidence is not mostly used for perpertration, instead it tends to serve as circumstantial evidence. Plant materials constitute the basis, among others, for linking a suspect or object to a crime scene or a victim, confirming or not confirming an alibi, determining the post-mortem interval, and determining the origin of food/object. Forensic botany entails field work, knowledge of plants, understanding ecosystem processes, and a basis understaning of geoscience. In this study, experiments with mammal cadavers were conducted to determine the occurence of an event. The simplest criterion characterising botanical evidence is its size. Therefore, macroremains include whole plants or their larger fragments (e.g. tree bark, leaves, seeds, prickles, and thorns), whereas microscopic evidence includes palynomorphs (spores and pollen grains), diatoms, and tissues. Botanical methods allow for an analysis to be repeated multiple times and the test material is easy to collect in the field. Forensic botany can be supplemented with molecular analyses, which, although specific and sensitive, still require validation.
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Affiliation(s)
- Idalia Kasprzyk
- Institute of Biology and Biotechnology, College of Natural Sciences, University of Rzeszów, Al. Rejtana 16c, 35-959 Rzeszów, Poland.
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Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGD, Teixeira Mendes-Junior C. Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 2022; 45:e20220077. [PMID: 36121926 PMCID: PMC9514793 DOI: 10.1590/1678-4685-gmb-2022-0077] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | - Vitor Matheus Soares Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | | | | | - Celso Teixeira Mendes-Junior
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
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Gül F, Karadayı S, Yurdabakan Z, Özbek T, Karadayı B. Investigating changes in salivary microbiota due to dental treatment: A metagenomic analysis study for forensic purposes. Forensic Sci Int 2022; 340:111447. [PMID: 36116269 DOI: 10.1016/j.forsciint.2022.111447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/31/2022] [Indexed: 11/20/2022]
Abstract
The advent of next generation sequencing techniques as well as the existing traditional culture methods has enabled metagenomic studies on the usability of microbiomes for the forensic identification of individuals to gain momentum. However, before the utilization of microbiomes as a potential technique for real forensic case resolutions, it is necessary to understand the stability of the microbiota compositions in an individual's biological samples and the factors responsible for their variations. In the present study, we compared the microbiota compositions present in the saliva of individuals with active dental caries before and after treatment from a forensic and clinical perspective using an approach based on the sequencing of all the variable regions (V1-V9) of the bacterial 16 S rRNA gene. For this purpose, 10 individuals were included in the study comprising of 8 individuals between the ages of 18-50 years with at least 3 deep dentin caries as patients and 2 healthy individuals without any dental or gingival diseases as controls. Saliva samples were collected from the patients at two timepoints, before and after treatment, as well as from the healthy individuals (before and after control) at an interval of 1 month. The collected 20 saliva samples were subjected to metagenomic analysis using the MinION device, which was developed by Oxford Nanopore Technologies (ONT Oxford, UK). Bioinformatic analyses were performed on the obtained data and the results were evaluated using statistical comparison methods and alpha/beta diversity analyses within the scope of the study objective. On evaluation using the distance metrics, it was observed that the microbial compositions in the saliva of individuals with active caries remained relatively stable after treatment. However, the relative abundance levels of bacteria of 28 genera and species showed statistically significant differences before and after treatment (p < 0.05). As a result, although the composition of salivary microbiome remained relatively stable after caries treatment, there were significant changes in many types of bacteria, especially at the species level, between the BT and AT samples. Our results provide a framework for further forensic and clinical investigations regarding the factors that affect human salivary microbiome diversity.
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Affiliation(s)
- Feyza Gül
- Institute of Forensic Sciences and Legal Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
| | - Sukriye Karadayı
- Department of Medical Laboratory Techniques, Altınbaş University, Istanbul, Turkey.
| | - Zuhal Yurdabakan
- Department of Oral and Dentomaxillofacial Radiology, Faculty of Dentistry, Altınbaş University, Istanbul, Turkey.
| | - Tülin Özbek
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, Istanbul, Turkey.
| | - Beytullah Karadayı
- Department of Forensic Medicine, Cerrahpasa Medical Faculty, Istanbul University-Cerrahpaşa, Istanbul, Turkey.
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