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Noble PA, Pozhitkov A, Singh K, Woods E, Liu C, Levin M, Javan G, Wan J, Abouhashem AS, Mathew-Steiner SS, Sen CK. Unraveling the Enigma of Organismal Death: Insights, Implications, and Unexplored Frontiers. Physiology (Bethesda) 2024; 39:0. [PMID: 38624244 DOI: 10.1152/physiol.00004.2024] [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: 01/12/2024] [Revised: 03/21/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024] Open
Abstract
Significant knowledge gaps exist regarding the responses of cells, tissues, and organs to organismal death. Examining the survival mechanisms influenced by metabolism and environment, this research has the potential to transform regenerative medicine, redefine legal death, and provide insights into life's physiological limits, paralleling inquiries in embryogenesis.
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Affiliation(s)
- Peter A Noble
- Department of Microbiology, University of Alabama Birmingham, Birmingham, Alabama, United States
| | - Alexander Pozhitkov
- Division of Research Informatics, Beckman Research Institute, City of Hope, Duarte, California, United States
| | - Kanhaiya Singh
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Erik Woods
- Ossium Health, Indianapolis, Indiana, United States
| | - Chunyu Liu
- Institute for Human Performance, Upstate Medical University, Syracuse, New York, United States
| | - Michael Levin
- Department of Biology, Tufts University, Medford, Massachusetts, United States
| | - Gulnaz Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, Alabama, United States
| | - Jun Wan
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Ahmed Safwat Abouhashem
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Shomita S Mathew-Steiner
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
| | - Chandan K Sen
- Department of Surgery, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States
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Spychała K, Piecuch A, Szleszkowski Ł, Kadej M, Ogórek R. Microscopic fungi on the corpse - Promising tool requiring further research. Forensic Sci Int 2024; 361:112129. [PMID: 38986228 DOI: 10.1016/j.forsciint.2024.112129] [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: 07/17/2023] [Revised: 01/21/2024] [Accepted: 06/29/2024] [Indexed: 07/12/2024]
Abstract
Forensic microbiology is a relatively new area of forensic sciences. It considers the potential of microorganisms to be used in criminal investigations. As most studies involve the role of bacteria in fields like post-mortem interval estimation, personal identification or geolocation, the data on the role of fungi is comparatively scarce. Forensic mycology involves the application of fungi and their structures in forensic cases. The aim of this review is the evaluation of the current state of knowledge on fungi associated with human cadavers and their possible role in estimating the time since death. In accordance with the available reports, we focused on the relation between microscopic fungi isolated from human corpses and the cadaver condition e.g., the stage of decomposition. We also emphasised the contrast between the reported methodologies and attempted to standardise research methods in forensic mycology from sample collection to its storage, mycological analysis and identification of the obtained fungal cultures. Moreover, the potential usage of microscopic fungi in criminal cases was discussed based on various case reports.
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Affiliation(s)
- Klaudyna Spychała
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
| | - Agata Piecuch
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
| | - Łukasz Szleszkowski
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Radeckiego 4, Wrocław PL-50-345, Poland
| | - Marcin Kadej
- Centre for Forensic Biology and Entomology, Department of Invertebrate Biology, Evolution and Conservation, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 65, Wrocław PL-51-148, Poland.
| | - Rafał Ogórek
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [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: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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Iancu L, Bonicelli A, Procopio N. Decomposition in an extreme cold environment and associated microbiome-prediction model implications for the postmortem interval estimation. Front Microbiol 2024; 15:1392716. [PMID: 38803371 PMCID: PMC11128606 DOI: 10.3389/fmicb.2024.1392716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction The accurate estimation of postmortem interval (PMI), the time between death and discovery of the body, is crucial in forensic science investigations as it impacts legal outcomes. PMI estimation in extremely cold environments becomes susceptible to errors and misinterpretations, especially with prolonged PMIs. This study addresses the lack of data on decomposition in extreme cold by providing the first overview of decomposition in such settings. Moreover, it proposes the first postmortem microbiome prediction model for PMI estimation in cold environments, applicable even when the visual decomposition is halted. Methods The experiment was conducted on animal models in the second-coldest region in the United States, Grand Forks, North Dakota, and covered 23 weeks, including the winter months with temperatures as low as -39°C. Random Forest analysis models were developed to estimate the PMI based either uniquely on 16s rRNA gene microbial data derived from nasal swabs or based on both microbial data and measurable environmental parameters such as snow depth and outdoor temperatures, on a total of 393 samples. Results Among the six developed models, the best performing one was the complex model based on both internal and external swabs. It achieved a Mean Absolute Error (MAE) of 1.36 weeks and an R2 value of 0.91. On the other hand, the worst performing model was the minimal one that relied solely on external swabs. It had an MAE of 2.89 weeks and an R2 of 0.73. Furthermore, among the six developed models, the commonly identified predictors across at least five out of six models included the following genera: Psychrobacter (ASV1925 and ASV1929), Carnobacterium (ASV2872) and Pseudomonas (ASV1863). Discussion The outcome of this research provides the first microbial model able to predict PMI with an accuracy of 9.52 days over a six-month period of extreme winter conditions.
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Affiliation(s)
- Lavinia Iancu
- Department of Criminal Justice, University of North Dakota, Grand Forks, ND, United States
| | - Andrea Bonicelli
- Research Centre for Field Archaeology and Forensic Taphonomy, School of Law and Policing, Preston, United Kingdom
| | - Noemi Procopio
- Research Centre for Field Archaeology and Forensic Taphonomy, School of Law and Policing, Preston, United Kingdom
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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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Javan GT, Singh K, Finley SJ, Green RL, Sen CK. Complexity of human death: its physiological, transcriptomic, and microbiological implications. Front Microbiol 2024; 14:1345633. [PMID: 38282739 PMCID: PMC10822681 DOI: 10.3389/fmicb.2023.1345633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Human death is a complex, time-governed phenomenon that leads to the irreversible cessation of all bodily functions. Recent molecular and genetic studies have revealed remarkable experimental evidence of genetically programmed cellular death characterized by several physiological processes; however, the basic physiological function that occurs during the immediate postmortem period remains inadequately described. There is a paucity of knowledge connecting necrotic pathologies occurring in human organ tissues to complete functional loss of the human organism. Cells, tissues, organs, and organ systems show a range of differential resilience and endurance responses that occur during organismal death. Intriguingly, a persistent ambiguity in the study of postmortem physiological systems is the determination of the trajectory of a complex multicellular human body, far from life-sustaining homeostasis, following the gradual or sudden expiry of its regulatory systems. Recent groundbreaking investigations have resulted in a paradigm shift in understanding the cell biology and physiology of death. Two significant findings are that (i) most cells in the human body are microbial, and (ii) microbial cell abundance significantly increases after death. By addressing the physiological as well as the microbiological aspects of death, future investigations are poised to reveal innovative insights into the enigmatic biological activities associated with death and human decomposition. Understanding the elaborate crosstalk of abiotic and biotic factors in the context of death has implications for scientific discoveries important to informing translational knowledge regarding the transition from living to the non-living. There are important and practical needs for a transformative reestablishment of accepted models of biological death (i.e., artificial intelligence, AI) for more precise determinations of when the regulatory mechanisms for homeostasis of a living individual have ceased. In this review, we summarize mechanisms of physiological, genetic, and microbiological processes that define the biological changes and pathways associated with human organismal death and decomposition.
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Affiliation(s)
- Gulnaz T. Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Kanhaiya Singh
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sheree J. Finley
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Robert L. Green
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Chandan K. Sen
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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Xu G, Teng X, Gao XH, Zhang L, Yan H, Qi RQ. Advances in machine learning-based bacteria analysis for forensic identification: identity, ethnicity, and site of occurrence. Front Microbiol 2023; 14:1332857. [PMID: 38179452 PMCID: PMC10764511 DOI: 10.3389/fmicb.2023.1332857] [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: 11/03/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
When faced with an unidentified body, identifying the victim can be challenging, particularly if physical characteristics are obscured or masked. In recent years, microbiological analysis in forensic science has emerged as a cutting-edge technology. It not only exhibits individual specificity, distinguishing different human biotraces from various sites of occurrence (e.g., gastrointestinal, oral, skin, respiratory, and genitourinary tracts), each hosting distinct bacterial species, but also offers insights into the accident's location and the surrounding environment. The integration of machine learning with microbiomics provides a substantial improvement in classifying bacterial species compares to traditional sequencing techniques. This review discusses the use of machine learning algorithms such as RF, SVM, ANN, DNN, regression, and BN for the detection and identification of various bacteria, including Bacillus anthracis, Acetobacter aceti, Staphylococcus aureus, and Streptococcus, among others. Deep leaning techniques, such as Convolutional Neural Networks (CNN) models and derivatives, are also employed to predict the victim's age, gender, lifestyle, and racial characteristics. It is anticipated that big data analytics and artificial intelligence will play a pivotal role in advancing forensic microbiology in the future.
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Affiliation(s)
- Geyao Xu
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Xianzhuo Teng
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xing-Hua Gao
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Li Zhang
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Hongwei Yan
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Rui-Qun Qi
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
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Cláudia-Ferreira A, Barbosa DJ, Saegeman V, Fernández-Rodríguez A, Dinis-Oliveira RJ, Freitas AR. The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations. Microorganisms 2023; 11:2509. [PMID: 37894167 PMCID: PMC10608847 DOI: 10.3390/microorganisms11102509] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The relevance of postmortem microbiological examinations has been controversial for decades, but the boom in advanced sequencing techniques over the last decade is increasingly demonstrating their usefulness, namely for the estimation of the postmortem interval. This comprehensive review aims to present the current knowledge about the human postmortem microbiome (the necrobiome), highlighting the main factors influencing this complex process and discussing the principal applications in the field of forensic sciences. Several limitations still hindering the implementation of forensic microbiology, such as small-scale studies, the lack of a universal/harmonized workflow for DNA extraction and sequencing technology, variability in the human microbiome, and limited access to human cadavers, are discussed. Future research in the field should focus on identifying stable biomarkers within the dominant Bacillota and Pseudomonadota phyla, which are prevalent during postmortem periods and for which standardization, method consolidation, and establishment of a forensic microbial bank are crucial for consistency and comparability. Given the complexity of identifying unique postmortem microbial signatures for robust databases, a promising future approach may involve deepening our understanding of specific bacterial species/strains that can serve as reliable postmortem interval indicators during the process of body decomposition. Microorganisms might have the potential to complement routine forensic tests in judicial processes, requiring robust investigations and machine-learning models to bridge knowledge gaps and adhere to Locard's principle of trace evidence.
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Affiliation(s)
- Ana Cláudia-Ferreira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
| | - Daniel José Barbosa
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Veroniek Saegeman
- Department of Infection Control and Prevention, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Amparo Fernández-Rodríguez
- Microbiology Laboratory, Biology Service, Institute of Toxicology and Forensic Sciences, 28232 Madrid, Spain;
| | - Ricardo Jorge Dinis-Oliveira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Department of Public Health and Forensic Sciences, and Medical Education, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana R. Freitas
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Ķimsis J, Pokšāne A, Kazarina A, Vilcāne A, Petersone‐Gordina E, Zayakin P, Gerhards G, Ranka R. Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD. ENVIRONMENTAL MICROBIOLOGY REPORTS 2023; 15:383-391. [PMID: 37057308 PMCID: PMC10472514 DOI: 10.1111/1758-2229.13157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.
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Affiliation(s)
- Jānis Ķimsis
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | - Alise Pokšāne
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | - Alisa Kazarina
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | | | | | - Pawel Zayakin
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
| | | | - Renate Ranka
- Latvian Biomedical Research and Study CentreLaboratory of molecular microbiologyRigaLatvia
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10
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Iancu L, Muslim A, Aazmi S, Jitaru V. Postmortem skin microbiome signatures associated with human cadavers within the first 12 h at the morgue. Front Microbiol 2023; 14:1234254. [PMID: 37564294 PMCID: PMC10410280 DOI: 10.3389/fmicb.2023.1234254] [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: 06/04/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction Forensic microbiome studies expanded during the last decade, aiming to identify putative bacterial biomarkers to be used for the postmortem interval (PMI) estimation. Bacterial diversity and dynamics during decomposition are influenced by each individual's micro and macroenvironment, ante and postmortem conditions, varying across body sites and time. The skin, the largest organ of the human body, hosts a diverse microbial diversity, representing the first line of defense of a living individual. Targeting the investigation of the postmortem skin microbiome could help understanding the role of microbes during decomposition, and association with the ante and postmortem conditions. Methods The current study aimed to identify the postmortem skin microbiome signatures associated with eight human bodies, received at the Institute of Legal Medicine Iasi, Romania, during April and May 2021. A total of 162 samples (including triplicate) representing face and hands skin microbiome were investigated via Illumina MiSeq, upon arrival at the morgue (T0) and after 12 hours (T1). Results The taxonomic characteristics of the skin microbiota varied across different body sites. However, there were no significant differences in taxonomic profiles between collection time, T0 and T1, except for some dynamic changes in the abundance of dominant bacteria. Moreover, different microbial signatures have been associated with a specific cause of death, such as cardiovascular disease, while an elevated blood alcohol level could be associated with a decrease in bacterial richness and diversity. Discussion The places where the bodies were discovered seemed to play an important role in explaining the bacterial diversity composition. This study shows promising results towards finding common postmortem bacterial signatures associated with human cadavers within the first 12h at the morgue.
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Affiliation(s)
- Lavinia Iancu
- Department of Criminal Justice, University of North Dakota, Grand Forks, ND, United States
| | - Azdayanti Muslim
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, Selangor, Malaysia
- Institute for Biodiversity and Sustainable Development, Universiti Teknologi MARA (UiTM), Selangor, Malaysia
- Microbiome Health and Environment (MiHeaRT), Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor, Malaysia
| | - Shafiq Aazmi
- Microbiome Health and Environment (MiHeaRT), Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor, Malaysia
- School of Biology, Faculty of Applied Science, Universiti Teknologi MARA, Selangor, Malaysia
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Murugesan M, Manoj D, Johnson LR, James RI. Forensic Microbiology in India: A missing piece in the puzzle of criminal investigation system. Indian J Med Microbiol 2023; 44:100367. [PMID: 37356836 DOI: 10.1016/j.ijmmb.2023.100367] [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: 11/17/2022] [Revised: 02/26/2023] [Accepted: 03/31/2023] [Indexed: 06/27/2023]
Abstract
BACKGROUND Forensic Microbiology is an emerging branch of science that has great potential to assist criminal investigations. Having said that, microbial analysis is not performed routinely during forensic investigations in India. This could be attributed to lack of specific training and lack of evidence-based standard protocol. OBJECTIVES The authors attempt to highlight the key areas in forensic microbiology that need to be explored in a developing nation like India. CONTENT Forensic microbiology could help in linking a person to a crime, determining the cause of death, estimating postmortem interval (PMI), etc. Additionally, applications are being developed by forensic microbiologists across the globe to investigate the coordinated and dynamic changes in microbial activity which occur after the death of a human host. Such evidence from the human postmortem microbiome can aid in criminal investigations and administration of justice. These recent advances and developments have the potential to transform the field of forensic microbiology in a developing country.
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Affiliation(s)
- Malathi Murugesan
- Department of Infectious Diseases & Hospital Infection Control Officer, Meenakshi Mission Hospital & Research Centre, Madurai, Tamil Nadu - 625107, India.
| | - Daniel Manoj
- Department of Forensic Medicine & Toxicology, Christian Medical College Vellore, Tamil Nadu - 632004, India.
| | - Latif Rajesh Johnson
- Department of Forensic Medicine & Toxicology, Christian Medical College Vellore, Tamil Nadu - 632004, India.
| | - Ranjit Immanuel James
- Department of Forensic Medicine & Toxicology, Christian Medical College Vellore, Tamil Nadu - 632004, India.
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Javan GT, Finley SJ, Moretti M, Visonà SD, Mezzari MP, Green RL. COVID-19 and brain-heart-lung microbial fingerprints in Italian cadavers. Front Mol Biosci 2023; 10:1196328. [PMID: 37388248 PMCID: PMC10300556 DOI: 10.3389/fmolb.2023.1196328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/30/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction: The fact that SARS-CoV-2, the coronavirus that caused COVID-19, can translocate within days of infection to the brain and heart and that the virus can survive for months is well established. However, studies have not investigated the crosstalk between the brain, heart, and lungs regarding microbiota that simultaneously co-inhabit these organs during COVID-19 illness and subsequent death. Given the significant overlap of cause of death from or with SARS-CoV-2, we investigated the possibility of a microbial fingerprint regarding COVID-19 death. Methods: In the current study, the 16S rRNA V4 region was amplified and sequenced from 20 COVID-19-positive and 20 non-COVID-19 cases. Nonparametric statistics were used to determine the resulting microbiota profile and its association with cadaver characteristics. When comparing non-COVID-19 infected tissues versus those infected by COVID-19, there is statistical differences (p < 0.05) between organs from the infected group only. Results: When comparing the three organs, microbial richness was significantly higher in non-COVID-19-infected tissues than infected. Unifrac distance metrics showed more variance between control and COVID-19 groups in weighted analysis than unweighted; both were statistically different. Unweighted Bray-Curtis principal coordinate analyses revealed a near distinct two-community structure: one for the control and the other for the infected group. Both unweighted and weighted Bray-Curtis showed statistical differences. Deblur analyses demonstrated Firmicutes in all organs from both groups. Discussion: Data obtained from these studies facilitated the defining of microbiome signatures in COVID-19 decedents that could be identified as taxonomic biomarkers effective for predicting the occurrence, the co-infections involved in its dysbiosis, and the evolution of the virus.
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Affiliation(s)
- Gulnaz T. Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Sheree J. Finley
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Matteo Moretti
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Silvia D. Visonà
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Melissa P. Mezzari
- Alkek Center for Metagenomics and Microbiome Research, Baylor College of Medicine, Houston, TX, United States
| | - Robert L. Green
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
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Nilendu D. Toward Oral Thanatomicrobiology-An Overview of the Forensic Implications of Oral Microflora. Acad Forensic Pathol 2023; 13:51-60. [PMID: 37457549 PMCID: PMC10338735 DOI: 10.1177/19253621231176411] [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: 12/28/2022] [Accepted: 05/01/2023] [Indexed: 07/18/2023]
Abstract
Introduction The oral cavity is home to numerous microorganisms including bacteria, fungi, and viruses which together form the oral microflora. It is the second most diverse microbial site in the human body after the gastrointestinal tract. Microbial degradation is a common phenomenon that occurs after death, with the early and advanced stages of decomposition being closely associated with oral microbial activity. Methods This article reviews the current state of knowledge on the role of the oral microflora in postmortem events, and highlights the growing importance of terms such as forensic microbiology and thanatomicrobiome. This article also discusses next-generation sequencing, metagenomic sequencing studies, and RNA sequencing to study the oral thanatomicrobiome and epinecrotic communities in forensic oral genetics. Results The indigenous microorganisms in the oral cavity are among the first to respond to the process of decomposition. DNA/RNA sequencing is a relatively simple, precise, and cost-effective method to estimate biological diversity during various stages of postmortem decomposition. The field of thanatomicrobiology is rapidly evolving into a key area in forensic research. Conclusion This article briefly narrates oral microflora and its implications in forensic odontology. The role of microbial activity in postmortem events is gaining importance in forensic research, and further studies are needed to fully understand the potential applications of advanced technology in the study of the oral thanatomicrobiome.
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Affiliation(s)
- Debesh Nilendu
- Debesh Nilendu PhD, Department of Oral Medicine and Radiology, K. M. Shah Dental College and Hospital, Sumandeep Vidyapeeth Deemed to be University, Waghodia Road, Piparia, Taluk Waghodia, Vadodara, Gujarat 391760, India,
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Guo X, Gu L, Luo Y, Wang S, Luo H, Song F. A bibliometric analysis of microbial forensics from 1984 to 2022: progress and research trends. Front Microbiol 2023; 14:1186372. [PMID: 37260676 PMCID: PMC10227522 DOI: 10.3389/fmicb.2023.1186372] [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: 03/14/2023] [Accepted: 04/21/2023] [Indexed: 06/02/2023] Open
Abstract
Microbial forensics is a rapidly evolving discipline that has gained significant momentum in recent years. The study evaluated relevant results over the last four decades from 1984 to 2022 all over the world, aiming to analyze the growing trends and research orientations of microbial forensics. Using "microbial forensics" as the search topic in the Web of Science Core Collection, the systematic retrieval identified 579 documents relevant to the field and draw many statistical tables and maps to make the retrieval results visible. According to further bibliometric analysis, there are an increasing number of publications related to microbial forensics from the overall trend, with the highest number of publications recorded in 2021. In terms of the total number of articles, the USA and China were both the leading contributors to the field among 40 countries. The field has developed rapidly in recent years based on the development of next-generation sequencing. Over the course of its development, there are rich keywords in the research of scholars, which focus on diversity and identification. Moreover, despite the early hot topic being PCR (the use of PCR to probe microorganisms), in recent years, the topics, markers, and the potential application of microorganisms in forensic practice have become hot, which also indicates the future research directions of microbial forensic.
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De Alcaraz-Fossoul J, Wang Y, Liu R, Mancenido M, Marshall PA, Núñez C, Broatch J, Ferry L. Microbes in fingerprints: A source for dating crime evidence? Forensic Sci Int Genet 2023; 65:102883. [PMID: 37120981 DOI: 10.1016/j.fsigen.2023.102883] [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: 08/04/2022] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
Interest in the human microbiome has grown in recent years because of increasing applications to biomedicine and forensic science. However, the potential for dating evidence at a crime scene based upon time-dependent changes in microbial signatures has not been established, despite a relatively straightforward scientific process for isolating the microbiome. We hypothesize that modifications in microbial diversity, abundance, and succession can provide estimates of the time a surface was touched for investigative purposes. In this proof-of-concept research, the sequencing and analysis of the 16 S rRNA gene from microbes present in fresh and aged latent fingerprints deposited by three donors with pre- and post-washed hands is reported. The stability of major microbial phyla is confirmed while the dynamics of less abundant groups is described up to 21 days post-deposition. Most importantly, a phylum is suggested as the source for possible biological markers to date fingerprints: Deinococcus-Thermus.
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Affiliation(s)
- Josep De Alcaraz-Fossoul
- Forensic Science Department, Henry C. Lee College of Criminal Justice and Forensic Science, University of New Haven; West Haven, Connecticut 06516, United States.
| | - Yue Wang
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Ruoqian Liu
- School of Mathematical and Statistical Sciences, The College of Liberal Arts and Sciences, Arizona State University; Tempe, Arizona 85251, United States
| | - Michelle Mancenido
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Pamela Ann Marshall
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Celeste Núñez
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Jennifer Broatch
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Lara Ferry
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
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Castro AE, De Ungria MCA. Methods used in microbial forensics and epidemiological investigations for stronger health systems. Forensic Sci Res 2023; 7:650-661. [PMID: 36817258 PMCID: PMC9930754 DOI: 10.1080/20961790.2021.2023272] [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] [Indexed: 10/18/2022] Open
Abstract
This review discusses microbial forensics as an emerging science that finds application in protecting human health. It is important to distinguish naturally acquired infections from those caused by the intentional release of microorganisms to the environment. This information is crucial in formulating procedures against the spread of infectious diseases and prosecuting persons who may be involved in acts of biocrime, bioterrorism, or biowarfare. A comparison between epidemiological investigations and microbial forensic investigations is provided. In addition, a discussion on how microbial forensics strengthens health systems is included in this review. Microbial forensic investigations and epidemiologic examinations employ similar concepts and involve identifying and characterising the microbe of interest. Both fields require formulating an appropriate case definition, determining a pathogen's mode of transmission, and identifying the source(s) of infection. However, the two subdisciplines differ in their objectives. An epidemiological investigation aims to identify the pathogen's source to prevent the spread of the disease. Microbial forensics focuses on source-tracking to facilitate the prosecution of persons responsible for the spread of a pathogen. Both fields use molecular techniques in analysing and comparing DNA, gene products, and biomolecules to identify and characterise the microorganisms of interest. We included case studies to show methods used in microbial forensic investigations, a brief discussion of the public significance of microbial forensic systems, and a roadmap for establishing a system at a national level. This system is expected to strengthen a country's capacity to respond to public health emergencies. Several factors must be considered in establishing national microbial forensic systems. First is the inherent ubiquity, diversity, and adaptability of microorganisms that warrants the use of robust and accurate molecular typing systems. Second, the availability of facilities and scientists who have been trained in epidemiology, molecular biology, bioinformatics, and data analytics. Human resources and infrastructure are critical requirements because formulating strategies and allocating resources in times of infectious disease outbreaks must be data-driven. Establishing and maintaining a national microbial forensic system to strengthen capacities in conducting forensic and epidemiological investigations should be prioritised by all countries, accompanied by a national policy that sets the legislative framework and provides for the system's financial requirements.
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Affiliation(s)
- Arizaldo E. Castro
- Microbial Ecology of Terrestrial and Aquatic Systems Laboratory, Institute of Biology, University of the Philippines Diliman, Quezon City, Philippines,CONTACT Arizaldo E. Castro
| | - Maria Corazon A. De Ungria
- DNA Analysis Laboratory, Natural Sciences Research Institute, University of the Philippines Diliman, Quezon City, Philippines,Program on Biodiversity, Ethnicity, and Forensics, Philippine Genome Center, University of the Philippines Diliman, Quezon City, Philippines
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Stefano T, Francesca M, Guendalina G, Michele B, Chiara F, Salvatore A, Riccardo Z. Utility and diagnostic value of postmortem microbiology associated with histology for forensic purposes. Forensic Sci Int 2023; 342:111534. [PMID: 36528011 DOI: 10.1016/j.forsciint.2022.111534] [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: 02/24/2022] [Revised: 10/11/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
Nowadays, the diagnostic value of postmortem microbiological investigations is still a debated topic, but postmortem microbiology (PMM) remains a discipline with great forensic potential. To evaluate the usefulness and diagnostic-forensic value of postmortem microbiological cultures, it has been conducted a study on cadaveric material sampled during autopsy aiming to identify the correct cause of death. The study analyzed 45 cadavers subjected to judicial autopsy, divided into two groups based on the presence or absence of external or internal macroscopic autopsy signs suggesting infectious pathology. In the same cases, both the microbiological and conventional histological investigations have been simultaneously carried out. From the investigations, mono-bacterial, mono-fungal, mixed and negative cultures were observed. In mono-species microbiological growth, the histological epicrisis confirmed an infectious cause of death due to the presence of signs of acute infection with an aggressive infectious agent. In cases where growth was mixed, it was possible to distinguish between simple postmortal contamination and perimortem colonization. Finally, in some cases where the microbiology was negative, this has been essential in highlighting signs of a vital reaction to viral or parasitic infection. The joint and integrated evaluation of the laboratory results made it possible to correctly understand even those peculiar situations in which the PMM results alone would not have been significant. These methods, when combined, constitute an optimal forensic approach for the identification of the real cause of death and thus reduce the number of unsolved cases.
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Affiliation(s)
- Tambuzzi Stefano
- Laboratorio di Istopatologia Forense e Microbiologia Medico Legale - Sezione di Medicina Legale e delle Assicurazioni - Dipartimento di Scienze Biomediche per la Salute - Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133 Milano, Italy
| | - Maciocco Francesca
- Laboratorio di Immunoematologia e Medicina Trasfusionale (SIMT) - Azienda Ospedaliera S. Carlo Borromeo, Via Pio II, 3, 20153 Milano, Italy
| | - Gentile Guendalina
- Laboratorio di Istopatologia Forense e Microbiologia Medico Legale - Sezione di Medicina Legale e delle Assicurazioni - Dipartimento di Scienze Biomediche per la Salute - Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133 Milano, Italy.
| | - Boracchi Michele
- Laboratorio di Istopatologia Forense e Microbiologia Medico Legale - Sezione di Medicina Legale e delle Assicurazioni - Dipartimento di Scienze Biomediche per la Salute - Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133 Milano, Italy
| | - Faraone Chiara
- Laboratorio di Istopatologia Forense e Microbiologia Medico Legale - Sezione di Medicina Legale e delle Assicurazioni - Dipartimento di Scienze Biomediche per la Salute - Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133 Milano, Italy
| | - Andreola Salvatore
- Laboratorio di Istopatologia Forense e Microbiologia Medico Legale - Sezione di Medicina Legale e delle Assicurazioni - Dipartimento di Scienze Biomediche per la Salute - Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133 Milano, Italy
| | - Zoja Riccardo
- Laboratorio di Istopatologia Forense e Microbiologia Medico Legale - Sezione di Medicina Legale e delle Assicurazioni - Dipartimento di Scienze Biomediche per la Salute - Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133 Milano, Italy
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18
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Zhang F, Wang P, Zeng K, Yuan H, Wang Z, Li X, Yuan H, Du S, Guan D, Wang L, Zhao R. Postmortem submersion interval estimation of cadavers recovered from freshwater based on gut microbial community succession. Front Microbiol 2022; 13:988297. [PMID: 36532467 PMCID: PMC9756852 DOI: 10.3389/fmicb.2022.988297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 09/19/2023] Open
Abstract
Microbial community succession during decomposition has been proven to be a useful tool for postmortem interval (PMI) estimation. Numerous studies have shown that the intestinal microbial community presented chronological changes after death and was stable in terrestrial corpses with different causes of death. However, the postmortem pattern of intestinal microbial community succession in cadavers retrieved from water remains unclear. For immersed corpses, the postmortem submersion interval (PMSI) is a useful indicator of PMI. To provide reliable estimates of PMSI in forensic investigations, we investigated the gut microbial community succession of corpses submersed in freshwater and explored its potential application in forensic investigation. In this study, the intestinal microbial community of mouse submersed in freshwater that died of drowning or CO2 asphyxia (i.e., postmortem submersion) were characterized by 16S rDNA amplification and high-throughput sequencing, followed by bioinformatic analyses. The results demonstrated that the chronological changes in intestinal bacterial communities were not different between the drowning and postmortem submersion groups. α-diversity decreased significantly within 14 days of decomposition in both groups, and the β-diversity bacterial community structure ordinated chronologically, inferring the functional pathway and phenotype. To estimate PMSI, a regression model was established by random forest (RF) algorithm based on the succession of postmortem microbiota. Furthermore, 15 genera, including Proteus, Enterococcus, and others, were selected as candidate biomarkers to set up a concise predicted model, which provided a prediction of PMSI [MAE (± SE) = 0.818 (± 0.165) d]. Overall, our present study provides evidence that intestinal microbial community succession would be a valuable marker to estimate the PMSI of corpses submerged in an aquatic habitat.
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Affiliation(s)
- Fuyuan Zhang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Pengfei Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Kuo Zeng
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Huiya Yuan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Ziwei Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Xinjie Li
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Haomiao Yuan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Shukui Du
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Dawei Guan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Linlin Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Rui Zhao
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
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Bhattacharya C, Tierney BT, Ryon KA, Bhattacharyya M, Hastings JJA, Basu S, Bhattacharya B, Bagchi D, Mukherjee S, Wang L, Henaff EM, Mason CE. Supervised Machine Learning Enables Geospatial Microbial Provenance. Genes (Basel) 2022; 13:1914. [PMID: 36292799 PMCID: PMC9601318 DOI: 10.3390/genes13101914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/14/2022] [Accepted: 10/18/2022] [Indexed: 11/04/2022] Open
Abstract
The recent increase in publicly available metagenomic datasets with geospatial metadata has made it possible to determine location-specific, microbial fingerprints from around the world. Such fingerprints can be useful for comparing microbial niches for environmental research, as well as for applications within forensic science and public health. To determine the regional specificity for environmental metagenomes, we examined 4305 shotgun-sequenced samples from the MetaSUB Consortium dataset-the most extensive public collection of urban microbiomes, spanning 60 different cities, 30 countries, and 6 continents. We were able to identify city-specific microbial fingerprints using supervised machine learning (SML) on the taxonomic classifications, and we also compared the performance of ten SML classifiers. We then further evaluated the five algorithms with the highest accuracy, with the city and continental accuracy ranging from 85-89% to 90-94%, respectively. Thereafter, we used these results to develop Cassandra, a random-forest-based classifier that identifies bioindicator species to aid in fingerprinting and can infer higher-order microbial interactions at each site. We further tested the Cassandra algorithm on the Tara Oceans dataset, the largest collection of marine-based microbial genomes, where it classified the oceanic sample locations with 83% accuracy. These results and code show the utility of SML methods and Cassandra to identify bioindicator species across both oceanic and urban environments, which can help guide ongoing efforts in biotracing, environmental monitoring, and microbial forensics (MF).
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Affiliation(s)
- Chandrima Bhattacharya
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY 10065, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Integrated Design and Media, Center for Urban Science and Progress, NYU Tandon School of Engineering, Brooklyn, New York, NY 11201, USA
| | - Braden T. Tierney
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Krista A. Ryon
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Malay Bhattacharyya
- Center for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata 700108, India
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India
| | - Jaden J. A. Hastings
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065, USA
| | - Srijani Basu
- Department of Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Bodhisatwa Bhattacharya
- Department of Electrical and Electronics Engineering, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Debneel Bagchi
- Department of Metallurgy & Materials Engineering, Indian Institute of Engineering Science & Technology, Shibpur, Howrah 711103, India
| | - Somsubhro Mukherjee
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Lu Wang
- Department of Biological Sciences, National University of Singapore, Singapore 117558, Singapore
| | - Elizabeth M. Henaff
- Integrated Design and Media, Center for Urban Science and Progress, NYU Tandon School of Engineering, Brooklyn, New York, NY 11201, USA
| | - Christopher E. Mason
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10065, USA
- Integrated Design and Media, Center for Urban Science and Progress, NYU Tandon School of Engineering, Brooklyn, New York, NY 11201, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY 10065, USA
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MALDI-TOF Mass Spectrometry Analysis and Human Post-Mortem Microbial Community: A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074354. [PMID: 35410034 PMCID: PMC8998342 DOI: 10.3390/ijerph19074354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023]
Abstract
Introduction: The human post-mortem microbiome (HPM) plays a major role in the decomposition process. Successional changes in post-mortem bacterial communities have been recently demonstrated using high throughput metagenomic sequencing techniques, showing great potential as a post-mortem interval (PMI) predictor. The aim of this study is to verify the application of the mass spectrometry technique, better known as MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), as a cheap and quick method for microbe taxonomic identification and for studying the PM microbiome. Methods: The study was carried out on 18 human bodies, ranging from 4 months to 82 years old and with a PMI range from 24 h up to 15 days. The storage time interval in the coolers was included in the final PMI estimates. Using the PMI, the sample study was divided into three main groups: seven cases with a PMI < 72 h; six cases with a PMI of 72−168 h and five cases with a PMI > 168 h. For each body, microbiological swabs were sampled from five external anatomical sites (eyes, ears, nose, mouth, and rectum) and four internal organs (brain, spleen, liver, and heart). Results: The HPM became increasingly different from the starting communities over time in the internal organs as well as at skin sites; the HPM microbiome was mostly dominated by Firmicutes and Proteobacteria phyla; and a PM microbial turnover existed during decomposition, evolving with the PMI. Conclusions: MALDI-TOF is a promising method for PMI estimation, given its sample handling, good reproducibility, and high speed and throughput. Although several intrinsic and extrinsic factors can affect the structure of the HPM, MALDI-TOF can detect the overall microbial community turnover of most prevalent phyla during decomposition. Limitations are mainly related to its sensitivity due to the culture-dependent method and bias in the identification of new isolates.
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Sguazzi G, Mickleburgh HL, Ghignone S, Voyron S, Renò F, Migliario M, Sellitto F, Lovisolo F, Camurani G, Ogbanga N, Gino S, Procopio N. 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. [PMID: 35338895 DOI: 10.1016/j.fsigen.2022.102686] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 11/28/2022]
Abstract
Human DNA samples can remain unaltered for years and preserve important genetic information for forensic investigations. In fact, besides human genetic information, these extracts potentially contain additional valuable information: microbiome signatures. Forensic microbiology is rapidly becoming a significant tool for estimating post-mortem interval (PMI), and establishing cause of death and personal identity. To date, the possibility to recover unaltered microbiome signatures from human DNA extracts has not been proven. This study examines the microbiome signatures within human DNA extracts obtained from six cadavers with different PMIs, which were stored frozen for 5-16 years. Results demonstrated that the microbiome can be co-extracted with human DNA using forensic kits designed to extract the human host's DNA from different tissues and fluids during decomposition. We compared the microbial communities identified in these samples with microbial DNA recovered from two human cadavers donated to the Forensic Anthropology Center at Texas State University (FACTS) during multiple decomposition stages, to examine whether the microbial signatures recovered from "old" (up to 16 years) extracts are consistent with those identified in recently extracted microbial DNA samples. The V4 region of 16 S rRNA gene was amplified and sequenced using Illumina MiSeq for all DNA extracts. The results obtained from the human DNA extracts were compared with each other and with the microbial DNA from the FACTS samples. Overall, we found that the presence of specific microbial taxa depends on the decomposition stage, the type of tissue, and the depositional environment. We found no indications of contamination in the microbial signatures, or any alterations attributable to the long-term frozen storage of the extracts, demonstrating that older human DNA extracts are a reliable source of such microbial signatures. No shared Core Microbiome (CM) was identified amongst the total 18 samples, but we identified certain species in association with the different decomposition stages, offering potential for the use of microbial signatures co-extracted with human DNA samples for PMI estimation in future. Unveiling the new significance of older human DNA extracts brings with it important ethical-legal considerations. Currently, there are no shared legal frameworks governing the long-term storage and use of human DNA extracts obtained from crime scene evidence for additional research purposes. It is therefore important to create common protocols on the storage of biological material collected at crime scenes. We review existing legislation and guidelines, and identify some important limitations for the further development and application of forensic microbiomics.
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Affiliation(s)
- Giulia Sguazzi
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy; CRIMEDIM - Center for Research and Training in Disaster Medicine, Humanitarian Aid and Global Health, Università del Piemonte Orientale, Via Lanino, 1-28100 Novara, Italy
| | - Hayley L Mickleburgh
- Department of Cultural Sciences, Linnaeus University, Växjö, Sweden; Forensic Anthropology Center, Texas State University, San Marcos, TX, USA
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection (IPSP) - Turin Unit - National Research Council (CNR), 1-10125 Turin, Italy
| | - Samuele Voyron
- Institute for Sustainable Plant Protection (IPSP) - Turin Unit - National Research Council (CNR), 1-10125 Turin, Italy; Department of Life Sciences and Systems Biology, University of Torino, V.le P.A. Mattioli 25, 10125 Turin, Italy
| | - Filippo Renò
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Mario Migliario
- Department of Translational Medicine, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Federica Sellitto
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST, Newcastle Upon Tyne, UK
| | - Flavia Lovisolo
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Giulia Camurani
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Nengi Ogbanga
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST, Newcastle Upon Tyne, UK
| | - Sarah Gino
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Noemi Procopio
- Forensic Anthropology Center, Texas State University, San Marcos, TX, USA; Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST, Newcastle Upon Tyne, UK.
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22
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Speruda M, Piecuch A, Borzęcka J, Kadej M, Ogórek R. Microbial traces and their role in forensic science. J Appl Microbiol 2021; 132:2547-2557. [PMID: 34954826 DOI: 10.1111/jam.15426] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 11/27/2022]
Abstract
Forensic microbiology, also known as the microbiology of death, is an emerging branch of science that is still underused in criminal investigations. Some of the cases might be difficult to solve with commonly-used forensic methods, and then they become an operational field for microbiological and mycological analysis. The aim of our review is to present significant achievements of selected studies on the thanatomicrobiome (microorganisms found in the body, organs and fluids after death) and epinecrotic community (microorganisms found on decaying corpses) that can be used in forensic sciences. Research carried out as a part of the forensic microbiology deals with the thanatomicrobiome and the necrobiome - communities of microorganisms that live inside and outside of a putrefying corpse. Change of species composition observed in each community is a valuable feature that gives a lot of information related to the crime. It is mainly used in the estimation of post-mortem interval (PMI). In some criminal investigations, such noticeable changes in the microbiome and mycobiome can determine the cause or the actual place of death. The microbial traces found at the crime scene can also provide clear evidence of guilt. Nowadays, identification of microorganisms isolated from the body or environment is based on metagenome analysis and 16S rRNA gene amplicon-based sequencing for bacteria and ITS rRNA gene amplicon-based sequencing for fungi. Cultivation methods are still in use and seem to be more accurate; however, they require much more time to achieve a final result, which is an unwanted feature in any criminal investigation.
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Affiliation(s)
- Mateusz Speruda
- Department of Mycology and Genetics, University of Wroclaw, 51-148, Wroclaw, Poland
| | - Agata Piecuch
- Department of Mycology and Genetics, University of Wroclaw, 51-148, Wroclaw, Poland
| | - Justyna Borzęcka
- Department of Mycology and Genetics, University of Wroclaw, 51-148, Wroclaw, Poland
| | - Marcin Kadej
- Department of Invertebrate Biology, Evolution and Conservation, Laboratory of Forensic Biology and Entomology, University of Wrocław, Przybyszewskiego 65, 51-148, Wrocław, Poland
| | - Rafał Ogórek
- Department of Mycology and Genetics, University of Wroclaw, 51-148, Wroclaw, Poland
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23
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Gouello A, Dunyach-Remy C, Siatka C, Lavigne JP. Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences. Diagnostics (Basel) 2021; 12:diagnostics12010001. [PMID: 35054168 PMCID: PMC8774847 DOI: 10.3390/diagnostics12010001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/16/2023] Open
Abstract
The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.
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Affiliation(s)
- Audrey Gouello
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95037 Cergy-Pontoise, France;
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | - Catherine Dunyach-Remy
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | | | - Jean-Philippe Lavigne
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
- Correspondence: ; Tel.: +33-466683202
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24
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Jurkevitch E, Pasternak Z. A walk on the dirt: soil microbial forensics from ecological theory to the crime lab. FEMS Microbiol Rev 2021; 45:5937428. [PMID: 33098291 DOI: 10.1093/femsre/fuaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.
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Affiliation(s)
- Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Division of Identification and Forensic Science, Israel Police
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25
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Ahannach S, Spacova I, Decorte R, Jehaes E, Lebeer S. At the Interface of Life and Death: Post-mortem and Other Applications of Vaginal, Skin, and Salivary Microbiome Analysis in Forensics. Front Microbiol 2021; 12:694447. [PMID: 34394033 PMCID: PMC8355522 DOI: 10.3389/fmicb.2021.694447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
Microbial forensics represents a promising tool to strengthen traditional forensic investigative methods and fill related knowledge gaps. Large-scale microbiome studies indicate that microbial fingerprinting can assist forensics in areas such as trace evidence, source tracking, geolocation, and circumstances of death. Nevertheless, the majority of forensic microbiome studies focus on soil and internal organ samples, whereas the microbiome of skin, mouth, and especially vaginal samples that are routinely collected in sexual assault and femicide cases remain underexplored. This review discusses the current and emerging insights into vaginal, skin, and salivary microbiome-modulating factors during life (e.g., lifestyle and health status) and after death (e.g., environmental influences and post-mortem interval) based on next-generation sequencing. We specifically highlight the key aspects of female reproductive tract, skin, and mouth microbiome samples relevant in forensics. To fill the current knowledge gaps, future research should focus on the degree to which the post-mortem succession rate and profiles of vaginal, skin, and saliva microbiota are sensitive to abiotic and biotic factors, presence or absence of oxygen and other gases, and the nutrient richness of the environment. Application of this microbiome-related knowledge could provide valuable complementary data to strengthen forensic cases, for example, to shed light on the circumstances surrounding death with (post-mortem) microbial fingerprinting. Overall, this review synthesizes the present knowledge and aims to provide a framework to adequately comprehend the hurdles and potential application of vaginal, skin, and salivary post-mortem microbiomes in forensic investigations.
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Affiliation(s)
- Sarah Ahannach
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Irina Spacova
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
| | - Ronny Decorte
- Laboratory of Forensic Genetics, Department of Forensic Medicine, University Hospitals Leuven, Leuven, Belgium.,Department of Imaging and Pathology, Forensic Biomedical Sciences, KU Leuven, Leuven, Belgium
| | - Els Jehaes
- Forensic DNA Laboratory, Department of Forensic Medicine, Antwerp University Hospital, Edegem, Belgium
| | - Sarah Lebeer
- Department of Bioscience Engineering, Research Group Environmental Ecology and Applied Microbiology, University of Antwerp, Antwerp, Belgium
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26
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Hilal MG, Yu Q, Zhou R, Wang Y, Feng T, Li X, Li H. Exploring microbial communities, assessment methodologies and applications of animal's carcass decomposition: a review. FEMS Microbiol Ecol 2021; 97:6311132. [PMID: 34185048 DOI: 10.1093/femsec/fiab098] [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: 03/14/2021] [Accepted: 06/26/2021] [Indexed: 11/14/2022] Open
Abstract
Animals are an essential part of the ecosystem, and their carcasses are the nutrient patches or hotspots where nutrients accumulate for a long time. After death, the physical and chemical properties undergo alterations inside the carcass. The animal carcass is decomposed by many decomposers such as bacteria, fungi, microeukaryotes and insects. The role of microbial symbionts in living organisms is well explored and studied, but there is a scarcity of knowledge and research related to their role in decomposing animal carcasses. Microbes play an important role in carcass decomposition. The origins of microbial communities associated with a carcass, including the internal and external microbiome, are discussed in this review. The succession and methods used for the detection and exploration of decomposition-associated microbial communities have been briefly described. Also, the applications of carcass-associated microbial taxa have been outlined. This review is intended to understand the dynamics of microbial communities associated with the carcass and pave the way to estimate postmortem interval and its role in recycling nutrients.
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Affiliation(s)
- Mian Gul Hilal
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, PR China
| | - Qiaoling Yu
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Rui Zhou
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Yijie Wang
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Tianshu Feng
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Tianshui South Road #222, Lanzhou, Gansu 730000, PR China
| | - Huan Li
- Institute of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, China.,Center for Grassland Microbiome, Lanzhou University, Lanzhou 730000, China
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27
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The Epistemic Revolution Induced by Microbiome Studies: An Interdisciplinary View. BIOLOGY 2021; 10:biology10070651. [PMID: 34356506 PMCID: PMC8301382 DOI: 10.3390/biology10070651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/01/2021] [Accepted: 07/06/2021] [Indexed: 12/14/2022]
Abstract
Simple Summary This interdisciplinary study, conducted by experts in evolutionary biology, ecology, ecosystem studies, arts, medicine, forensic analyses, agriculture, law, and philosophy of science describe how microbiome studies are convergently affecting the concepts and practices of diverse fields and practices, that now consider microbiomes within their legitimate scope. Consequently, it describes what seems to be an ongoing pluridisciplinary epistemic revolution, with the potential to fundamentally change how we understand the world through an ecologization of pre-existing concepts, a greater focus on interactions, the use of multi-scalar interaction networks as explanatory frameworks, the reconceptualization of the usual definitions of individuals, and a de-anthropocentrification of our perception of phenomena. Abstract Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An ‘epistemic revolution induced by microbiome studies’ seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.
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28
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Dell'Annunziata F, Francesca M, Pepa MED, Folliero V, Luongo L, Bocelli S, Guida F, Mascolo P, Campobasso CP, Maione S, Franci G, Galdiero M. Postmortem interval assessment by MALDI-TOF mass spectrometry analysis in murine cadavers. J Appl Microbiol 2021; 132:707-714. [PMID: 34251733 PMCID: PMC9291851 DOI: 10.1111/jam.15210] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/26/2022]
Abstract
Aims This study assessed the use of matrix‐assisted laser desorption/ionization time of flight (MALDI‐TOF) mass spectrometry as an alternative method to identify species associated with the thanatomicrobiota and epinecrotic communities. Methods and Results The study was conducted on 10 murine cadavers, and microbiological swabs were collected from five external anatomical sites (eyes, ears, nose, mouth and rectum) and four internal organs (brain, spleen, liver, heart), during 16 and 30 days, for the thanatomicrobiota and epinecrotic communities, respectively. Our results revealed that the postmortem microbiota associated with the external cavities showed changes over time and reduced taxonomic diversity. The internal organs, initially sterile, showed signs of microbial invasion at 3 and 10 days postmortem for the liver‐spleen and heart‐brain, respectively. The postmortem microbiota was mainly dominated by Firmicutes and Proteobacteria. Conclusions MALDI‐TOF is a promising method for estimating postmortem interval (PMI), associated with rapid sample handling, good reproducibility and high productivity. Significance and Impact of the Study This study investigated microbial changes during the decomposition process and proposed a simple strategy for PMI estimation. Results introducing the application of the MALDI‐TOF method in the field of forensic.
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Affiliation(s)
- Federica Dell'Annunziata
- Microbiology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Martora Francesca
- Microbiology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Maria Elena Della Pepa
- Microbiology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Veronica Folliero
- Microbiology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Livio Luongo
- Pharmacology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy.,IRCSS, NEUROMED, Pozzilli, Italy
| | - Serena Bocelli
- Pharmacology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Francesca Guida
- Pharmacology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Pasquale Mascolo
- Legal Medicine Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Carlo Pietro Campobasso
- Legal Medicine Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
| | - Sabatino Maione
- Pharmacology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy.,IRCSS, NEUROMED, Pozzilli, Italy
| | - Gianluigi Franci
- Microbiology Section, Department of Medicine, Surgery and Dentistry Scuola Medica Salernitana, University of Salerno, Salerno, Italy
| | - Marilena Galdiero
- Microbiology Section, Department of Experimental Medicine, University of Study of Campania "Luigi Vanvitelli", Napoli, Italy
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29
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Newsome TM, Barton B, Buck JC, DeBruyn J, Spencer E, Ripple WJ, Barton PS. Monitoring the dead as an ecosystem indicator. Ecol Evol 2021; 11:5844-5856. [PMID: 34141188 PMCID: PMC8207411 DOI: 10.1002/ece3.7542] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 12/21/2022] Open
Abstract
Dead animal biomass (carrion) is present in all terrestrial ecosystems, and its consumption, decomposition, and dispersal can have measurable effects on vertebrates, invertebrates, microbes, parasites, plants, and soil. But despite the number of studies examining the influence of carrion on food webs, there has been no attempt to identify how general ecological processes around carrion might be used as an ecosystem indicator. We suggest that knowledge of scavenging and decomposition rates, scavenger diversity, abundance, and behavior around carrion, along with assessments of vegetation, soil, microbe, and parasite presence, can be used individually or in combination to understand food web dynamics. Monitoring carrion could also assist comparisons of ecosystem processes among terrestrial landscapes and biomes. Although there is outstanding research needed to fully integrate carrion ecology and monitoring into ecosystem management, we see great potential in using carrion as an ecosystem indicator of an intact and functional food web.
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Affiliation(s)
- Thomas M. Newsome
- School of Life and Environmental SciencesThe University of SydneySydneyNSWAustralia
| | - Brandon Barton
- Department of Biological SciencesMississippi State UniversityMississippi StateMSUSA
| | - Julia C. Buck
- Biology and Marine BiologyUniversity of North Carolina WilmingtonWilmingtonNCUSA
| | - Jennifer DeBruyn
- Biosystems Engineering and Soil ScienceUniversity of TennesseeKnoxvilleTNUSA
| | - Emma Spencer
- School of Life and Environmental SciencesThe University of SydneySydneyNSWAustralia
| | - William J. Ripple
- Department of Forest Ecosystems and SocietyOregon State UniversityCorvallisORUSA
| | - Philip S. Barton
- School of ScienceFederation University AustraliaMt HelenVICAustralia
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30
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Jordan D, Mills D. Past, Present, and Future of DNA Typing for Analyzing Human and Non-Human Forensic Samples. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.646130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Forensic DNA analysis has vastly evolved since the first forensic samples were evaluated by restriction fragment length polymorphism (RFLP). Methodologies advanced from gel electrophoresis techniques to capillary electrophoresis and now to next generation sequencing (NGS). Capillary electrophoresis was and still is the standard method used in forensic analysis. However, dependent upon the information needed, there are several different techniques that can be used to type a DNA fragment. Short tandem repeat (STR) fragment analysis, Sanger sequencing, SNapShot, and capillary electrophoresis-single strand conformation polymorphism (CE-SSCP) are a few of the techniques that have been used for the genetic analysis of DNA samples. NGS is the newest and most revolutionary technology and has the potential to be the next standard for genetic analysis. This review briefly encompasses many of the techniques and applications that have been utilized for the analysis of human and nonhuman DNA samples.
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31
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Roy D, Tomo S, Purohit P, Setia P. Microbiome in Death and Beyond: Current Vistas and Future Trends. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.630397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Forensic medicine has, for a long time, been relying on biochemical, anthropologic, and histopathologic evidences in solving various investigations. However, depending on the method used, lengthy sample processing time, scanty sample, and less sensitivity and accuracy pervade these procedures. Accordingly, newer arenas such as the thanatomicrobiome have come forward to aid in its quandaries; furthermore, the parallel advances in genomic and proteomic techniques have complemented and are still emerging to be used in forensic experiments and investigations. Postmortem interval (PMI) is one of the most important aspects of medico-legal investigations. The current trend in PMI estimation is toward genomic analyses of autopsy samples. Similarly, determination of cause of death, although a domain of medical sciences, is being targeted as the next level of forensic casework. With the current trend in laboratory sciences moving to the discovery of newer disease-specific markers for diagnostic and prognostic purposes, the same is being explored for the determination of the cause of death by using techniques such as Real-Time PCR, DNA micro-array, to Next-Gen Sequencing. Establishing an individual’s biological profile has been done using medicolegal methods and anthropology as well as bar-bodies/Davidson bodies (gender determination); and in cases where the determination of age/gender is a challenge using morphological characteristics; the recent advances in the field of genomics and proteomics have played a significant role, e.g., use of mitochondrial DNA in age estimation and in maternity disputes. The major hurdle forensic medical research faces is the fact that most of the studies are conducted in animal models, which are often difficult to mimic in human and real-time scenarios. Additionally, the high accuracy required in criminal investigations to be used in a court of law as evidence has prevented these results to come out of the labs and be used to the optimum. The current review aims at giving a comprehensive and critical account of the various molecular biology techniques including “thanatogenomics,” currently being utilized in the veritable fields of forensic medicine.
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32
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Aquila I, Ricci P, Bonetta CF, Sacco MA, Longhini F, Torti C, Mazzitelli M, Garofalo E, Bruni A, Trecarichi EM, Serapide F, Gratteri S, Quirino A, Barreca GS, Abenavoli L, Arena V, Oliva A, Giancotti A, Iavicoli I, Liberto MC, Matera G. Analysis of the persistence time of the SARS-CoV-2 virus in the cadaver and the risk of passing infection to autopsy staff. Med Leg J 2021; 89:40-53. [PMID: 33475037 DOI: 10.1177/0025817220980601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The activity of the SARS-CoV-2 virus has not yet been studied in a post-mortem setting. The absence of these data has led to the prohibition of exposure of infected corpses during burial procedures. Our aim was to assess the virus's persistence and the possibility of transmission in the post-mortem phase including autopsy staff. The sample group included 29 patients who were admitted to our Covid-19 Centre who died during hospitalisation and the autopsy staff. All the swabs were subjected to a one-step real-time reverse transcription polymerase chain reaction with cycle threshold (Ct) values. Swab collection was performed at 2 h, 4 h, 6 h, 12 h, over 24 since death. The following were the analysis of patients' swabs: 10 cases were positive 2 h after death; 10 cases positive 4 h after death; 9 cases were found positive 6 h after death; 7 cases positive 12 h after death; 9 cases remained positive 24 h after death. The swabs performed on all the forensic pathologist staff on duty who performed the autopsies were negative. The choice to avoid rituals and the display of corpses before and at the burial procedures given appears cautiously valid due to the persistence of the SARS-CoV-2 virus in the post-mortem period. Although the caution in choosing whether or not to perform an autopsy on infected corpses is acceptable, not to perform autopsies is not biologically supported.
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Affiliation(s)
- Isabella Aquila
- Institute of Legal Medicine, Department of Surgical and Medical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Pietrantonio Ricci
- Institute of Legal Medicine, Department of Surgical and Medical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Carlo Filippo Bonetta
- Institute of Legal Medicine, Department of Surgical and Medical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Matteo Antonio Sacco
- Institute of Legal Medicine, Department of Surgical and Medical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Federico Longhini
- Intensive Care Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Carlo Torti
- Infectious and Tropical Diseases Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Maria Mazzitelli
- Infectious and Tropical Diseases Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Eugenio Garofalo
- Intensive Care Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Andrea Bruni
- Intensive Care Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Infectious and Tropical Diseases Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Francesca Serapide
- Infectious and Tropical Diseases Unit, Department of Medical and Surgical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Santo Gratteri
- Institute of Legal Medicine, Department of Surgical and Medical Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Angela Quirino
- Clinical Microbiology Unit, Department of Health Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Giorgio Settimo Barreca
- Clinical Microbiology Unit, Department of Health Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Ludovico Abenavoli
- Department of Health Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Vincenzo Arena
- Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Istituto di Anatomia Patologica, Università Cattolica Del Sacro Cuore, Rome, Italy
| | - Antonio Oliva
- Department of Health Surveillance and Bioethics, Section of Legal Medicine, Fondazione Policlinico A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Aida Giancotti
- Clinical Microbiology Unit, Department of Health Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Ivo Iavicoli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Maria Carla Liberto
- Clinical Microbiology Unit, Department of Health Sciences, University "Magna Graecia" of Catanzaro, Italy
| | - Giovanni Matera
- Clinical Microbiology Unit, Department of Health Sciences, University "Magna Graecia" of Catanzaro, Italy
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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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34
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Lukiw WJ, Arceneaux L, Li W, Bond T, Zhao Y. Gastrointestinal (GI)-Tract Microbiome Derived Neurotoxins and their Potential Contribution to Inflammatory Neurodegeneration in Alzheimer's Disease (AD). JOURNAL OF ALZHEIMER'S DISEASE & PARKINSONISM 2021; 11:525. [PMID: 34457996 PMCID: PMC8395586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The human gastrointestinal (GI)-tract microbiome is a rich, complex and dynamic source of microorganisms that possess a staggering diversity and complexity. Importantly there is a significant variability in microbial complexity even amongst healthy individuals-this has made it difficult to link specific microbial abundance patterns with age-related neurological disease. GI-tract commensal microorganisms are generally beneficial to human metabolism and immunity, however enterotoxigenic forms of microbes possess significant potential to secrete what are amongst the most neurotoxic and pro-inflammatory biopolymers known. These include toxic glycolipids such as lipopolysaccharide (LPS), enterotoxins, microbial-derived amyloids and small non-coding RNA. One major microbial species of the GI-tract microbiome, about ~100-fold more abundant than Escherichia coli in deep GI-tract regions is Bacteroides fragilis, an anaerobic, rod-shaped Gram-negative bacterium. B. fragilis can secrete: (i) a particularly potent, pro-inflammatory and unique LPS subtype (BF-LPS); and (ii) a zinc-metalloproteinase known as B. fragilis-toxin (BFT) or fragilysin. Ongoing studies indicate that BF-LPS and/or BFT disrupt paracellular-and transcellular-barriers by cleavage of intercellular-proteins resulting in 'leaky' barriers. These barriers: (i) become defective and more penetrable with aging and disease; and (ii) permit entry of microbiome-derived neurotoxins into the systemic-circulation from which they next transit the blood-brain barrier and gain access to the CNS. Here LPS accumulates and significantly alters homeostatic patterns of gene expression. The affinity of LPS for neuronal nuclei is significantly enhanced in the presence of amyloid beta 42 (Aβ42) peptides. Recent research on the appearance of the brain thanatomicrobiome at the time of death and the increasing likelihood of a complex brain microbiome are reviewed and discussed. This paper will also highlight some recent advances in this extraordinary research area that links the pro-inflammatory exudates of the GI-tract microbiome with innate-immune disturbances and inflammatory-signaling within the CNS with reference to Alzheimer's disease (AD) wherever possible.
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Affiliation(s)
- Walter J. Lukiw
- LSU Neuroscience Center, Louisiana State University Health
Sciences Center, New Orleans, LA, United States,Department of Ophthalmology, LSU Health Sciences Center,
New Orleans, LA, United States,Department of Neurology, Louisiana State University Health
Sciences Center, New Orleans, LA, United States,Corresponding author: Dr. Walter J. Lukiw, LSU
Neuroscience Center, Louisiana State University Health Sciences Center, New
Orleans, LA, United States,
| | - Lisa Arceneaux
- LSU Neuroscience Center, Louisiana State University Health
Sciences Center, New Orleans, LA, United States
| | - Wenhong Li
- LSU Neuroscience Center, Louisiana State University Health
Sciences Center, New Orleans, LA, United States,Department of Pharmacology, School of Pharmacy, Jiangxi
University of Traditional Chinese Medicine (TCM), Nanchang, China
| | - Taylor Bond
- LSU Neuroscience Center, Louisiana State University Health
Sciences Center, New Orleans, LA, United States
| | - Yuhai Zhao
- LSU Neuroscience Center, Louisiana State University Health
Sciences Center, New Orleans, LA, United States,Department of Anatomy and Cell Biology, Louisiana State
University, New Orleans, LA, United States
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35
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Impact of the Human Microbiome in Forensic Sciences: a Systematic Review. Appl Environ Microbiol 2020; 86:AEM.01451-20. [PMID: 32887714 DOI: 10.1128/aem.01451-20] [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] [Indexed: 12/16/2022] Open
Abstract
Numerous studies relate differences in microbial communities to human health and disease; however, little is known about microbial changes that occur postmortem or the possible applications of microbiome analysis in the field of forensic science. The aim of this review was to study the microbiome and its applications in forensic sciences and to determine the main lines of investigation that are emerging, as well as its possible contributions to the forensic field. A systematic review of the human microbiome in relation to forensic science was carried out by following PRISMA guidelines. This study sheds light on the role of microbiome research in the postmortem interval during the process of decomposition, identifying death caused by drowning or sudden death, locating the geographical location of death, establishing a connection between the human microbiome and personal items, sexual contact, and the identification of individuals. Actinomycetaceae, Bacteroidaceae, Alcaligenaceae, and Bacilli play an important role in determining the postmortem interval. Aeromonas can be used to determine the cause of death, and Corynebacterium or Helicobacter pylori can be used to ascertain personal identity or geographical location. Several studies point to a promising future for microbiome analysis in the different fields of forensic science, opening up an important new area of research.
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Abstract
The human microbiome has been identified as having a key role in health and numerous diseases. Trillions of microbial cells and viral particles comprise the microbiome, each representing modifiable working elements of an intricate bioactive ecosystem. The significance of the human microbiome as it relates to human biology has progressed through culture-dependent (for example, media-based methods) and, more recently, molecular (for example, genetic sequencing and metabolomic analysis) techniques. The latter have become increasingly popular and evolved from being used for taxonomic identification of microbiota to elucidation of functional capacity (sequencing) and metabolic activity (metabolomics). This review summarises key elements of the human microbiome and its metabolic capabilities within the context of health and disease.
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Affiliation(s)
- Wiley Barton
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61C996, Ireland.,APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, T12YT20, Ireland.,VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, P61C996, Ireland
| | - Orla O'Sullivan
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61C996, Ireland.,APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, T12YT20, Ireland.,VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, P61C996, Ireland
| | - Paul D Cotter
- Department of Food Biosciences, Teagasc Food Research Centre, Moorepark, Fermoy, Cork, P61C996, Ireland.,APC Microbiome Ireland, University College Cork, National University of Ireland, Cork, T12YT20, Ireland.,VistaMilk SFI Research Centre, Teagasc, Moorepark, Fermoy, Cork, P61C996, Ireland
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37
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Bishop AH. The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases. FEMS Microbiol Lett 2019; 366:5303725. [PMID: 30689874 DOI: 10.1093/femsle/fnz021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/26/2019] [Indexed: 12/28/2022] Open
Abstract
The microorganisms with which we share our world go largely unnoticed. We are, however, beginning to be able to exploit their apparently silent presence as witnesses to events that are of legal concern. This information can be used to link forensic samples to criminal events and even perpetrators. Once dead, our bodies are rapidly colonised, internally and externally. The progress of these events can be charted to inform how long and even by what means a person has died. A small number of microbial species could actually be the cause of such deaths as a result of biocrime or bioterrorism. The procedures and techniques to respond to such attacks have matured in the last 20 years. The capability now exists to identify malicious intent, characterise the threat agent to isolate level and potentially link it to perpetrators with a high level of confidence.
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Affiliation(s)
- A H Bishop
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Devon, PL4 8AA, UK
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38
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Keenan SW, DeBruyn JM. Changes to vertebrate tissue stable isotope (δ 15N) composition during decomposition. Sci Rep 2019; 9:9929. [PMID: 31289347 PMCID: PMC6617491 DOI: 10.1038/s41598-019-46368-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/26/2019] [Indexed: 01/10/2023] Open
Abstract
During carcass decomposition, tissues undergo biochemical changes: Cells autolyze, enteric microbes ferment cellular products, and tissues degrade. Ultimately, decomposition fluids are released as an ephemeral nitrogen (N) and carbon source to the surrounding environment. However, decomposition fluids are δ15N-enriched relative to body tissues, leading to a disconnect between starting tissue composition and ending fluid composition. It remains largely unknown when or if tissues exhibit δ15N enrichment postmortem despite the importance of tissue stable isotopes to ecologists. To test our hypothesis that tissues would become progressively δ15N-enriched during decay, soft tissues and bone were collected from beaver carcasses at five time points. All soft tissues, including muscle, were significantly δ15N-enriched compared to fresh tissues, but were not as enriched as decomposition fluids. Tissue breakdown is initially dominated by anaerobic autolysis and later by microbe and insect infiltration, and partly explains decay fluid isotopic enrichment. We speculate that after rupture, preferential volatilization of δ15N-depleted compounds (especially ammonia) contributes to further enrichment. These results constrain the timing, rate, and potential mechanisms driving carcass isotopic enrichment during decay, and suggest that found carcasses (e.g., road kill) should be used with caution for inferring trophic ecology as decay can result in significant postmortem δ15N enrichment.
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Affiliation(s)
- Sarah W Keenan
- University of Tennessee, Department of Biosystems Engineering and Soil Science, 2506 E.J. Chapman Drive, Knoxville, TN, 37996, USA. .,South Dakota School of Mines & Technology, Department of Geology and Geological Engineering, 501 East St. Joseph Street, Rapid City, SD, 57701, USA.
| | - Jennifer M DeBruyn
- University of Tennessee, Department of Biosystems Engineering and Soil Science, 2506 E.J. Chapman Drive, Knoxville, TN, 37996, USA
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Burcham ZM, Schmidt CJ, Pechal JL, Brooks CP, Rosch JW, Benbow ME, Jordan HR. Detection of critical antibiotic resistance genes through routine microbiome surveillance. PLoS One 2019; 14:e0213280. [PMID: 30870464 PMCID: PMC6417727 DOI: 10.1371/journal.pone.0213280] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 02/18/2019] [Indexed: 12/29/2022] Open
Abstract
Population-based public health data on antibiotic resistance gene carriage is poorly surveyed. Research of the human microbiome as an antibiotic resistance reservoir has primarily focused on gut associated microbial communities, but data have shown more widespread microbial colonization across organs than originally believed, with organs previously considered as sterile being colonized. Our study demonstrates the utility of postmortem microbiome sampling during routine autopsy as a method to survey antibiotic resistance carriage in a general population. Postmortem microbial sampling detected pathogens of public health concern including genes for multidrug efflux pumps, carbapenem, methicillin, vancomycin, and polymixin resistances. Results suggest that postmortem assessments of host-associated microbial communities are useful in acquiring community specific data while reducing selective-participant biases.
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Affiliation(s)
- Zachary M. Burcham
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States of America
| | - Carl J. Schmidt
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States of America
| | - Jennifer L. Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, United States of America
| | - Christopher P. Brooks
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States of America
| | - Jason W. Rosch
- Department of Infectious Disease, St. Jude Children’s Research Hospital, Memphis, TN, United States of America
| | - M. Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, United States of America
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, United States of America
| | - Heather R. Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States of America
- * E-mail:
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Mora-Ortiz M, Trichard M, Oregioni A, Claus SP. Thanatometabolomics: introducing NMR-based metabolomics to identify metabolic biomarkers of the time of death. Metabolomics 2019; 15:37. [PMID: 30834988 PMCID: PMC6476858 DOI: 10.1007/s11306-019-1498-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/21/2019] [Indexed: 01/15/2023]
Abstract
INTRODUCTION Death is the permanent cessation of the critical functions of the organism as a whole. However, the shutdown of a complex biological organism does not abruptly terminate at time of death. New high-throughput technologies allow the systematic investigation of the biochemical modulations occurring after death. Recent genomics studies have demonstrated that genes remain active after death, triggering upregulation of some genes and initiating feedback loops. These genes were mostly involved in pathways related to immunity, inflammation and cancer. These genetic modulations suggest many biochemical events persist after death, which can be captured using a metabolomics approach. OBJECTIVES This proof of concept work aimed to determine whether NMR spectroscopy could identify metabolomics changes occurring after death, and characterise the nature of these metabolomics modulations. METHODS High-resolution 1H-NMR spectroscopy was applied to six biological matrices: heart, kidney, liver, spleen, skin and white adipose tissue of ten adult mice at three different type points. RESULTS Forty-three metabolites were associated with post mortem metabolomics modulations. Kidney, heart and spleen showed the highest metabolic perturbations. Conversely, skin and white adipose tissue were the least altered matrices. Early metabolic modulations were associated with energy metabolism and DNA synthesis, by contrast, late metabolomics modulations were associated with microbial metabolism. CONCLUSIONS NMR has proven potential to determine the time of death based on post-mortem metabolomics modulations. This could be useful in the context of transplants, forensic studies and as internal quality control in metabolomics studies. Further investigations are required to validate these findings in humans in order to determine which compounds robustly reflect post-mortem metabolic fluctuations to accurately determine the time of death.
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Affiliation(s)
- Marina Mora-Ortiz
- Department of Food and Nutritional Sciences, The University of Reading, Whiteknights Campus, Reading, RG6 6AP, UK.
- Department of Twin Research, Kings College London, St Thomas' Hospital Campus, 3rd Floor South Wing Block D, Westminster Bridge Road, London, SE1 7EH, UK.
| | - Marianne Trichard
- Département Biologie Alimentaire à l'Ecole Nationale Supérieure de Chimie, Biologie et Physique de Bordeaux (ENSCBP), 33600, Pessac, France
| | - Alain Oregioni
- MRC Biomedical NMR Centre, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Sandrine P Claus
- Department of Food and Nutritional Sciences, The University of Reading, Whiteknights Campus, Reading, RG6 6AP, UK
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Lawrence KE, Lam KC, Morgun A, Shulzhenko N, Löhr CV. Effect of temperature and time on the thanatomicrobiome of the cecum, ileum, kidney, and lung of domestic rabbits. J Vet Diagn Invest 2019; 31:155-163. [PMID: 30741115 DOI: 10.1177/1040638719828412] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Knowledge of changes in the composition of microbial communities (microbiota) in tissues after death, over time, is critical to correctly interpret results of microbiologic testing from postmortem examinations. Limited information is available about postmortem changes of the microbiota and the associated microbial genes (microbiome) of internal organs in any species. We examined the effect of time and ambient temperature on the postmortem microbiome (thanatomicrobiome) of tissues typically sampled for microbiologic testing during autopsies. Twenty rabbits were euthanized and their bodies stored at 4°C or 20°C for 6 or 48 h. Ileum, cecum, kidney, and lung tissue were sampled. Bacterial DNA abundance was determined by RT-qPCR. Microbiome diversity was determined by 16S rRNA gene sequencing. By relative abundance of the microbiome composition, intestinal tissues were clearly separated from lungs and kidneys, which were similar to each other, over all times and temperatures. Only cecal thanatomicrobiomes had consistently high concentrations and consistent composition in all conditions. In lungs and kidneys, but not intestine, proteobacteria were highly abundant at specific times and temperatures. Thanatomicrobiome variation was not explained by minor subclinical lesions identified upon microscopic examination of tissues. Bacterial communities typically found in the intestine were not identified at extra-intestinal sites in the first 48 h at 4°C and only in small amounts at 20°C. However, changes in tissue-specific microbiomes during the postmortem interval should be considered when interpreting results of microbiologic testing.
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Affiliation(s)
- Kelsey E Lawrence
- Department of Biomedical Sciences, College of Veterinary Medicine (Lawrence, Shulzhenko, Löhr).,Department of Bioresource Research, College of Agriculture (Lam), Oregon State University, Corvallis, OR.,College of Pharmacy (Morgun), Oregon State University, Corvallis, OR.,Current addresses: Willamette Valley Animal Hospital, Tualatin, OR (Lawrence).,Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD (Lam)
| | - Khiem C Lam
- Department of Biomedical Sciences, College of Veterinary Medicine (Lawrence, Shulzhenko, Löhr).,Department of Bioresource Research, College of Agriculture (Lam), Oregon State University, Corvallis, OR.,College of Pharmacy (Morgun), Oregon State University, Corvallis, OR.,Current addresses: Willamette Valley Animal Hospital, Tualatin, OR (Lawrence).,Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD (Lam)
| | - Andrey Morgun
- Department of Biomedical Sciences, College of Veterinary Medicine (Lawrence, Shulzhenko, Löhr).,Department of Bioresource Research, College of Agriculture (Lam), Oregon State University, Corvallis, OR.,College of Pharmacy (Morgun), Oregon State University, Corvallis, OR.,Current addresses: Willamette Valley Animal Hospital, Tualatin, OR (Lawrence).,Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD (Lam)
| | - Natalia Shulzhenko
- Department of Biomedical Sciences, College of Veterinary Medicine (Lawrence, Shulzhenko, Löhr).,Department of Bioresource Research, College of Agriculture (Lam), Oregon State University, Corvallis, OR.,College of Pharmacy (Morgun), Oregon State University, Corvallis, OR.,Current addresses: Willamette Valley Animal Hospital, Tualatin, OR (Lawrence).,Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD (Lam)
| | - Christiane V Löhr
- Department of Biomedical Sciences, College of Veterinary Medicine (Lawrence, Shulzhenko, Löhr).,Department of Bioresource Research, College of Agriculture (Lam), Oregon State University, Corvallis, OR.,College of Pharmacy (Morgun), Oregon State University, Corvallis, OR.,Current addresses: Willamette Valley Animal Hospital, Tualatin, OR (Lawrence).,Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD (Lam)
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Javan GT, Finley SJ, Tuomisto S, Hall A, Benbow ME, Mills D. An interdisciplinary review of the thanatomicrobiome in human decomposition. Forensic Sci Med Pathol 2018; 15:75-83. [PMID: 30519986 DOI: 10.1007/s12024-018-0061-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/19/2018] [Indexed: 01/21/2023]
Abstract
Death does not occur instantaneously and organs do not decompose at the same rate or in the same way. Nulligravid human uteri and prostate glands are the last internal organs to deteriorate during decomposition; however, the reason for this very important observation is still enigmatic. Recent studies have elucidated that the composition and abundance of microbes in the human thanatomicrobiome (microbiome of death) varies by organ and changes as a function of time and temperature. The ileocecal area has the largest absolute postmortem burden that spreads to the liver and spleen and continues to the heart and brain depending on the cause of death. To truly understand the mechanisms of microbial assembly during decomposition, a thorough examination of different strategies utilized by the trillions of microbes that colonize decaying tissues is needed from a multi-organ and multidisciplinary approach. In this review, we highlight interdisciplinary research and provide an overview of human decomposition investigations of thanatomicrobiomic changes in internal organs.
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Affiliation(s)
- Gulnaz T Javan
- Physical Sciences Department, Forensic Science Program, Alabama State University, 915 S. Jackson St., Hatch Hall Building Room 251, Montgomery, AL, 36104, USA.
| | - Sheree J Finley
- Physical Sciences Department, Forensic Science Program, Alabama State University, 915 S. Jackson St., Hatch Hall Building Room 251, Montgomery, AL, 36104, USA
| | - Sari Tuomisto
- Faculty of Medicine and Life Sciences, Department of Forensic Medicine, University of Tampere, Tampere, Finland
| | - Ashley Hall
- Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Chicago, IL, USA
| | - M Eric Benbow
- Department of Entomology and Department of Osteopathic Medicine, Michigan State University, East Lansing, MI, USA
| | - DeEtta Mills
- Department of Biological Sciences, Florida International University, Miami, FL, USA
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Iancu L, Junkins EN, Necula-Petrareanu G, Purcarea C. Characterizing forensically important insect and microbial community colonization patterns in buried remains. Sci Rep 2018; 8:15513. [PMID: 30341329 PMCID: PMC6195615 DOI: 10.1038/s41598-018-33794-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/06/2018] [Indexed: 02/08/2023] Open
Abstract
During violent criminal actions in which the perpetrator disposes of the victim's remains by burial, the analysis of insects and bacterial colonization patterns could be necessary for postmortem interval (PMI) estimation. Our research aimed to assess the decomposition process of buried rat carcasses from shallow graves (40 cm), the diversity and dynamics of insects and bacteria throughout the decomposition stages, and the environmental parameters' influence on these variations. The results provide further insight on decomposition in soil and contribute to a broader understanding of the factors involved in decomposition by qualitatively and quantitatively analysing the decomposer community (bacteria and insects). Additionally, two bacterial taxa, Enterococcus faecalis and Clostridium paraputrificum that were investigated for the first time as PMI indicators using quantitative polymerase chain reaction (qPCR) showed differential abundance over time, promising data for PMI estimation. The current study on the decomposition of buried rat carcasses in a natural environment will strengthen the current knowledge on decomposed remains from shallow graves and represents an effort to quantify insect and bacterial taxa as PMI estimators.
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Affiliation(s)
- Lavinia Iancu
- Institute of Biology Bucharest, Romanian Academy, Splaiul Independentei, 296, 060031, Bucharest, Romania.
| | - Emily N Junkins
- University of Oklahoma, Department of Microbiology and Plant Biology, 770 Van Vleet Oval, Norman, OK, 73019-0390, United States of America
| | | | - Cristina Purcarea
- Institute of Biology Bucharest, Romanian Academy, Splaiul Independentei, 296, 060031, Bucharest, Romania
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44
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Oliveira M, Amorim A. Microbial forensics: new breakthroughs and future prospects. Appl Microbiol Biotechnol 2018; 102:10377-10391. [PMID: 30302518 PMCID: PMC7080133 DOI: 10.1007/s00253-018-9414-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/14/2018] [Accepted: 09/16/2018] [Indexed: 12/17/2022]
Abstract
Recent advances in genetic data generation, through massive parallel sequencing (MPS), storage and analysis have fostered significant progresses in microbial forensics (or forensic microbiology). Initial applications in circumstances of biocrime, bioterrorism and epidemiology are now accompanied by the prospect of using microorganisms (i) as ancillary evidence in criminal cases; (ii) to clarify causes of death (e.g., drownings, toxicology, hospital-acquired infections, sudden infant death and shaken baby syndromes); (iii) to assist human identification (skin, hair and body fluid microbiomes); (iv) for geolocation (soil microbiome); and (v) to estimate postmortem interval (thanatomicrobiome and epinecrotic microbial community). When compared with classical microbiological methods, MPS offers a diverse range of advantages and alternative possibilities. However, prior to its implementation in the forensic context, critical efforts concerning the elaboration of standards and guidelines consolidated by the creation of robust and comprehensive reference databases must be undertaken.
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Affiliation(s)
- Manuela Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal. .,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Júlio Amaral de Carvalho,45, 4200-135, Porto, Portugal. .,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4200-135, Porto, Portugal.
| | - António Amorim
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,Ipatimup - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Rua Júlio Amaral de Carvalho,45, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, 4200-135, Porto, Portugal
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45
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Wescott DJ. Recent advances in forensic anthropology: decomposition research. Forensic Sci Res 2018; 3:327-342. [PMID: 30788450 PMCID: PMC6374978 DOI: 10.1080/20961790.2018.1488571] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 06/12/2018] [Indexed: 12/28/2022] Open
Abstract
Decomposition research is still in its infancy, but significant advances have occurred within forensic anthropology and other disciplines in the past several decades. Decomposition research in forensic anthropology has primarily focused on estimating the postmortem interval (PMI), detecting clandestine remains, and interpreting the context of the scene. Additionally, while much of the work has focused on forensic-related questions, an interdisciplinary focus on the ecology of decomposition has also advanced our knowledge. The purpose of this article is to highlight some of the fundamental shifts that have occurred to advance decomposition research, such as the role of primary extrinsic factors, the application of decomposition research to the detection of clandestine remains and the estimation of the PMI in forensic anthropology casework. Future research in decomposition should focus on the collection of standardized data, the incorporation of ecological and evolutionary theory, more rigorous statistical analyses, examination of extended PMIs, greater emphasis on aquatic decomposition and interdisciplinary or transdisciplinary research, and the use of human cadavers to get forensically reliable data.
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Affiliation(s)
- Daniel J Wescott
- Department of Anthropology, Texas State University, Forensic Anthropology Center at Texas State, San Marcos, TX, USA
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Eom YB. Microbial Forensics: Bioterrorism and Biocrime. BIOMEDICAL SCIENCE LETTERS 2018; 24:55-63. [DOI: 10.15616/bsl.2018.24.2.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/16/2018] [Accepted: 05/29/2018] [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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47
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Viero A, Montisci M, Pelletti G, Vanin S. Crime scene and body alterations caused by arthropods: implications in death investigation. Int J Legal Med 2018; 133:307-316. [PMID: 29938388 PMCID: PMC6342896 DOI: 10.1007/s00414-018-1883-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/18/2018] [Indexed: 11/26/2022]
Abstract
The activity of arthropods on corpses has been largely investigated, since they can produce information to reconstruct the peri-mortem events. However, the feeding/movement activity of insects around the crime scene, among the clothes and on the body, can also cause some alterations that can lead to wrong reconstruction and misinterpretations. This article summarises all the post-mortem arthropods artefacts related to the scene (i.e. fly artefacts and floor stripes) and the body (i.e. skin and other soft tissue alterations, bone alterations and hair alterations) that can mislead the forensic pathologist, discussing macroscopic and microscopic findings derived from forensic casework and from experimental laboratory studies, in order to provide a useful instrument to avoid misinterpretations and evaluation errors. Finally, some procedural notes for the documentation and the interpretation of findings are proposed.
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Affiliation(s)
- A Viero
- Legal Medicine and Toxicology, University-Hospital of Padova, Via Falloppio, 50, 35121, Padova, Italy
| | - M Montisci
- Legal Medicine and Toxicology, University-Hospital of Padova, Via Falloppio, 50, 35121, Padova, Italy
| | - G Pelletti
- Department of Medical and Surgical Sciences, Unit of Legal Medicine, University of Bologna, Bologna, Italy
| | - S Vanin
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Huddersfield, UK.
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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. [PMID: 29747223 DOI: 10.1111/lam.13005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 04/05/2018] [Accepted: 04/16/2018] [Indexed: 12/27/2022]
Abstract
Recent studies have revealed distinct thanatomicrobiome (microbiome of death) signatures in human body sites after death. Thanatomicrobiome studies suggest that microbial succession after death may have the potential to reveal important postmortem biomarkers for the identification of time of death. We surveyed the postmortem microbiomes of cardiac tissues from 10 corpses with varying times of death (6-58 h) using amplicon-based sequencing of the 16S rRNA gene' V1-2 and V4 hypervariable regions. The results demonstrated that amplicons had statistically significant (P < 0·05) sex-dependent changes. Clostridium sp., Pseudomonas sp., Pantoea sp. and Streptococcus sp. had the highest enrichment for both V1-2 and V4 regions. Interestingly, the results also show that V4 amplicons had higher abundance of Clostridium sp. and Pseudomonas sp. in female hearts compared to males. In addition, Streptococcus sp. was solely found in male heart samples. The distinction between sexes was further supported by principle coordinate analysis, which revealed microbes in female hearts formed a distinctive cluster separate from male cadavers for both hypervariable regions. This study provides data that demonstrates that two hypervariable regions show discriminatory power for sex differences in postmortem heart samples. SIGNIFICANCE AND IMPACT OF THE STUDY The findings represent preliminary data of the first thanatomicrobiome investigation of a comparison between 16S rRNA gene V1-2 and V4 amplicon signatures in corpse heart tissues. The results demonstrated that V4 hypervariable region amplicons had statistically significant (P < 0·05) sex-dependent microbial diversity. For example, Streptococcus sp. was solely found in male postmortem heart tissues. Interestingly, the results also show that V4 amplicons had higher abundance of Clostridium sp. and Pseudomonas sp. in female heart tissues compared to males. The finding of Clostridium sp. supports the postmortem clostridium effect in corpse heart tissues.
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Affiliation(s)
- C R Bell
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL, USA
| | - J E Wilkinson
- RTL Genomics, Research and Testing Laboratory, Lubbock, TX, USA
| | - B K Robertson
- Microbiology Program, Department of Biological Sciences, College of Science, Technology, Engineering and Mathematics, Alabama State University, Montgomery, AL, USA
| | - G T Javan
- Forensic Science Program, Department of Physical Sciences, Alabama State University, Montgomery, AL, USA
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Zhou W, Bian Y. Thanatomicrobiome composition profiling as a tool for forensic investigation. Forensic Sci Res 2018; 3:105-110. [PMID: 30483658 PMCID: PMC6197100 DOI: 10.1080/20961790.2018.1466430] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/29/2018] [Indexed: 12/22/2022] Open
Abstract
Thanatomicrobiome, or the postmortem microbiome, has been recognized as a useful microbial marker of the time and location of host death. In this mini-review, we compare the experimental methods commonly applied to thanatomicrobiome studies to the state-of-the-art methodologies in the microbiome field. Then, we review present findings in thanatomicrobiome studies, focusing on the diversity of the thanatomicrobiome composition and prediction models that have been proposed. Finally, we discuss potential improvements and future directions of the field.
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Affiliation(s)
- Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Yingnan Bian
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Shanghai, China
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50
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Microbial Forensics: Beyond a Fascination. DNA FINGERPRINTING: ADVANCEMENTS AND FUTURE ENDEAVORS 2018. [PMCID: PMC7121623 DOI: 10.1007/978-981-13-1583-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Microbiology has seen a great transition from culture-based identification of microbes using various biochemical and microscopic observations to identify and functionally characterize the microbes by just collecting the DNA and sequencing it. This advancement has not only moved in and around microbiology but has found its applications in fields which were earlier considered to be the remote ones. Forensics is one such field, where tracing the leftover evidence on a crime scene can lead to the identification and prosecution of the culprit. When leftover microbes in the biological material or objects used by the culprit or the person in question are used to correlate the identity of the individual, it takes us to the new field of science—“microbial forensics.” Technological advances in the field of forensics, molecular biology, and microbiology have all helped to refine the techniques of collecting and processing of the samples for microbiological identification using DNA-based methods followed by its inference in the form of evidence. Studies have supported the assumption that skin or surface microflora of an individual is somewhat related with the microflora found on the objects used by that individual and efforts are ongoing to see if this is found consistently in various surroundings and with different individuals. Once established, this technique would facilitate accurate identification and differentiation of an individual or suspect to guide investigations along with conventional evidence. Legal investigations are not only the field where microbial forensic could help. Agriculture, defense, public health, tourism, etc. are the fields wherein microbial forensics with different names based on the fields are helping out and have potential to further support other fields.
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