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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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Yang F, Zhang X, Hu S, Nie H, Gui P, Zhong Z, Guo Y, Zhao X. Changes in Microbial Communities Using Pigs as a Model for Postmortem Interval Estimation. Microorganisms 2023; 11:2811. [PMID: 38004822 PMCID: PMC10672931 DOI: 10.3390/microorganisms11112811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/06/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
Microbial communities can undergo significant successional changes during decay and decomposition, potentially providing valuable insights for determining the postmortem interval (PMI). The microbiota produce various gases that cause cadaver bloating, and rupture releases nutrient-rich bodily fluids into the environment, altering the soil microbiota around the carcasses. In this study, we aimed to investigate the underlying principles governing the succession of microbial communities during the decomposition of pig carcasses and the soil beneath the carcasses. At early decay, the phylum Firmicutes and Bacteroidota were the most abundant in both the winter and summer pig rectum. However, Proteobacteria became the most abundant in the winter pig rectum in late decay. Using genus as a biomarker to estimate the PMI could get the MAE from 1.375 days to 2.478 days based on the RF model. The abundance of bacterial communities showed a decreasing trend with prolonged decomposition time. There were statistically significant differences in microbial diversity in the two periods (pre-rupture and post-rupture) of the four groups (WPG 0-8Dvs. WPG 16-40D, p < 0.0001; WPS 0-16Dvs. WPS 24-40D, p = 0.003; SPG 0D vs. SPG 8-40D, p = 0.0005; and SPS 0D vs. SPS 8-40D, p = 0.0208). Most of the biomarkers in the pre-rupture period belong to obligate anaerobes. In contrast, the biomarkers in the post-rupture period belong to aerobic bacteria. Furthermore, the genus Vagococcus shows a similar increase trend, whether in winter or summer. Together, these results suggest that microbial succession was predictable and can be developed into a forensic tool for estimating the PMI.
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Affiliation(s)
- Fan Yang
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; (F.Y.); (S.H.); (H.N.)
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China; (X.Z.); (Y.G.)
| | - Sheng Hu
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; (F.Y.); (S.H.); (H.N.)
| | - Hao Nie
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; (F.Y.); (S.H.); (H.N.)
| | - Peng Gui
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.G.); (Z.Z.)
| | - Zengtao Zhong
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (P.G.); (Z.Z.)
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha 410013, China; (X.Z.); (Y.G.)
| | - Xingchun Zhao
- Institute of Forensic Science, Ministry of Public Security, Beijing 100038, China; (F.Y.); (S.H.); (H.N.)
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Cláudia-Ferreira A, Barbosa DJ, Saegeman V, Fernández-Rodríguez A, Dinis-Oliveira RJ, Freitas AR. The Future Is Now: Unraveling the Expanding Potential of Human (Necro)Microbiome in Forensic Investigations. Microorganisms 2023; 11:2509. [PMID: 37894167 PMCID: PMC10608847 DOI: 10.3390/microorganisms11102509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/24/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The relevance of postmortem microbiological examinations has been controversial for decades, but the boom in advanced sequencing techniques over the last decade is increasingly demonstrating their usefulness, namely for the estimation of the postmortem interval. This comprehensive review aims to present the current knowledge about the human postmortem microbiome (the necrobiome), highlighting the main factors influencing this complex process and discussing the principal applications in the field of forensic sciences. Several limitations still hindering the implementation of forensic microbiology, such as small-scale studies, the lack of a universal/harmonized workflow for DNA extraction and sequencing technology, variability in the human microbiome, and limited access to human cadavers, are discussed. Future research in the field should focus on identifying stable biomarkers within the dominant Bacillota and Pseudomonadota phyla, which are prevalent during postmortem periods and for which standardization, method consolidation, and establishment of a forensic microbial bank are crucial for consistency and comparability. Given the complexity of identifying unique postmortem microbial signatures for robust databases, a promising future approach may involve deepening our understanding of specific bacterial species/strains that can serve as reliable postmortem interval indicators during the process of body decomposition. Microorganisms might have the potential to complement routine forensic tests in judicial processes, requiring robust investigations and machine-learning models to bridge knowledge gaps and adhere to Locard's principle of trace evidence.
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Affiliation(s)
- Ana Cláudia-Ferreira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
| | - Daniel José Barbosa
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Veroniek Saegeman
- Department of Infection Control and Prevention, University Hospitals Leuven, 3000 Leuven, Belgium;
| | - Amparo Fernández-Rodríguez
- Microbiology Laboratory, Biology Service, Institute of Toxicology and Forensic Sciences, 28232 Madrid, Spain;
| | - Ricardo Jorge Dinis-Oliveira
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Department of Public Health and Forensic Sciences, and Medical Education, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ana R. Freitas
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), CESPU, CRL, 4585-116 Gandra, Portugal; (A.C.-F.); (R.J.D.-O.)
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- UCIBIO—Applied Molecular Biosciences Unit, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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Iancu L, Muslim A, Aazmi S, Jitaru V. Postmortem skin microbiome signatures associated with human cadavers within the first 12 h at the morgue. Front Microbiol 2023; 14:1234254. [PMID: 37564294 PMCID: PMC10410280 DOI: 10.3389/fmicb.2023.1234254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023] Open
Abstract
Introduction Forensic microbiome studies expanded during the last decade, aiming to identify putative bacterial biomarkers to be used for the postmortem interval (PMI) estimation. Bacterial diversity and dynamics during decomposition are influenced by each individual's micro and macroenvironment, ante and postmortem conditions, varying across body sites and time. The skin, the largest organ of the human body, hosts a diverse microbial diversity, representing the first line of defense of a living individual. Targeting the investigation of the postmortem skin microbiome could help understanding the role of microbes during decomposition, and association with the ante and postmortem conditions. Methods The current study aimed to identify the postmortem skin microbiome signatures associated with eight human bodies, received at the Institute of Legal Medicine Iasi, Romania, during April and May 2021. A total of 162 samples (including triplicate) representing face and hands skin microbiome were investigated via Illumina MiSeq, upon arrival at the morgue (T0) and after 12 hours (T1). Results The taxonomic characteristics of the skin microbiota varied across different body sites. However, there were no significant differences in taxonomic profiles between collection time, T0 and T1, except for some dynamic changes in the abundance of dominant bacteria. Moreover, different microbial signatures have been associated with a specific cause of death, such as cardiovascular disease, while an elevated blood alcohol level could be associated with a decrease in bacterial richness and diversity. Discussion The places where the bodies were discovered seemed to play an important role in explaining the bacterial diversity composition. This study shows promising results towards finding common postmortem bacterial signatures associated with human cadavers within the first 12h at the morgue.
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Affiliation(s)
- Lavinia Iancu
- Department of Criminal Justice, University of North Dakota, Grand Forks, ND, United States
| | - Azdayanti Muslim
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, Jalan Hospital, Selangor, Malaysia
- Institute for Biodiversity and Sustainable Development, Universiti Teknologi MARA (UiTM), Selangor, Malaysia
- Microbiome Health and Environment (MiHeaRT), Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor, Malaysia
| | - Shafiq Aazmi
- Microbiome Health and Environment (MiHeaRT), Faculty of Applied Sciences, Universiti Teknologi MARA, Selangor, Malaysia
- School of Biology, Faculty of Applied Science, Universiti Teknologi MARA, Selangor, Malaysia
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Bambaradeniya TB, Magni PA, Dadour IR. A Summary of Concepts, Procedures and Techniques Used by Forensic Entomologists and Proxies. INSECTS 2023; 14:536. [PMID: 37367352 DOI: 10.3390/insects14060536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/28/2023]
Abstract
Forensic entomology is a branch of forensic science that incorporates insects as a part of solving crime. Insect-based evidence recovered at a crime scene can be used to estimate the minimum postmortem interval, determine if a carcass/corpse has been relocated, and contribute to the cause and manner of death. The current review summarises the stepwise usage of forensic entomology methods at a crime scene and in the laboratory, including specimen collection and rearing, identification, xenobiotic detection, documentation, and referencing previous research and casework. It also provides three standards for the collection of insects when attending a crime scene. The Gold standard attributes to a forensic entomologist (FE) who is likely to be well-trained attending a scene. The subsequent standards (Silver and Bronze) have been added because the authors believe that this information is currently missing in the literature. The purpose is so that an attending crime scene agent/proxy with some basic knowledge and some simple tools can recover almost all the insect information required by an FE to make the best estimation of the minimum postmortem interval.
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Affiliation(s)
- Tharindu B Bambaradeniya
- School of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, WA 6150, Australia
| | - Paola A Magni
- School of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, WA 6150, Australia
- Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Ian R Dadour
- School of Medical, Molecular & Forensic Sciences, Murdoch University, Murdoch, WA 6150, Australia
- Source Certain, P.O. Box 1570, Wangara, WA 6947, Australia
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Elastic fiber degradation as a possible indicator for PMI estimation on mummified and corified skin: a pilot study. Int J Legal Med 2023; 137:519-535. [PMID: 36434263 DOI: 10.1007/s00414-022-02915-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/09/2022] [Indexed: 11/26/2022]
Abstract
Mummified and corified bodies are particularly complex scenarios to investigate, starting from identifying the post-mortem interval (PMI), even more so in indoor environments. In these bodies, the skin has the peculiar feature to resist for a long time. Among its components, there are elastic fibers, which are characterized by intrinsic resistance to post-mortem degenerative phenomena. Starting from these considerations, we investigated microscopically the persistence, detectability, and changes of elastic fibers in the skin of mummified and corified bodies with different known PMI. The aim was to evaluate whether they could provide an additional tool to aid in PMI estimation in these cases. Therefore, we collected skin samples from mummified or corified bodies found in a domestic environment with different known PMI, as well as from corified bodies that had been exhumed after 11 years of burial. Histochemical staining specific for elastic fibers, namely, Weigert's resorcin fuchsin, showed their prolonged persistence and a progressive and different degradation between mummified and corified skin as a function of PMI. Moreover, on the whole, we observed greater preservation of elastic fibers in mummified skin than in corified one at the same PMI. Therefore, histological analysis of elastic fibers in mummified and corified skin may help to provide valuable aid in estimating PMI, especially in those particular cases where more reliable alternatives are lacking.
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7
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Wang S, Chen W, Shang Y, Ren L, Zhang X, Guo Y, Zhang C. High-throughput sequencing to evaluate the effects of methamphetamine on the succession of the bacterial community to estimate the postmortem interval. Forensic Sci Res 2023; 7:736-747. [PMID: 36817241 PMCID: PMC9930777 DOI: 10.1080/20961790.2022.2046368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In forensic medical examinations, estimating the postmortem interval (PMI) is an important factor. Methamphetamine (MA) is a synthetic stimulant that is commonly abused, and estimation of the PMI after MA abuse has become one of the main tasks in forensic investigation. Microorganisms play a vital role in carrion decomposition. Analysing the bacterial succession patterns can be used as a forensic tool to estimate the PMI. The present study aimed to analyse bacterial succession changes during the decomposition of MA to estimate the PMI. We analysed bacterial communities in rabbits treated with three different concentrations of MA (0, 22.5, and 90 mg/kg) under the natural conditions of 20 °C and 70% humidity by sequencing 16S rRNA gene amplicons using the Illumina MiSeq system. We obtained 2 374 209 high-quality sequences and 2 937 operational taxonomic units (OTUs). The relative abundances of the bacterial communities varied markedly in response to different MA concentrations. Interestingly, in response to the different concentrations of MA, Bacteroidetes became disparate in the rectum in the late PMI. Increased numbers of bacterial taxa were identified in the rectum and buccal cavity samples, except at the highest concentration of MA in the rectum samples when PMI was 0-h, than were present in live rabbits. Meanwhile, the PMI correlated significantly with bacterial succession at different taxonomic levels. Our results suggested that bacterial community succession could be used as a "microbial clock" to estimate the PMI in cases of MA-related death; however, further study is required to gain a deeper understanding of this concept.
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Affiliation(s)
- Shujuan Wang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Wei Chen
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yanjie Shang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Lipin Ren
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Xiangyan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Yadong Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Changquan Zhang
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China,CONTACT Changquan Zhang
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Li W, Xing Y, Gan L, Peng W, Deng S. Exploring the value of microorganisms in the appendix for inferring postmortem interval in Sprague-Dawley rats using high-throughput sequencing. J Forensic Sci 2023; 68:163-175. [PMID: 36440674 DOI: 10.1111/1556-4029.15173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 10/30/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022]
Abstract
Various microorganisms play an important role in daily functions in the body and continue to flourish after death. Our prior investigation using frozen cadavers revealed that the appendix, rather than the transverse colon, was a superior sampling site for intestinal bacteria because the appendiceal flora had higher diversity than that in the transverse colon in the majority of experimental periods after death. We sought to explore out more about whether the appendicular flora is significantly related to postmortem interval (PMI) at natural temperatures following the host's death. In this work, we employed high-throughput sequencing to evaluate the contents of rats' appendices within 2 weeks after death and then utilized the random forest algorithm to build a PMI prediction model after completing basic visual analyses on the sequencing data. The findings revealed that Firmicutes was the absolute dominant species of appendicular flora; alpha-diversity of appendix flora first increased and then decreased, with the highest point appearing at 36 h after death; and the primary metabolic functions were carbohydrate metabolism, amino acid metabolism, as well as cofactors and vitamin metabolism. Finally, a random forest regression model for PMI prediction was built by the training data at the family level, with the mean absolute error of 10.27 h for prediction within 14 days postmortem, and the test set data subsequently proved the model's reliability. Changes in appendicular flora were strongly related to the PMI following rats' deaths, so we have reason to believe that the appendicular flora is valuable in predicting PMI.
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Affiliation(s)
- Weihan Li
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Yu Xing
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Li Gan
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Wenli Peng
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Shixiong Deng
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
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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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Tozzo P, Amico I, Delicati A, Toselli F, Caenazzo L. Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review. Diagnostics (Basel) 2022; 12:2641. [PMID: 36359484 PMCID: PMC9689864 DOI: 10.3390/diagnostics12112641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 08/12/2023] Open
Abstract
The determination of the Post-Mortem Interval (PMI) is an issue that has always represented a challenge in the field of forensic science. Different innovative approaches, compared to the more traditional ones, have been tried over the years, without succeeding in being validated as successful methods for PMI estimation. In the last two decades, innovations in sequencing technologies have made it possible to generate large volumes of data, allowing all members of a bacterial community to be sequenced. The aim of this manuscript is to provide a review regarding new advances in PMI estimation through cadaveric microbiota identification using 16S rRNA sequencing, in order to correlate specific microbiome profiles obtained from different body sites to PMI. The systematic review was performed according to PRISMA guidelines. For this purpose, 800 studies were identified through database searching (Pubmed). Articles that dealt with PMI estimation in correlation with microbiome composition and contained data about species, body site of sampling, monitoring time and sequencing method were selected and ultimately a total of 25 studies were considered. The selected studies evaluated the contribution of the various body sites to determine PMI, based on microbiome sequencing, in human and animal models. The results of this systematic review highlighted that studies conducted on both animals and humans yielded results that were promising. In order to fully exploit the potential of the microbiome in the estimation of PMI, it would be desirable to identify standardized body sampling sites and specific sampling methods in order to align data obtained by different research groups.
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Affiliation(s)
- Pamela Tozzo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35121 Padova, Italy
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11
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Kumari P, Prakash P, Yadav S, Saran V. Microbiome analysis: An emerging forensic investigative tool. Forensic Sci Int 2022; 340:111462. [PMID: 36155349 DOI: 10.1016/j.forsciint.2022.111462] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 12/30/2022]
Abstract
Microbial diversity's potential has been investigated in medical and therapeutic studies throughout the last few decades. However, its usage in forensics is increasing due to its effectiveness in circumstances when traditional approaches fail to provide a decisive opinion or are insufficient in forming a concrete opinion. The application of human microbiome may serve in detecting the type of stains of saliva and vaginal fluid, as well as in attributing the stains to the individual. Similarly, the microbiome makeup of a soil sample may be utilised to establish geographic origin or to associate humans, animals, or things with a specific area, additionally microorganisms influence the decay process which may be used in depicting the Time Since death. Further in detecting the traces of the amount and concentration of alcohol, narcotics, and other forensically relevant compounds in human body or visceral tissues as they also affect the microbial community within human body. Beside these, there is much more scope of microbiomes to be explored in terms of forensic investigation, this review focuses on multidimensional approaches to human microbiomes from a forensic standpoint, implying the potential of microbiomes as an emerging tool for forensic investigations such as individual variability via skin microbiomes, reconstructing crime scene, and linking evidence to individual.
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Affiliation(s)
- Pallavi Kumari
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India.
| | - Poonam Prakash
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Shubham Yadav
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - Vaibhav Saran
- Department of Forensic Science, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
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12
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Zhang J, Liu W, Simayijiang H, Hu P, Yan J. Application of Microbiome in Forensics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022:S1672-0229(22)00096-1. [PMID: 36031058 PMCID: PMC10372919 DOI: 10.1016/j.gpb.2022.07.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/29/2022] [Indexed: 06/04/2023]
Abstract
Recent advances in next-generation sequencing technology and improvements in bioinformatics have expanded the scope of microbiome analysis as a forensic tool. Microbiome research is concerned with the study of the compositional profile and diversity of microbial flora as well as the interactions between microbes, hosts, and the environment. It has opened up many new possibilities for forensic analysis. In this review, we discuss various applications of microbiomes in forensics, including identification of individuals, geolocation inference, post-mortem interval (PMI) estimation, and others.
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Affiliation(s)
- Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Wenli Liu
- Beijing Center for Physical and Chemical Analysis, Beijing 100089, China
| | | | - Ping Hu
- Key Laboratory of Environment and Health (HUST), Ministry of Education & Ministry of Environmental Protection, and State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan 030001, China.
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13
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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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14
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Dmitrijs F, Guo J, Huang Y, Liu Y, Fang X, Jiang K, Zha L, Cai J, Fu X. Bacterial Succession in Microbial Biofilm as a Potential Indicator for Postmortem Submersion Interval Estimation. Front Microbiol 2022; 13:951707. [PMID: 35942315 PMCID: PMC9356301 DOI: 10.3389/fmicb.2022.951707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/13/2022] [Indexed: 11/18/2022] Open
Abstract
Bacteria acts as the main decomposer during the process of biodegradation by microbial communities in the ecosystem. Numerous studies have revealed the bacterial succession patterns during carcass decomposition in the terrestrial setting. The machine learning algorithm-generated models based on such temporal succession patterns have been developed for the postmortem interval (PMI) estimation. However, the bacterial succession that occurs on decomposing carcasses in the aquatic environment is poorly understood. In the forensic practice, the postmortem submersion interval (PMSI), which approximately equals to the PMI in most of the common drowning cases, has long been problematic to determine. In the present study, bacterial successions in the epinecrotic biofilm samples collected from the decomposing swine cadavers submerged in water were analyzed by sequencing the variable region 4 (V4) of 16S rDNA. The succession patterns between the repeated experimental settings were repeatable. Using the machine learning algorithm for establishing random forest (RF) models, the microbial community succession patterns in the epinecrotic biofilm samples taken during the 56-day winter trial and 21-day summer trial were determined to be used as the PMSI predictors with the mean absolute error (MAE) of 17.87 ± 2.48 ADD (≈1.3 day) and 20.59 ± 4.89 ADD (≈0.7 day), respectively. Significant differences were observed between the seasons and between the substrates. The data presented in this research suggested that the influences of the environmental factors and the aquatic bacterioplankton on succession patterns of the biofilm bacteria were of great significance. The related mechanisms of such influence need to be further studied and clarified in depth to consider epinecrotic biofilm as a reliable predictor in the forensic investigations.
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Affiliation(s)
- Finkelbergs Dmitrijs
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Juanjuan Guo
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
- Department of Vascular Surgery, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yecao Huang
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Yafei Liu
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Xinyue Fang
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Kankan Jiang
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Lagabaiyila Zha
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
| | - Jifeng Cai
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
- Jifeng Cai
| | - Xiaoliang Fu
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, China
- Department of Forensic Medicine, School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoliang Fu
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15
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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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16
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Shi Y, Zou Y, Xiong Y, Zhang S, Song M, An X, Liu C, Zhang W, Chen S. Host Gasdermin D restrains systemic endotoxemia by capturing Proteobacteria in the colon of high-fat diet-feeding mice. Gut Microbes 2021; 13:1946369. [PMID: 34275417 PMCID: PMC8288038 DOI: 10.1080/19490976.2021.1946369] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Gasdermin D (GSDMD) functions as a key pyroptotic executor through its secreted N-terminal domain (GSDMD-N). However, the functional relevance and mechanistic basis of the precise roles of host colonic GSDMD in high-fat diet (HFD)-induced gut dysbiosis and systemic endotoxemia remain elusive. In this study, we demonstrate that HFD feeding triggers GSDMD-N secretion of both T-lymphocytes and enterocytes in mouse colons. GSDMD deficiency aggravates HFD-induced systemic endotoxemia, gut barrier impairment, and colonic inflammation. More importantly, active GSDMD-N kills the Proteobacteria phylum via directly interacting with Cardiolipin. Mechanistically, we identify that the Glu236 (a known residue for GSDMD protein cleavage) is a bona fide important site for the bacterial recognition of GSDMD. Collectively, our findings explain the mechanism by which colonic GSDMD-N maintains low levels of HFD-induced metabolic endotoxemia. A GSDMD-N mimetic containing an exposed Glu236 site could be an attractive strategy for the treatment of HFD-induced metabolic endotoxemia.
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Affiliation(s)
- Yujie Shi
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yixin Zou
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yonghong Xiong
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Shiyao Zhang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China,Wenxiang Zhang State Key Laboratory of Natural Medicines, China Pharmaceutical University, #639 Longmian Avenue, Nanjing211198, China
| | - Mingming Song
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Xiaofei An
- Department of Endocrinology, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Chang Liu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Wenxiang Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,School of Life Science and Technology, China Pharmaceutical University, Nanjing, China,Wenxiang Zhang State Key Laboratory of Natural Medicines, China Pharmaceutical University, #639 Longmian Avenue, Nanjing211198, China
| | - Siyu Chen
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, China,School of Life Science and Technology, China Pharmaceutical University, Nanjing, China,CONTACT Siyu Chen
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17
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Gouello A, Dunyach-Remy C, Siatka C, Lavigne JP. Analysis of Microbial Communities: An Emerging Tool in Forensic Sciences. Diagnostics (Basel) 2021; 12:diagnostics12010001. [PMID: 35054168 PMCID: PMC8774847 DOI: 10.3390/diagnostics12010001] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 01/16/2023] Open
Abstract
The objective of forensic sciences is to find clues in a crime scene in order to reconstruct the scenario. Classical samples include DNA or fingerprints, but both have inherent limitations and can be uninformative. Another type of sample has emerged recently in the form of the microbiome. Supported by the Human Microbiome Project, the characteristics of the microbial communities provide real potential in forensics. They are highly specific and can be used to differentiate and classify the originating body site of a human biological trace. Skin microbiota is also highly specific and different between individuals, leading to its possibility as an identification tool. By extension, the possibilities of the microbial communities to be deposited on everyday objects has also been explored. Other uses include the determination of the post-mortem interval or the analysis of soil communities. One challenge is that the microbiome changes over time and can be influenced by many environmental and lifestyle factors. This review offers an overview of the main methods and applications to demonstrate the benefit of the microbiome to provide forensically relevant information.
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Affiliation(s)
- Audrey Gouello
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95037 Cergy-Pontoise, France;
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | - Catherine Dunyach-Remy
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
| | | | - Jean-Philippe Lavigne
- Bacterial Infection and Chronic Infection, INSERM U1047, Department of Microbiology and Hospital Infection, University Hospital Nîmes, Université de Montpellier, 30908 Nimes, France;
- Correspondence: ; Tel.: +33-466683202
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18
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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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19
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Miguel MA, Kim SH, Lee SS, Cho YI. Impact of Soil Microbes and Oxygen Availability on Bacterial Community Structure of Decomposing Poultry Carcasses. Animals (Basel) 2021; 11:2937. [PMID: 34679958 PMCID: PMC8532636 DOI: 10.3390/ani11102937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 10/07/2021] [Indexed: 11/16/2022] Open
Abstract
The impact of soil with an intact microbial community and oxygen availability on moisture content, soil pH, and bacterial communities during decomposition of poultry carcasses was investigated. Poultry carcasses were decomposed in soil with or without a microbial community, under aerobic or anaerobic conditions. The samples collected in each microcosm burial set-up were analyzed by targeted 16S rRNA amplicon sequencing and Amplicon sequence variants (ASV) method. Our results showed that moisture was high in the burial set-ups under anaerobic conditions and pH was high in the burial set-ups under aerobic conditions. Meanwhile, the Chao1 and Shannon index significantly differed between the different burial set-ups and across different time points. In addition, bacterial taxa composition during the early period of decomposition differed from that of the late period. A total of 23 phyla, 901 genera, and 1992 species were identified. Firmicutes was the most dominant phyla in all burial set-ups throughout the decomposition. At day 60, Pseudogracilibacillus was dominant in the burial set-ups under aerobic conditions, while Lentibacillus dominated in the burial set-ups under anaerobic conditions. This study demonstrated that the soil microbial community and availability of oxygen significantly affected the changes in moisture content, pH, and bacterial composition during the decomposition process.
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Affiliation(s)
| | | | | | - Yong-Il Cho
- Department of Animal Science and Technology, Sunchon National University, Suncheon 57922, Korea; (M.A.M.); (S.-H.K.); (S.-S.L.)
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20
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Iancu L, Angelescu IR, Paun VI, Henríquez-Castillo C, Lavin P, Purcarea C. Microbiome pattern of Lucilia sericata (Meigen) (Diptera: Calliphoridae) and feeding substrate in the presence of the foodborne pathogen Salmonella enterica. Sci Rep 2021; 11:15296. [PMID: 34315964 PMCID: PMC8316364 DOI: 10.1038/s41598-021-94761-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/16/2021] [Indexed: 12/04/2022] Open
Abstract
The microbial diversity and quantitative dynamics during the insect’s development stages constitute recently developed putative tools in forensic and medical studies. Meanwhile, little is known on the role of insects in spreading foodborne pathogenic bacteria and on the impact of these pathogens on the overall insects and feeding substrate microbiome composition. Here, we provide the first characterization of the bacterial communities harbored in adult and immature stages of Lucilia sericata, one of the first colonizers of decomposed human remains, in the presence of the foodborne pathogen Salmonella enterica using 16S rRNA Illumina sequencing and qPCR. The pathogen transmission from the wild adults to the second generation was observed, with a 101.25× quantitative increase. The microbial patterns from both insect and liver samples were not influenced by the artificial introduction of this pathogenic foodborne bacteria, being dominated by Firmicutes and Proteobacteria. Overall, our results provided a first detailed overview of the insect and decomposed substrate microbiome in the presence of a human pathogen, advancing the knowledge on the role of microbes as postmortem interval estimators and the transmission of pathogenic bacteria.
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Affiliation(s)
- Lavinia Iancu
- Department of Microbiology, Institute of Biology Bucharest of Romanian Academy, Splaiul Independentei, 296, 060031, Bucharest, Romania. .,Department of Criminal Justice, University of North Dakota, Grand Forks, ND, 58202, USA.
| | - Iulia Roxana Angelescu
- Department of Microbiology, Institute of Biology Bucharest of Romanian Academy, Splaiul Independentei, 296, 060031, Bucharest, Romania
| | - Victoria Ioana Paun
- Department of Microbiology, Institute of Biology Bucharest of Romanian Academy, Splaiul Independentei, 296, 060031, Bucharest, Romania
| | - Carlos Henríquez-Castillo
- Laboratorio de Fisiología y Genética Marina, Centro de Estudios Avanzados en Zonas Áridas, 1781421, Coquimbo, Chile.,Facultad de Ciencias del Mar, Universidad Católica del Norte, 1781421, Coquimbo, Chile
| | - Paris Lavin
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile.,Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Antofagasta, Chile
| | - Cristina Purcarea
- Department of Microbiology, Institute of Biology Bucharest of Romanian Academy, Splaiul Independentei, 296, 060031, Bucharest, Romania
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21
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Junkins EN, Stevenson BS. Using Plate-Wash PCR and High-Throughput Sequencing to Measure Cultivated Diversity for Natural Product Discovery Efforts. Front Microbiol 2021; 12:675798. [PMID: 34354680 PMCID: PMC8329497 DOI: 10.3389/fmicb.2021.675798] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/28/2021] [Indexed: 12/16/2022] Open
Abstract
Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Sequence-based data indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete and more complex, understanding of which organisms were present compared to what was eventually detected during cultivation. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against an already multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.
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Affiliation(s)
- Emily N Junkins
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Bradley S Stevenson
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
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22
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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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Yang R, Lin S, Dong Y, Ye H, Zhang T. Effect of microorganisms on the fingerprint of the volatile compounds in pine nut (Pinus koraiensis) peptide powder during storage. J Food Biochem 2021; 45:e13653. [PMID: 33792061 DOI: 10.1111/jfbc.13653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/25/2021] [Accepted: 01/31/2021] [Indexed: 11/28/2022]
Abstract
Pine nut (Pinus koraiensis) peptide (PNP) powder possesses promising bioactivities. However, the powder may have the quality problem of becoming sticky and smelly. Therefore, the volatile compounds' fingerprint of PNP powder was established by headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). The essential spoilage microorganisms were confirmed by 16S rDNA amplicon sequencing. The antioxidant activity, which presents PNP powder's quality, decreased during storage with the highest value of (1.88 ± 0.18) × 1014 at day 30. Fifty-nine significantly changed signals were detected; eight compounds were considered as volatile marker compounds. Besides, Firmicutes and Cyanobacteria were the essential spoilage microorganisms in PNP powder at the phylum level. Significantly, unidentified_Chloroplast, which belongs to Cyanobacteria, had a positive correlation with volatile marker compounds. The results proved that microorganisms indeed affect volatile compounds of PNP powder and induced off-flavor, including hexanal, which can be used as the detection indicator for the quality control of PNP powder. PRACTICAL APPLICATIONS: In the present study, we controlled the influence of moisture migration on PNP powder and investigated microorganisms' effects on volatile compounds of PNP powder. HS-GC-IMS could be used to establish fingerprints of volatile compounds in PNP powder. 16S rDNA amplicon sequencing method could be used to screen the dominant spoilage bacteria in PNP powder and established essential spoilage microorganisms of PNP powder. This work provides a reference for category identification of PNP powder, which was infected by spoilage bacteria or not, and stored at day 0 or 30 days. Hexanal can be considered as the volatile marker compound generated from microorganisms. It helps to realize the controllability of PNP powder storage and prolongs the shelf life of PNP powder.
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Affiliation(s)
- Ruiwen Yang
- College of Food Science and Engineering, Jilin University, Changchun, P.R. China
| | - Songyi Lin
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, P.R. China
| | - Yifei Dong
- National Engineering Research Center of Seafood, School of Food Science and Technology, Dalian Polytechnic University, Dalian, P.R. China
| | - Haiqing Ye
- College of Food Science and Engineering, Jilin University, Changchun, P.R. China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, P.R. China
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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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Zhou R, Wang Y, Hilal MG, Yu Q, Feng T, Li H. Temporal succession of water microbiomes and resistomes during carcass decomposition in a fish model. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123795. [PMID: 33264900 DOI: 10.1016/j.jhazmat.2020.123795] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/13/2020] [Accepted: 08/25/2020] [Indexed: 06/12/2023]
Abstract
Carcass decomposition in water may cause serious environmental pollution, which poses a great threat to water quality and public health. However, water microbial community succession and antibiotic resistance genes (ARGs) during carcass decomposition process are less explored. Using high-throughput sequencing and high-throughput quantitative PCR techniques, the temporal succession of water bacterial communities and ARGs profiles in experimental groups (fish carcasses) and control groups (no carcasses) containing two different types of water (the Yellow River water and tap water) in different successional stages were studied. Our results showed that NH3-N concentration in the corpse groups has greatly risen and exceeded more than 28 times on average over the safety thresholds of water quality. Some potential pathogenic genera Comamonas, Bacteroides and Pseudomonas significantly increased during carcass decomposition process. The bacterial communities of the Yellow River water and tap water in the experimental groups exhibited similar succession patterns, and community dissimilarities between the two groups decreased and smaller over time, indicating that bacterial community convergence. NH3-N, NO3-N and time were three most important factors in determining bacteria community structures. The influence of water type on corpse bacterial community structures was significant but weak. The gene copy number of seven detected ARGs (cmlA1-01, floR, sul1, sul2, tetG-01, tetM-01 and tetQ) in the experimental groups was more abundant than that in the control groups. The ARGs concentrations in the corpse groups were even enriched 19-fold (minimum) to 148-fold (maximum) compared to the gene tetQ of the Yellow River water in the control groups on the initial stage. Redundancy analysis (RDA) indicated that Bacteroidetes and Firmicutes were significantly correlated with all detected ARGs. This study emphasizes that cadaver degradation leads to the deterioration of nitrogen pollution, the abundance increase of potential pathogens, and the transfer of ARGs from dead animals to water environment, thereby uncovering the harmful effects of related water pollution for human health.
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Affiliation(s)
- Rui Zhou
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Yijie Wang
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Mian Gul Hilal
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Tianshu Feng
- School of Public Health, Lanzhou University, Lanzhou, 730000, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, 730000, China; Center for Grassland Microbiome, Lanzhou University, Lanzhou, 730000, China.
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Muletz‐Wolz CR, Wilson Rankin E, McGrath‐Blaser S, Venkatraman M, Maldonado JE, Gruner DS, Fleischer RC. Identification of novel bacterial biomarkers to detect bird scavenging by invasive rats. Ecol Evol 2021; 11:1814-1828. [PMID: 33614005 PMCID: PMC7882976 DOI: 10.1002/ece3.7171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Rapid advances in genomic tools for use in ecological contexts and non-model systems allow unprecedented insight into interactions that occur beyond direct observation. We developed an approach that couples microbial forensics with molecular dietary analysis to identify species interactions and scavenging by invasive rats on native and introduced birds in Hawaii. First, we characterized bacterial signatures of bird carcass decay by conducting 16S rRNA high-throughput sequencing on chicken (Gallus gallus domesticus) tissues collected over an 11-day decomposition study in natural Hawaiian habitats. Second, we determined if field-collected invasive black rats (Rattus rattus; n = 51, stomach and fecal samples) had consumed birds using molecular diet analysis with two independent PCR assays (mitochondrial Cytochrome Oxidase I and Cytochrome b genes) and Sanger sequencing. Third, we characterized the gut microbiome of the same rats using 16S rRNA high-throughput sequencing and identified 15 bacterial taxa that were (a) detected only in rats that consumed birds (n = 20/51) and (b) were indicative of decaying tissue in the chicken decomposition experiment. We found that 18% of rats (n = 9/51) likely consumed birds as carrion by the presence of bacterial biomarkers of decayed tissue in their gut microbiome. One species of native bird (Myadestes obscurus) and three introduced bird species (Lophura leucomelanos, Meleagris gallopavo, Zosterops japonicus) were detected in the rats' diets, with individuals from these species (except L. nycthemera) likely consumed through scavenging. Bacterial biomarkers of bird carcass decay can persist through rat digestion and may serve as biomarkers of scavenging. Our approach can be used to reveal trophic interactions that are challenging to measure through direct observation.
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Affiliation(s)
- Carly R. Muletz‐Wolz
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | - Erin Wilson Rankin
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of EntomologyUniversity of MarylandCollege ParkMDUSA
- Department of EntomologyUniversity of CaliforniaRiversideCAUSA
| | - Sarah McGrath‐Blaser
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
| | - Madhvi Venkatraman
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
- Department of EntomologyUniversity of MarylandCollege ParkMDUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
| | | | - Robert C. Fleischer
- Center for Conservation GenomicsSmithsonian Conservation Biology InstituteNational Zoological ParkWashingtonDCUSA
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Li H, Zhang S, Liu R, Yuan L, Wu D, Yang E, Yang H, Ullah S, Ishaq HM, Liu H, Wang Z, Xu J. Potential use of molecular and structural characterization of the gut bacterial community for postmortem interval estimation in Sprague Dawley rats. Sci Rep 2021; 11:225. [PMID: 33420339 PMCID: PMC7794466 DOI: 10.1038/s41598-020-80633-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 12/23/2020] [Indexed: 01/15/2023] Open
Abstract
Once the body dies, the indigenous microbes of the host begin to break down the body from the inside and play a key role thereafter. This study aimed to investigate the probable shift in the composition of the rectal microbiota at different time intervals up to 15 days after death and to explore bacterial taxa important for estimating the time since death. At the phylum level, Proteobacteria and Firmicutes showed major shifts when checked at 11 different intervals and emerged at most of the postmortem intervals. At the species level, Enterococcus faecalis and Proteus mirabilis showed a downward and upward trend, respectively, after day 5 postmortem. The phylum-, family-, genus-, and species-taxon richness decreased initially and then increased considerably. The turning point occurred on day 9, when the genus, rather than the phylum, family, or species, provided the most information for estimating the time since death. We constructed a prediction model using genus-level data from high-throughput sequencing, and seven bacterial taxa, namely, Enterococcus, Proteus, Lactobacillus, unidentified Clostridiales, Vagococcus, unidentified Corynebacteriaceae, and unidentified Enterobacteriaceae, were included in this model. The abovementioned bacteria showed potential for estimating the shortest time since death.
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Affiliation(s)
- Huan Li
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Siruo Zhang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Ruina Liu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Lu Yuan
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Di Wu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - E Yang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Han Yang
- Xi'an Chest Hospital, Xi'an, China
| | - Shakir Ullah
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Hafiz Muhammad Ishaq
- Faculty of Veterinary and Animal Sciences, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Hailong Liu
- The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Jiru Xu
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, China.
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Harrison L, Kooienga E, Speights C, Tomberlin J, Lashley M, Barton B, Jordan H. Microbial succession from a subsequent secondary death event following mass mortality. BMC Microbiol 2020; 20:309. [PMID: 33050884 PMCID: PMC7557037 DOI: 10.1186/s12866-020-01969-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 09/08/2020] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND Each death event can be characterized by its associated microbes - a living community of bacteria composed of carcass, soil, and insect-introduced bacterial species - a necrobiome. With the possibility for close succession of these death events, it may be beneficial to characterize how the magnitude of an initial death event may impact the decomposition and necrobiomes of subsequent death events in close proximity. In this paper we hope to characterize the microbial communities associated with a proximate subsequent death event, and distinguish any changes within those communities based on the magnitude of an initial death event and the biomass of preexisting carcass (es) undergoing decomposition. For this experiment, 6 feral swine carcasses in containers were placed in the vicinity of preexisting and ongoing carcass decomposition at sites of three different scales of decomposing carcass biomass. Swab samples were collected from the skin and eye sockets of the container pigs and subjected to 16 s rRNA sequencing and OTU assignment. RESULTS PERMANOVA analysis of the bacterial taxa showed that there was no significant difference in the bacterial communities based on initial mortality event biomass size, but we did see a change in the bacterial communities over time, and slight differences between the skin and ocular cavity communities. Even without soil input, necrobiome communities can change rapidly. Further characterization of the bacterial necrobiome included utilization of the Random Forest algorithm to identify the most important predictors for time of decomposition. Sample sets were also scanned for notable human and swine-associated pathogens. CONCLUSIONS The applications from this study are many, ranging from establishing the environmental impacts of mass mortality events to understanding the importance of scavenger, and scavenger microbial community input on decomposition.
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Affiliation(s)
- Lindsay Harrison
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Emilia Kooienga
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Cori Speights
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Jeffery Tomberlin
- Department of Entomology, Texas A&M University, Minnie Bell Heep Center, Suite 412, College Station, TX, 77843, USA
| | - Marcus Lashley
- Department of Wildlife, Fisheries and Aquaculture, Mississippi State University, Box 9680, Mississippi State, MS, 39762, USA
| | - Brandon Barton
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA
| | - Heather Jordan
- Department of Biological Sciences, Mississippi State University, PO Box GY, Mississippi State, MS, 39762, USA.
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Dash HR, Das S. Thanatomicrobiome and epinecrotic community signatures for estimation of post-mortem time interval in human cadaver. Appl Microbiol Biotechnol 2020; 104:9497-9512. [PMID: 33001249 DOI: 10.1007/s00253-020-10922-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 09/15/2020] [Accepted: 09/21/2020] [Indexed: 12/12/2022]
Abstract
Estimation of post-mortem time interval (PMI) is a key parameter in the forensic investigation which poses a huge challenge to the medico-legal experts. The succession of microbes within different parts of the human body after death has shown huge potential in the determination of PMI. Human body harbors trillions of microorganisms as commensals. With the death of an individual when biological functions are stopped, these microorganisms behave contrarily along with the invasion of degrading microbes from the environment. Human cadaver becomes a rich source of nutrients due to autolysis of cells, which attracts various invading microorganisms as well as macroorganisms. At different stages of degradation, the succession of microorganisms differs significantly which can be explored for accurate PMI estimation. With the advent of microbial genomics technique and reduction in the cost of DNA sequencing, thanatomicrobiome and epinecrotic community analysis have gained huge attention in PMI estimation. The article summarizes different sources of microorganisms in a human cadaver, their succession pattern, and analytical techniques for application in the field of microbial forensics. KEY POINTS: • Thanatomicrobiome and epinecrotic microbiome develop in postmortem human body. • Lack of metabolic, immune, neuroendocrine systems facilitate microbial succession. • Analysis of postmortem microbial communities predicts accurate PMI.
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Affiliation(s)
- Hirak Ranjan Dash
- Forensic Science Laboratory, Bhadbhada Road, Bhopal, Madhya Pradesh, 462003, India.
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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Cheng Y, Li Y, Xiong Y, Zou Y, Chen S, Zhang W, Liu C, Shi Y. Liver-specific knockdown of ANGPTL8 alters the structure of the gut microbiota in mice. ANN MICROBIOL 2020. [DOI: 10.1186/s13213-020-01599-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Purpose
To investigate the effect of liver-specific knockdown of ANGPTL8 on the structure of the gut microbiota.
Methods
We constructed mice with liver-specific ANGPTL8 knockdown by using an adeno-associated virus serotype 8 (AAV8) system harbouring an ANGPTL8 shRNA. We analysed the structure and function of the gut microbiome through pyrosequencing and KEGG (Kyoto Encyclopedia of Genes and Genomes) functional prediction.
Results
Compared with controls, ANGPTL8 shRNA reduced the Simpson index and Shannon index (p < 0.01) of the gut microbiota in mice. At the phylum level, the sh-ANGPTL8 group showed a healthier gut microbiota composition than controls (Bacteroidetes: controls 67.52%, sh-ANGPTL8 80.75%; Firmicutes: controls 10.96%, sh-ANGPTL8 8.58%; Proteobacteria: controls 9.29%, sh-ANGPTL8 0.98%; F/B ratio: controls 0.16, sh-ANGPTL8 0.11). PCoA and UPGMA analysis revealed a significant difference in microbiota composition, while KEGG analysis revealed a significant difference in microbiota function between controls and the sh-ANGPTL8 group.
Conclusion
Our results revealed that inhibition of ANGPTL8 signalling altered the structure of the gut microbiome, which might further affect the metabolism of mice. We have thus identified ANGPTL8 as a novel hepatogenic hormone potentially involving the liver-gut axis and regulating the structure of the gut microbiota.
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Qu D, Qiao DF, Klintschar M, Qu Z, Yue X. High-throughput 16S rDNA sequencing assisting in the detection of bacterial pathogen candidates: a fatal case of necrotizing fasciitis in a child. Int J Legal Med 2020; 135:399-407. [PMID: 32895762 DOI: 10.1007/s00414-020-02421-x] [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: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/19/2022]
Abstract
Postmortem detection of pathogens in infectious deaths is quite important for diagnosing the cause of death and public health. However, it is difficult to detect possible bacterial pathogens in forensic practice using conventional methods like bacterial culture, especially in cases with putrefaction and antibiotic treatment. We report a fatal case caused by necrotizing fasciitis due to bacterial infection. An 8-year-old girl was found dead during sleep 4 days after a minor trauma to her left knee. The gross autopsy suggested that bacterial soft tissue infection might be the cause of death, and the microscopic examination confirmed the diagnosis. The slight putrefaction found at gross autopsy might interfere through postmortem bacterial translocation and reproduction with bacterial culture. High-throughput 16S rDNA sequencing was employed to identify possible pathogens. Bacterial DNA sequencing results suggested Streptococcus pyogenes and Staphylococcus, typical pathogens of necrotizing fasciitis in the tissue. 16S rDNA sequencing might thus be a useful tool for accurate detection of pathogens in forensic practice.
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Affiliation(s)
- Dong Qu
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.,Institute of Legal Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Dong-Fang Qiao
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Michael Klintschar
- Institute of Legal Medicine, Hannover Medical School, 30625, Hannover, Germany
| | - Zhi Qu
- Institute for Epidemiology, Social Medicine and Health Systems Research, Hannover Medical School, 30625, Hannover, Germany
| | - Xia Yue
- Department of Forensic Pathology, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
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Procopio N, Ghignone S, Voyron S, Chiapello M, Williams A, Chamberlain A, Mello A, Buckley M. Soil Fungal Communities Investigated by Metabarcoding Within Simulated Forensic Burial Contexts. Front Microbiol 2020; 11:1686. [PMID: 32793158 PMCID: PMC7393272 DOI: 10.3389/fmicb.2020.01686] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/29/2020] [Indexed: 01/01/2023] Open
Abstract
Decomposition of animal bodies in the burial environment plays a key role in the biochemistry of the soil, altering the balance of the local microbial populations present before the introduction of the carcass. Despite the growing number of studies on decomposition and soil bacterial populations, less is known on its effects on fungal communities. Shifts in the fungal populations at different post-mortem intervals (PMIs) could provide insights for PMI estimation and clarify the role that specific fungal taxa have at specific decomposition stages. In this study, we buried pig carcasses over a period of 1- to 6-months, and we sampled the soil in contact with each carcass at different PMIs. We performed metabarcoding analysis of the mycobiome targeting both the internal transcribed spacer (ITS) 1 and 2, to elucidate which one was more suitable for this purpose. Our results showed a decrease in the fungal taxonomic richness associated with increasing PMIs, and the alteration of the soil fungal signature even after 6 months post-burial, showing the inability of soil communities to restore their original composition within this timeframe. The results highlighted taxonomic trends associated with specific PMIs, such as the increase of the Mortierellomycota after 4- and 6-months and of Ascomycota particularly after 2 months, and the decrease of Basidiomycota from the first to the last time point. We have found a limited number of taxa specifically associated with the carrion and not present in the control soil, showing that the major contributors to the recorded changes are originated from the soil and were not introduced by the carrion. As this is the first study conducted on burial graves, it sets the baseline for additional studies to investigate the role of fungal communities on prolonged decomposition periods and to identify fungal biomarkers to improve the accuracy of PMI prediction for forensic applications.
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Affiliation(s)
- Noemi Procopio
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Stefano Ghignone
- Istituto per la Protezione Sostenibile delle Piante, CNR, Turin, Italy
| | - Samuele Voyron
- Istituto per la Protezione Sostenibile delle Piante, CNR, Turin, Italy
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Università degli Studi di Torino, Turin, Italy
| | - Marco Chiapello
- Istituto per la Protezione Sostenibile delle Piante, CNR, Turin, Italy
| | - Anna Williams
- School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Andrew Chamberlain
- School of Natural Sciences, The University of Manchester, Manchester, United Kingdom
| | - Antonietta Mello
- Istituto per la Protezione Sostenibile delle Piante, CNR, Turin, Italy
| | - Michael Buckley
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
- School of Natural Sciences, The University of Manchester, Manchester, United Kingdom
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Dangerfield CR, Frehner EH, Buechley ER, Şekercioğlu ÇH, Brazelton WJ. Succession of bacterial communities on carrion is independent of vertebrate scavengers. PeerJ 2020; 8:e9307. [PMID: 32566404 PMCID: PMC7293191 DOI: 10.7717/peerj.9307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 05/17/2020] [Indexed: 11/20/2022] Open
Abstract
The decomposition of carrion is carried out by a suite of macro- and micro-organisms who interact with each other in a variety of ecological contexts. The ultimate result of carrion decomposition is the recycling of carbon and nutrients from the carrion back into the ecosystem. Exploring these ecological interactions among animals and microbes is a critical aspect of understanding the nutrient cycling of an ecosystem. Here we investigate the potential impacts that vertebrate scavenging may have on the microbial community of carrion. In this study, we placed seven juvenile domestic cow carcasses in the Grassy Mountain region of Utah, USA and collected tissue samples at periodic intervals. Using high-depth environmental sequencing of the 16S rRNA gene and camera trap data, we documented the microbial community shifts associated with decomposition and with vertebrate scavenger visitation. The remarkable scarcity of animals at our study site enabled us to examine natural carrion decomposition in the near absence of animal scavengers. Our results indicate that the microbial communities of carcasses that experienced large amounts of scavenging activity were not significantly different than those carcasses that observed very little scavenging activity. Rather, the microbial community shifts reflected changes in the stage of decomposition similar to other studies documenting the successional changes of carrion microbial communities. Our study suggests that microbial community succession on carrion follows consistent patterns that are largely unaffected by vertebrate scavenging.
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Affiliation(s)
- Cody R Dangerfield
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Ethan H Frehner
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA
| | - Evan R Buechley
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.,HawkWatch International, Salt Lake City, UT, USA
| | - Çağan H Şekercioğlu
- School of Biological Sciences, University of Utah, Salt Lake City, UT, USA.,Department of Molecular Biology and Genetics, Ko University, Istanbul, Turkey
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Tozzo P, Scrivano S, Sanavio M, Caenazzo L. The Role of DNA Degradation in the Estimation of Post-Mortem Interval: A Systematic Review of the Current Literature. Int J Mol Sci 2020; 21:ijms21103540. [PMID: 32429539 PMCID: PMC7278928 DOI: 10.3390/ijms21103540] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/11/2020] [Accepted: 05/15/2020] [Indexed: 02/03/2023] Open
Abstract
The determination of the post-mortal interval (PMI) is an extremely discussed topic in the literature and of deep forensic interest, for which various types of methods have been proposed. The aim of the manuscript is to provide a review of the studies on the post-mortem DNA degradation used for estimating PMI. This review has been performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and the PRISMA Guidelines. Several analytical techniques have been proposed to analyse the post-mortem DNA degradation in order to use it to estimate the PMI. Studies focused mainly on animal models and on particular tissues. The results have been mixed: while on the one hand literature data in this field have confirmed that in the post-mortem several degradation processes involve nucleic acids, on the other hand some fundamental aspects are still little explored: the influence of ante and post-mortem factors on DNA degradation, the feasibility and applicability of a multiparametric mathematical model that takes into account DNA degradation and the definition of one or more target organs in order to standardize the results on human cases under standard conditions.
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Affiliation(s)
- Pamela Tozzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35122 Padova, Italy;
- Correspondence: ; Tel.: +39-0498272234
| | - Salvatore Scrivano
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (S.S.); (M.S.)
| | - Matteo Sanavio
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35122 Padova, Italy; (S.S.); (M.S.)
| | - Luciana Caenazzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35122 Padova, Italy;
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Li H, Yang E, Zhang S, Zhang J, Yuan L, Liu R, Ullah S, Wang Q, Mushtaq N, Shi Y, An C, Wang Z, Xu J. Molecular characterization of gut microbial shift in SD rats after death for 30 days. Arch Microbiol 2020; 202:1763-1773. [PMID: 32350549 DOI: 10.1007/s00203-020-01889-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/26/2020] [Accepted: 04/15/2020] [Indexed: 01/06/2023]
Abstract
To observe the temporal shifts of the intestinal microbial community structure and diversity in rats for 30 days after death. Rectal swabs were collected from rats before death (BD) and on day 1, 5, 10, 15, 20, 25, and 30 after death (AD). Bacteria genomic DNA was extracted and V3 + V4 regions of 16S rRNA gene were amplified by PCR. The amplicons were sequenced at Illumina MiSeq sequencing platform. The bacterial diversity and richness showed similar results from day 1 to 5 and day 10 to 25 all presenting downtrend, while from day 5 to 10 showed slightly increased. The relative abundance of Firmicutes and Proteobacteria displayed inverse variation in day 1, 5, 10 and that was the former decreased, the latter increased. Bacteroidetes, Spirochaete and TM7 in day 15, 20, 25, 30 was significantly decline comparing with BD. Enterococcus and Proteus displayed reduced trend over day 1, 5, 10 and day 10, 15, 20, 25, respectively, while Sporosarcina showed obvious elevation during day 15, 20, 25. Accordingly, there was a certain correlation between intestinal flora succession and the time of death. The results suggested that intestinal flora may be potential indicator to aid estimation of post-mortem interval (PMI).
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Affiliation(s)
- Huan Li
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - E Yang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Siruo Zhang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Jing Zhang
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Lu Yuan
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Ruina Liu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Shakir Ullah
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Qi Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China.,Teaching and Research Section of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Nosheen Mushtaq
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Yi Shi
- Shaanxi Provincial Centre for Disease Control and Prevention, Xi'an, People's Republic of China
| | - Cuihong An
- Shaanxi Provincial Centre for Disease Control and Prevention, Xi'an, People's Republic of China
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China.
| | - Jiru Xu
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China.
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Time Series Resolution of the Fish Necrobiome Reveals a Decomposer Succession Involving Toxigenic Bacterial Pathogens. mSystems 2020; 5:5/2/e00145-20. [PMID: 32345738 PMCID: PMC7190384 DOI: 10.1128/msystems.00145-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The microbial decomposition of animal tissues is an important ecological process that impacts nutrient cycling in natural environments. We studied the microbial decomposition of a common North American fish (rainbow darters) over four time points, combining 16S rRNA gene and shotgun metagenomic sequence data to obtain both taxonomic and functional perspectives. Our data revealed a strong community succession that was reproduced across different fish and environments. Decomposition time point was the main driver of community composition and functional potential; fish environmental origin (upstream or downstream of a wastewater treatment plant) had a secondary effect. We also identified strains related to the putative pathogen Aeromonas veronii as dominant members of the decomposition community. These bacteria peaked early in decomposition and coincided with the metagenomic abundance of hemolytic toxin genes. Our work reveals a strong decomposer succession in wild-caught fish, providing functional and taxonomic insights into the vertebrate necrobiome. Despite progress understanding microbial communities involved in terrestrial vertebrate decomposition, little is known about the microbial decomposition of aquatic vertebrates from a functional and environmental context. Here, we analyzed temporal changes in the “necrobiome” of rainbow darters, which are common North American fish that are sensitive indicators of water quality. By combining 16S rRNA gene and shotgun metagenomic sequence data from four time points, we studied the progression of decomposers from both taxonomic and functional perspectives. The 16S rRNA gene profiles revealed strong community succession, with early decomposition stages associated with Aeromonas and Clostridium taxa and later stages dominated by members of the Rikenellaceae (i.e., Alistipes/Acetobacteroides genera). These results were reproducible and independent of environmental perturbation, given that exposure to wastewater treatment plant effluent did not substantially influence the necrobiome composition of fish or the associated water sample microbiota. Metagenomic analysis revealed significant changes throughout decomposition in degradation pathways for amino acids, carbohydrates/glycans, and other compounds, in addition to putrefaction pathways for production of putrescine, cadaverine, and indole. Binning of contigs confirmed a predominance of Aeromonas genome assemblies, including those from novel strains related to the pathogen Aeromonas veronii. These bins of Aeromonas genes also encoded known hemolysin toxins (e.g., aerolysin) that were particularly abundant early in the process, potentially contributing to host cell lysis during decomposition. Overall, our results demonstrate that wild-caught fish have a reproducible decomposer succession and that the fish necrobiome serves as a potential source of putative pathogens and toxigenic bacteria. IMPORTANCE The microbial decomposition of animal tissues is an important ecological process that impacts nutrient cycling in natural environments. We studied the microbial decomposition of a common North American fish (rainbow darters) over four time points, combining 16S rRNA gene and shotgun metagenomic sequence data to obtain both taxonomic and functional perspectives. Our data revealed a strong community succession that was reproduced across different fish and environments. Decomposition time point was the main driver of community composition and functional potential; fish environmental origin (upstream or downstream of a wastewater treatment plant) had a secondary effect. We also identified strains related to the putative pathogen Aeromonas veronii as dominant members of the decomposition community. These bacteria peaked early in decomposition and coincided with the metagenomic abundance of hemolytic toxin genes. Our work reveals a strong decomposer succession in wild-caught fish, providing functional and taxonomic insights into the vertebrate necrobiome.
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Liu R, Gu Y, Shen M, Li H, Zhang K, Wang Q, Wei X, Zhang H, Wu D, Yu K, Cai W, Wang G, Zhang S, Sun Q, Huang P, Wang Z. Predicting postmortem interval based on microbial community sequences and machine learning algorithms. Environ Microbiol 2020; 22:2273-2291. [PMID: 32227435 DOI: 10.1111/1462-2920.15000] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/18/2020] [Accepted: 03/22/2020] [Indexed: 11/29/2022]
Abstract
Microbes play an essential role in the decomposition process but were poorly understood in their succession and behaviour. Previous researches have shown that microbes show predictable behaviour that starts at death and changes during the decomposition process. Research of such behaviour enhances the understanding of decomposition and benefits estimating the postmortem interval (PMI) in forensic investigations, which is critical but faces multiple challenges. In this study, we combined microbial community characterization, microbiome sequencing from different organs (i.e. brain, heart and cecum) and machine learning algorithms [random forest (RF), support vector machine (SVM) and artificial neural network (ANN)] to investigate microbial succession pattern during corpse decomposition and estimate PMI in a mouse corpse system. Microbial communities exhibited significant differences between the death point and advanced decay stages. Enterococcus faecalis, Anaerosalibacter bizertensis, Lactobacillus reuteri, and so forth were identified as the most informative species in the decomposition process. Furthermore, the ANN model combined with the postmortem microbial data set from the cecum, which was the best combination among all candidates, yielded a mean absolute error of 1.5 ± 0.8 h within 24-h decomposition and 14.5 ± 4.4 h within 15-day decomposition. This integrated model can serve as a reliable and accurate technology in PMI estimation.
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Affiliation(s)
- Ruina Liu
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yuexi Gu
- School of Mathematics and Statistics, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Mingwang Shen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, 710061, China
| | - Huan Li
- Department of Microbiology and immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Kai Zhang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Qi Wang
- Chongqing Medical University, College of Basic Medicine, Department of Forensic Medicine, Chongqing, 400016, China
| | - Xin Wei
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Haohui Zhang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Di Wu
- 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
| | - Wumin Cai
- 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
| | - Siruo Zhang
- Department of Microbiology and immunology, School of Basic Medical Sciences, Xi'an Jiaotong University, Xi'an, China
| | - Qinru Sun
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Ping Huang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, 200063, China
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, 710061, China
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Zhou J, Nelson TM, Rodriguez Lopez C, Sarma RR, Zhou SJ, Rollins LA. A comparison of nonlethal sampling methods for amphibian gut microbiome analyses. Mol Ecol Resour 2020; 20:844-855. [PMID: 31990452 DOI: 10.1111/1755-0998.13139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/03/2019] [Accepted: 01/20/2020] [Indexed: 12/27/2022]
Abstract
Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.
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Affiliation(s)
- Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia
| | - Tiffanie Maree Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Griffith University, Southport, Qld, Australia
| | - Carlos Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Roshmi Rekha Sarma
- School of Biological, Earth and Environmental Sciences, Ecology & Evolution Research Centre, Biological Sciences South (E26) UNSW, University of New South Wales, Kensington, NSW, Australia
| | - Shao Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia
| | - Lee Ann Rollins
- School of Biological, Earth and Environmental Sciences, Ecology & Evolution Research Centre, Biological Sciences South (E26) UNSW, University of New South Wales, Kensington, NSW, Australia
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39
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Succession of oral microbiota community as a tool to estimate postmortem interval. Sci Rep 2019; 9:13063. [PMID: 31506511 PMCID: PMC6737051 DOI: 10.1038/s41598-019-49338-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/22/2019] [Indexed: 12/21/2022] Open
Abstract
The establishment of postmortem interval is one of the most important aspects of forensic expertise. Microbes may provide a novel way to estimate the postmortem intervals in order to avoid many of these limitations. The oral cavity harbors one of the most diverse microbiomes that play a key role in the decomposition of corpses. In this study, the oral bacterial community showed obvious changes in relative abundance during the process of mice decomposition. Meanwhile, at different taxonomic levels, specific bacteria were found to be significantly correlated with the postmortem interval. Linear regression models between relative abundance and the postmortem interval were constructed. Among these species, Gamma-proteobacteria and Proteus were the best ones that can be used to infer the postmortem interval, especially late postmortem interval. Therefore, we suggest that succession of oral microbial community can be developed as a forensic tool for estimating the postmortem interval.
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40
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Fungal succession during mammalian cadaver decomposition and potential forensic implications. Sci Rep 2019; 9:12907. [PMID: 31501472 PMCID: PMC6733900 DOI: 10.1038/s41598-019-49361-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 08/24/2019] [Indexed: 02/02/2023] Open
Abstract
The necrobiome is the postmortem community that includes bacteria, fungi, arthropods, and other cadaver-associated organisms. It has been suggested as biological evidence for forensic investigation. Fungi form distinctive mildew spots in colonizing decomposing bodies, converting them into moldy cadavers. However, the postmortem fungal community consists of more than these visible species. Characterizing the succession pattern of the fungal community during decomposition is valuable not only for understanding the ecosystem composition of the cadaver decomposition islands but also for contributing to forensic investigations. In the present study, the fungal composition of pig cadavers and succession patterns during decomposition were investigated with high-throughput sequencing. The succession patterns were easier to discern in outdoor cadavers, compared with those that were placed indoors. The metabarcoding approach revealed trends linking particular fungal taxa with specific postmortem intervals (PMIs). Dominant species increased notably in cadavers and soil. Furthermore, the succession of the soil community was driven by the cadaver decomposition. Significant mycoflora differences were observed between environmental and cadaveric soil. The results obtained suggested that postputrefaction mycoflora have considerable potential for PMI estimation, particularly in cases that involve heavily decomposed bodies. In addition, the diversity of fungal communities revealed by the metabarcoding approach allowed us to discriminate the sites of cadaver decomposition, implying that postputrefaction mycoflora may be helpful in identifying the environment in which a cadaver has been placed, or the original location from which a cadaver has been moved. Our results provide an important step towards developing fungal evidence for use in forensic science and add to the growing body of work on postmortem microbial communities.
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41
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He J, Guo J, Fu X, Cai J. Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation. Braz J Microbiol 2019; 50:999-1010. [PMID: 31364013 DOI: 10.1007/s42770-019-00119-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.
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Affiliation(s)
- Jing He
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Juanjuan Guo
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Xiaoliang Fu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Jifeng Cai
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China.
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42
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Burcham ZM, Pechal JL, Schmidt CJ, Bose JL, Rosch JW, Benbow ME, Jordan HR. Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model. Front Microbiol 2019; 10:745. [PMID: 31057499 PMCID: PMC6482229 DOI: 10.3389/fmicb.2019.00745] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/25/2019] [Indexed: 01/26/2023] Open
Abstract
Decomposing remains are a nutrient-rich ecosystem undergoing constant change due to cell breakdown and abiotic fluxes, such as pH level and oxygen availability. These environmental fluxes affect bacterial communities who respond in a predictive manner associated with the time since organismal death, or the postmortem interval (PMI). Profiles of microbial taxonomic turnover and transmigration are currently being studied in decomposition ecology, and in the field of forensic microbiology as indicators of the PMI. We monitored bacterial community structural and functional changes taking place during decomposition of the intestines, bone marrow, lungs, and heart in a highly controlled murine model. We found that organs presumed to be sterile during life are colonized by Clostridium during later decomposition as the fluids from internal organs begin to emulsify within the body cavity. During colonization of previously sterile sites, gene transcripts for multiple metabolism pathways were highly abundant, while transcripts associated with stress response and dormancy increased as decomposition progressed. We found our model strengthens known bacterial taxonomic succession data after host death. This study is one of the first to provide data of expressed bacterial community genes, alongside transmigration and structural changes of microbial species during laboratory controlled vertebrate decomposition. This is an important dataset for studying the effects of the environment on bacterial communities in an effort to determine which bacterial species and which bacterial functional pathways, such as amino acid metabolism, provide key changes during stages of decomposition that relate to the PMI. Finding unique PMI species or functions can be useful for determining time since death in forensic investigations.
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Affiliation(s)
- Zachary M Burcham
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, East Lansing, MI, United States
| | - Carl J Schmidt
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Jeffrey L Bose
- Department of Microbiology, Molecular Genetics, and Immunology, University of Kansas Medical Center, Kansas City, KS, United States
| | - Jason W Rosch
- Department of Infectious Disease, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - M Eric Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, United States.,Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, United States
| | - Heather R Jordan
- Department of Biological Sciences, Mississippi State University, Starkville, MS, United States
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Wu Y, Shi L, Li Q, Wu J, Peng W, Li H, Chen K, Ren Y, Fu X. Microbiota Diversity in Human Colorectal Cancer Tissues Is Associated with Clinicopathological Features. Nutr Cancer 2019; 71:214-222. [PMID: 30843732 DOI: 10.1080/01635581.2019.1578394] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Yaxin Wu
- Department of Gastroenterology, Central Hospital of Dazhou City, Sichuan, China
| | - Lei Shi
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Qing Li
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Jiao Wu
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Wei Peng
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Huan Li
- Department of Gastroenterology, the Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Kequan Chen
- Department of Gastroenterology, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yixing Ren
- Department of Gastrointestinal surgery, the Affiliated Hospital of North Sichuan Medical College, Sichuan, China
| | - Xiangsheng Fu
- Department of Gastroenterology, the Affiliated Hospital of North Sichuan Medical College, Sichuan, China
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44
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Environmental microbiology: Perspectives for legal and occupational medicine. Leg Med (Tokyo) 2018; 35:34-43. [DOI: 10.1016/j.legalmed.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/09/2018] [Accepted: 09/23/2018] [Indexed: 11/18/2022]
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45
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Iancu L, Junkins EN, Necula-Petrareanu G, Purcarea C. Characterizing forensically important insect and microbial community colonization patterns in buried remains. Sci Rep 2018; 8:15513. [PMID: 30341329 PMCID: PMC6195615 DOI: 10.1038/s41598-018-33794-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 10/06/2018] [Indexed: 02/08/2023] Open
Abstract
During violent criminal actions in which the perpetrator disposes of the victim's remains by burial, the analysis of insects and bacterial colonization patterns could be necessary for postmortem interval (PMI) estimation. Our research aimed to assess the decomposition process of buried rat carcasses from shallow graves (40 cm), the diversity and dynamics of insects and bacteria throughout the decomposition stages, and the environmental parameters' influence on these variations. The results provide further insight on decomposition in soil and contribute to a broader understanding of the factors involved in decomposition by qualitatively and quantitatively analysing the decomposer community (bacteria and insects). Additionally, two bacterial taxa, Enterococcus faecalis and Clostridium paraputrificum that were investigated for the first time as PMI indicators using quantitative polymerase chain reaction (qPCR) showed differential abundance over time, promising data for PMI estimation. The current study on the decomposition of buried rat carcasses in a natural environment will strengthen the current knowledge on decomposed remains from shallow graves and represents an effort to quantify insect and bacterial taxa as PMI estimators.
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Affiliation(s)
- Lavinia Iancu
- Institute of Biology Bucharest, Romanian Academy, Splaiul Independentei, 296, 060031, Bucharest, Romania.
| | - Emily N Junkins
- University of Oklahoma, Department of Microbiology and Plant Biology, 770 Van Vleet Oval, Norman, OK, 73019-0390, United States of America
| | | | - Cristina Purcarea
- Institute of Biology Bucharest, Romanian Academy, Splaiul Independentei, 296, 060031, Bucharest, Romania
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Wu Y, Wu J, Chen T, Li Q, Peng W, Li H, Tang X, Fu X. Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis in Mice via a Toll-Like Receptor 4/p21-Activated Kinase 1 Cascade. Dig Dis Sci 2018; 63:1210-1218. [PMID: 29508166 DOI: 10.1007/s10620-018-4999-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/23/2018] [Indexed: 12/27/2022]
Abstract
BACKGROUND The underlying pathogenic mechanism of Fusobacterium nucleatum in the carcinogenesis of colorectal cancer has been poorly understood. METHODS Using C57BL/6-ApcMin/+ mice, we investigated gut microbial structures with F. nucleatum, antibiotics, and Toll-like receptor 4 (TLR4) antagonist TAK-242 treatment. In addition, we measured intestinal tumor formation and the expression of TLR4, p21-activated kinase 1 (PAK1), phosphorylated-PAK1 (p-PAK1), phosphorylated-β-catenin S675 (p-β-catenin S675), and cyclin D1 in mice with different treatments. RESULTS Fusobacterium nucleatum and antibiotics treatment altered gut microbial structures in mice. In addition, F. nucleatum invaded into the intestinal mucosa in large amounts but were less abundant in the feces of F. nucleatum-fed mice. The average number and size of intestinal tumors in F. nucleatum groups was significantly increased compared to control groups in ApcMin/+ mice (P < 0.05). The expression of TLR4, PAK1, p-PAK1, p-β-catenin S675, and cyclin D1 was significantly increased in F. nucleatum groups compared to the control groups (P < 0.05). Moreover, TAK-242 significantly decreased the average number and size of intestinal tumors compared to F. nucleatum groups (P < 0.05). The expression of p-PAK1, p-β-catenin S675, and cyclin D1 was also significantly decreased in the TAK-242-treated group compared to F. nucleatum groups (P < 0.05). CONCLUSIONS Fusobacterium nucleatum potentiates intestinal tumorigenesis in ApcMin/+ mice via a TLR4/p-PAK1/p-β-catenin S675 cascade. Fusobacterium nucleatum-induced intestinal tumorigenesis can be inhibited by TAK-242, implicating TLR4 as a potential target for the prevention and therapy of F. nucleatum-related colorectal cancer.
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Affiliation(s)
- Yaxin Wu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.,Endoscopy Center, The Affiliated Hospital of Southwest Medical University, Street Taiping 25#, Luzhou, 646000, Sichuan, China
| | - Jiao Wu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.,Endoscopy Center, The Affiliated Hospital of Southwest Medical University, Street Taiping 25#, Luzhou, 646000, Sichuan, China
| | - Ting Chen
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.,Endoscopy Center, The Affiliated Hospital of Southwest Medical University, Street Taiping 25#, Luzhou, 646000, Sichuan, China
| | - Qing Li
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.,Endoscopy Center, The Affiliated Hospital of Southwest Medical University, Street Taiping 25#, Luzhou, 646000, Sichuan, China
| | - Wei Peng
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.,Endoscopy Center, The Affiliated Hospital of Southwest Medical University, Street Taiping 25#, Luzhou, 646000, Sichuan, China
| | - Huan Li
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.,Endoscopy Center, The Affiliated Hospital of Southwest Medical University, Street Taiping 25#, Luzhou, 646000, Sichuan, China
| | - Xiaowei Tang
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Xiangsheng Fu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China. .,Endoscopy Center, The Affiliated Hospital of Southwest Medical University, Street Taiping 25#, Luzhou, 646000, Sichuan, China.
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47
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Chen Y, Peng Y, Yu J, Chen T, Wu Y, Shi L, Li Q, Wu J, Fu X. Invasive Fusobacterium nucleatum activates beta-catenin signaling in colorectal cancer via a TLR4/P-PAK1 cascade. Oncotarget 2018; 8:31802-31814. [PMID: 28423670 PMCID: PMC5458249 DOI: 10.18632/oncotarget.15992] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/20/2017] [Indexed: 12/15/2022] Open
Abstract
The underlying mechanism of Fusobacterium nucleatum (Fn) in the carcinogenesis of colorectal cancer (CRC) is poorly understood. Here, we examined Fn abundance in CRC tissues, as well as β-catenin, TLR4 and PAK1 protein abundance in Fn positive and Fn negative CRCs. Furthermore, we isolated a strain of Fn (F01) from a CRC tissue and examined whether Fn (F01) infection of colon cancer cells activated β-catenin signaling via the TLR4/P-PAK1/P-β-catenin S675 cascade. Invasive Fn was abundant in 62.2% of CRC tissues. TLR4, PAK1 and nuclear β-catenin proteins were more abundant within Fn-positive over Fn-negative CRCs (P < 0.05). Fn and its lipopolysaccharide induced a significant increase in TLR4/P-PAK1/P-β-catenin S675/C-myc/CyclinD1 protein abundance, as well as in the nuclear translocation of β-catenin. Furthermore, inhibition of TLR4 or PAK1 prior to challenge with Fn significantly decreased protein abundance of P-β-catenin S675, C-myc and Cyclin D1, as well as nuclear β-catenin accumulation. Inhibition of TLR4 significantly decreased P-PAK1 protein abundance, and for the first time, we observed an interaction between TLR4 and P-PAK1 using immunoprecipitation. Our data suggest that invasive Fn activates β-catenin signaling via a TLR4/P-PAK1/P-β-catenin S675 cascade in CRC. Furthermore, TLR4 and PAK1 could be potential pharmaceutical targets for the treatment of Fn-related CRCs.
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Affiliation(s)
- Yongyu Chen
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
| | - Yan Peng
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
| | - Jiahui Yu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
| | - Ting Chen
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
| | - Yaxin Wu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
| | - Lei Shi
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
| | - Qing Li
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
| | - Jiao Wu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
| | - Xiangsheng Fu
- Department of Gastroenterology, The Affiliated Hospital of Southwest Medical University, Sichuan, 646000, China
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Fialho VS, Rodrigues VB, Elliot SL. Nesting strategies and disease risk in necrophagous beetles. Ecol Evol 2018; 8:3296-3310. [PMID: 29607025 PMCID: PMC5869311 DOI: 10.1002/ece3.3919] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/11/2018] [Accepted: 01/16/2018] [Indexed: 01/28/2023] Open
Abstract
While the effects of carcass decomposition on microorganisms have been demonstrated in recent years, little is known of how this impacts necrophagous insects. A common assumption is that insects that exploit carcasses are exposed to a high density of potentially harmful microorganisms, but no field data have so far validated this. Necrophagous beetles such as the Scarabaeinae have complex nesting behaviors with elaborate parental care. So here, we begin to explore whether this conjunction of life history and nesting behavior represents an adaptive response to the threat posed by microbes in these environments, mainly by entomopathogens. We evaluated the density and distribution of fungi and bacteria from soil near the carcasses, and their ability to infect and kill insects that are in contact with this soil during the decomposition process. Our data showed an increase in the density and activity of opportunistic or facultative pathogens during the apex of decomposition, when there is a predominance of necrophagous insects. Meanwhile, the survivorship of bait insects decreased when in contact with soil from this period of decomposition, indicating a potential risk of infection. However, the density and activity of these microorganisms decreased with distance from the carcass, mainly with depth, which would benefit tunneller beetles in particular. We have thus provided the first field data to show that necrophagous insects are indeed exposed to high densities of potentially harmful microorganisms. Furthermore, we propose that some parental care strategies may have arisen not only as a response to competition, but also as adaptations that reduce the risks of disease. Although we have focused on carrion feeders, we suggest that the same occurs with coprophagous beetles, as both carrion and dung are nutrient‐rich resources.
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Affiliation(s)
| | | | - Simon Luke Elliot
- Department of Entomology Universidade Federal de Viçosa Viçosa Minas Gerais Brazil
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Chen S, Li X, Liu L, Liu C, Han X. Ophiopogonin D alleviates high‐fat diet‐induced metabolic syndrome and changes the structure of gut microbiota in mice. FASEB J 2018; 32:1139-1153. [PMID: 29084766 DOI: 10.1096/fj.201700741rr] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Siyu Chen
- Department of Biochemistry and Molecular BiologyKey Laboratory of Human Functional Genomics of Jiangsu ProvinceNanjing Medical University Nanjing Jiangsu China
- School of Life Sciences, China Pharmaceutical University Nanjing Jiangsu China
| | - Xiao Li
- Department of Pathology First Affiliated Hospital with Nanjing Medical University Nanjing Jiangsu China
| | - Li Liu
- Department of Geriatrics First Affiliated Hospital with Nanjing Medical University Nanjing Jiangsu China
| | - Chang Liu
- School of Life Sciences, China Pharmaceutical University Nanjing Jiangsu China
| | - Xiao Han
- Department of Biochemistry and Molecular BiologyKey Laboratory of Human Functional Genomics of Jiangsu ProvinceNanjing Medical University Nanjing Jiangsu China
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50
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Monitoring of post-mortem changes of saliva N-glycosylation by nano LC/MS. Anal Bioanal Chem 2017; 410:45-56. [DOI: 10.1007/s00216-017-0702-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/25/2017] [Accepted: 10/10/2017] [Indexed: 01/01/2023]
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