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Franceschetti L, Lodetti G, Blandino A, Amadasi A, Bugelli V. Exploring the role of the human microbiome in forensic identification: opportunities and challenges. Int J Legal Med 2024; 138:1891-1905. [PMID: 38594499 PMCID: PMC11306296 DOI: 10.1007/s00414-024-03217-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
Abstract
Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition. This review explores the potential of microbiome analysis in forensic human identification, evaluating its applications, advantages, limitations, and future prospects. The uniqueness of an individual's microbial community, particularly the skin microbiota, can provide distinctive biological markers for identification purposes, while technological advancements like 16 S rRNA sequencing and metagenomic shotgun sequencing are enhancing the specificity of microbial identification, enabling detailed analysis of these complex ecological communities. Despite these promising findings, current research has not yet achieved a level of identification probability that could establish microbial analysis as a stand-alone evidence tool. Therefore, it is presently considered ancillary to traditional methods, contributing to a more comprehensive biological profile of individuals.
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Affiliation(s)
- Lorenzo Franceschetti
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, via Luigi Mangiagalli 37, Milan, 20133, Italy.
| | - Giorgia Lodetti
- Institute of Legal Medicine, Department of Biomedical Sciences for Health, University of Milan, via Luigi Mangiagalli 37, Milan, 20133, Italy
| | | | - Alberto Amadasi
- Institute of Legal Medicine and Forensic Sciences, University Medical Centre Charité, University of Berlin, Turmstr. 21, Building N, Berlin, 10559, Germany
| | - Valentina Bugelli
- Department of Medicine and Surgery, Section of Forensic Medicine, University of Parma, Parma, Italy
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2
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Spychała K, Piecuch A, Szleszkowski Ł, Kadej M, Ogórek R. Microscopic fungi on the corpse - Promising tool requiring further research. Forensic Sci Int 2024; 361:112129. [PMID: 38986228 DOI: 10.1016/j.forsciint.2024.112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 01/21/2024] [Accepted: 06/29/2024] [Indexed: 07/12/2024]
Abstract
Forensic microbiology is a relatively new area of forensic sciences. It considers the potential of microorganisms to be used in criminal investigations. As most studies involve the role of bacteria in fields like post-mortem interval estimation, personal identification or geolocation, the data on the role of fungi is comparatively scarce. Forensic mycology involves the application of fungi and their structures in forensic cases. The aim of this review is the evaluation of the current state of knowledge on fungi associated with human cadavers and their possible role in estimating the time since death. In accordance with the available reports, we focused on the relation between microscopic fungi isolated from human corpses and the cadaver condition e.g., the stage of decomposition. We also emphasised the contrast between the reported methodologies and attempted to standardise research methods in forensic mycology from sample collection to its storage, mycological analysis and identification of the obtained fungal cultures. Moreover, the potential usage of microscopic fungi in criminal cases was discussed based on various case reports.
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Affiliation(s)
- Klaudyna Spychała
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
| | - Agata Piecuch
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
| | - Łukasz Szleszkowski
- Department of Forensic Medicine, Wroclaw Medical University, Mikulicza-Radeckiego 4, Wrocław PL-50-345, Poland
| | - Marcin Kadej
- Centre for Forensic Biology and Entomology, Department of Invertebrate Biology, Evolution and Conservation, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 65, Wrocław PL-51-148, Poland.
| | - Rafał Ogórek
- Department of Mycology and Genetics, Faculty of Biological Sciences, University of Wrocław, Przybyszewskiego 63, Wroclaw PL-51-148, Poland
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3
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Won C, Yim SS. Emerging methylation-based approaches in microbiome engineering. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:96. [PMID: 38987811 PMCID: PMC11238421 DOI: 10.1186/s13068-024-02529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over various biological processes such as DNA replication, uptake, and gene regulation in bacteria. In this review, we explore recent advances in characterizing bacterial epigenomes, accompanied by emerging strategies that harness bacterial epigenetics to elucidate and engineer diverse bacterial species with precision and effectiveness. Furthermore, we delve into the potential of epigenetic modifications to steer microbial functions and influence community dynamics, offering promising opportunities for understanding and modulating microbiomes. Additionally, we investigate the extensive diversity of DNA methyltransferases and emphasize their potential utility in the context of the human microbiome. In summary, this review highlights the potential of DNA methylation as a powerful toolkit for engineering microbiomes.
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Affiliation(s)
- Changhee Won
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sung Sun Yim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
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Wang X, Le C, Jin X, Feng Y, Chen L, Huang X, Tian S, Wang Q, Ji J, Liu Y, Zhang H, Huang J, Ren Z. Estimating postmortem interval based on oral microbial community succession in rat cadavers. Heliyon 2024; 10:e31897. [PMID: 38882314 PMCID: PMC11177140 DOI: 10.1016/j.heliyon.2024.e31897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/18/2024] Open
Abstract
The accurate estimation of the postmortem interval has been one of the crucial issues to be solved in forensic research, and it is influenced by various factors in the process of decay. With the development of high-throughput sequencing technology, forensic microbiology has become the major hot topic in forensic science, which provides new research options for postmortem interval estimation. The oral microbial community is one of the most diverse of microbiomes, ranking as the second most abundant microbiota following the gastrointestinal tract. It is remarkable that oral microorganisms have a significant function in the decay process of cadavers. Therefore, we collected outdoor soil to simulate the death environment and focused on the relationship between oral microbial community succession and PMI in rats above the soil. In addition, linear regression models and random forest regression models were developed for the relationship between the relative abundance of oral microbes and PMI. We also identified a number of microorganisms that may be important to estimate PMI, including: Ignatzschineria, Morganella, Proteus, Lysinibacillus, Pseudomonas, Globicatella, Corynebacterium, Streptococcus, Rothia, Aerococcus, Staphylococcus, and so on.
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Affiliation(s)
- Xiaoxue Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Cuiyun Le
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Yuhang Feng
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Li Chen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Xiaolan Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Shunyi Tian
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jingyan Ji
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Yubo Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, 550004, Guizhou, China
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Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
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Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
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Iancu L, Bonicelli A, Procopio N. Decomposition in an extreme cold environment and associated microbiome-prediction model implications for the postmortem interval estimation. Front Microbiol 2024; 15:1392716. [PMID: 38803371 PMCID: PMC11128606 DOI: 10.3389/fmicb.2024.1392716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/22/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction The accurate estimation of postmortem interval (PMI), the time between death and discovery of the body, is crucial in forensic science investigations as it impacts legal outcomes. PMI estimation in extremely cold environments becomes susceptible to errors and misinterpretations, especially with prolonged PMIs. This study addresses the lack of data on decomposition in extreme cold by providing the first overview of decomposition in such settings. Moreover, it proposes the first postmortem microbiome prediction model for PMI estimation in cold environments, applicable even when the visual decomposition is halted. Methods The experiment was conducted on animal models in the second-coldest region in the United States, Grand Forks, North Dakota, and covered 23 weeks, including the winter months with temperatures as low as -39°C. Random Forest analysis models were developed to estimate the PMI based either uniquely on 16s rRNA gene microbial data derived from nasal swabs or based on both microbial data and measurable environmental parameters such as snow depth and outdoor temperatures, on a total of 393 samples. Results Among the six developed models, the best performing one was the complex model based on both internal and external swabs. It achieved a Mean Absolute Error (MAE) of 1.36 weeks and an R2 value of 0.91. On the other hand, the worst performing model was the minimal one that relied solely on external swabs. It had an MAE of 2.89 weeks and an R2 of 0.73. Furthermore, among the six developed models, the commonly identified predictors across at least five out of six models included the following genera: Psychrobacter (ASV1925 and ASV1929), Carnobacterium (ASV2872) and Pseudomonas (ASV1863). Discussion The outcome of this research provides the first microbial model able to predict PMI with an accuracy of 9.52 days over a six-month period of extreme winter conditions.
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Affiliation(s)
- Lavinia Iancu
- Department of Criminal Justice, University of North Dakota, Grand Forks, ND, United States
| | - Andrea Bonicelli
- Research Centre for Field Archaeology and Forensic Taphonomy, School of Law and Policing, Preston, United Kingdom
| | - Noemi Procopio
- Research Centre for Field Archaeology and Forensic Taphonomy, School of Law and Policing, Preston, United Kingdom
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Zerekidze A, Li M, Refisch A, Shameya J, Sobanski T, Walter M, Wagner G. Impact of Toxoplasma gondii and Human Microbiome on Suicidal Behavior: A Systematic Review. J Clin Med 2024; 13:593. [PMID: 38276099 PMCID: PMC10816148 DOI: 10.3390/jcm13020593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Suicide remains a persistent global health challenge, resisting widespread prevention efforts. According to previous findings, toxoplasmosis is particularly associated with altered decision making, which could lead to risk-taking behavior, thereby increasing the likelihood for suicidal behavior (SB). In addition, discussion about the role of microbiome in psychiatric disorders has emerged lately, which also makes it relevant to investigate its role in the context of SB. Therefore, two systematic reviews are integrated in this paper, and the existing knowledge is comprehensively summarized regarding the association between microbial pathogens and SB. METHODS We conducted a systematic search with keywords including SB and Toxoplasma gondii (Suicid* AND Toxoplasm*) and microbiome (Suicid* AND Microbiome AND Microbiota) throughout PubMed and Scopus to retrieve related studies up to 9 November 2023, identifying 24 eligible records. The subjects of the included studies had to have fulfilled the criteria of an SB disorder as defined by DSM-5, and death cases needed to have been defined as suicide. RESULTS Most studies reported significant association between toxoplasmosis and SB, suggesting a higher likelihood of SB in the infected population. Regarding the microbiome, only very few studies investigated an association between SB and alterations in the microbiome. Based on six included studies, there were some indications of a link between changes in the microbiome and SB. CONCLUSION The cognitive aspects of decision making in T. gondii-infected individuals with SB should be further investigated to unravel the underlying mechanisms. Further sufficiently powered studies are needed to establish a link between SB and alterations in the microbiome.
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Affiliation(s)
- Ani Zerekidze
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
| | - Meng Li
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
- Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
| | - Alexander Refisch
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
- Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
| | - Justina Shameya
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
| | - Thomas Sobanski
- Department of Psychiatry, Psychotherapy and Psychosomatic Medicine, Center for Mental Health, Thueringen-Kliniken “Georgius Agricola”, 07318 Saalfeld, Germany;
| | - Martin Walter
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
- Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
- German Center for Mental Health (DZPG), Partner Site Jena, 07743 Jena, Germany
| | - Gerd Wagner
- Department of Psychiatry and Psychotherapy, Jena Center for Mental Health, Jena University Hospital, 07743 Jena, Germany
- Circuits Underlying Mental Health (C-I-R-C), Jena-Magdeburg-Halle, 07743 Jena, Germany
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Javan GT, Singh K, Finley SJ, Green RL, Sen CK. Complexity of human death: its physiological, transcriptomic, and microbiological implications. Front Microbiol 2024; 14:1345633. [PMID: 38282739 PMCID: PMC10822681 DOI: 10.3389/fmicb.2023.1345633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Human death is a complex, time-governed phenomenon that leads to the irreversible cessation of all bodily functions. Recent molecular and genetic studies have revealed remarkable experimental evidence of genetically programmed cellular death characterized by several physiological processes; however, the basic physiological function that occurs during the immediate postmortem period remains inadequately described. There is a paucity of knowledge connecting necrotic pathologies occurring in human organ tissues to complete functional loss of the human organism. Cells, tissues, organs, and organ systems show a range of differential resilience and endurance responses that occur during organismal death. Intriguingly, a persistent ambiguity in the study of postmortem physiological systems is the determination of the trajectory of a complex multicellular human body, far from life-sustaining homeostasis, following the gradual or sudden expiry of its regulatory systems. Recent groundbreaking investigations have resulted in a paradigm shift in understanding the cell biology and physiology of death. Two significant findings are that (i) most cells in the human body are microbial, and (ii) microbial cell abundance significantly increases after death. By addressing the physiological as well as the microbiological aspects of death, future investigations are poised to reveal innovative insights into the enigmatic biological activities associated with death and human decomposition. Understanding the elaborate crosstalk of abiotic and biotic factors in the context of death has implications for scientific discoveries important to informing translational knowledge regarding the transition from living to the non-living. There are important and practical needs for a transformative reestablishment of accepted models of biological death (i.e., artificial intelligence, AI) for more precise determinations of when the regulatory mechanisms for homeostasis of a living individual have ceased. In this review, we summarize mechanisms of physiological, genetic, and microbiological processes that define the biological changes and pathways associated with human organismal death and decomposition.
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Affiliation(s)
- Gulnaz T. Javan
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Kanhaiya Singh
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Sheree J. Finley
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Robert L. Green
- Department of Physical and Forensic Sciences, Alabama State University, Montgomery, AL, United States
| | - Chandan K. Sen
- Department of Surgery, School of Medicine, McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, United States
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She JJ, Liu WX, Ding XM, Guo G, Han J, Shi FY, Lau HCH, Ding CG, Xue WJ, Shi W, Liu GX, Zhang Z, Hu CH, Chen Y, Wong CC, Yu J. Defining the biogeographical map and potential bacterial translocation of microbiome in human 'surface organs'. Nat Commun 2024; 15:427. [PMID: 38199995 PMCID: PMC10781665 DOI: 10.1038/s41467-024-44720-6] [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: 05/28/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
The microbiome in a specific human organ has been well-studied, but few reports have investigated the multi-organ microbiome as a whole. Here, we aim to analyse the intra-individual inter-organ and intra-organ microbiome in deceased humans. We collected 1608 samples from 53 sites of 7 surface organs (oral cavity, esophagus, stomach, small intestine, appendix, large intestine and skin; n = 33 subjects) and performed microbiome profiling, including 16S full-length sequencing. Microbial diversity varied dramatically among organs, and core microbial species co-existed in different intra-individual organs. We deciphered microbial changes across distinct intra-organ sites, and identified signature microbes, their functional traits, and interactions specific to each site. We revealed significant microbial heterogeneity between paired mucosa-lumen samples of stomach, small intestine, and large intestine. Finally, we established the landscape of inter-organ relationships of microbes along the digestive tract. Therefore, we generate a catalogue of bacterial composition, diversity, interaction, functional traits, and bacterial translocation in human at inter-organ and intra-organ levels.
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Affiliation(s)
- Jun-Jun She
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China.
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China.
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China.
- Yulin Hospital, First Affiliated Hospital of Xi'an Jiao Tong University, Yulin, China.
| | - Wei-Xin Liu
- Institute of Digestive Disease and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xiao-Ming Ding
- Department of Kidney Transplantation, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Institute of Organ Transplantation, Xi'an Jiao Tong University, Xi'an, China
| | - Gang Guo
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Jing Han
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Fei-Yu Shi
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Harry Cheuk-Hay Lau
- Institute of Digestive Disease and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chen-Guang Ding
- Department of Kidney Transplantation, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Institute of Organ Transplantation, Xi'an Jiao Tong University, Xi'an, China
| | - Wu-Jun Xue
- Department of Kidney Transplantation, The First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Institute of Organ Transplantation, Xi'an Jiao Tong University, Xi'an, China
| | - Wen Shi
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Gai-Xia Liu
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Zhe Zhang
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Chen-Hao Hu
- Department of General Surgery, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Yinnan Chen
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China
- Department of Talent Highland, First Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Chi Chun Wong
- Institute of Digestive Disease and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jun Yu
- Center for Gut Microbiome Research, Med-X Institute Centre, First Affiliated Hospital of Xi'an Jiao Tong University, Xian, China.
- Institute of Digestive Disease and The Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Musisi E, Wyness A, Eldirdiri S, Dombay E, Mtafya B, Ntinginya NE, Heinrich N, Kibiki GS, Hoelscher M, Boeree M, Aarnoutse R, Gillespie SH, Sabiiti W. Effect of seven anti-tuberculosis treatment regimens on sputum microbiome: a retrospective analysis of the HIGHRIF study 2 and PanACEA MAMS-TB clinical trials. THE LANCET. MICROBE 2023; 4:e913-e922. [PMID: 37832571 DOI: 10.1016/s2666-5247(23)00191-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 05/18/2023] [Accepted: 06/14/2023] [Indexed: 10/15/2023]
Abstract
BACKGROUND Respiratory tract microbiota has been described as the gatekeeper for respiratory health. We aimed to assess the impact of standard-of-care and experimental anti-tuberculosis treatment regimens on the respiratory microbiome and implications for treatment outcomes. METHODS In this retrospective study, we analysed the sputum microbiome of participants with tuberculosis treated with six experimental regimens versus standard-of-care who were part of the HIGHRIF study 2 (NCT00760149) and PanACEA MAMS-TB (NCT01785186) clinical trials across a 3-month treatment follow-up period. Samples were from participants in Mbeya, Kilimanjaro, Bagamoyo, and Dar es Salaam, Tanzania. Experimental regimens were composed of different combinations of rifampicin (R), isoniazid (H), pyrazinamide (Z), ethambutol (E), moxifloxacin (M), and a new drug, SQ109 (Q). Reverse transcription was used to create complementary DNA for each participant's total sputum RNA and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina metagenomic technique. Qiime was used to analyse the amplicon sequence variants and estimate alpha diversity. Descriptive statistics were applied to assess differences in alpha diversity pre-treatment and post-treatment initiation and the effect of each treatment regimen. FINDINGS Sequence data were obtained from 397 pre-treatment and post-treatment samples taken between Sept 26, 2008, and June 30, 2015, across seven treatment regimens. Pre-treatment microbiome (206 genera) was dominated by Firmicutes (2860 [44%] of 6500 amplicon sequence variants [ASVs]) at the phylum level and Streptococcus (2340 [36%] ASVs) at the genus level. Two regimens had a significant depressing effect on the microbiome after 2 weeks of treatment, HR20mg/kgZM (Shannon diversity index p=0·0041) and HR35mg/kgZE (p=0·027). Gram-negative bacteria were the most sensitive to bactericidal activity of treatment with the highest number of species suppressed being under the moxifloxacin regimen. By week 12 after treatment initiation, microbiomes had recovered to pre-treatment level except for the HR35mg/kgZE regimen and for genus Mycobacterium, which did not show recovery across all regimens. Tuberculosis culture conversion to negative by week 8 of treatment was associated with clearance of genus Neisseria, with a 98% reduction of the pre-treatment level. INTERPRETATION HR20mg/kgZM was effective against tuberculosis without limiting microbiome recovery, which implies a shorter efficacious anti-tuberculosis regimen with improved treatment outcomes might be achieved without harming the commensal microbiota. FUNDING European and Developing Countries Clinical Trials Partnership and German Ministry of Education and Research.
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Affiliation(s)
- Emmanuel Musisi
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Adam Wyness
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK; Scottish Association of Marine Science, Oban, UK
| | - Sahar Eldirdiri
- Department of Microbiology, Kettering General Hospital, Kettering, UK
| | - Evelin Dombay
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Bariki Mtafya
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK; National Institute for Medical Research, Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Nyanda E Ntinginya
- National Institute for Medical Research, Mbeya Medical Research Centre, Mbeya, Tanzania
| | - Norbert Heinrich
- Division of Infectious Diseases and Tropical Medicine, University Hospital, University of Munich (LMU), Munich, Germany
| | - Gibson S Kibiki
- Kilimanjaro Clinical Research Institute, Moshi, Tanzania; Africa Research Excellence Fund (AREF), London, UK
| | - Michael Hoelscher
- Division of Infectious Diseases and Tropical Medicine, University Hospital, University of Munich (LMU), Munich, Germany; Fraunhofer ITMP, Immunology, Infection and Pandemic Research, Munich, Germany
| | - Martin Boeree
- Department of Lung Diseases, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Rob Aarnoutse
- Department of Pharmacy, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Stephen H Gillespie
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK
| | - Wilber Sabiiti
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, UK.
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11
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Heinrich F, Mertz KD, Glatzel M, Beer M, Krasemann S. Using autopsies to dissect COVID-19 pathogenesis. Nat Microbiol 2023; 8:1986-1994. [PMID: 37798476 DOI: 10.1038/s41564-023-01488-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 09/04/2023] [Indexed: 10/07/2023]
Abstract
The emergence of SARS-CoV-2 has resulted in millions of deaths as a result of COVID-19. Suitable models were missing at the beginning of the pandemic, and studies investigating disease pathogenesis relied on patients who had succumbed to COVID-19. Since then, autopsies of patients have substantially contributed to our understanding of the pathogenesis of COVID-19 and associated major organ complications. Here we summarize how autopsies have complemented experimental studies, mainly in animal models, and how they have facilitated critical knowledge of COVID-19 to improve daily clinical practice and develop therapeutic interventions. Employing advanced histopathologic and molecular genetic methods in post-mortem tissues, the COVID-19 pandemic has highlighted the importance of autopsies for virology research and clinical practice in current and emerging infectious diseases.
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Affiliation(s)
- Fabian Heinrich
- Institute of Legal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kirsten D Mertz
- Institute of Pathology, Kantonsspital Baselland, Liestal, Switzerland
- University of Basel, Basel, Switzerland
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Susanne Krasemann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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12
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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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Brockbals L, Garrett-Rickman S, Fu S, Ueland M, McNevin D, Padula MP. Estimating the time of human decomposition based on skeletal muscle biopsy samples utilizing an untargeted LC-MS/MS-based proteomics approach. Anal Bioanal Chem 2023; 415:5487-5498. [PMID: 37423904 PMCID: PMC10444689 DOI: 10.1007/s00216-023-04822-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 06/16/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023]
Abstract
Accurate estimation of the postmortem interval (PMI) is crucial in forensic medico-legal investigations to understand case circumstances (e.g. narrowing down list of missing persons or include/exclude suspects). Due to the complex decomposition chemistry, estimation of PMI remains challenging and currently often relies on the subjective visual assessment of gross morphological/taphonomic changes of a body during decomposition or entomological data. The aim of the current study was to investigate the human decomposition process up to 3 months after death and propose novel time-dependent biomarkers (peptide ratios) for the estimation of decomposition time. An untargeted liquid chromatography tandem mass spectrometry-based bottom-up proteomics workflow (ion mobility separated) was utilized to analyse skeletal muscle, collected repeatedly from nine body donors decomposing in an open eucalypt woodland environment in Australia. Additionally, general analytical considerations for large-scale proteomics studies for PMI determination are raised and discussed. Multiple peptide ratios (human origin) were successfully proposed (subgroups < 200 accumulated degree days (ADD), < 655 ADD and < 1535 ADD) as a first step towards generalised, objective biochemical estimation of decomposition time. Furthermore, peptide ratios for donor-specific intrinsic factors (sex and body mass) were found. Search of peptide data against a bacterial database did not yield any results most likely due to the low abundance of bacterial proteins within the collected human biopsy samples. For comprehensive time-dependent modelling, increased donor number would be necessary along with targeted confirmation of proposed peptides. Overall, the presented results provide valuable information that aid in the understanding and estimation of the human decomposition processes.
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Affiliation(s)
- Lana Brockbals
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Samara Garrett-Rickman
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Shanlin Fu
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Maiken Ueland
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Dennis McNevin
- Centre for Forensic Science, School of Mathematical and Physical Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Matthew P Padula
- School of Life Sciences, Faculty of Science, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
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14
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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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15
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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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16
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De Alcaraz-Fossoul J, Wang Y, Liu R, Mancenido M, Marshall PA, Núñez C, Broatch J, Ferry L. Microbes in fingerprints: A source for dating crime evidence? Forensic Sci Int Genet 2023; 65:102883. [PMID: 37120981 DOI: 10.1016/j.fsigen.2023.102883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/02/2023]
Abstract
Interest in the human microbiome has grown in recent years because of increasing applications to biomedicine and forensic science. However, the potential for dating evidence at a crime scene based upon time-dependent changes in microbial signatures has not been established, despite a relatively straightforward scientific process for isolating the microbiome. We hypothesize that modifications in microbial diversity, abundance, and succession can provide estimates of the time a surface was touched for investigative purposes. In this proof-of-concept research, the sequencing and analysis of the 16 S rRNA gene from microbes present in fresh and aged latent fingerprints deposited by three donors with pre- and post-washed hands is reported. The stability of major microbial phyla is confirmed while the dynamics of less abundant groups is described up to 21 days post-deposition. Most importantly, a phylum is suggested as the source for possible biological markers to date fingerprints: Deinococcus-Thermus.
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Affiliation(s)
- Josep De Alcaraz-Fossoul
- Forensic Science Department, Henry C. Lee College of Criminal Justice and Forensic Science, University of New Haven; West Haven, Connecticut 06516, United States.
| | - Yue Wang
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Ruoqian Liu
- School of Mathematical and Statistical Sciences, The College of Liberal Arts and Sciences, Arizona State University; Tempe, Arizona 85251, United States
| | - Michelle Mancenido
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Pamela Ann Marshall
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Celeste Núñez
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Jennifer Broatch
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
| | - Lara Ferry
- School of Mathematical and Natural Sciences, New College of Interdisciplinary Arts and Sciences, Arizona State University; Glendale, Arizona 85306, United States
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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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18
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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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Du QX, Zhang S, Long FH, Lu XJ, Wang L, Cao J, Jin QQ, Ren K, Zhang J, Huang P, Sun JH. Combining with lab-on-chip technology and multi-organ fusion strategy to estimate post-mortem interval of rat. Front Med (Lausanne) 2023; 9:1083474. [PMID: 36703889 PMCID: PMC9871555 DOI: 10.3389/fmed.2022.1083474] [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: 10/29/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023] Open
Abstract
Background The estimation of post-mortem interval (PMI) is one of the most important problems in forensic pathology all the time. Although many classical methods can be used to estimate time since death, accurate and rapid estimation of PMI is still a difficult task in forensic practice, so the estimation of PMI requires a faster, more accurate, and more convenient method. Materials and methods In this study, an experimental method, lab-on-chip, is used to analyze the characterizations of polypeptide fragments of the lung, liver, kidney, and skeletal muscle of rats at defined time points after death (0, 1, 2, 3, 5, 7, 9, 12, 15, 18, 21, 24, 27, and 30 days). Then, machine learning algorithms (base model: LR, SVM, RF, GBDT, and MLPC; ensemble model: stacking, soft voting, and soft-weighted voting) are applied to predict PMI with single organ. Multi-organ fusion strategy is designed to predict PMI based on multiple organs. Then, the ensemble pruning algorithm determines the best combination of multi-organ. Results The kidney is the best single organ for predicting the time of death, and its internal and external accuracy is 0.808 and 0.714, respectively. Multi-organ fusion strategy dramatically improves the performance of PMI estimation, and its internal and external accuracy is 0.962 and 0.893, respectively. Finally, the best organ combination determined by the ensemble pruning algorithm is all organs, such as lung, liver, kidney, and skeletal muscle. Conclusion Lab-on-chip is feasible to detect polypeptide fragments and multi-organ fusion is more accurate than single organ for PMI estimation.
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Affiliation(s)
- Qiu-xiang Du
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
| | - Shuai Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
| | - Fei-hao Long
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
| | - Xiao-jun Lu
- Criminal Investigation Detachment, Baotou Public Security Bureau, Baotou, Inner Mongolia, China
| | - Liang Wang
- National Center for Liver Cancer, Second Military Medical University, Shanghai, China
| | - Jie Cao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
| | - Qian-qian Jin
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
| | - Kang Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
| | - Ji Zhang
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Ping Huang
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
| | - Jun-hong Sun
- Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, China
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20
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Xiang Q, Su Q, Li Q, Liu J, Du Y, Shi H, Li Z, Ma Y, Niu Y, Chen L, Liu C, Zhao J. Microbial community analyses provide a differential diagnosis for the antemortem and postmortem injury of decayed cadaver: An animal model. J Forensic Leg Med 2023; 93:102473. [PMID: 36580880 DOI: 10.1016/j.jflm.2022.102473] [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: 10/21/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
Differentiating antemortem injury from postmortem injury of decayed cadavers is one of the difficult issues in forensic science. Forensic pathologists identify antemortem injury according to the macroscopic and microscopic vital reactions taken place after being injured. However, the decomposition would render those vital reactions ineffective. Microbiomes have been widely used in forensic science due to their succession with time and sensitivity to vary of environment. In this study, microbiomes were introduced to determine whether the bacterial communities can be used to distinguish between the ante- and postmortem injuries through an animal experiment. Our findings showed that the differences of bacterial community were increasingly apparent from the 6th to 9th day after the wound created when the types of wounds were unidentified by morphological examination due to decomposition. The biomarkers at the genus level could effectively distinguish between injury types, Among them, Enterococcus and Enterobacter were only observed in the antemortem injured group, while Staphylococcus and Acinetobacter were only in the postmortem injured group. It is possible to tell whether cadaveric injuries developed before or after death by detecting differences in the bacterial communities of putrefying wounds. This study provides a new perspective for the differences between ante- and postmortem injuries and provides a promising method for us to identify the ante- and postmortem wounds, especially in decomposed cadavers.
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Affiliation(s)
- Qingqing Xiang
- School of Forensic Medicine, Kunming Medical University, Chunrong Road West 1168, Chenggong District, Kunming, 650500, China
| | - Qin Su
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University & Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan 2nd Road 74, Yuexiu District, Guangzhou, 510275, PR China; Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China
| | - Qi Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University & Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan 2nd Road 74, Yuexiu District, Guangzhou, 510275, PR China
| | - Jingjian Liu
- Department of Anatomy, North Sichuan Medical College, Nanchong, 637000, China
| | - Yukun Du
- School of Forensic Medicine, Southern Medical University, Shaitai Road South 1023-1063, Baiyun District, Guangzhou, 510515, China
| | - He Shi
- Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China
| | - Zhigang Li
- Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China
| | - Yanbin Ma
- Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China
| | - Yong Niu
- Section of Forensic Sciences, Criminal Investigation Department, Ministry of Public Security, Chang' an Avenue 14, Dongcheng District, Beijing, 100741, China
| | - Lifang Chen
- School of Forensic Medicine, Kunming Medical University, Chunrong Road West 1168, Chenggong District, Kunming, 650500, China.
| | - Chao Liu
- Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China.
| | - Jian Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University & Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan 2nd Road 74, Yuexiu District, Guangzhou, 510275, PR China; Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China.
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21
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Tarone AM, Mann AE, Zhang Y, Zascavage RR, Mitchell EA, Morales E, Rusch TW, Allen MS. The devil is in the details: Variable impacts of season, BMI, sampling site temperature, and presence of insects on the post-mortem microbiome. Front Microbiol 2022; 13:1064904. [PMID: 36569070 PMCID: PMC9768039 DOI: 10.3389/fmicb.2022.1064904] [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: 10/08/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Post-mortem microbial communities are increasingly investigated as proxy evidence for a variety of factors of interest in forensic science. The reported predictive power of the microbial community to determine aspects of the individual's post-mortem history (e.g., the post-mortem interval) varies substantially among published research. This observed variation is partially driven by the local environment or the individual themselves. In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. Materials and methods In the current study, we investigated the impact of BMI, sex, insect activity, season, repeat sampling, decomposition time, and temperature on the microbial community sampled from donated human remains in San Marcos, TX using a high-throughput gene-fragment metabarcoding approach. Results We found that season, temperature at the sampling site, BMI, and sex had a significant effect on the post-mortem microbiome, the presence of insects has a homogenizing influence on the total bacterial community, and that community consistency from repeat sampling decreases as the decomposition process progresses. Moreover, we demonstrate the importance of temperature at the site of sampling on the abundance of important diagnostic taxa. Conclusion The results of this study suggest that while the bacterial community or specific bacterial species may prove to be useful for forensic applications, a clearer understanding of the mechanisms underpinning microbial decomposition will greatly increase the utility of microbial evidence in forensic casework.
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Affiliation(s)
- Aaron M. Tarone
- Department of Entomology, Texas A&M University, College Station, TX, United States
| | - Allison E. Mann
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States,Department of Biological Sciences, Clemson University, Clemson, SC, United States
| | - Yan Zhang
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Roxanne R. Zascavage
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Elizabeth A. Mitchell
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Edgar Morales
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States
| | - Travis W. Rusch
- Department of Entomology, Texas A&M University, College Station, TX, United States,Center for Grain and Animal Health Research, USDA Agricultural Research Service, Manhattan, KS, United States
| | - Michael S. Allen
- Department of Microbiology, Immunology, and Genetics, University of North Texas Health Science Center, Fort Worth, TX, United States,*Correspondence: Michael S. Allen,
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22
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Zhang F, Wang P, Zeng K, Yuan H, Wang Z, Li X, Yuan H, Du S, Guan D, Wang L, Zhao R. Postmortem submersion interval estimation of cadavers recovered from freshwater based on gut microbial community succession. Front Microbiol 2022; 13:988297. [PMID: 36532467 PMCID: PMC9756852 DOI: 10.3389/fmicb.2022.988297] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/21/2022] [Indexed: 09/19/2023] Open
Abstract
Microbial community succession during decomposition has been proven to be a useful tool for postmortem interval (PMI) estimation. Numerous studies have shown that the intestinal microbial community presented chronological changes after death and was stable in terrestrial corpses with different causes of death. However, the postmortem pattern of intestinal microbial community succession in cadavers retrieved from water remains unclear. For immersed corpses, the postmortem submersion interval (PMSI) is a useful indicator of PMI. To provide reliable estimates of PMSI in forensic investigations, we investigated the gut microbial community succession of corpses submersed in freshwater and explored its potential application in forensic investigation. In this study, the intestinal microbial community of mouse submersed in freshwater that died of drowning or CO2 asphyxia (i.e., postmortem submersion) were characterized by 16S rDNA amplification and high-throughput sequencing, followed by bioinformatic analyses. The results demonstrated that the chronological changes in intestinal bacterial communities were not different between the drowning and postmortem submersion groups. α-diversity decreased significantly within 14 days of decomposition in both groups, and the β-diversity bacterial community structure ordinated chronologically, inferring the functional pathway and phenotype. To estimate PMSI, a regression model was established by random forest (RF) algorithm based on the succession of postmortem microbiota. Furthermore, 15 genera, including Proteus, Enterococcus, and others, were selected as candidate biomarkers to set up a concise predicted model, which provided a prediction of PMSI [MAE (± SE) = 0.818 (± 0.165) d]. Overall, our present study provides evidence that intestinal microbial community succession would be a valuable marker to estimate the PMSI of corpses submerged in an aquatic habitat.
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Affiliation(s)
- Fuyuan Zhang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Pengfei Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Kuo Zeng
- Institute of Evidence Law and Forensic Science, China University of Political Science and Law, Beijing, China
| | - Huiya Yuan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Ziwei Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Xinjie Li
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Haomiao Yuan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Shukui Du
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Dawei Guan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Linlin Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Rui Zhao
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
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23
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Zhao X, Zhong Z, Hua Z. Estimation of the post-mortem interval by modelling the changes in oral bacterial diversity during decomposition. J Appl Microbiol 2022; 133:3451-3464. [PMID: 35950442 PMCID: PMC9825971 DOI: 10.1111/jam.15771] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/23/2022] [Accepted: 05/27/2022] [Indexed: 01/11/2023]
Abstract
AIMS Decomposition, a complicated process, depends on several factors, including carrion insects, bacteria and the environment. However, the composition of and variation in oral bacteria over long periods of decomposition remain unclear. The current study aims to illustrate the composition of oral bacteria and construct an informative model for estimating the post-mortem interval (PMI) during decomposition. METHODS AND RESULTS Samples were collected from rats' oral cavities for 59 days, and 12 time points in the PMI were selected to detect bacterial community structure by sequencing the V3-V4 region of the bacterial 16S ribosomal RNA (16S rRNA) gene on the Ion S5 XL platform. The results indicated that microorganisms in the oral cavity underwent great changes during decomposition, with a tendency for variation to first decrease and then increase at day 24. Additionally, to predict the PMI, an informative model was established using the random forest algorithm. Three genera of bacteria (Atopostipes, Facklamia and Cerasibacillus) were linearly correlated at all 12 time points in the 59-day period. Planococcaceae was selected as the best feature for the last 6 time points. The R2 of the model reached 93.94%, which suggested high predictive accuracy. Furthermore, to predict the functions of the oral microbiota, PICRUSt results showed that energy metabolism was increased on day 3 post-mortem and carbohydrate metabolism surged significantly on days 3 and 24 post-mortem. CONCLUSIONS Overall, our results suggested that post-mortem oral microbial community data can serve as a forensic resource to estimate the PMI over long time periods. SIGNIFICANCE AND IMPACT OF THE STUDY The results of the present study are beneficial for estimating the PMI. Identifying changes in the bacterial community is of great significance for further understanding the applicability of oral flora in forensic medicine.
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Affiliation(s)
- Xingchun Zhao
- School of BiopharmacyChina Pharmaceutical UniversityNanjingP.R. China,National Engineering Laboratory for Forensic ScienceBeijingP.R. China,Institute of Forensic ScienceMinistry of Public SecurityBeijingP.R. China,Key Laboratory of Forensic Genetics of Ministry of Public SecurityBeijingP.R. China
| | - Zengtao Zhong
- Department of MicrobiologyCollege of Life SciencesNanjing Agricultural UniversityNanjingP.R. China
| | - Zichun Hua
- School of BiopharmacyChina Pharmaceutical UniversityNanjingP.R. China
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24
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Liu R, Wang Q, Zhang K, Wu H, Wang G, Cai W, Yu K, Sun Q, Fan S, Wang Z. Analysis of Postmortem Intestinal Microbiota Successional Patterns with Application in Postmortem Interval Estimation. MICROBIAL ECOLOGY 2022; 84:1087-1102. [PMID: 34775524 DOI: 10.1007/s00248-021-01923-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms play a vital role in the decomposition of vertebrate remains in natural nutrient cycling, and the postmortem microbial succession patterns during decomposition remain unclear. The present study used hierarchical clustering based on Manhattan distances to analyze the similarities and differences among postmortem intestinal microbial succession patterns based on microbial 16S rDNA sequences in a mouse decomposition model. Based on the similarity, seven different classes of succession patterns were obtained. Generally, the normal intestinal flora in the cecum was gradually decreased with changes in the living conditions after death, while some facultative anaerobes and obligate anaerobes grew and multiplied upon oxygen consumption. Furthermore, a random forest regression model was developed to predict the postmortem interval based on the microbial succession trend dataset. The model demonstrated a mean absolute error of 20.01 h and a squared correlation coefficient of 0.95 during 15-day decomposition. Lactobacillus, Dubosiella, Enterococcus, and the Lachnospiraceae NK4A136 group were considered significant biomarkers for this model according to the ranked list. The present study explored microbial succession patterns in terms of relative abundances and variety, aiding in the prediction of postmortem intervals and offering some information on microbial behaviors in decomposition ecology.
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Affiliation(s)
- Ruina Liu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qi Wang
- College of Basic Medicine, Department of Forensic Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Kai Zhang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hao Wu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Gongji Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Wumin Cai
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Kai Yu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qinru Sun
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Shuanliang Fan
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
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25
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Mason AR, McKee-Zech HS, Hoeland KM, Davis MC, Campagna SR, Steadman DW, DeBruyn JM. Body Mass Index (BMI) Impacts Soil Chemical and Microbial Response to Human Decomposition. mSphere 2022; 7:e0032522. [PMID: 36135386 PMCID: PMC9599287 DOI: 10.1128/msphere.00325-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Microorganisms are key decomposers of vertebrate mortalities, breaking down body tissues and impacting decomposition progress. During human decomposition, both extrinsic environmental factors and intrinsic cadaver-related factors have the potential to impact microbial decomposers either directly or indirectly via altered physical or chemical conditions. While extrinsic factors (e.g., temperature, humidity) explain some variation in microbial response during human decomposition in terrestrial settings, recent work has noted that even under the same environmental conditions, individuals can have different decomposition patterns, highlighting the potential for intrinsic factors to impact microbial decomposers. The goal of this study was to investigate the effects of several intrinsic factors (age, sex, diseases at time of death, and body mass index [BMI]) on chemical and microbial changes in decomposition-impacted soils. In a field study conducted at the University of Tennessee Anthropology Research Facility, soils were collected from the decomposition-impacted area surrounding 19 deceased human individuals through the end of active decomposition. Soil physicochemical parameters were measured, and microbial (bacterial and fungal) communities were assessed via amplicon sequencing. BMI was shown to explain some variation in soil pH and microbial response to human decomposition. Hierarchical linear mixed (HLM) effects models revealed that BMI category significantly explained variation in pH response within decomposition-impacted soils over time (HLM F = 9.647; P < 0.001). Additionally, the relative abundance of soil Saccharomycetes in decomposition soils under underweight donors displayed little to no changes (mean maximum change in relative abundance, +6.6%), while all other BMI categories displayed an increased relative abundance of these organisms over time (normal, +50.6%; overweight, +64.4%; and obese, +64.6%) (HLM F = 3.441; P = 0.11). Together, these results reveal intrinsic factors influencing decomposition patterns, especially within the soil environment, and suggest BMI is an important factor for controlling decomposition processes. IMPORTANCE This work begins to address questions about interindividual variation in vertebrate decomposition attributed to intrinsic factors, that is, properties of the carcass or cadaver itself. Most research on factors affecting decomposition has focused on the extrinsic environment, such as temperature or humidity. While these extrinsic factors do explain some variation in decomposition patterns, interindividual variability is still observed. Understanding how intrinsic factors influence microbial decomposers will help reveal the ecological impacts of decomposition. This work also has forensic applications, as soil chemical and biological changes have been suggested as indicators of postmortem interval. We reveal factors that explain variation in the decomposition environment that should be considered in these estimates. This is particularly important as we consider the implications of variations in human populations due to diet, age, BMI, disease, toxicological loading, etc. on forensic investigations dealing with decomposing remains.
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Affiliation(s)
- Allison R. Mason
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | | | | | - Mary C. Davis
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA
| | - Shawn R. Campagna
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee, USA
| | - Dawnie W. Steadman
- Department of Anthropology, University of Tennessee, Knoxville, Tennessee, USA
| | - Jennifer M. DeBruyn
- Department of Biosystems Engineering and Soil Science, University of Tennessee, Knoxville, Tennessee, USA
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26
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Deel HL, Montoya S, King K, Emmons AL, Huhn C, Lynne AM, Metcalf JL, Bucheli SR. The microbiome of fly organs and fly-human microbial transfer during decomposition. Forensic Sci Int 2022; 340:111425. [DOI: 10.1016/j.forsciint.2022.111425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 08/03/2022] [Accepted: 08/13/2022] [Indexed: 11/30/2022]
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27
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von Hoermann C, Weithmann S, Sikorski J, Nevo O, Szpila K, Grzywacz A, Grunwald JE, Reckel F, Overmann J, Steiger S, Ayasse M. Linking bacteria, volatiles and insects on carrion: the role of temporal and spatial factors regulating inter-kingdom communication via volatiles. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220555. [PMID: 36061525 PMCID: PMC9428529 DOI: 10.1098/rsos.220555] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Multi-kingdom community complexity and the chemically mediated dynamics between bacteria and insects have recently received increased attention in carrion research. However, the strength of these inter-kingdom interactions and the factors that regulate them are poorly studied. We used 75 piglet cadavers across three forest regions to survey the relationship between three actors (epinecrotic bacteria, volatile organic compounds (VOCs) and flies) during the first 4 days of decomposition and the factors that regulate this interdependence. The results showed a dynamic bacterial change during decomposition (temperature-time index) and across the forest management gradient, but not between regions. Similarly, VOC emission was dynamic across a temperature-time index and the forest management gradient but did not differ between regions. However, fly occurrence was dynamic across both space and time. The strong interdependence between the three actors was mainly regulated by the temperature-time index and the study regions, thereby revealing regulation at temporal and spatial scales. Additionally, the actor interdependence was stable across a gradient of forest management intensity. By combining different actors of decomposition, we have expanded our knowledge of the holistic mechanisms regulating carrion community dynamics and inter-kingdom interactions, an important precondition for better describing food web dynamics and entire ecosystem functions.
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Affiliation(s)
- Christian von Hoermann
- Department of Conservation and Research, Bavarian Forest National Park, Grafenau, Germany
| | - Sandra Weithmann
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
| | - Johannes Sikorski
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Omer Nevo
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
- Institute of Biodiversity, Friedrich Schiller University, Jena, Germany
| | - Krzysztof Szpila
- Department of Ecology and Biogeography, Nicolaus Copernicus University, Torun, Poland
| | - Andrzej Grzywacz
- Department of Ecology and Biogeography, Nicolaus Copernicus University, Torun, Poland
| | - Jan-Eric Grunwald
- Bavarian State Criminal Police Office, SG 204, Microtraces/Biology, 80636 Munich, Germany
| | - Frank Reckel
- Bavarian State Criminal Police Office, SG 204, Microtraces/Biology, 80636 Munich, Germany
| | - Jörg Overmann
- Department of Microbial Ecology and Diversity Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany
| | - Sandra Steiger
- Department of Evolutionary Animal Ecology, University of Bayreuth, Bayreuth, Germany
| | - Manfred Ayasse
- Institute of Evolutionary Ecology and Conservation Genomics, University of Ulm, Ulm, Germany
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28
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Microbiota succession throughout life from the cradle to the grave. Nat Rev Microbiol 2022; 20:707-720. [PMID: 35906422 DOI: 10.1038/s41579-022-00768-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/21/2022] [Indexed: 11/08/2022]
Abstract
Associations between age and the human microbiota are robust and reproducible. The microbial composition at several body sites can predict human chronological age relatively accurately. Although it is largely unknown why specific microorganisms are more abundant at certain ages, human microbiota research has elucidated a series of microbial community transformations that occur between birth and death. In this Review, we explore microbial succession in the healthy human microbiota from the cradle to the grave. We discuss the stages from primary succession at birth, to disruptions by disease or antibiotic use, to microbial expansion at death. We address how these successions differ by body site and by domain (bacteria, fungi or viruses). We also review experimental tools that microbiota researchers use to conduct this work. Finally, we discuss future directions for studying the microbiota's relationship with age, including designing consistent, well-powered, longitudinal studies, performing robust statistical analyses and improving characterization of non-bacterial microorganisms.
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29
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Khalikov AA, Kildyushov EM, Kuznetsov KO, Rahmatullina GR. [Estimation of time since death with the postmortem microbiome: a modern view and approaches to solving the problem]. Sud Med Ekspert 2022; 65:49-53. [PMID: 35613449 DOI: 10.17116/sudmed20226503149] [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: 11/18/2022]
Abstract
The aim of the review is to summarize and update the data of modern studies devoted to determining the post-mortem interval (PMI) with the use of microorganisms, as well as disclosing prospects for further study in the presented direction. Estimating the time elapsed since death based on the postmortem microbiome has great potential for accurate determination of PMI, but all methods currently used have their limitations. The dynamics of changes in microbial communities due to the influence of many external and internal factors significantly complicates the process of interpreting the results. The change of microbial communities in the human corpse has shown promising results for the assessment of PMI, but to date there is no evidence of the repeatability of such a continuity in various geographic and ecological conditions. The question of conducting new, large-scale studies, taking in all the factors that could affect the posthumous microbiome, is becoming urgent.
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Affiliation(s)
| | - E M Kildyushov
- Pirogov Russian National Research Medical University, Moscow, Russia
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30
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MALDI-TOF Mass Spectrometry Analysis and Human Post-Mortem Microbial Community: A Pilot Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19074354. [PMID: 35410034 PMCID: PMC8998342 DOI: 10.3390/ijerph19074354] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 02/04/2023]
Abstract
Introduction: The human post-mortem microbiome (HPM) plays a major role in the decomposition process. Successional changes in post-mortem bacterial communities have been recently demonstrated using high throughput metagenomic sequencing techniques, showing great potential as a post-mortem interval (PMI) predictor. The aim of this study is to verify the application of the mass spectrometry technique, better known as MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), as a cheap and quick method for microbe taxonomic identification and for studying the PM microbiome. Methods: The study was carried out on 18 human bodies, ranging from 4 months to 82 years old and with a PMI range from 24 h up to 15 days. The storage time interval in the coolers was included in the final PMI estimates. Using the PMI, the sample study was divided into three main groups: seven cases with a PMI < 72 h; six cases with a PMI of 72−168 h and five cases with a PMI > 168 h. For each body, microbiological swabs were sampled from five external anatomical sites (eyes, ears, nose, mouth, and rectum) and four internal organs (brain, spleen, liver, and heart). Results: The HPM became increasingly different from the starting communities over time in the internal organs as well as at skin sites; the HPM microbiome was mostly dominated by Firmicutes and Proteobacteria phyla; and a PM microbial turnover existed during decomposition, evolving with the PMI. Conclusions: MALDI-TOF is a promising method for PMI estimation, given its sample handling, good reproducibility, and high speed and throughput. Although several intrinsic and extrinsic factors can affect the structure of the HPM, MALDI-TOF can detect the overall microbial community turnover of most prevalent phyla during decomposition. Limitations are mainly related to its sensitivity due to the culture-dependent method and bias in the identification of new isolates.
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Kaszubinski SF, Receveur JP, Nestle ED, Pechal JL, Benbow ME. Microbial community succession of submerged bones in an aquatic habitat. J Forensic Sci 2022; 67:1565-1578. [PMID: 35349167 DOI: 10.1111/1556-4029.15036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/06/2022] [Accepted: 03/08/2022] [Indexed: 01/04/2023]
Abstract
After death, microbes (including bacteria and fungi) colonize carrion from a variety of sources during the decomposition process. The predictable succession of microbes could be useful for forensics, such as postmortem submersion interval estimation (PMSI) for aquatic deaths. However, gaps exist in our understanding of microbial succession on submerged bone, particularly regarding longer-term decomposition (>1 year), fungal composition, and differences between internal and external microbial communities. To further explore this potential forensic tool, we described the postmortem microbial communities (bacteria and fungi) on and within submerged bones using targeted amplicon sequencing. We hypothesized predictable successional patterns of microbial colonization would be detected on the surface and within submerged bones, which would eventually converge to a similar microbial community. To best replicate forensic contexts, we sampled bones from replicate swine (Sus scrofa domesticus) carcasses submerged in a freshwater pond, every three months for nearly two years. Microbial bone (internal vs. external) community structure (taxa abundance and diversity) of bones differed for both bacteria and fungi, but internal and external communities did not converge to a similar structure. PMSI estimation models built with random forest regression of postmortem microbiomes were highly accurate (>80% variation explained in PMSI) and showed promise for forensic purposes. Overall, we provide further evidence that internal and external bone microbial communities submerged in an aquatic habitat are distinct and each community undergoes predictable succession, demonstrating potential utility in forensics for modeling PMSI in unattended deaths and/or cold cases.
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Affiliation(s)
- Sierra F Kaszubinski
- Department of Integrative Biology, Michigan State University, East Lansing, Michigan, USA
| | - Joseph P Receveur
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA
| | - Emily D Nestle
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA
| | - M Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, Michigan, USA.,Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, Michigan, USA.,Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, Michigan, USA
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32
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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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Du Y, Chen JQ, Liu Q, Fu JC, Lin CX, Lin LH, Li H, Qu YF, Ji X. Dietary Correlates of Oral and Gut Microbiota in the Water Monitor Lizard, Varanus salvator (Laurenti, 1768). Front Microbiol 2022; 12:771527. [PMID: 35069477 PMCID: PMC8770915 DOI: 10.3389/fmicb.2021.771527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 11/30/2021] [Indexed: 12/11/2022] Open
Abstract
Numerous studies have demonstrated that food shapes the structure and composition of the host’s oral and gut microbiota. The disorder of oral and gut microbiota may trigger various host diseases. Here, we collected oral and gut samples from wild water monitor lizards (Varanus salvator) and their captive conspecifics fed with bullfrogs, eggs, and depilated chicken, aiming to examine dietary correlates of oral and gut microbiota. We used the 16S rRNA gene sequencing technology to analyze the composition of the microbiota. Proteobacteria and Bacteroidota were the dominant phyla in the oral microbiota, and so were in the gut microbiota. The alpha diversity of microbiota was significantly higher in the gut than in the oral cavity, and the alpha diversity of oral microbiota was higher in captive lizards than in wild conspecifics. Comparing the relative abundance of oral and gut bacteria and their gene functions, differences among different animal groups presumably resulted from human contact in artificial breeding environments and complex food processing. Differences in gene function might be related to the absolute number and/or the taxonomic abundance of oral and gut microorganisms in the wild and the water environment. This study provides not only basic information about the oral and gut microbiota of captive and wild water monitor lizards, but also an inference that feeding on frogs and aquatic products and reducing human exposure help water monitor lizards maintain a microbiota similar to that in the wild environment.
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Affiliation(s)
- Yu Du
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Jun-Qiong Chen
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qian Liu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jian-Chao Fu
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Chi-Xian Lin
- Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,MOE Key Laboratory of Utilization and Conservation for Tropical Marine Bioresources, Hainan Tropical Ocean University, Sanya, China
| | - Long-Hui Lin
- Hangzhou Key Laboratory for Ecosystem Protection and Restoration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hong Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yan-Fu Qu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiang Ji
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China.,Hainan Key Laboratory of Herpetological Research, College of Fisheries and Life Science, Hainan Tropical Ocean University, Sanya, China.,Zhejiang Provincial Key Laboratory for Water Environment and Marine Biological Resources Protection, College of Life and Environmental Sciences, Wenzhou University, Wenzhou, China
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Kateete DP, Mbabazi MM, Nakazzi F, Katabazi FA, Kigozi E, Ssengooba W, Nakiyingi L, Namiiro S, Okwera A, Joloba ML, Muwonge A. Sputum microbiota profiles of treatment-naïve TB patients in Uganda before and during first-line therapy. Sci Rep 2021; 11:24486. [PMID: 34966183 PMCID: PMC8716532 DOI: 10.1038/s41598-021-04271-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 12/14/2021] [Indexed: 11/23/2022] Open
Abstract
Information on microbiota dynamics in pulmonary tuberculosis (TB) in Africa is scarce. Here, we sequenced sputa from 120 treatment-naïve TB patients in Uganda, and investigated changes in microbiota of 30 patients with treatment-response follow-up samples. Overall, HIV-status and anti-TB treatment were associated with microbial structural and abundance changes. The predominant phyla were Bacteroidetes, Firmicutes, Proteobacteria, Fusobacteria and Actinobacteria, accounting for nearly 95% of the sputum microbiota composition; the predominant genera across time were Prevotella, Streptococcus, Veillonella, Haemophilus, Neisseria, Alloprevotella, Porphyromonas, Fusobacterium, Gemella, and Rothia. Treatment-response follow-up at month 2 was characterized by a reduction in abundance of Mycobacterium and Fretibacterium, and an increase in Ruminococcus and Peptococcus; month 5 was characterized by a reduction in Tannerella and Fusobacterium, and an increase in members of the family Neisseriaceae. The microbiota core comprised of 44 genera that were stable during treatment. Hierarchical clustering of this core's abundance distinctly separated baseline (month 0) samples from treatment follow-up samples (months 2/5). We also observed a reduction in microbial diversity with 9.1% (CI 6-14%) of the structural variation attributed to HIV-status and anti-TB treatment. Our findings show discernible microbiota signals associated with treatment with potential to inform anti-TB treatment response monitoring.
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Affiliation(s)
- David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda.
| | - Monica M Mbabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Faith Nakazzi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fred A Katabazi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edgar Kigozi
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Willy Ssengooba
- BSL-3 Mycobacteriology Laboratory, Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Lydia Nakiyingi
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
- Infectious Diseases Institute, Makerere University College of Health Sciences, Mulago Hospital Complex, Kampala, Uganda
| | - Sharon Namiiro
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Alphonse Okwera
- TB Clinics, Mulago National Referral Hospital, Kampala, Uganda
| | - Moses L Joloba
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | - Adrian Muwonge
- Division of Genetics and Genomics, The Roslin Institute, University of Edinburgh, Edinburg, UK.
- Division of Infection and Immunity, The Roslin Institute, University of Edinburgh, Edinburg, UK.
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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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Gouello A, Dunyach-Remy C, Siatka C, Lavigne JP. Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences. Diagnostics (Basel) 2021; 12:diagnostics12010001. [PMID: 35054168 PMCID: PMC8774847 DOI: 10.3390/diagnostics12010001] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/16/2023] Open
Abstract
The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.
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Affiliation(s)
- Audrey Gouello
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95037 Cergy-Pontoise, France;
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | - Catherine Dunyach-Remy
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | | | - Jean-Philippe Lavigne
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
- Correspondence: ; Tel.: +33-466683202
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Wang Y, Wang M, Luo C, Li L, Xu W, Hu G, Wang Y, Amendt J, Wang J. Dynamics of insects, microorganisms and muscle mRNA on pig carcasses and their significances in estimating PMI. Forensic Sci Int 2021; 329:111090. [PMID: 34752998 DOI: 10.1016/j.forsciint.2021.111090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 11/18/2022]
Abstract
The accurate estimate of the postmortem interval (PMI) is of vital significance in the investigation of homicide cases. In this study, three pig carcasses were placed in the field to study the pattern of insect succession, the change of microorganisms and the degradation of muscle tissue RNA during the decomposition process. The results showed that insects could quickly colonize the carcasses and still exist on them until the end of the experiment (41 days). Their development and succession patterns are useful indicators for PMI estimation. The diversity of rectal microorganisms decreased with the decomposition time. In different decomposition periods, significant differences in the rectal and soil microbial composition and relative abundance were found, which could be used to estimate the PMI with an accuracy of 3-4 days. The RNA of muscle tissue was found to have a time-dependent relationship with the PMI. Ppia and Gapdh showed a linear upward trend within 10 h after the death, followed by a gradual downward trend from 10 to 240 h. The expression of β-actin gene showed a gradual downward trend during 0-240 h. This is the first study in China to analyze the changes of insects, muscle RNA and microorganisms on pig carcasses in the same natural environment, which provide basic data for the PMI estimation.
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Affiliation(s)
- Yu Wang
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Man Wang
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Chengliang Luo
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Liangliang Li
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Wang Xu
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Guoliang Hu
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Yinghui Wang
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China
| | - Jens Amendt
- Institute of Forensic Medicine, University of Frankfurt, Kennedyallee, Frankfurt/Main, Germany.
| | - Jiangfeng Wang
- Department of Forensic Medicine, Soochow University, Ganjiang East Road, Suzhou, China.
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Caenazzo L, Tozzo P. Microbiome Forensic Biobanking: A Step toward Microbial Profiling for Forensic Human Identification. Healthcare (Basel) 2021; 9:1371. [PMID: 34683051 PMCID: PMC8544459 DOI: 10.3390/healthcare9101371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/04/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
In recent years many studies have highlighted the great potential of microbial analysis in human identification for forensic purposes, with important differences in microbial community composition and function across different people and locations, showing a certain degree of uncertainty. Therefore, further studies are necessary to enable forensic scientists to evaluate the risk of microbial transfer and recovery from various items and to further critically evaluate the suitability of current human DNA recovery protocols for human microbial profiling for identification purposes. While the establishment and development of microbiome research biobanks for clinical applications is already very structured, the development of studies on the applicability of microbiome biobanks for forensic purposes is still in its infancy. The creation of large population microbiome biobanks, specifically dedicated to forensic human identification, could be worthwhile. This could also be useful to increase the practical applications of forensic microbiology for identification purposes, given that this type of evidence is currently absent from most real casework investigations and judicial proceedings in courts.
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Affiliation(s)
| | - Pamela Tozzo
- Laboratory of Forensic Genetics, Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
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Hu L, Xing Y, Jiang P, Gan L, Zhao F, Peng W, Li W, Tong Y, Deng S. Predicting the postmortem interval using human intestinal microbiome data and random forest algorithm. Sci Justice 2021; 61:516-527. [PMID: 34482931 DOI: 10.1016/j.scijus.2021.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/20/2021] [Accepted: 06/22/2021] [Indexed: 01/04/2023]
Abstract
Gradual changes in microbial communities in a human body after death can be used to determine postmortem interval (PMI). In this study, gut microflora samples were collected from the vermiform appendix and the transverse colon of human cadavers with PMIs between 5 and 192 h. The results revealed that the appendix might be an excellent intestinal sampling site and the appendix flora had an inferred succession rule during human body decomposition. Firmicutes, Bacteroidetes, and their respective subclasses showed a predictable successionrule in relative abundance over time. A Random Forest regression model was developed to correlate human gut microbiota with PMI. We believe that our findings have increased the knowledge of the composition and abundance of the gut microbiota in human corpses, and suggest that the use of the human appendix microbial succession may be a potential method for forensic estimation of the time of death.
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Affiliation(s)
- Lai Hu
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Yu Xing
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Pu Jiang
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Li Gan
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Fan Zhao
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Wenli Peng
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Weihan Li
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Yanqiu Tong
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China; School of Humanities, Chongqing Jiaotong University, #66 Xuefu Road, Chongqing 400016, China
| | - Shixiong Deng
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China.
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Deel H, Emmons AL, Kiely J, Damann FE, Carter DO, Lynne A, Knight R, Xu ZZ, Bucheli S, Metcalf JL. A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition. mSphere 2021; 6:e0045521. [PMID: 34259562 PMCID: PMC8386422 DOI: 10.1128/msphere.00455-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/21/2021] [Indexed: 11/20/2022] Open
Abstract
The bones of decomposing vertebrates are colonized by a succession of diverse microbial communities. If this succession is similar across individuals, microbes may provide clues about the postmortem interval (PMI) during forensic investigations in which human skeletal remains are discovered. Here, we characterize the human bone microbial decomposer community to determine whether microbial succession is a marker for PMI. Six human donor subjects were placed outdoors to decompose on the soil surface at the Southeast Texas Applied Forensic Science facility. To also assess the effect of seasons, three decedents were placed each in the spring and summer. Once ribs were exposed through natural decomposition, a rib was collected from each body for eight time points at 3 weeks apart. We discovered a core bone decomposer microbiome dominated by taxa in the phylum Proteobacteria and evidence that these bone-invading microbes are likely sourced from the surrounding decomposition environment, including skin of the cadaver and soils. Additionally, we found significant overall differences in bone microbial community composition between seasons. Finally, we used the microbial community data to develop random forest models that predict PMI with an accuracy of approximately ±34 days over a 1- to 9-month time frame of decomposition. Typically, anthropologists provide PMI estimates based on qualitative information, giving PMI errors ranging from several months to years. Previous work has focused on only the characterization of the bone microbiome decomposer community, and this is the first known data-driven, quantitative PMI estimate of terrestrially decomposed human skeletal remains using microbial abundance information. IMPORTANCE Microbes are known to facilitate vertebrate decomposition, and they can do so in a repeatable, predictable manner. The succession of microbes in the skin and associated soil can be used to predict time since death during the first few weeks of decomposition. However, when remains are discovered after months or years, often the only evidence are skeletal remains. To determine if microbial succession in bone would be useful for estimating time since death after several months, human subjects were placed to decompose in the spring and summer seasons. Ribs were collected after 1 to 9 months of decomposition, and the bone microbial communities were characterized. Analysis revealed a core bone decomposer microbial community with some differences in microbial assembly occurring between seasons. These data provided time since death estimates of approximately ±34 days over 9 months. This may provide forensic investigators with a tool for estimating time since death of skeletal remains, for which there are few current methods.
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Affiliation(s)
- Heather Deel
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Alexandra L. Emmons
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jennifer Kiely
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | | | - David O. Carter
- Laboratory of Forensic Taphonomy, Forensic Sciences Unit, Chaminade University of Honolulu, Honolulu, Hawaii, USA
- School of Natural Sciences and Mathematics, Chaminade University of Honolulu, Honolulu, Hawaii, USA
| | - Aaron Lynne
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Rob Knight
- Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Zhenjiang Zech Xu
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - Sibyl Bucheli
- Department of Biological Sciences, Sam Houston State University, Huntsville, Texas, USA
| | - Jessica L. Metcalf
- Program in Cell & Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
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Jurkevitch E, Pasternak Z. A walk on the dirt: soil microbial forensics from ecological theory to the crime lab. FEMS Microbiol Rev 2021; 45:5937428. [PMID: 33098291 DOI: 10.1093/femsre/fuaa053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Forensics aims at using physical evidence to solve investigations with science-based principles, thus operating within a theoretical framework. This however is often rather weak, the exception being DNA-based human forensics that is well anchored in theory. Soil is a most commonly encountered, easily and unknowingly transferred evidence but it is seldom employed as soil analyses require extensive expertise. In contrast, comparative analyses of soil bacterial communities using nucleic acid technologies can efficiently and precisely locate the origin of forensic soil traces. However, this application is still in its infancy, and is very rarely used. We posit that understanding the theoretical bases and limitations of their uses is essential for soil microbial forensics to be judiciously implemented. Accordingly, we review the ecological theory and experimental evidence explaining differences between soil microbial communities, i.e. the generation of beta diversity, and propose to integrate a bottom-up approach of interactions at the microscale, reflecting historical contingencies with top-down mechanisms driven by the geographic template, providing a potential explanation as to why bacterial communities map according to soil types. Finally, we delimit the use of soil microbial forensics based on the present technologies and ecological knowledge, and propose possible venues to remove existing bottlenecks.
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Affiliation(s)
- Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Zohar Pasternak
- Division of Identification and Forensic Science, Israel Police
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42
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Čížková D, Ďureje Ľ, Piálek J, Kreisinger J. Experimental validation of small mammal gut microbiota sampling from faeces and from the caecum after death. Heredity (Edinb) 2021; 127:141-150. [PMID: 34045683 PMCID: PMC8322053 DOI: 10.1038/s41437-021-00445-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 02/04/2023] Open
Abstract
Data on the gut microbiota (GM) of wild animals are key to studies on evolutionary biology (host-GM interactions under natural selection), ecology and conservation biology (GM as a fitness component closely connected to the environment). Wildlife GM sampling often requires non-invasive techniques or sampling from dead animals. In a controlled experiment profiling microbial 16S rRNA in 52 house mice (Mus musculus) from eight families and four genetic backgrounds, we studied the effects of live- and snap-trapping on small mammal GM and evaluated the suitability of microbiota from non-fresh faeces as a proxy for caecal GM. We compared CM from individuals sampled 16-18 h after death with those in live traps and caged controls, and caecal and faecal GM collected from mice in live-traps. Sampling delay did not affect GM composition, validating data from fresh cadavers or snap-trapped animals. Animals trapped overnight displayed a slight but significant difference in GM composition to the caged controls, though the change only had negligible effect on GM diversity, composition and inter-individual divergence. Hence, the trapping process appears not to bias GM profiling. Despite their significant difference, caecal and faecal microbiota were correlated in composition and, to a lesser extent, diversity. Both showed congruent patterns of inter-individual divergence following the natural structure of the dataset. Thus, the faecal microbiome represents a good non-invasive proxy of the caecal microbiome, making it suitable for detecting biologically relevant patterns. However, care should be taken when analysing mixed datasets containing both faecal and caecal samples.
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Affiliation(s)
- Dagmar Čížková
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Ľudovít Ďureje
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jaroslav Piálek
- grid.418095.10000 0001 1015 3316Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Jakub Kreisinger
- grid.4491.80000 0004 1937 116XFaculty of Science, Department of Zoology, Charles University, Prague, Czech Republic
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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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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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45
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Díez López C, Kayser M, Vidaki A. Estimating the Time Since Deposition of Saliva Stains With a Targeted Bacterial DNA Approach: A Proof-of-Principle Study. Front Microbiol 2021; 12:647933. [PMID: 34149638 PMCID: PMC8206545 DOI: 10.3389/fmicb.2021.647933] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 04/14/2021] [Indexed: 01/04/2023] Open
Abstract
Information on the time when a stain was deposited at a crime scene can be valuable in forensic investigations. It can link a DNA-identified stain donor with a crime or provide a post-mortem interval estimation in cases with cadavers. The available methods for estimating stain deposition time have limitations of different types and magnitudes. In this proof-of-principle study we investigated for the first time the use of microbial DNA for this purpose in human saliva stains. First, we identified the most abundant and frequent bacterial species in saliva using publicly available 16S rRNA gene next generation sequencing (NGS) data from 1,848 samples. Next, we assessed time-dependent changes in 15 identified species using de-novo 16S rRNA gene NGS in the saliva stains of two individuals exposed to indoor conditions for up to 1 year. We selected four bacterial species, i.e., Fusobacterium periodonticum, Haemophilus parainfluenzae, Veillonella dispar, and Veillonella parvula showing significant time-dependent changes and developed a 4-plex qPCR assay for their targeted analysis. Then, we analyzed the saliva stains of 15 individuals exposed to indoor conditions for up to 1 month. Bacterial counts generally increased with time and explained 54.9% of the variation (p = <2.2E–16). Time since deposition explained ≥86.5% and ≥88.9% of the variation in each individual and species, respectively (p = <2.2E–16). Finally, based on sample duplicates we built and tested multiple linear regression models for predicting the stain deposition time at an individual level, resulting in an average mean absolute error (MAE) of 5 days (ranging 3.3–7.8 days). Overall, the deposition time of 181 (81.5%) stains was correctly predicted within 1 week. Prediction models were also assessed in stains exposed to similar conditions up to 1 month 7 months later, resulting in an average MAE of 8.8 days (ranging 3.9–16.9 days). Our proof-of-principle study suggests the potential of the DNA profiling of human commensal bacteria as a method of estimating saliva stains time since deposition in the forensic scenario, which may be expanded to other forensically relevant tissues. The study considers practical applications of this novel approach, but various forensic developmental validation and implementation criteria will need to be met in more dedicated studies in the future.
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Affiliation(s)
- Celia Díez López
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
| | - Athina Vidaki
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam, Netherlands
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46
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Bisker C, Taylor G, Carney H, Ralebitso-Senior TK. A Combined Application of Molecular Microbial Ecology and Elemental Analyses Can Advance the Understanding of Decomposition Dynamics. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.605817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Introducing animal carbon-source to soil initiates biochemical and microbial processes that lead to its decomposition and recycling, which subsequently cause successional shifts in soil microbial community. To investigate the use of soil microbial community to inform criminal investigation, this study was designed to mimic clandestine graves. It compared the decomposition of stillborn piglets (Sus scrofa domesticus), as human analogues, to oak (Quercus robur) leaf litter and soil-only controls outdoors for 720 days. Environmental and edaphic parameters were monitored and showed soil microbial community alignment with temperature seasonality, which highlighted the importance of this abiotic factor. Denaturing gradient gel electrophoresis (DGGE) data were used to calculate Hill numbers and diversity indices of the bacterial 16S rRNA community did not distinguish mammalian- from plant-based decomposition consistently during the first or second year of the study. In contrast, the fungal 18S rRNA community allowed clear differentiation between different treatments (beta diversity) throughout the 720-day experiment and suggested the moment of the decomposing mammalian skin rupture. 16S rRNA-based NGS facilitated the identification of e.g., Pirellulaceae, Acidobacteria ii1-15_order and Candidatus xiphinematobacter as Year 2 bacterial markers of gravesoil at family, order and species taxonomic levels, respectively, and confirmed the similarity of the calculated Hill diversity metrics with those derived from DGGE profiling. Parallel soil elemental composition was measured by portable X-ray Fluorescence where calcium profiles for the piglet-associated soils were distinct from those without carrion. Also, soil calcium content and PMI correlated positively during the first year then negatively during the second. This study is one of the first to apply a multidisciplinary approach based on molecular and physicochemical analytical techniques to assess decomposition. It highlights the recognised potential of using soil microbial community in forensic investigations and provides a proof-of-concept for the application of a combined molecular and elemental approach to further understand the dynamics of decomposition. In addition, it sets the scene for further research in different conditions based on Hill numbers metrics instead of the classic ecological indices for soil necrobiome richness, diversity and evenness.
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47
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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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48
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Stewart JD, Kremer P, Shakya KM, Conway M, Saad A. Outdoor Atmospheric Microbial Diversity Is Associated With Urban Landscape Structure and Differs From Indoor-Transit Systems as Revealed by Mobile Monitoring and Three-Dimensional Spatial Analysis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.620461] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Microbes are abundant inhabitants of the near-surface atmosphere in urban areas. The distribution of microbial communities may benefit or hinder human wellbeing and ecosystem function. Surveys of airborne microbial diversity are uncommon in both natural and built environments and those that investigate diversity are stationary in the city, thus missing continuous exposure to microbes that covary with three-dimensional urban structure. Individuals in cities are generally mobile and would be exposed to diverse urban structures outdoors and within indoor-transit systems in a day. We used mobile monitoring of microbial diversity and geographic information system spatial analysis, across Philadelphia, Pennsylvania, USA in outdoor and indoor-transit (subways and train cars) environments. This study identifies to the role of the three-dimensional urban landscape in structuring atmospheric microbiomes and employs mobile monitoring over ~1,920 kilometers to measure continuous biodiversity. We found more diverse communities outdoors that significantly differ from indoor-transit air in microbial community structure, function, likely source environment, and potentially pathogenic fraction of the community. Variation in the structure of the urban landscape was associated with diversity and function of the near-surface atmospheric microbiome in outdoor samples.
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49
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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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50
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Gwenzi W. The 'thanato-resistome' - The funeral industry as a potential reservoir of antibiotic resistance: Early insights and perspectives. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141120. [PMID: 32836113 PMCID: PMC7381411 DOI: 10.1016/j.scitotenv.2020.141120] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 07/18/2020] [Accepted: 07/18/2020] [Indexed: 05/03/2023]
Abstract
The funeral industry is a potential reservoir of antibiotic resistance. The occurrence, human exposure and health risks of antibiotic resistance in the funeral industry were examined. The funeral industry harbours antibiotic resistance to multiple common and last-resort antibiotics, hence constitutes the 'thanato-resistome'. Hydrological processes, air-borne particulates and vectors disseminate antibiotic resistance, while horizontal gene transfer circulates antibiotic resistance among resistomes, forming a complex network. Ingestion, inhalation of air-borne particulates, dermal intake and clothes of workers contribute to human exposure. Human health risks include; development of drug resistance in previously susceptible pathogens, and increased morbidity and mortality caused by increased pathogenicity and outbreaks of multi-drug resistant infections. Ecological risks include the proliferation of resistant organisms at the expense of susceptible ones, thereby disrupting ecosystem structure and function, including biogeochemical cycles. Barring inferential data, quantitative evidence linking antibiotic resistance to human infections is weak. This reflects the lack of systematic quantitative studies, rather than the absence of such health risks. Quantitative risk assessment is constrained by lack of quantitative data on antibiotic resistance in various reservoirs and exposure routes. A framework for risk assessment and mitigation is proposed. Finally, ten hypotheses and emerging tools such as genomics, in silico techniques and big data analytics are highlighted.
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Affiliation(s)
- Willis Gwenzi
- Biosystems and Environmental Engineering Research Group, Department of Soil Science and Agricultural Engineering, Faculty of Agriculture, University of Zimbabwe, P.O. Box MP167, Mount Pleasant, Harare, Zimbabwe.
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