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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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2
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Moitas B, Caldas IM, Sampaio-Maia B. Microbiology and postmortem interval: a systematic review. Forensic Sci Med Pathol 2024; 20:696-715. [PMID: 37843744 PMCID: PMC11297127 DOI: 10.1007/s12024-023-00733-z] [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] [Accepted: 10/04/2023] [Indexed: 10/17/2023]
Abstract
This systematic review aims to learn if and how it is possible to use the human microbiome to indicate the time elapsed after death. Articles were searched on the PubMed database using predefined data fields and keywords; reviews, systematic reviews, and meta-analyses were excluded. The final selection included 14 papers (out of 144). The results indicated that the microorganisms present in the cadaveric island succeed predictably over time, with markers between the stages of decomposition constituting a potential innovative tool for postmortem interval (PMI) estimation. The human microbiome has the potential to be used for PMI estimation and may present advantages as microbes are present in all seasons, in all habitats, including the most extreme ones, and because microbial communities respond predictably to environmental changes.
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Affiliation(s)
- Bruna Moitas
- Departamento de Ciências da Saúde Pública e Forenses e Educação Médica, Faculdade de Medicina, Universidade do Porto, Porto, Portugal
| | - Inês Morais Caldas
- Faculdade de Medicina Dentária da Universidade do Porto, Porto, Portugal.
- CFE - Centre of Functional Ecology, University of Coimbra, Coimbra, Portugal.
- 1H-TOXRUN - One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, 4585-116, Gandra, Portugal.
| | - Benedita Sampaio-Maia
- Faculdade de Medicina Dentária da Universidade do Porto, Porto, Portugal
- i3S - Instituto de Investigação e Inovação Em Saúde, Universidade do Porto, Porto, Portugal
- INEB - Instituto Nacional de Engenharia Biomédica, Universidade do Porto, Porto, Portugal
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3
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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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Weisensee KE, Tica CI, Atwell MM, Ehrett C, Smith DH, Carbajales-Dale P, Claflin P, Nisbet N. geoFOR: A collaborative forensic taphonomy database for estimating the postmortem interval. Forensic Sci Int 2024; 355:111934. [PMID: 38277912 DOI: 10.1016/j.forsciint.2024.111934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 11/03/2023] [Accepted: 01/14/2024] [Indexed: 01/28/2024]
Abstract
Accurately assessing the postmortem interval (PMI), or the time since death, remains elusive within forensic science research and application. This paper introduces geoFOR, a web-based collaborative application that utilizes ArcGIS and machine learning to deliver improved PMI predictions. The geoFOR application provides a standardized, collaborative forensic taphonomy database that gives practitioners a readily available tool to enter case information that automates the collection of environmental data and delivers a PMI prediction using statistically robust methods. After case submission, the cross-validating machine learning PMI predictive model results in a R² value of 0.82. Contributors receive a predicted PMI with an 80% confidence interval. The geoFOR database currently contains 2529 entries from across the U.S. and includes cases from medicolegal investigations and longitudinal studies from human decomposition facilities. We present the overall findings of the data collected so far and compare results from medicolegal cases and longitudinal studies to highlight previously poorly understood limitations involved in the difficult task of PMI estimation. This novel approach for building a reference dataset of human decomposition is forensically and geographically representative of the realities in which human remains are discovered which allows for continual improvement of PMI estimations as more data is captured. It is our goal that the geoFOR data repository follow the principles of Open Science and be made available to forensic researchers to test, refine, and improve PMI models. Mass collaboration and data sharing can ultimately address enduring issues associated with accurately estimating the PMI within medicolegal death investigations.
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Affiliation(s)
- Katherine E Weisensee
- Department of Sociology, Anthropology and Criminal Justice, Clemson University, Clemson, SC, USA.
| | - Cristina I Tica
- Department of Anthropology and Applied Archaeology, Eastern New Mexico University, Portales, NM, USA
| | - Madeline M Atwell
- Department of Sociology, Anthropology and Criminal Justice, Clemson University, Clemson, SC, USA
| | - Carl Ehrett
- Watt Family Innovation Center, Clemson University, Clemson, SC, USA
| | - D Hudson Smith
- Watt Family Innovation Center, Clemson University, Clemson, SC, USA
| | | | - Patrick Claflin
- Clemson Center for Geospatial Technologies, Clemson University, Clemson, SC, USA
| | - Noah Nisbet
- Watt Family Innovation Center, Clemson University, Clemson, SC, USA
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Zerekidze A, Li M, Refisch A, Shameya J, Sobanski T, Walter M, Wagner G. Impact of Toxoplasma gondii and Human Microbiome on Suicidal Behavior: A Systematic Review. J Clin Med 2024; 13:593. [PMID: 38276099 PMCID: PMC10816148 DOI: 10.3390/jcm13020593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Suicide remains a persistent global health challenge, resisting widespread prevention efforts. According to previous findings, toxoplasmosis is particularly associated with altered decision making, which could lead to risk-taking behavior, thereby increasing the likelihood for suicidal behavior (SB). In addition, discussion about the role of microbiome in psychiatric disorders has emerged lately, which also makes it relevant to investigate its role in the context of SB. Therefore, two systematic reviews are integrated in this paper, and the existing knowledge is comprehensively summarized regarding the association between microbial pathogens and SB. METHODS We conducted a systematic search with keywords including SB and Toxoplasma gondii (Suicid* AND Toxoplasm*) and microbiome (Suicid* AND Microbiome AND Microbiota) throughout PubMed and Scopus to retrieve related studies up to 9 November 2023, identifying 24 eligible records. The subjects of the included studies had to have fulfilled the criteria of an SB disorder as defined by DSM-5, and death cases needed to have been defined as suicide. RESULTS Most studies reported significant association between toxoplasmosis and SB, suggesting a higher likelihood of SB in the infected population. Regarding the microbiome, only very few studies investigated an association between SB and alterations in the microbiome. Based on six included studies, there were some indications of a link between changes in the microbiome and SB. CONCLUSION The cognitive aspects of decision making in T. gondii-infected individuals with SB should be further investigated to unravel the underlying mechanisms. Further sufficiently powered studies are needed to establish a link between SB and alterations in the microbiome.
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Affiliation(s)
- Ani Zerekidze
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
| | - Meng Li
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
- Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
| | - Alexander Refisch
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
- Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
| | - Justina Shameya
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
| | - Thomas Sobanski
- Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, Center for Mental Health, Thueringen-Kliniken “Georgius Agricola”, 07318 Saalfeld, Germany;
| | - Martin Walter
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
- Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
- German Center for Mental Health (DZPG), Partner Site Jena, 07743 Jena, Germany
| | - Gerd Wagner
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
- Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
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6
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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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Yang F, Zhang X, Hu S, Nie H, Gui P, Zhong Z, Guo Y, Zhao X. Changes in Microbial Communities Using Pigs as a Model for Postmortem Interval Estimation. Microorganisms 2023; 11:2811. [PMID: 38004822 PMCID: PMC10672931 DOI: 10.3390/microorganisms11112811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Microbial communities can undergo significant successional changes during decay and decomposition, potentially providing valuable insights for determining the postmortem interval (PMI). The microbiota produce various gases that cause cadaver bloating, and rupture releases nutrient-rich bodily fluids into the environment, altering the soil microbiota around the carcasses. In this study, we aimed to investigate the underlying principles governing the succession of microbial communities during the decomposition of pig carcasses and the soil beneath the carcasses. At early decay, the phylum Firmicutes and Bacteroidota were the most abundant in both the winter and summer pig rectum. However, Proteobacteria became the most abundant in the winter pig rectum in late decay. Using genus as a biomarker to estimate the PMI could get the MAE from 1.375 days to 2.478 days based on the RF model. The abundance of bacterial communities showed a decreasing trend with prolonged decomposition time. There were statistically significant differences in microbial diversity in the two periods (pre-rupture and post-rupture) of the four groups (WPG 0-8Dvs. WPG 16-40D, p < 0.0001; WPS 0-16Dvs. WPS 24-40D, p = 0.003; SPG 0D vs. SPG 8-40D, p = 0.0005; and SPS 0D vs. SPS 8-40D, p = 0.0208). Most of the biomarkers in the pre-rupture period belong to obligate anaerobes. In contrast, the biomarkers in the post-rupture period belong to aerobic bacteria. Furthermore, the genus Vagococcus shows a similar increase trend, whether in winter or summer. Together, these results suggest that microbial succession was predictable and can be developed into a forensic tool for estimating the PMI.
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Affiliation(s)
- Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; (F.Y.); (S.H.); (H.N.)
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China; (X.Z.); (Y.G.)
| | - Sheng Hu
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; (F.Y.); (S.H.); (H.N.)
| | - Hao Nie
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; (F.Y.); (S.H.); (H.N.)
| | - Peng Gui
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.G.); (Z.Z.)
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.G.); (Z.Z.)
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China; (X.Z.); (Y.G.)
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; (F.Y.); (S.H.); (H.N.)
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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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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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10
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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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11
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Liu R, Zhang K, Li H, Sun Q, Wei X, Li H, Zhang S, Fan S, Wang Z. Dissecting the microbial community structure of internal organs during the early postmortem period in a murine corpse model. BMC Microbiol 2023; 23:38. [PMID: 36765295 PMCID: PMC9912631 DOI: 10.1186/s12866-023-02786-0] [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: 12/28/2021] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Microorganisms distribute and proliferate both inside and outside the body, which are the main mediators of decomposition after death. However, limited information is available on the postmortem microbiota changes of extraintestinal body sites in the early decomposition stage of mammalian corpses. RESULTS This study investigated microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition in male C57BL/6 J mice by 16S rRNA sequencing. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 h than that at 0.5 or 4 h. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific. CONCLUSION The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 h in internal organs may inform a new direction for organ transplantation.
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Affiliation(s)
- Ruina Liu
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Kai Zhang
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Huan Li
- grid.452910.bXi’an Mental Health Center Hospital, Xi’an, 710061 China
| | - Qinru Sun
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Xin Wei
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Huiyu Li
- grid.43169.390000 0001 0599 1243College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Siruo Zhang
- grid.440288.20000 0004 1758 0451Department of Clinical Laboratory, Shaanxi Provincial People’s Hospital, Shaanxi Xi’an, 710068 People’s Republic of China ,grid.43169.390000 0001 0599 1243Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Shaanxi Xi’an, 710061 People’s Republic of China
| | - Shuanliang Fan
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
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12
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Chen D, Guo J, Li A, Sun C, Lin H, Lin H, Yang C, Wang W, Gao J. Metabolic fluorine labeling and hotspot imaging of dynamic gut microbiota in mice. SCIENCE ADVANCES 2023; 9:eabg6808. [PMID: 36706178 PMCID: PMC9882976 DOI: 10.1126/sciadv.abg6808] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Real-time localization and microbial activity information of indigenous gut microbiota over an extended period of time remains a challenge with existing visualizing methods. Here, we report a metabolic fluorine labeling (MEFLA)-based strategy for monitoring the dynamic gut microbiota via 19F magnetic resonance imaging (19F MRI). In situ labeling of different microbiota subgroups is achieved by using a panel of peptidoglycan-targeting MEFLA probes containing 19F atoms of different chemical shifts, and subsequent real-time in vivo imaging is accomplished by multiplexed hotspot 19F MRI with high sensitivity and unlimited penetration. Using this method, we realize extended visualization (>24 hours) of native gut microbes located at different intestinal sections and semiquantitative analysis of their metabolic dynamics modulated by various conditions, such as the host death and different β-lactam antibiotics. Our strategy holds great potential for noninvasive and real-time assessing of the metabolic activities and locations of the highly dynamic gut microbiota.
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Affiliation(s)
- Dongxia Chen
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Junnan Guo
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ao Li
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chengjie Sun
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Huibin Lin
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Hongyu Lin
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Wei Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Jinhao Gao
- Department of Chemical Biology, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, Fujian Provincial Key Laboratory of Chemical Biology, and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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13
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Mason AR, Taylor LS, DeBruyn JM. Microbial ecology of vertebrate decomposition in terrestrial ecosystems. FEMS Microbiol Ecol 2023; 99:6985004. [PMID: 36631293 DOI: 10.1093/femsec/fiad006] [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: 09/20/2022] [Revised: 12/13/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023] Open
Abstract
Vertebrate decomposition results in an ephemeral disturbance of the surrounding environment. Microbial decomposers are recognized as key players in the breakdown of complex organic compounds, controlling carbon and nutrient fate in the ecosystem and potentially serving as indicators of time since death for forensic applications. As a result, there has been increasing attention on documenting the microbial communities associated with vertebrate decomposition, or the 'necrobiome'. These necrobiome studies differ in the vertebrate species, microhabitats (e.g. skin vs. soil), and geographic locations studied, but many are narrowly focused on the forensic application of microbial data, missing the larger opportunity to understand the ecology of these communities. To further our understanding of microbial dynamics during vertebrate decomposition and identify knowledge gaps, there is a need to assess the current works from an ecological systems perspective. In this review, we examine recent work pertaining to microbial community dynamics and succession during vertebrate (human and other mammals) decomposition in terrestrial ecosystems, through the lens of a microbial succession ecological framework. From this perspective, we describe three major microbial microhabitats (internal, external, and soil) in terms of their unique successional trajectories and identify three major knowledge gaps that remain to be addressed.
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Affiliation(s)
- Allison R Mason
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Lois S Taylor
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, TN 37996, United States
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14
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Yuan H, Wang Z, Wang Z, Zhang F, Guan D, Zhao R. Trends in forensic microbiology: From classical methods to deep learning. Front Microbiol 2023; 14:1163741. [PMID: 37065115 PMCID: PMC10098119 DOI: 10.3389/fmicb.2023.1163741] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Accepted: 03/08/2023] [Indexed: 04/18/2023] Open
Abstract
Forensic microbiology has been widely used in the diagnosis of causes and manner of death, identification of individuals, detection of crime locations, and estimation of postmortem interval. However, the traditional method, microbial culture, has low efficiency, high consumption, and a low degree of quantitative analysis. With the development of high-throughput sequencing technology, advanced bioinformatics, and fast-evolving artificial intelligence, numerous machine learning models, such as RF, SVM, ANN, DNN, regression, PLS, ANOSIM, and ANOVA, have been established with the advancement of the microbiome and metagenomic studies. Recently, deep learning models, including the convolutional neural network (CNN) model and CNN-derived models, improve the accuracy of forensic prognosis using object detection techniques in microorganism image analysis. This review summarizes the application and development of forensic microbiology, as well as the research progress of machine learning (ML) and deep learning (DL) based on microbial genome sequencing and microbial images, and provided a future outlook on forensic microbiology.
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Affiliation(s)
- Huiya Yuan
- Department of Forensic Analytical Toxicology, 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
| | - Zhi Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Fuyuan Zhang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Dawei Guan
- Liaoning Province Key Laboratory of Forensic Bio-Evidence Science, Shenyang, China
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- *Correspondence: Dawei Guan
| | - Rui Zhao
- Liaoning Province Key Laboratory of Forensic Bio-Evidence Science, Shenyang, China
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Rui Zhao
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15
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Li W, Xing Y, Gan L, Peng W, Deng S. Exploring the value of microorganisms in the appendix for inferring postmortem interval in Sprague-Dawley rats using high-throughput sequencing. J Forensic Sci 2023; 68:163-175. [PMID: 36440674 DOI: 10.1111/1556-4029.15173] [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: 07/04/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022]
Abstract
Various microorganisms play an important role in daily functions in the body and continue to flourish after death. Our prior investigation using frozen cadavers revealed that the appendix, rather than the transverse colon, was a superior sampling site for intestinal bacteria because the appendiceal flora had higher diversity than that in the transverse colon in the majority of experimental periods after death. We sought to explore out more about whether the appendicular flora is significantly related to postmortem interval (PMI) at natural temperatures following the host's death. In this work, we employed high-throughput sequencing to evaluate the contents of rats' appendices within 2 weeks after death and then utilized the random forest algorithm to build a PMI prediction model after completing basic visual analyses on the sequencing data. The findings revealed that Firmicutes was the absolute dominant species of appendicular flora; alpha-diversity of appendix flora first increased and then decreased, with the highest point appearing at 36 h after death; and the primary metabolic functions were carbohydrate metabolism, amino acid metabolism, as well as cofactors and vitamin metabolism. Finally, a random forest regression model for PMI prediction was built by the training data at the family level, with the mean absolute error of 10.27 h for prediction within 14 days postmortem, and the test set data subsequently proved the model's reliability. Changes in appendicular flora were strongly related to the PMI following rats' deaths, so we have reason to believe that the appendicular flora is valuable in predicting PMI.
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Affiliation(s)
- Weihan Li
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Yu Xing
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Li Gan
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Wenli Peng
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Shixiong Deng
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
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16
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Liu R, Wang Q, Zhang K, Wu H, Wang G, Cai W, Yu K, Sun Q, Fan S, Wang Z. Analysis of Postmortem Intestinal Microbiota Successional Patterns with Application in Postmortem Interval Estimation. MICROBIAL ECOLOGY 2022; 84:1087-1102. [PMID: 34775524 DOI: 10.1007/s00248-021-01923-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms play a vital role in the decomposition of vertebrate remains in natural nutrient cycling, and the postmortem microbial succession patterns during decomposition remain unclear. The present study used hierarchical clustering based on Manhattan distances to analyze the similarities and differences among postmortem intestinal microbial succession patterns based on microbial 16S rDNA sequences in a mouse decomposition model. Based on the similarity, seven different classes of succession patterns were obtained. Generally, the normal intestinal flora in the cecum was gradually decreased with changes in the living conditions after death, while some facultative anaerobes and obligate anaerobes grew and multiplied upon oxygen consumption. Furthermore, a random forest regression model was developed to predict the postmortem interval based on the microbial succession trend dataset. The model demonstrated a mean absolute error of 20.01 h and a squared correlation coefficient of 0.95 during 15-day decomposition. Lactobacillus, Dubosiella, Enterococcus, and the Lachnospiraceae NK4A136 group were considered significant biomarkers for this model according to the ranked list. The present study explored microbial succession patterns in terms of relative abundances and variety, aiding in the prediction of postmortem intervals and offering some information on microbial behaviors in decomposition ecology.
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Affiliation(s)
- Ruina Liu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qi Wang
- College of Basic Medicine, Department of Forensic Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Kai Zhang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hao Wu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Gongji Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Wumin Cai
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kai Yu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qinru Sun
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Shuanliang Fan
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
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17
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Tozzo P, Amico I, Delicati A, Toselli F, Caenazzo L. Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review. Diagnostics (Basel) 2022; 12:2641. [PMID: 36359484 PMCID: PMC9689864 DOI: 10.3390/diagnostics12112641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 08/12/2023] Open
Abstract
The determination of the Post-Mortem Interval (PMI) is an issue that has always represented a challenge in the field of forensic science. Different innovative approaches, compared to the more traditional ones, have been tried over the years, without succeeding in being validated as successful methods for PMI estimation. In the last two decades, innovations in sequencing technologies have made it possible to generate large volumes of data, allowing all members of a bacterial community to be sequenced. The aim of this manuscript is to provide a review regarding new advances in PMI estimation through cadaveric microbiota identification using 16S rRNA sequencing, in order to correlate specific microbiome profiles obtained from different body sites to PMI. The systematic review was performed according to PRISMA guidelines. For this purpose, 800 studies were identified through database searching (Pubmed). Articles that dealt with PMI estimation in correlation with microbiome composition and contained data about species, body site of sampling, monitoring time and sequencing method were selected and ultimately a total of 25 studies were considered. The selected studies evaluated the contribution of the various body sites to determine PMI, based on microbiome sequencing, in human and animal models. The results of this systematic review highlighted that studies conducted on both animals and humans yielded results that were promising. In order to fully exploit the potential of the microbiome in the estimation of PMI, it would be desirable to identify standardized body sampling sites and specific sampling methods in order to align data obtained by different research groups.
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Affiliation(s)
- Pamela Tozzo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35121 Padova, Italy
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18
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Mason AR, McKee-Zech HS, Hoeland KM, Davis MC, Campagna SR, Steadman DW, DeBruyn JM. Body Mass Index (BMI) Impacts Soil Chemical and Microbial Response to Human Decomposition. mSphere 2022; 7:e0032522. [PMID: 36135386 PMCID: PMC9599287 DOI: 10.1128/msphere.00325-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Microorganisms are key decomposers of vertebrate mortalities, breaking down body tissues and impacting decomposition progress. During human decomposition, both extrinsic environmental factors and intrinsic cadaver-related factors have the potential to impact microbial decomposers either directly or indirectly via altered physical or chemical conditions. While extrinsic factors (e.g., temperature, humidity) explain some variation in microbial response during human decomposition in terrestrial settings, recent work has noted that even under the same environmental conditions, individuals can have different decomposition patterns, highlighting the potential for intrinsic factors to impact microbial decomposers. The goal of this study was to investigate the effects of several intrinsic factors (age, sex, diseases at time of death, and body mass index [BMI]) on chemical and microbial changes in decomposition-impacted soils. In a field study conducted at the University of Tennessee Anthropology Research Facility, soils were collected from the decomposition-impacted area surrounding 19 deceased human individuals through the end of active decomposition. Soil physicochemical parameters were measured, and microbial (bacterial and fungal) communities were assessed via amplicon sequencing. BMI was shown to explain some variation in soil pH and microbial response to human decomposition. Hierarchical linear mixed (HLM) effects models revealed that BMI category significantly explained variation in pH response within decomposition-impacted soils over time (HLM F = 9.647; P < 0.001). Additionally, the relative abundance of soil Saccharomycetes in decomposition soils under underweight donors displayed little to no changes (mean maximum change in relative abundance, +6.6%), while all other BMI categories displayed an increased relative abundance of these organisms over time (normal, +50.6%; overweight, +64.4%; and obese, +64.6%) (HLM F = 3.441; P = 0.11). Together, these results reveal intrinsic factors influencing decomposition patterns, especially within the soil environment, and suggest BMI is an important factor for controlling decomposition processes. IMPORTANCE This work begins to address questions about interindividual variation in vertebrate decomposition attributed to intrinsic factors, that is, properties of the carcass or cadaver itself. Most research on factors affecting decomposition has focused on the extrinsic environment, such as temperature or humidity. While these extrinsic factors do explain some variation in decomposition patterns, interindividual variability is still observed. Understanding how intrinsic factors influence microbial decomposers will help reveal the ecological impacts of decomposition. This work also has forensic applications, as soil chemical and biological changes have been suggested as indicators of postmortem interval. We reveal factors that explain variation in the decomposition environment that should be considered in these estimates. This is particularly important as we consider the implications of variations in human populations due to diet, age, BMI, disease, toxicological loading, etc. on forensic investigations dealing with decomposing remains.
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Affiliation(s)
- Allison R. Mason
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | | | | | - Mary C. Davis
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Dawnie W. Steadman
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
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19
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Wang Z, Zhang F, Wang L, Yuan H, Guan D, Zhao R. Advances in artificial intelligence-based microbiome for PMI estimation. Front Microbiol 2022; 13:1034051. [PMID: 36267183 PMCID: PMC9577360 DOI: 10.3389/fmicb.2022.1034051] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Postmortem interval (PMI) estimation has always been a major challenge in forensic science. Conventional methods for predicting PMI are based on postmortem phenomena, metabolite or biochemical changes, and insect succession. Because postmortem microbial succession follows a certain temporal regularity, the microbiome has been shown to be a potentially effective tool for PMI estimation in the last decade. Recently, artificial intelligence (AI) technologies shed new lights on forensic medicine through analyzing big data, establishing prediction models, assisting in decision-making, etc. With the application of next-generation sequencing (NGS) and AI techniques, it is possible for forensic practitioners to improve the dataset of microbial communities and obtain detailed information on the inventory of specific ecosystems, quantifications of community diversity, descriptions of their ecological function, and even their application in legal medicine. This review describes the postmortem succession of the microbiome in cadavers and their surroundings, and summarizes the application, advantages, problems, and future strategies of AI-based microbiome analysis for PMI estimation.
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Affiliation(s)
- Ziwei Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Fuyuan Zhang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, 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
| | - 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
| | - 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
- *Correspondence: Dawei Guan,
| | - 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
- Rui Zhao,
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20
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Javan GT, Wells T, Allen J, Visona S, Moretti M, Tipton C, Scott L, Finley SJ. Correlation between postmortem microbial signatures and substance abuse disorders. PLoS One 2022; 17:e0274401. [PMID: 36155553 PMCID: PMC9512198 DOI: 10.1371/journal.pone.0274401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/26/2022] [Indexed: 11/18/2022] Open
Abstract
The microbiota gut-brain-axis is a bidirectional circuit that links the neural, endocrine, and immunological systems with gut microbial communities. The gut microbiome plays significant roles in human mind and behavior, specifically pain perception, learning capacity, memory, and temperament. Studies have shown that disruptions in the gut microbiota have been associated with substance use disorders. The interplay of gut microbiota in substance abuse disorders has not been elucidated; however, postmortem microbiome profiles may produce promising avenues for future forensic investigations. The goal of the current study was to determine gut microbiome composition in substance abuse disorder cases using transverse colon tissues of 21 drug overdose versus 19 non-overdose-related cases. We hypothesized that postmortem samples of the same cause of death will reveal similar microbial taxonomic relationships. We compared microbial diversity profiles using amplicon-based sequencing of the 16S rRNA gene V4 hypervariable region. The results demonstrated that the microbial abundance in younger-aged cases were found to have significantly more operational taxonomic units than older cases. Using weighted UniFrac analysis, the influence of substances in overdose cases was found to be a significant factor in determining microbiome similarity. The results also revealed that samples of the same cause of death cluster together, showing a high degree of similarity between samples and a low degree of similarity among samples of different causes of death. In conclusion, our examination of human transverse colon microflora in decomposing remains extends emerging literature on postmortem microbial communities, which will ultimately contribute to advanced knowledge of human putrefaction.
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Affiliation(s)
- Gulnaz T. Javan
- Department of Physical Sciences and Forensic Science Programs, Alabama State University, Montgomery, Alabama, United States of America
- * E-mail:
| | - Tiara Wells
- Department of Physical Sciences and Forensic Science Programs, Alabama State University, Montgomery, Alabama, United States of America
| | - Jamese Allen
- Department of Physical Sciences and Forensic Science Programs, Alabama State University, Montgomery, Alabama, United States of America
| | - Silvia Visona
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Matteo Moretti
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Craig Tipton
- RTL Genomics, Lubbock, Texas, United States of America
- Department of Biological Sciences, Texas Tech University, Lubbock, Texas, United States of America
| | - Latia Scott
- Department of Biological Sciences, Delaware State University, Dover, Delaware, United States of America
- College of Agriculture, Virginia State University, Petersburg, Virginia, United States of America
| | - Sheree J. Finley
- Department of Physical Sciences and Forensic Science Programs, Alabama State University, Montgomery, Alabama, United States of America
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21
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Dash HR, Das S. Microbial community signatures for estimation of postmortem time intervals. ADVANCES IN APPLIED MICROBIOLOGY 2022; 118:91-113. [PMID: 35461664 DOI: 10.1016/bs.aambs.2022.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The human body provides a complex ecosystem for symbiotic habitation of a huge number of microorganisms. These commensal microorganisms provide a huge benefit to the living host by acting against many deadly infections. Once the host dies, many changes in the complex ecosystem of the human body take place. The personalized microbes of a human body undergo successional change as many exogenous microbes attack the nutrient-rich cadaver after death. The succession pattern change of microbes in human cadaver allows postulating different models for estimation of Postmortem time interval (PMI). Estimation of PMI has a broad prospect from the criminal investigation point of view. Though many techniques are being used nowadays to estimate PMI, all of them have their pros and cons. With the advent of advanced molecular biological techniques, studies on the thanatomicrobiome of a human cadaver have gained pace and provide a superior alternative for conventional methods of PMI estimation. This chapter summarizes the recent advancements in the changes in signature microflora postmortem with change in human microenvironment to postulate a consensus model for estimation of PMI.
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Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India.
| | - Surajit Das
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, India.
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22
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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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23
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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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24
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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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25
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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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