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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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Huang X, Zeng J, Li S, Chen J, Wang H, Li C, Zhang S. 16S rRNA, metagenomics and 2bRAD-M sequencing to decode human thanatomicrobiome. Sci Data 2024; 11:736. [PMID: 38971804 PMCID: PMC11227556 DOI: 10.1038/s41597-024-03518-3] [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: 12/25/2023] [Accepted: 06/13/2024] [Indexed: 07/08/2024] Open
Abstract
Microorganisms are essential in the decomposition of corpses and play a significant role in forensic science. However, previous studies have primarily focused on animal remains, specifically the gut, skin, and burial environment. Insufficient research has been conducted on the microbiota of human cadavers, especially in cases of advanced decomposition and additional tissues, resulting in a lack of relevant reference data. In this study, the microbiota of eight cadavers at different stages of decomposition were detected using 16S rRNA, metagenomic sequencing and 2bRAD-M sequencing. Nine different sites, including oral and nasal cavities, heart, liver, spleen, lung, kidney, muscle and gut, were analysed and the efficacy of these methods was evaluated. The results showed that 16S rRNA sequencing was the most cost-effective method for the study of cadavers in the early stages of decomposition, whereas for cadaveric tissues in the late stages of decomposition, 2bRAD-M could overcome host contamination more effectively than metagenomic sequencing. This paves the way for new opportunities in data retrieval and promotes in-depth investigations into the microbiota.
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Affiliation(s)
- Xin Huang
- Institute of Forensic Science, Fudan University, Shanghai, 200032, PR China
| | - Jianye Zeng
- Institute of Forensic Science, Fudan University, Shanghai, 200032, PR China
| | - Shilin Li
- Institute of Forensic Science, Fudan University, Shanghai, 200032, PR China
| | - Ji Chen
- Institute of Forensic Science, Fudan University, Shanghai, 200032, PR China
| | - Hongyan Wang
- The State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Chengtao Li
- Institute of Forensic Science, Fudan University, Shanghai, 200032, PR China.
| | - Suhua Zhang
- Institute of Forensic Science, Fudan University, Shanghai, 200032, PR China.
- Department of Forensic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, PR China.
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3
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von Konow I, Eliasson A, Nilsson J, Malm T. Impact of prolonged storage time on homograft ultrastructures: an attempt to find optimal guidelines for homograft processing. Cell Tissue Bank 2024; 25:649-662. [PMID: 38386211 PMCID: PMC11142956 DOI: 10.1007/s10561-024-10127-2] [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: 10/20/2023] [Accepted: 01/10/2024] [Indexed: 02/23/2024]
Abstract
According to guidelines, total ischemic time for homografts at processing must be kept short to avoid degeneration. Many homografts are discarded due to practical inability to finish all steps from procurement to cryopreservation within the time limit. Although, several studies have shown that homografts with prolonged ischemic time show adequate quality and performance. Twenty aortic and 12 pulmonary homografts were collected and biopsies were retrieved at preparation (day 0) and after 1, 2, 3, 4, 7, 14, 21, 28, and 60 days in antibiotic decontamination at 4 °C. Biopsies were prepared for light microscopy (LM) and transmission electron microscopy (TEM). Assessment generated scores for cells, elastin, and collagen. Relative differences between times were compared with Wilcoxon signed rank test. Bonferroni corrected p value of 0.0056 was considered significant. LM could only reveal decrease in cell count at 60 days in aortic homografts, no other differences was detected. TEM showed affected cell appearance in day 3 and day 4 and beyond for aortic and pulmonary homografts respectively. Elastin appearance was affected at day 60 for aortic and day 21 for pulmonary homografts. Collagen appearance was affected at day 28 for aortic homografts, with no significant differences in pulmonary homografts. Cell degeneration starts early after homograft procurement, but elastic and collagen fibers are more resistant to degeneration. Overall structure integrity as seen in LM was not affected at all, while TEM could reveal small degeneration signs in individual elastic fibers and collagen bundles at 21 and 28 days respectively.
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Affiliation(s)
- Ida von Konow
- Department of Cardiothoracic Surgery, Skane University Hospital, Lund, Sweden.
- Department of Clinical Sciences, Thoracic Surgery, Lund University, Lund, Sweden.
- Tissue Bank Lund, Skane University Hospital, Lund, Sweden.
| | | | - Johan Nilsson
- Department of Cardiothoracic Surgery, Skane University Hospital, Lund, Sweden
- Department of Translational Medicine, Thoracic Surgery and Bioinformatics, Lund University, Lund, Sweden
| | - Torsten Malm
- Department of Clinical Sciences, Thoracic Surgery, Lund University, Lund, Sweden
- Tissue Bank Lund, Skane University Hospital, Lund, Sweden
- Department of Pediatric Cardiac Surgery Unit, Skane University Hospital, Lund, Sweden
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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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Tidwell TL. Life in Suspension with Death: Biocultural Ontologies, Perceptual Cues, and Biomarkers for the Tibetan Tukdam Postmortem Meditative State. Cult Med Psychiatry 2024:10.1007/s11013-023-09844-2. [PMID: 38393648 DOI: 10.1007/s11013-023-09844-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/05/2023] [Indexed: 02/25/2024]
Abstract
This article presents two cases from a collaborative study among Tibetan monastic populations in India on the postdeath meditative state called tukdam (thugs dam). Entered by advanced Tibetan Buddhist practitioners through a variety of different practices, this state provides an ontological frame that is investigated by two distinct intellectual traditions-the Tibetan Buddhist and medical tradition on one hand and the Euroamerican biomedical and scientific tradition on the other-using their respective means of inquiry. Through the investigation, the traditions enact two paradigms of the body at the time of death alongside attendant conceptualizations of what constitutes life itself. This work examines when epistemologies of these two traditions might converge, under what ontological contexts, and through which correlated indicators of evidence. In doing so, this work explores how these two intellectual traditions might answer how the time course and characteristics of physiological changes during the postmortem period might exhibit variation across individuals. Centrally, this piece presents an epistemological inquiry delineating the types of valid evidence that constitute exceptional processes post-clinical death and their potential ontological implications.
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Affiliation(s)
- Tawni L Tidwell
- Center for Healthy Minds, University of Wisconsin-Madison, 625 W. Washington Ave., Madison, WI, 53703, USA.
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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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7
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Cieśla J, Skrobisz J, Niciński B, Kloc M, Mazur K, Pałasz A, Javan GT, Tomsia M. The smell of death. State-of-the-art and future research directions. Front Microbiol 2023; 14:1260869. [PMID: 37779703 PMCID: PMC10538644 DOI: 10.3389/fmicb.2023.1260869] [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: 07/18/2023] [Accepted: 08/30/2023] [Indexed: 10/03/2023] Open
Abstract
The decomposition of a body is inseparably associated with the release of several types of odors. This phenomenon has been used in the training of sniffer dogs for decades. The odor profile associated with decomposition consists of a range of volatile organic compounds (VOCs), chemical composition of which varies over time, temperature, environmental conditions, and the type of microorganisms, and insects colonizing the carcass. Mercaptans are responsible for the bad smell associated with corpses; however, there are no unified recommendations for conducting forensic analysis based on the detectable odor of revealed corpses and previous research on VOCs shows differing results. The aim of this review is to systematize the current knowledge on the type of volatile organic compounds related to the decomposition process, depending on a few variables. This knowledge will improve the methods of VOCs detection and analysis to be used in modern forensic diagnostics and improve the methods of training dogs for forensic applications.
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Affiliation(s)
- Julia Cieśla
- Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Julia Skrobisz
- Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Bartosz Niciński
- Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Magdalena Kloc
- Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Katarzyna Mazur
- Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Artur Pałasz
- Department of Histology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
| | - Gulnaz T. Javan
- Department of Physical and Forensic Science Programs, Alabama State University, Montgomery, AL, United States
| | - Marcin Tomsia
- Department of Forensic Medicine and Forensic Toxicology, Faculty of Medical Sciences in Katowice, Medical University of Silesia, Katowice, Poland
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8
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Tambuzzi S, Maciocco F, Gentile G, Boracchi M, Bailo P, Marchesi M, Zoja R. Applications of microbiology to different forensic scenarios - A narrative review. J Forensic Leg Med 2023; 98:102560. [PMID: 37451142 DOI: 10.1016/j.jflm.2023.102560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
In contrast to other forensic disciplines, forensic microbiology is still too often considered a "side activity" and is not able to make a real and concrete contribution to forensic investigations. Indeed, the various application aspects of this discipline still remain a niche activity and, as a result, microbiological investigations are often omitted or only approximated, in part due to poor report in the literature. However, in certain situations, forensic microbiology can prove to be extremely effective, if not crucial, when all other disciplines fail. Precisely because microorganisms can represent forensic evidence, in this narrative review all the major pathological forensic applications described in the literature have been presented. The goal of our review is to highlight the versatility and transversality of microbiology in forensic science and to provide a comprehensive source of literature to refer to when needed.
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Affiliation(s)
- Stefano Tambuzzi
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| | - Francesca Maciocco
- Azienda Ospedaliera "San Carlo Borromeo", Servizio di Immunoematologia e Medicina Trasfusionale (SIMT), Via Pio II°, n. 3, Milano, Italy
| | - Guendalina Gentile
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy.
| | - Michele Boracchi
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| | | | - Matteo Marchesi
- ASST Papa Giovanni XXIII, Piazza OMS 1, 24127, Bergamo, Italy
| | - Riccardo Zoja
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
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9
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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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Singh P, Ali W, Sandhu S, Mishra S, Singh US, Verma AK, Singh M, Kaleem Ahmad M, Kumari S. Post-mortem interval estimation using miRNAs of road traffic accident cases: A forensic molecular approach. Sci Justice 2023; 63:485-492. [PMID: 37453780 DOI: 10.1016/j.scijus.2023.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/12/2023] [Accepted: 04/28/2023] [Indexed: 07/18/2023]
Abstract
In forensic examination accurate estimation of post-mortem interval (PMI) is a challenging task, particularly in the advanced stages of decomposition. The existing methods (algor mortis, livor mortis, rigor mortis, putrefaction etc) used for estimating PMI rely on analyzing the physical, biochemical, and metabolic changes that occur in the corpse after death. While these methods have shown some level of effectiveness in estimating PMI during the early stages of decomposition, accurate estimation becomes increasingly challenging during the later stages of putrefaction when the body undergoes significant changes. Recently, microRNA (miRNA) profiling due to its relatively small size and stability has emerged as a promising tool in several areas of forensics. This study demonstrates the potential of miRNA for PMI estimation in advanced stages of death. In this study, miRNA-195, miRNA-206, and miRNA-378 were selected as target miRNAs and miRNA-1 as reference miRNA. Left ventricle tissue (5 g) of the heart from 20 forensic autopsies of traffic accident victims (18-32 years) were collected and processed. The samples were held at room temperature for eight different time intervals (12, 24, 48, 72, 96, 120, 168 and 196 h), and RNA was extracted from all the samples using Trizol-based RNA isolation protocol, followed by cDNA synthesis and amplification with commercially available specific miRNA probes in Real-Time PCR (RT-PCR), Ct was calculated. The result showed that miRNAs were associated with PMI. Over time, there were substantial changes in the Ct values of all three miRNAs, with significant reductions observed at 196 h compared to 12 h. miRNA-206 demonstrated significant changes at multiple time intervals, while miRNA-1 remained stable for up to 196 h and thus holds caas an endogenous marker. In conclusion, miRNA has the potential to serve as a valuable tool for estimating PMI, especially during the advanced stages of decomposition, when used in conjunction with established techniques. However, further validation of the study is required to obtain more accurate estimates of PMI.
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Affiliation(s)
- Paurabhi Singh
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Wahid Ali
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Sangram Sandhu
- Department of Prosthodontics, King George's Medical University, Lucknow, India.
| | - Sridhar Mishra
- Department of Pathology, Dr. Ram Manohar Lohiya Institute of Medical Sciences, Lucknow, India
| | - Uma Shankar Singh
- Department of Pathology, King George's Medical University, Lucknow, India
| | - Anoop K Verma
- Department of Forensic Medicine and Toxicology, King George's Medical University, Lucknow, India.
| | - Mousami Singh
- Department of Forensic Medicine and Toxicology, King George's Medical University, Lucknow, India.
| | - M Kaleem Ahmad
- Department of Biochemistry, King George's Medical University, Lucknow, India.
| | - Sangeeta Kumari
- Department of Forensic Medicine and Toxicology, King George's Medical University, Lucknow, India.
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11
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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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12
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Silva NIO, Albery GF, Arruda MS, Oliveira GFG, Costa TA, de Mello ÉM, Moreira GD, Reis EV, da Silva SA, Silva MC, de Almeida MG, Becker DJ, Carlson CJ, Vasilakis N, Hanley KA, Drumond BP. Ecological drivers of sustained enzootic yellow fever virus transmission in Brazil, 2017-2021. PLoS Negl Trop Dis 2023; 17:e0011407. [PMID: 37276217 PMCID: PMC10270639 DOI: 10.1371/journal.pntd.0011407] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 06/15/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023] Open
Abstract
Beginning December 2016, sylvatic yellow fever (YF) outbreaks spread into southeastern Brazil, and Minas Gerais state experienced two sylvatic YF waves (2017 and 2018). Following these massive YF waves, we screened 187 free-living non-human primate (NHPs) carcasses collected throughout the state between January 2019 and June 2021 for YF virus (YFV) using RTqPCR. One sample belonging to a Callithrix, collected in June 2020, was positive for YFV. The viral strain belonged to the same lineage associated with 2017-2018 outbreaks, showing the continued enzootic circulation of YFV in the state. Next, using data from 781 NHPs carcasses collected in 2017-18, we used generalized additive mixed models (GAMMs) to identify the spatiotemporal and host-level drivers of YFV infection and intensity (an estimation of genomic viral load in the liver of infected NHP). Our GAMMs explained 65% and 68% of variation in virus infection and intensity, respectively, and uncovered strong temporal and spatial patterns for YFV infection and intensity. NHP infection was higher in the eastern part of Minas Gerais state, where 2017-2018 outbreaks affecting humans and NHPs were concentrated. The odds of YFV infection were significantly lower in NHPs from urban areas than from urban-rural or rural areas, while infection intensity was significantly lower in NHPs from urban areas or the urban-rural interface relative to rural areas. Both YFV infection and intensity were higher during the warm/rainy season compared to the cold/dry season. The higher YFV intensity in NHPs in warm/rainy periods could be a result of higher exposure to vectors and/or higher virus titers in vectors during this time resulting in the delivery of a higher virus dose and higher viral replication levels within NHPs. Further studies are needed to better test this hypothesis and further compare the dynamics of YFV enzootic cycles between different seasons.
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Affiliation(s)
| | - Gregory F. Albery
- Department of Biology, Georgetown University, Washington, DC, United States of America
| | - Matheus Soares Arruda
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Thaís Alkifeles Costa
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Érica Munhoz de Mello
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Laboratório de Zoonoses—Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Dias Moreira
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Erik Vinícius Reis
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Simone Agostinho da Silva
- Laboratório de Zoonoses—Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Marlise Costa Silva
- Laboratório de Zoonoses—Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Munique Guimarães de Almeida
- Laboratório de Zoonoses—Centro de Controle de Zoonoses, Prefeitura de Belo Horizonte, Belo Horizonte, Minas Gerais, Brazil
| | - Daniel J. Becker
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Colin J. Carlson
- Department of Biology, Georgetown University, Washington, DC, United States of America
- Center for Global Health Science and Security, Georgetown University, Washington, D.C., United States of America
| | - Nikos Vasilakis
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Center for Vector-Borne and Zoonotic Diseases, The University of Texas Medical Branch, Galveston, Texas, United States of America
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Betânia Paiva Drumond
- Department of Microbiology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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13
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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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14
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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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15
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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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16
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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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17
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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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18
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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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19
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Landman WJM, Buter GJ, Dijkman R, van Eck JHH. In vivo typing of Escherichia coli obtained from laying chickens with the E. coli peritonitis syndrome. Avian Pathol 2021; 50:436-446. [PMID: 34351217 DOI: 10.1080/03079457.2021.1962004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
RESEARCH HIGHLIGHTS Even at high doses not any E. coli strain can induce EPSSubstantial differences in virulence exist within very virulent E. coli strainsThe embryo lethality test is a useful alternative for biotyping E. coli in laying hensBroiler colibacillosis may represent a source of EPS strains for layers and vice versa.
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Affiliation(s)
| | | | | | - J H H van Eck
- Department of Population Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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20
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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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21
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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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22
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Gates L, Klein NJ, Sebire NJ, Alber DG. Characterising Post-mortem Bacterial Translocation Under Clinical Conditions Using 16S rRNA Gene Sequencing in Two Animal Models. Front Microbiol 2021; 12:649312. [PMID: 34135873 PMCID: PMC8200633 DOI: 10.3389/fmicb.2021.649312] [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: 01/04/2021] [Accepted: 04/29/2021] [Indexed: 12/19/2022] Open
Abstract
Sudden unexpected death in infancy (SUDI) is the sudden and unexpected death of an apparently healthy infant occurring within the first year of life where the cause is not immediately obvious. It is believed that a proportion of unexplained infant deaths are due to an infection that remains undiagnosed. The interpretation of post-mortem microbiology results is difficult due to the potential false-positives, a source of which is post-mortem bacterial translocation. Post-mortem bacterial translocation is the spread of viable bacteria from highly colonised sites to extra-intestinal tissues. We hypothesise that although post-mortem bacterial translocation occurs, when carcasses are kept under controlled routine clinical conditions it is not extensive and can be defined using 16S rRNA gene sequencing. With this knowledge, implementation of the 16S rRNA gene sequencing technique into routine clinical diagnostics would allow a more reliable retrospective diagnosis of ante-mortem infection. Therefore, the aim of this study was to establish the extent of post-mortem bacterial translocation in two animal models to establish a baseline sequencing signal for the post-mortem process. To do this we used 16S rRNA gene sequencing in two animal models over a 2 week period to investigate (1) the bacterial community succession in regions of high bacterial colonisation, and (2) the bacterial presence in visceral tissues routinely sampled during autopsy for microbiological investigation. We found no evidence for significant and consistent post-mortem bacterial translocation in the mouse model. Although bacteria were detected in tissues in the piglet model, we did not find significant and consistent evidence for post-mortem bacterial translocation from the gastrointestinal tract or nasal cavity. These data do not support the concept of significant post-mortem translocation as part of the normal post-mortem process.
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Affiliation(s)
- Lily Gates
- Department of Infection, Immunity and Inflammation, University College London Institute of Child Health, London, United Kingdom
| | - Nigel J Klein
- Department of Infection, Immunity and Inflammation, University College London Institute of Child Health, London, United Kingdom
| | - Neil J Sebire
- Histopathology, Great Ormond Street Hospital, London, United Kingdom
| | - Dagmar G Alber
- Department of Infection, Immunity and Inflammation, University College London Institute of Child Health, London, United Kingdom
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23
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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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24
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Coscia A, Bardanzellu F, Caboni E, Fanos V, Peroni DG. When a Neonate Is Born, So Is a Microbiota. Life (Basel) 2021; 11:life11020148. [PMID: 33669262 PMCID: PMC7920069 DOI: 10.3390/life11020148] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
In recent years, the role of human microbiota as a short- and long-term health promoter and modulator has been affirmed and progressively strengthened. In the course of one’s life, each subject is colonized by a great number of bacteria, which constitute its specific and individual microbiota. Human bacterial colonization starts during fetal life, in opposition to the previous paradigm of the “sterile womb”. Placenta, amniotic fluid, cord blood and fetal tissues each have their own specific microbiota, influenced by maternal health and habits and having a decisive influence on pregnancy outcome and offspring outcome. The maternal microbiota, especially that colonizing the genital system, starts to influence the outcome of pregnancy already before conception, modulating fertility and the success rate of fertilization, even in the case of assisted reproduction techniques. During the perinatal period, neonatal microbiota seems influenced by delivery mode, drug administration and many other conditions. Special attention must be reserved for early neonatal nutrition, because breastfeeding allows the transmission of a specific and unique lactobiome able to modulate and positively affect the neonatal gut microbiota. Our narrative review aims to investigate the currently identified pre- and peri-natal factors influencing neonatal microbiota, before conception, during pregnancy, pre- and post-delivery, since the early microbiota influences the whole life of each subject.
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Affiliation(s)
- Alessandra Coscia
- Neonatology Unit, Department of Public Health and Pediatrics, Università degli Studi di Torino, 10124 Turin, Italy;
| | - Flaminia Bardanzellu
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU and University of Cagliari, SS 554 km 4,500, 09042 Monserrato, Italy; (E.C.); (V.F.)
- Correspondence:
| | - Elisa Caboni
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU and University of Cagliari, SS 554 km 4,500, 09042 Monserrato, Italy; (E.C.); (V.F.)
| | - Vassilios Fanos
- Neonatal Intensive Care Unit, Department of Surgical Sciences, AOU and University of Cagliari, SS 554 km 4,500, 09042 Monserrato, Italy; (E.C.); (V.F.)
| | - Diego Giampietro Peroni
- Clinical and Experimental Medicine Department, Section of Pediatrics, University of Pisa, Via Roma, 55, 56126 Pisa PI, Italy;
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25
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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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26
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Lutz H, Vangelatos A, Gottel N, Osculati A, Visona S, Finley SJ, Gilbert JA, Javan GT. Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver. Front Microbiol 2020; 11:569630. [PMID: 33363519 PMCID: PMC7752770 DOI: 10.3389/fmicb.2020.569630] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Human thanatomicrobiota studies have shown that microorganisms inhabit and proliferate externally and internally throughout the body and are the primary mediators of putrefaction after death. Yet little is known about the source and diversity of the thanatomicrobiome or the underlying factors leading to delayed decomposition exhibited by reproductive organs. The use of the V4 hypervariable region of bacterial 16S rRNA gene sequences for taxonomic classification ("barcoding") and phylogenetic analyses of human postmortem microbiota has recently emerged as a possible tool in forensic microbiology. The goal of this study was to apply a 16S rRNA barcoding approach to investigate variation among different organs, as well as the extent to which microbial associations among different body organs in human cadavers can be used to predict forensically important determinations, such as cause and time of death. We assessed microbiota of organ tissues including brain, heart, liver, spleen, prostate, and uterus collected at autopsy from criminal casework of 40 Italian cadavers with times of death ranging from 24 to 432 h. Both the uterus and prostate had a significantly higher alpha diversity compared to other anatomical sites, and exhibited a significantly different microbial community composition from non-reproductive organs, which we found to be dominated by the bacterial orders MLE1-12, Saprospirales, and Burkholderiales. In contrast, reproductive organs were dominated by Clostridiales, Lactobacillales, and showed a marked decrease in relative abundance of MLE1-12. These results provide insight into the observation that the uterus and prostate are the last internal organs to decay during human decomposition. We conclude that distinct community profiles of reproductive versus non-reproductive organs may help guide the application of forensic microbiology tools to investigations of human cadavers.
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Affiliation(s)
- Holly Lutz
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | | | - Neil Gottel
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Antonio Osculati
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Silvia Visona
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Sheree J Finley
- Physical Sciences Department, Forensic Science Programs, Alabama State University, Montgomery, AL, United States
| | - Jack A Gilbert
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, United States.,Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, United States
| | - Gulnaz T Javan
- Physical Sciences Department, Forensic Science Programs, Alabama State University, Montgomery, AL, United States
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27
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Ceciliason AS, Andersson MG, Nyberg S, Sandler H. Histological quantification of decomposed human livers: a potential aid for estimation of the post-mortem interval? Int J Legal Med 2020; 135:253-267. [PMID: 33236207 PMCID: PMC7782410 DOI: 10.1007/s00414-020-02467-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/12/2020] [Indexed: 10/29/2022]
Abstract
The objective of this study was to determine if a novel scoring-based model for histological quantification of decomposed human livers could improve the precision of post-mortem interval (PMI) estimation for bodies from an indoor setting. The hepatic decomposition score (HDS) system created consists of five liver scores (HDS markers): cell nuclei and cell structure of hepatocytes, bile ducts, portal triad, and architecture. A total of 236 forensic autopsy cases were divided into a training dataset (n = 158) and a validation dataset (n = 78). All cases were also scored using the total body score (TBS) method. We specified a stochastic relationship between the log-transformed accumulated degree-days (log10ADD) and the taphonomic findings, using a multivariate regression model to compute the likelihood function. Three models were applied, based on (i) five HDS markers, (ii) three partial body scores (head, trunk, limbs), or (iii) a combination of the two. The predicted log10ADD was compared with the true log10ADD for each case. The fitted models performed equally well in the training dataset and the validation dataset. The model comprising both scoring methods had somewhat better precision than either method separately. Our results indicated that the HDS system was statistically robust. Combining the HDS markers with the partial body scores resulted in a better representation of the decomposition process and might improve PMI estimation of decomposed human remains.
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Affiliation(s)
- Ann-Sofie Ceciliason
- Forensic Medicine, Department of Surgical Sciences, Uppsala University Hospital, Uppsala University, SE-751 85, Uppsala, Sweden.
| | - M Gunnar Andersson
- Department of Chemistry, Environment and Feed Hygiene, The National Veterinary Institute, SE-751 89, Uppsala, Sweden
| | - Sofia Nyberg
- Department of Forensic Medicine, The National Board of Forensic Medicine, Box 1024, SE-751 40, Uppsala, Sweden
| | - Håkan Sandler
- Forensic Medicine, Department of Surgical Sciences, Uppsala University Hospital, Uppsala University, SE-751 85, Uppsala, Sweden.,Department of Forensic Medicine, The National Board of Forensic Medicine, Box 1024, SE-751 40, Uppsala, Sweden
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28
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Dawson BM, Barton PS, Wallman JF. Contrasting insect activity and decomposition of pigs and humans in an Australian environment: A preliminary study. Forensic Sci Int 2020; 316:110515. [DOI: 10.1016/j.forsciint.2020.110515] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 09/09/2020] [Accepted: 09/10/2020] [Indexed: 12/21/2022]
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29
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Dash HR, Das S. Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time interval in human cadaver. Appl Microbiol Biotechnol 2020; 104:9497-9512. [PMID: 33001249 DOI: 10.1007/s00253-020-10922-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022]
Abstract
Estimation of post-mortem time interval (PMI) is a key parameter in the forensic investigation which poses a huge challenge to the medico-legal experts. The succession of microbes within different parts of the human body after death has shown huge potential in the determination of PMI. Human body harbors trillions of microorganisms as commensals. With the death of an individual when biological functions are stopped, these microorganisms behave contrarily along with the invasion of degrading microbes from the environment. Human cadaver becomes a rich source of nutrients due to autolysis of cells, which attracts various invading microorganisms as well as macroorganisms. At different stages of degradation, the succession of microorganisms differs significantly which can be explored for accurate PMI estimation. With the advent of microbial genomics technique and reduction in the cost of DNA sequencing, thanatomicrobiome and epinecrotic community analysis have gained huge attention in PMI estimation. The article summarizes different sources of microorganisms in a human cadaver, their succession pattern, and analytical techniques for application in the field of microbial forensics. KEY POINTS: • Thanatomicrobiome and epinecrotic microbiome develop in postmortem human body. • Lack of metabolic, immune, neuroendocrine systems facilitate microbial succession. • Analysis of postmortem microbial communities predicts accurate PMI.
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Affiliation(s)
- Hirak Ranjan Dash
- Forensic Science Laboratory, Bhadbhada Road, Bhopal, Madhya Pradesh, 462003, India.
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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30
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Oostra RJ, Gelderman T, Groen WJM, Uiterdijk HG, Cammeraat ELH, Krap T, Wilk LS, Lüschen M, Morriën WE, Wobben F, Duijst WLJM, Aalders MCG. Amsterdam Research Initiative for Sub-surface Taphonomy and Anthropology (ARISTA) - A taphonomic research facility in the Netherlands for the study of human remains. Forensic Sci Int 2020; 317:110483. [PMID: 32947241 DOI: 10.1016/j.forsciint.2020.110483] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 11/27/2022]
Abstract
A taphonomic research facility for the study of human remains was recently realized in Amsterdam, the Netherlands, to systematically investigate the decomposition of the human body under known conditions. Governmental authorization was obtained to make use of the body donation program of the Amsterdam University Medical Centers, location Academic Medical Center, for this specific purpose. In contrast to the small number of comparable initiatives elsewhere, this facility specifically allows for the study of buried bodies e.g. with the use of telemetry and remote sensing. Here, we discuss the concept of body donation in the Netherlands, its role in taphonomic research, and the sequence of events that preceded the realization of this facility, which is the first of its kind in Europe. In addition to offering novel research options to the scientific community, we hope that it will also pave the way for the successful realization of similar initiatives in other locations.
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Affiliation(s)
- Roelof-Jan Oostra
- Dept. of Medical Biology, section Clinical Anatomy and Embryology, Amsterdam University Medical Centers - location Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, P.O.Box 22660, 1100 DD, Amsterdam, the Netherlands; CLHC-Amsterdam Center for Forensic Science and Medicine, Science Park - Building 904 (Room C2.243), 1098 XH, Amsterdam, the Netherlands.
| | - Tamara Gelderman
- Ars Cogniscendi Foundation for Legal and Forensic Medicine, Zuiderzeestraatweg 404, 8091 PB, Wezep, the Netherlands; Dept. of Criminal Law and Criminology, Faculty of Law, Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands.
| | - W J Mike Groen
- Laboratory for Human Osteoarchaeology, Faculty of Archaeology, Leiden University, PO Box 9514, 2300 RA, Leiden, the Netherlands; Forensic Anthropology and Archaeology Unit, Division of Special Services and Expertise, Netherlands Forensic Institute, PO Box 24044, 2490 AA, The Hague, the Netherlands; CLHC-Amsterdam Center for Forensic Science and Medicine, Science Park - Building 904 (Room C2.243), 1098 XH, Amsterdam, the Netherlands.
| | - H Gepke Uiterdijk
- AMC Research Office, Amsterdam University Medical Centers - location Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, PO Box 22660, 1100 DD, Amsterdam, the Netherlands; CLHC-Amsterdam Center for Forensic Science and Medicine, Science Park - Building 904 (Room C2.243), 1098 XH, Amsterdam, the Netherlands.
| | - Erik L H Cammeraat
- Dept. of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands.
| | - Tristan Krap
- Dept. of Medical Biology, section Clinical Anatomy and Embryology, Amsterdam University Medical Centers - location Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, P.O.Box 22660, 1100 DD, Amsterdam, the Netherlands; Ars Cogniscendi Foundation for Legal and Forensic Medicine, Zuiderzeestraatweg 404, 8091 PB, Wezep, the Netherlands; Department of Life Sciences and Technology-Biotechnology-Forensic Science, Van Hall Larenstein, University of Applied Sciences, PO Box 1528, 8901 BV, Leeuwarden, the Netherlands; Dept. of Criminal Law and Criminology, Faculty of Law, Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands; CLHC-Amsterdam Center for Forensic Science and Medicine, Science Park - Building 904 (Room C2.243), 1098 XH, Amsterdam, the Netherlands.
| | - Leah S Wilk
- Dept. of Biomedical Engineering and Physics, Amsterdam University Medical Centers - location Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, P.O.Box 22660, 1100 DD, Amsterdam, the Netherlands; CLHC-Amsterdam Center for Forensic Science and Medicine, Science Park - Building 904 (Room C2.243), 1098 XH, Amsterdam, the Netherlands.
| | - Mark Lüschen
- Team Special Search Techniques, Division Special Operations, Central Forensic Service Center, Netherlands National Police, Hoofdstraat 54, 3972 LB Driebergen-Rijsenburg, the Netherlands; CLHC-Amsterdam Center for Forensic Science and Medicine, Science Park - Building 904 (Room C2.243), 1098 XH, Amsterdam, the Netherlands.
| | - W Elly Morriën
- Dept. of Ecosystem and Landscape Dynamics, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE, Amsterdam, the Netherlands.
| | - Frans Wobben
- Asset Data & Monitoring, Sweco Nederland B.V., K.P. van der Mandelelaan 41-43, 3062 MB, Rotterdam, the Netherlands.
| | - Wilma L J M Duijst
- Ars Cogniscendi Foundation for Legal and Forensic Medicine, Zuiderzeestraatweg 404, 8091 PB, Wezep, the Netherlands; Dept. of Criminal Law and Criminology, Faculty of Law, Maastricht University, PO Box 616, 6200 MD, Maastricht, the Netherlands; CLHC-Amsterdam Center for Forensic Science and Medicine, Science Park - Building 904 (Room C2.243), 1098 XH, Amsterdam, the Netherlands.
| | - Maurice C G Aalders
- Dept. of Biomedical Engineering and Physics, Amsterdam University Medical Centers - location Academic Medical Center, University of Amsterdam, Meibergdreef 15, 1105 AZ, Amsterdam, P.O.Box 22660, 1100 DD, Amsterdam, the Netherlands; CLHC-Amsterdam Center for Forensic Science and Medicine, Science Park - Building 904 (Room C2.243), 1098 XH, Amsterdam, the Netherlands.
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31
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Javan GT, Hanson E, Finley SJ, Visonà SD, Osculati A, Ballantyne J. Identification of cadaveric liver tissues using thanatotranscriptome biomarkers. Sci Rep 2020; 10:6639. [PMID: 32313164 PMCID: PMC7170907 DOI: 10.1038/s41598-020-63727-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 03/31/2020] [Indexed: 01/10/2023] Open
Abstract
Thanatotranscriptome studies involve the examination of mRNA transcript abundance and gene expression patterns in the internal organs of deceased humans. Postmortem gene expression is indicative of the cellular status of a corpse at the time of death, a portion of which may represent a cascade of molecular events occasioned by death. Specific gene biomarkers identify perceptible transcriptional changes induced by stochastic responses to the cessation of biological functions. Transcriptome analyses of postmortem mRNA from a tissue fragment may determine unique molecular identifiers for specific organs and demonstrate unique patterns of gene expression that can provide essential contextual anatomical information. We evaluated the impact of targeted transcriptome analysis using RNA sequencing to reveal global changes in postmortem gene expression in liver tissues from 27 Italian and United States corpses: 3.5-hour-old to 37-day-old. We found that our single blind study using eight liver tissue-specific gene biomarkers (e.g. AMBP and AHSG) is highly specific, with autopsy-derived organ samples correctly identified as tissues originating from postmortem livers. The results demonstrate that 98–100% of sequencing reads were mapped to these liver biomarkers. Our findings indicate that gene expression signatures of mRNA exposed up to 37 days of autolysis, can be used to validate the putative identity of tissue fragments.
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Affiliation(s)
- Gulnaz T Javan
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, USA.
| | - Erin Hanson
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
| | - Sheree J Finley
- Forensic Science Program, Physical Sciences Department, Alabama State University, Montgomery, AL, USA
| | - Silvia D Visonà
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Antonio Osculati
- Department of Public Health, Experimental and Forensic Medicine, University of Pavia, Pavia, Italy
| | - Jack Ballantyne
- National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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Lukiw WJ, Li W, Bond T, Zhao Y. Facilitation of Gastrointestinal (GI) Tract Microbiome-Derived Lipopolysaccharide (LPS) Entry Into Human Neurons by Amyloid Beta-42 (Aβ42) Peptide. Front Cell Neurosci 2019; 13:545. [PMID: 31866832 PMCID: PMC6908466 DOI: 10.3389/fncel.2019.00545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/22/2019] [Indexed: 01/01/2023] Open
Abstract
Human gastrointestinal (GI)-tract microbiome-derived lipopolysaccharide (LPS): (i) has been recently shown to target, accumulate within, and eventually encapsulate neuronal nuclei of the human central nervous system (CNS) in Alzheimer's disease (AD) brain; and (ii) this action appears to impede and restrict the outward flow of genetic information from neuronal nuclei. It has previously been shown that in LPS-encased neuronal nuclei in AD brain there is a specific disruption in the output and expression of two AD-relevant, neuron-specific markers encoding the cytoskeletal neurofilament light (NF-L) chain protein and the synaptic phosphoprotein synapsin-1 (SYN1) involved in the regulation of neurotransmitter release. The biophysical mechanisms involved in the facilitation of the targeting of LPS to neuronal cells and nuclei and eventual nuclear envelopment and functional disruption are not entirely clear. In this "Perspectives article" we discuss current advances, and consider future directions in this research area, and provide novel evidence in human neuronal-glial (HNG) cells in primary culture that the co-incubation of LPS with amyloid-beta 42 (Aβ42) peptide facilitates the association of LPS with neuronal cells. These findings: (i) support a novel pathogenic role for Aβ42 peptides in neurons via the formation of pores across the nuclear membrane and/or a significant biophysical disruption of the neuronal nuclear envelope; and (ii) advance the concept that the Aβ42 peptide-facilitated entry of LPS into brain neurons, accession of neuronal nuclei, and down-regulation of neuron-specific components such as NF-L and SYN1 may contribute significantly to neuropathological deficits as are characteristically observed in AD-affected brain.
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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, Louisiana State University Health Sciences Center, New Orleans, LA, United States
- Department of Neurology, 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 Health Sciences Center, New Orleans, LA, United States
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