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Foster NR, Taylor D, Hoogewerff J, Aberle MG, de Caritat P, Roffey P, Edwards R, Malik A, Waycott M, Young JM. The secret hidden in dust: Assessing the potential to use biological and chemical properties of the airborne fraction of soil for provenance assignment and forensic casework. Forensic Sci Int Genet 2023; 67:102931. [PMID: 37659257 DOI: 10.1016/j.fsigen.2023.102931] [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: 09/30/2022] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/04/2023]
Abstract
The airborne fraction of soil (dust) is both ubiquitous in nature and contains localised biological and chemical signatures, making it a potential medium for forensic intelligence. Metabarcoding of dust can yield biological communities unique to the site of interest, similarly, geochemical analyses can uncover elements and minerals within dust that can be matched to a geographic location. Combining these analyses presents multiple lines of evidence as to the origin of dust collected from items of interest. In this work, we investigated whether bacterial and fungal communities in dust change through time and whether they are comparable to soil samples of the same site. We integrated dust metabarcoding into a framework amenable to forensic casework, (i.e., using calibrated log-likelihood ratios) to predict the origin of dust samples using models constructed from both dust samples and soil samples from the same site. Furthermore, we tested whether both metabarcoding and geochemical/mineralogical analyses could be conducted on a single swabbed sample, for situations where sampling is limited. We found both analyses could generate results from a single swabbed sample and found biological and chemical signatures unique to sites. However, we did find significant variation within sites, where this did not always correlate with time but was a random effect of sampling. This variation within sites was not greater than between sites and so did not influence site discrimination. When modelling bacterial and fungal diversity using calibrated log-likelihood ratios, we found samples were correctly predicted using dust 67% and 56% of the time and using soil 56% and 22% of the time for bacteria and fungi communities respectively. Incorrect predictions were related to within site variability, highlighting limitations to assigning dust provenance using metabarcoding of soil.
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Affiliation(s)
- Nicole R Foster
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia.
| | - Duncan Taylor
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia; Forensic Science SA, GPO Box 2790, Adelaide, SA 5001, Australia
| | - Jurian Hoogewerff
- National Centre for Forensic Studies, University of Canberra, Bruce Australian Capital Territory 2617, Australia
| | - Michael G Aberle
- National Centre for Forensic Studies, University of Canberra, Bruce Australian Capital Territory 2617, Australia
| | - Patrice de Caritat
- National Centre for Forensic Studies, University of Canberra, Bruce Australian Capital Territory 2617, Australia; Geoscience Australia, GPO Box 378, Canberra Australian Capital Territory 2601, Australia
| | - Paul Roffey
- National Centre for Forensic Studies, University of Canberra, Bruce Australian Capital Territory 2617, Australia; Australian Federal Police, GPO Box 401, Canberra Australian Capital Territory 2601, Australia
| | - Robert Edwards
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
| | - Arif Malik
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Michelle Waycott
- School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jennifer M Young
- College of Science and Engineering, Flinders University, GPO Box 2100, Adelaide, SA 5001, Australia
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2
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Tambuzzi S, Maciocco F, Gentile G, Boracchi M, Bailo P, Marchesi M, Zoja R. Applications of microbiology to different forensic scenarios - A narrative review. J Forensic Leg Med 2023; 98:102560. [PMID: 37451142 DOI: 10.1016/j.jflm.2023.102560] [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: 12/21/2022] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
In contrast to other forensic disciplines, forensic microbiology is still too often considered a "side activity" and is not able to make a real and concrete contribution to forensic investigations. Indeed, the various application aspects of this discipline still remain a niche activity and, as a result, microbiological investigations are often omitted or only approximated, in part due to poor report in the literature. However, in certain situations, forensic microbiology can prove to be extremely effective, if not crucial, when all other disciplines fail. Precisely because microorganisms can represent forensic evidence, in this narrative review all the major pathological forensic applications described in the literature have been presented. The goal of our review is to highlight the versatility and transversality of microbiology in forensic science and to provide a comprehensive source of literature to refer to when needed.
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Affiliation(s)
- Stefano Tambuzzi
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| | - Francesca Maciocco
- Azienda Ospedaliera "San Carlo Borromeo", Servizio di Immunoematologia e Medicina Trasfusionale (SIMT), Via Pio II°, n. 3, Milano, Italy
| | - Guendalina Gentile
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy.
| | - Michele Boracchi
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| | | | - Matteo Marchesi
- ASST Papa Giovanni XXIII, Piazza OMS 1, 24127, Bergamo, Italy
| | - Riccardo Zoja
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
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3
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Moitas B, Caldas IM, Sampaio-Maia B. Forensic microbiology and geographical location: a systematic review. AUST J FORENSIC SCI 2023. [DOI: 10.1080/00450618.2023.2191993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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4
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Zhang J, Liu W, Simayijiang H, Hu P, Yan J. Application of Microbiome in Forensics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00096-1. [PMID: 36031058 PMCID: PMC10372919 DOI: 10.1016/j.gpb.2022.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/29/2022] [Indexed: 06/04/2023]
Abstract
Recent advances in next-generation sequencing technology 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 microbiomes in forensics, including identification of individuals, geolocation inference, post-mortem interval (PMI) estimation, and others.
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Affiliation(s)
- Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Wenli Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | | | - Ping Hu
- Key Laboratory of Environment and Health (HUST), Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
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Guo Z, Bao Y, Liu J. Environmental Difference and Spatial Distance Affect the Fidelity of Variation Source of Microbial Community Structure in Air-Dried Soils. Microorganisms 2022; 10:microorganisms10040672. [PMID: 35456724 PMCID: PMC9031423 DOI: 10.3390/microorganisms10040672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
Air-dried soil archives are important for microbial ecology research, although the process of air-drying preservation inevitably destroys the original microbial information in soils. Only upon fully understanding the limitations of air-dried soil can it play a greater role. The value of air-dried soil depends on the fidelity of microbial community structure information in the air-dried soil relative to that in fresh soil. To evaluate this, high-throughput sequencing was applied to investigate the microbial community of fresh soils and 227 days air-dried archives from typical farmland under a large spatial scale, and PERMANOVA was used to analyze the explanation proportion (EP) of the spatial factor on the microbial community structure in any paired-fresh or air-dried soils. The results show that for any paired soils, the value of EP ranged from 42.4% to 97.9% (p < 0.001). Importantly, taking fresh soil as a reference, the value of EP declined in air-dried soils (effect size r = 0.79, p < 0.001). Furthermore, the standardized difference in EP between fresh and air-dried soil (NDEP) was used to characterize the fidelity of variance source of microbial community structure in air-dried soils, and correlation tests showed that NDEP was negatively correlated with spatial distance (r = −0.21, p < 0.01) and with environmental difference (r = −0.37, p < 0.001). Further analyses show that larger NDEP was observed at a spatial distance <25 km or an environmental difference <0.58. Variance partitioning analysis showed that 28.0% of the variation in NDEP could be explained, with environmental difference constituting 14.0% and the interaction between the environmental difference and spatial distance constituting the remaining 14.0%. Soil texture was the most important factor for predicting NDEP, followed by soil pH and annual average temperature. This study not only emphasizes the possible decline in EP when using air-dried soils to reveal microbial community patterns, but also implies that air-dried soil is more suitable for addressing scientific questions under a large spatial scale or environmental differences.
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Affiliation(s)
- Zhiying Guo
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Correspondence:
| | - Yuanyuan Bao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
| | - Jie Liu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China; (Y.B.); (J.L.)
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Efeoğlu FG, Çakan H, Kara U, Daş T. Forensic Microbiological Analysis of Soil and the Physical Evidence Buried in Soil Obtained from Several Towns in Istanbul. Cureus 2022; 14:e22329. [PMID: 35317034 PMCID: PMC8934109 DOI: 10.7759/cureus.22329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/17/2022] [Indexed: 11/23/2022] Open
Abstract
Background The identification of bacterial species in the soil can be used for the differentiation of soil samples and physical evidence. This study aims to evaluate the importance of identifying microorganisms in the soil for forensic sciences. The study covered 20 regions identified and marked outside the settlement areas within the boundaries of Istanbul. Methodology Big and wide soil and forest areas were preferred. Four types of physical evidence samples were collected from the identified areas at the end of the first, second, and third months and then analyzed. The collected samples were physically embedded in the soil. In this study, 10 g of soil sample and four pieces of physical evidence (fabric, rubber, metal, and wood), sized 5 × 5 cm and buried 20-30 cm deep in the soil, contaminated with soil were collected for analysis and stored in sterile conditions. The microbiological identification analyses were conducted at the end of the predefined period and in the predefined order using first phenotypic (e.g., microscopic and macroscopic), followed by culture methods using advanced diagnostic analyses, such as API and matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Results In the soil samples and the physical evidence samples collected, 83% bacteria and 17% fungus were identified. A database was set up for the study findings. Conclusions The presence of microorganisms in the soil and physical evidence samples contaminated with soil, which is crucial in the evaluation of criminal cases, was determined using microbiological analysis.
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Assessment of the link between evidence and crime scene through soil bacterial and fungal microbiome: A mock case in forensic study. Forensic Sci Int 2021; 329:111060. [PMID: 34736047 DOI: 10.1016/j.forsciint.2021.111060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/10/2021] [Accepted: 10/19/2021] [Indexed: 01/28/2023]
Abstract
In forensic studies, soil traces can be used to find clues to the origin of an unknown sample or the relationship between a crime scene and a suspect and can provide invaluable evidence as they frequently adhere to objects, with high persistence. In this study, it was aimed to investigate the potential of the bacterial and fungal microbiome diversity of the soil to be used as legitimate evidence in the resolution of homicide cases. Within the scope of a mock homicide case scenario, a total of 12 soil samples were collected, including two evidence samples, three crime scene samples and seven non-crime scene related control samples. Both bacterial and fungal microbiome profiles of these samples were analysed using Illumina NovaSeq platform. The resulting sequences were analysed using QIIME 2 microbiome bioinformatics platform. Beta diversity analysis was performed to determine the difference between samples. In bacterial community analyses, it has been observed that it is difficult to distinguish evidence samples and crime scene samples from control samples at phylum and class level, whereas differentiation could be made at genus and species level. Fungal community analyses allowed to distinguish evidence samples and crime scene samples from control samples at both phylum and class and genus and species level. Principal coordinate analysis (PCoA) results showed that distance between evidence samples and crime scene reference samples was closer to each other than non-crime scene related control samples. The results of this study showed that bacterial and especially fungal DNA in soil has the potential to contribute effectively to the resolution of forensic cases. Thus, it has been understood that it is possible to establish a relationship between the case and the crime scene with the help of microbiome analyses on soil samples obtained in homicide cases.
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8
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Robinson JM, Pasternak Z, Mason CE, Elhaik E. Forensic Applications of Microbiomics: A Review. Front Microbiol 2021; 11:608101. [PMID: 33519756 PMCID: PMC7838326 DOI: 10.3389/fmicb.2020.608101] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023] Open
Abstract
The rise of microbiomics and metagenomics has been driven by advances in genomic sequencing technology, improved microbial sampling methods, and fast-evolving approaches in bioinformatics. Humans are a host to diverse microbial communities in and on their bodies, which continuously interact with and alter the surrounding environments. Since information relating to these interactions can be extracted by analyzing human and environmental microbial profiles, they have the potential to be relevant to forensics. In this review, we analyzed over 100 papers describing forensic microbiome applications with emphasis on geolocation, personal identification, trace evidence, manner and cause of death, and inference of the postmortem interval (PMI). We found that although the field is in its infancy, utilizing microbiome and metagenome signatures has the potential to enhance the forensic toolkit. However, many of the studies suffer from limited sample sizes and model accuracies, and unrealistic environmental settings, leaving the full potential of microbiomics to forensics unexplored. It is unlikely that the information that can currently be elucidated from microbiomics can be used by law enforcement. Nonetheless, the research to overcome these challenges is ongoing, and it is foreseeable that microbiome-based evidence could contribute to forensic investigations in the future.
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Affiliation(s)
- Jake M Robinson
- Department of Landscape, University of Sheffield, Sheffield, United Kingdom.,Healthy Urban Microbiome Initiative (HUMI), Adelaide, SA, Australia
| | - Zohar Pasternak
- Quality Assurance and Evidence Unit, Division of Identification and Forensic Science (DIFS), National Headquarters of the Israel Police, Jerusalem, Israel
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, United States.,The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, United States
| | - Eran Elhaik
- Department of Biology, Lund University, Lund, Sweden
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9
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Young JM, Linacre A. Massively parallel sequencing is unlocking the potential of environmental trace evidence. Forensic Sci Int Genet 2020; 50:102393. [PMID: 33157385 DOI: 10.1016/j.fsigen.2020.102393] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/03/2020] [Accepted: 09/07/2020] [Indexed: 01/16/2023]
Abstract
Massively parallel sequencing (MPS) has revolutionised the field of genomics enabling substantial advances in human DNA profiling. Further, the advent of MPS now allows biological signatures to be obtained from complex DNA mixtures and trace amounts of low biomass samples. Environmental samples serve as ideal forms of contact trace evidence as detection at a scene can establish a link between a suspect, location and victim. Many studies have applied MPS technology to characterise the biodiversity within high biomass environmental samples (such as soil and water) to address questions related to ecology, conservation, climate change and human health. However, translation of these tools to forensic science remains in its infancy, due in part to the merging of traditional forensic ecology practices with unfamiliar DNA technologies and complex datasets. In addition, people and objects also carry low biomass environmental signals which have recently been shown to reflect a specific individual or location. The sensitivity, and reducing cost, of MPS is now unlocking the power of both high and low biomass environmental DNA (eDNA) samples as useful sources of genetic information in forensic science. This paper discusses the potential of eDNA to forensic science by reviewing the most explored applications that are leading the integration of this technology into the field. We introduce novel areas of forensic ecology that could also benefit from these tools with a focus on linking a suspect to a scene or establishing provenance of an unknown sample and discuss the current limitations and validation recommendations to achieve translation of eDNA into casework.
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Affiliation(s)
- J M Young
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia.
| | - A Linacre
- College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia
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10
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Foran DR, Badgley AJ. Bacterial Profiling of Soil For Forensic Investigations: Consideration of Ex Situ Changes in Questioned and Known Soil Samples. J Forensic Sci 2019; 65:471-480. [PMID: 31584712 DOI: 10.1111/1556-4029.14202] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/02/2019] [Accepted: 09/06/2019] [Indexed: 11/30/2022]
Abstract
Soil, being diverse and ubiquitous, can potentially link a suspect or victim to a crime scene. Recently scientists have examined the microbial makeup of soil for determining its origin, and differentiating soil samples is well-established. However, when soil is transferred to evidence its microbial makeup may change over time, leading to false exclusions. In this research, "known" soils from diverse habitats were stored under controlled conditions, while evidence soils were aged on mock evidence. Limited quantities of soil were also assayed. Bacterial profiles were produced using next-generation sequencing of the 16S rRNA gene. Overall, known soils stored open at room temperature were more similar to evidence soils over time than were known soils stored bagged and/or frozen. Evidence soils, even as little as 1 mg, associated with the correct habitat 99% of the time, accentuating the importance of considering ex situ microbial changes in soil for its successful use as forensic evidence.
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Affiliation(s)
- David R Foran
- Forensic Science Program, School of Criminal Justice and Department of Integrative Biology, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
| | - Alyssa J Badgley
- Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
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11
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Journey history reconstruction from the soils and sediments on footwear: An empirical approach. Sci Justice 2019; 59:306-316. [DOI: 10.1016/j.scijus.2018.11.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 11/02/2018] [Accepted: 11/04/2018] [Indexed: 11/23/2022]
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12
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Eom YB. Microbial Forensics: Human Identification. BIOMEDICAL SCIENCE LETTERS 2018; 24:292-304. [DOI: 10.15616/bsl.2018.24.4.292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 09/01/2023]
Affiliation(s)
- Yong-Bin Eom
- Department of Biomedical Laboratory Science, College of Medical Sciences, Soonchunhyang University, Asan, Chungnam 31538, Korea
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13
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Badgley AJ, Jesmok EM, Foran DR. Time Radically Alters Ex Situ Evidentiary Soil 16S Bacterial Profiles Produced Via Next-Generation Sequencing,. J Forensic Sci 2018; 63:1356-1365. [PMID: 29464695 DOI: 10.1111/1556-4029.13753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Revised: 12/27/2017] [Accepted: 01/22/2018] [Indexed: 11/29/2022]
Abstract
Previous research has revealed the potential of soil bacterial profiling for forensic purposes; however, investigators have not thoroughly examined fluctuations in microbial profiles from soil aged on evidence. In this research, soils collected from multiple habitats were placed on evidence items and sampled over time, and then bacterial profiles were generated via next-generation sequencing of the 16S rRNA locus. Bacterial abundance charts and nonmetric multidimensional scaling plots provided visual representation of bacterial profiles temporally, while supervised classification was used to statistically associate evidence to a source. The ex situ evidence soils displayed specific, consistent taxonomic changes as they aged, resulting in their drift in multidimensional space, but never toward a different habitat. Ninety-five percent of the 364 evidentiary profiles statistically classified to the correct habitat, with misclassification generally stemming from evidence type and increased age. Ultimately, understanding bacterial changes that occur temporally in ex situ soils should enhance their use in forensic investigations.
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Affiliation(s)
- Alyssa J Badgley
- Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
| | - Ellen M Jesmok
- Forensic Science Program, School of Criminal Justice, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
| | - David R Foran
- Forensic Science Program, School of Criminal Justice and Department of Integrative Biology, Michigan State University, 655 Auditorium Road, 560 Baker Hall, East Lansing, MI, 48824
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Young JM, Austin JJ, Weyrich LS. Soil DNA metabarcoding and high-throughput sequencing as a forensic tool: considerations, potential limitations and recommendations. FEMS Microbiol Ecol 2016; 93:fiw207. [DOI: 10.1093/femsec/fiw207] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/14/2016] [Accepted: 10/06/2016] [Indexed: 11/14/2022] Open
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Abstract
ABSTRACT
Soil microbial forensics can be defined as the study of how microorganisms can be applied to forensic investigations. The field of soil microbial forensics is of increasing interest and applies techniques commonly used in diverse disciplines in order to identify microbes and determine their abundances, complexities, and interactions with soil and surrounding objects. Emerging new techniques are also providing insights into the complexity of microbes in soil. Soil may harbor unique microbes that may reflect specific physical and chemical characteristics indicating site specificity. While applications of some of these techniques in the field of soil microbial forensics are still in early stages, we are still gaining insight into how microorganisms may be more robustly used in forensic investigations.
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16
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Young JM, Weyrich LS, Cooper A. High-throughput Sequencing of Trace Quantities of Soil Provides Reproducible and Discriminative Fungal DNA Profiles. J Forensic Sci 2016; 61:478-484. [PMID: 27404621 DOI: 10.1111/1556-4029.12996] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 04/26/2015] [Accepted: 05/10/2015] [Indexed: 11/28/2022]
Abstract
High-throughput sequencing (HTS) offers improved resolution between forensic soil samples by characterizing individual taxa present; however, the heterogeneous distribution of taxa in soils, and limited quantity of material available, may hinder the reliability of HTS in casework. Using HTS of the internal transcribed spacer, we examined the effect of soil mass (50, 150, and 250 mg) on fungal DNA profiles, focusing on reproducibility and discriminatory power between close proximity soils, and samples with similar textural classification. The results show that reduced soil mass had no significant effect on sample differentiation and that 150 mg soil provides the most reproducible DNA profiles across different soil types. In addition, Ascomycota was identified as a robust fungal target for forensic intelligence as this phylum was detected consistently across all samples regardless of sample quantity. Overall, this study highlights the value of trace quantities of soil for use in forensic casework.
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Affiliation(s)
- Jennifer M Young
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Darling Building, North Terrace Campus, Adelaide, SA, 5005, Australia
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Darling Building, North Terrace Campus, Adelaide, SA, 5005, Australia
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Darling Building, North Terrace Campus, Adelaide, SA, 5005, Australia
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17
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Predicting the origin of soil evidence: High throughput eukaryote sequencing and MIR spectroscopy applied to a crime scene scenario. Forensic Sci Int 2015; 251:22-31. [DOI: 10.1016/j.forsciint.2015.03.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 03/10/2015] [Indexed: 12/22/2022]
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18
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Young JM, Weyrich LS, Cooper A. Forensic soil DNA analysis using high-throughput sequencing: A comparison of four molecular markers. Forensic Sci Int Genet 2014; 13:176-84. [DOI: 10.1016/j.fsigen.2014.07.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/25/2014] [Accepted: 07/28/2014] [Indexed: 01/17/2023]
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19
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Nishi E, Tashiro Y, Sakai K. Discrimination among individuals using terminal restriction fragment length polymorphism profiling of bacteria derived from forensic evidence. Int J Legal Med 2014; 129:425-33. [DOI: 10.1007/s00414-014-1092-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 10/01/2014] [Indexed: 10/24/2022]
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20
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Araújo ASF, Borges CD, Tsai SM, Cesarz S, Eisenhauer N. Soil bacterial diversity in degraded and restored lands of Northeast Brazil. Antonie van Leeuwenhoek 2014; 106:891-9. [DOI: 10.1007/s10482-014-0258-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 08/08/2014] [Indexed: 01/27/2023]
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Khodakova AS, Smith RJ, Burgoyne L, Abarno D, Linacre A. Random whole metagenomic sequencing for forensic discrimination of soils. PLoS One 2014; 9:e104996. [PMID: 25111003 PMCID: PMC4128759 DOI: 10.1371/journal.pone.0104996] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/15/2014] [Indexed: 11/19/2022] Open
Abstract
Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.
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Affiliation(s)
| | - Renee J. Smith
- School of Biological Sciences, Flinders University, Adelaide, Australia
| | - Leigh Burgoyne
- School of Biological Sciences, Flinders University, Adelaide, Australia
| | - Damien Abarno
- School of Biological Sciences, Flinders University, Adelaide, Australia
- Forensic Science South Australia, Adelaide, Australia
| | - Adrian Linacre
- School of Biological Sciences, Flinders University, Adelaide, Australia
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Giampaoli S, Berti A, Di Maggio R, Pilli E, Valentini A, Valeriani F, Gianfranceschi G, Barni F, Ripani L, Romano Spica V. The environmental biological signature: NGS profiling for forensic comparison of soils. Forensic Sci Int 2014; 240:41-7. [DOI: 10.1016/j.forsciint.2014.02.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Revised: 02/11/2014] [Accepted: 02/25/2014] [Indexed: 10/25/2022]
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Young JM, Rawlence NJ, Weyrich LS, Cooper A. Limitations and recommendations for successful DNA extraction from forensic soil samples: A review. Sci Justice 2014; 54:238-44. [DOI: 10.1016/j.scijus.2014.02.006] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 01/12/2014] [Accepted: 02/18/2014] [Indexed: 11/15/2022]
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Nakanishi H, Shojo H, Ohmori T, Hara M, Takada A, Adachi N, Saito K. Identification of feces by detection of Bacteroides genes. Forensic Sci Int Genet 2012; 7:176-9. [PMID: 23068949 DOI: 10.1016/j.fsigen.2012.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2012] [Revised: 08/18/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
Abstract
In forensic science, the identification of feces is very important in a variety of crime investigations. However, no sensitive and simple fecal identification method using molecular biological techniques has been reported. Here, we focused on the fecal bacteria, Bacteroides uniformis, Bacteroides vulgatus and Bacteroides thetaiotaomicron, and developed a novel fecal identification method by detection of the gene sequences specific to these bacteria in various body (feces, blood, saliva, semen, urine, vaginal fluids and skin surfaces) and forensic (anal adhesions) specimens. Bacterial gene detection was performed by real-time PCR using a minor groove binding probe to amplify the RNA polymerase β-subunit gene of B. uniformis and B. vulgatus, and the α-1-6 mannanase gene of B. thetaiotaomicron. At least one of these bacteria was detected in the feces of 20 donors; the proportions of B. uniformis, B. vulgatus and B. thetaiotaomicron were 95, 85 and 60%, respectively. Bacteroides vulgatus was also detected in one of six vaginal fluid samples, but B. thetaiotaomicron and B. uniformis were not detected in body samples other than feces. Further, we applied this method to forensic specimens from 18 donors. Eighteen anal adhesions also contained at least one of three bacteria; B. uniformis, B. vulgatus and B. thetaiotaomicron were detected in 89, 78 and 56%, respectively, of the specimens. Thus, these bacteria were present at a high frequency in the fecal and forensic specimens, while either B. uniformis or B. vulgatus was detected in all samples. Therefore, B. uniformis and B. vulgatus represent more appropriate target species than B. thetaiotaomicron for the identification of fecal material. If B. vulgatus and/or B. uniformis are detected, it is likely that the sample contains feces. Taken together, our results suggest that the use of molecular biological techniques will aid the detection of feces in forensic practice, although it is possible that the samples contained both feces and vaginal fluid.
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Affiliation(s)
- Hiroaki Nakanishi
- Forensic Science Laboratory of Yamanashi Prefectural Police H.Q., 312-4 Kubonakajima, Isawa, Fuefuki, Yamanashi 406-0036, Japan.
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Using oral microbial DNA analysis to identify expirated bloodspatter. Int J Legal Med 2010; 124:569-76. [PMID: 20162292 DOI: 10.1007/s00414-010-0426-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2009] [Accepted: 01/21/2010] [Indexed: 10/19/2022]
Abstract
Distinguishing expirated bloodstains (blood forced by airflow out of the nose, mouth or a chest wound) from impact spatter (blood from gunshots, explosives, blunt force trauma and/or machinery accidents) is an important challenge in forensic science. Streptococcal bacteria are only found in the human mouth and saliva. This study developed a polymerase chain reaction (PCR) method that detects DNA from these bacteria as a sensitive tool to detect the presence of saliva. The PCR method was very specific to human oral streptococci, with no PCR product being made from human DNA or DNA from other microbes that were tested. It was also very sensitive, detecting as little as 60 fg of target DNA. The PCR amplification gave product with 99 out of 100 saliva samples tested. PCR was not inhibited by the presence of blood and could detect target DNA in expirated bloodstains in a range of materials and for up to 92 days after deposit on cardboard or cotton fabric. In a blind trial, the PCR method was able to distinguish three mock forensic samples that contained expirated blood from four that did not. Our data show that bacteria present in the oral cavity can be detected in bloodstains that contain saliva and therefore can potentially be used as a marker in forensic work to distinguish mouth-expirated bloodstains from other types of bloodstains.
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