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Bouilloud M, Galan M, Pradel J, Loiseau A, Ferrero J, Gallet R, Roche B, Charbonnel N. Exploring the potential effects of forest urbanization on the interplay between small mammal communities and their gut microbiota. Anim Microbiome 2024; 6:16. [PMID: 38528597 DOI: 10.1186/s42523-024-00301-y] [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: 01/29/2024] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
Urbanization significantly impacts wild populations, favoring urban dweller species over those that are unable to adapt to rapid changes. These differential adaptative abilities could be mediated by the microbiome, which may modulate the host phenotype rapidly through a high degree of flexibility. Conversely, under anthropic perturbations, the microbiota of some species could be disrupted, resulting in dysbiosis and negative impacts on host fitness. The links between the impact of urbanization on host communities and their gut microbiota (GM) have only been scarcely explored. In this study, we tested the hypothesis that the bacterial composition of the GM could play a role in host adaptation to urban environments. We described the GM of several species of small terrestrial mammals sampled in forested areas along a gradient of urbanization, using a 16S metabarcoding approach. We tested whether urbanization led to changes in small mammal communities and in their GM, considering the presence and abundance of bacterial taxa and their putative functions. This enabled to decipher the processes underlying these changes. We found potential impacts of urbanization on small mammal communities and their GM. The urban dweller species had a lower bacterial taxonomic diversity but a higher functional diversity and a different composition compared to urban adapter species. Their GM assembly was mostly governed by stochastic effects, potentially indicating dysbiosis. Selection processes and an overabundance of functions were detected that could be associated with adaptation to urban environments despite dysbiosis. In urban adapter species, the GM functional diversity and composition remained relatively stable along the urbanization gradient. This observation can be explained by functional redundancy, where certain taxa express the same function. This could favor the adaptation of urban adapter species in various environments, including urban settings. We can therefore assume that there are feedbacks between the gut microbiota and host species within communities, enabling rapid adaptation.
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Affiliation(s)
- Marie Bouilloud
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France.
- Centre de Biologie pour la Gestion des Populations, 750 Avenue Agropolis, 34988, Montferrier sur Lez, France.
| | - Maxime Galan
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Pradel
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Anne Loiseau
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Julien Ferrero
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Romain Gallet
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
| | - Benjamin Roche
- MIVEGEC, IRD, CNRS, Univ Montpellier, Montpellier, France
| | - Nathalie Charbonnel
- CBGP, IRD, CIRAD, INRAE, Institut Agro, Univ Montpellier, Montpellier, France
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Li N, Liang XR, Zhou SD, Dang LH, Li J, An GS, Ren K, Jin QQ, Liang XH, Cao J, Du QX, Wang YY, Sun JH. Exploring postmortem succession of rat intestinal microbiome for PMI based on machine learning algorithms and potential use for humans. Forensic Sci Int Genet 2023; 66:102904. [PMID: 37307769 DOI: 10.1016/j.fsigen.2023.102904] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 03/02/2023] [Accepted: 06/05/2023] [Indexed: 06/14/2023]
Abstract
The microbial communities may undergo a meaningful successional change during the progress of decay and decomposition that could aid in determining the post-mortem interval (PMI). However, there are still challenges to applying microbiome-based evidence in law enforcement practice. In this study, we attempted to investigate the principles governing microbial community succession during decomposition of rat and human corpse, and explore their potential use for PMI of human cadavers. A controlled experiment was conducted to characterize temporal changes in microbial communities associated with rat corpses as they decomposed for 30 days. Obvious differences of microbial community structures were observed among different stages of decomposition, especially between decomposition of 0-7d and 9-30d. Thus, a two-layer model for PMI prediction was developed based on the succession of bacteria by combining classification and regression models using machine learning algorithms. Our results achieved 90.48% accuracy for discriminating groups of PMI 0-7d and 9-30d, and yielded a mean absolute error of 0.580d within 7d decomposition and 3.165d within 9-30d decomposition. Furthermore, samples from human cadavers were collected to gain the common succession of microbial community between rats and humans. Based on the 44 shared genera of rats and humans, a two-layer model of PMI was rebuilt to be applied for PMI prediction of human cadavers. Accurate estimates indicated a reproducible succession of gut microbes across rats and humans. Together these results suggest that microbial succession was predictable and can be developed into a forensic tool for estimating PMI.
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Affiliation(s)
- Na Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Xin-Rui Liang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Shi-Dong Zhou
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Li-Hong Dang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Jian Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Guo-Shuai An
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Kang Ren
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Qian-Qian Jin
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Xin-Hua Liang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Jie Cao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Qiu-Xiang Du
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China
| | - Ying-Yuan Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China.
| | - Jun-Hong Sun
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030604, Shanxi, China.
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Liu R, Zhang K, Li H, Sun Q, Wei X, Li H, Zhang S, Fan S, Wang Z. Dissecting the microbial community structure of internal organs during the early postmortem period in a murine corpse model. BMC Microbiol 2023; 23:38. [PMID: 36765295 PMCID: PMC9912631 DOI: 10.1186/s12866-023-02786-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND Microorganisms distribute and proliferate both inside and outside the body, which are the main mediators of decomposition after death. However, limited information is available on the postmortem microbiota changes of extraintestinal body sites in the early decomposition stage of mammalian corpses. RESULTS This study investigated microbial composition variations among different organs and the relationship between microbial communities and time since death over 1 day of decomposition in male C57BL/6 J mice by 16S rRNA sequencing. During 1 day of decomposition, Agrobacterium, Prevotella, Bacillus, and Turicibacter were regarded as time-relevant genera in internal organs at different timepoints. Pathways associated with lipid, amino acid, carbohydrate and terpenoid and polyketide metabolism were significantly enriched at 8 h than that at 0.5 or 4 h. The microbiome compositions and postmortem metabolic pathways differed by time since death, and more importantly, these alterations were organ specific. CONCLUSION The dominant microbes differed by organ, while they tended toward similarity as decomposition progressed. The observed thanatomicrobiome variation by body site provides new knowledge into decomposition ecology and forensic microbiology. Additionally, the microbes detected at 0.5 h in internal organs may inform a new direction for organ transplantation.
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Affiliation(s)
- Ruina Liu
- College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Kai Zhang
- College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Huan Li
- Xi’an Mental Health Center Hospital, Xi’an, 710061 China
| | - Qinru Sun
- College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Xin Wei
- College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Huiyu Li
- College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Siruo Zhang
- Department of Clinical Laboratory, Shaanxi Provincial People’s Hospital, Shaanxi Xi’an, 710068 People’s Republic of China
- Department of Microbiology and Immunology, School of Basic Medical Sciences, Xi’an Jiaotong University, Shaanxi Xi’an, 710061 People’s Republic of China
| | - Shuanliang Fan
- College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
| | - Zhenyuan Wang
- College of Forensic Medicine, Xi’an Jiaotong University, Xi’an, 710061 China
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Xiang Q, Su Q, Li Q, Liu J, Du Y, Shi H, Li Z, Ma Y, Niu Y, Chen L, Liu C, Zhao J. Microbial community analyses provide a differential diagnosis for the antemortem and postmortem injury of decayed cadaver: An animal model. J Forensic Leg Med 2023; 93:102473. [PMID: 36580880 DOI: 10.1016/j.jflm.2022.102473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/23/2022] [Indexed: 12/25/2022]
Abstract
Differentiating antemortem injury from postmortem injury of decayed cadavers is one of the difficult issues in forensic science. Forensic pathologists identify antemortem injury according to the macroscopic and microscopic vital reactions taken place after being injured. However, the decomposition would render those vital reactions ineffective. Microbiomes have been widely used in forensic science due to their succession with time and sensitivity to vary of environment. In this study, microbiomes were introduced to determine whether the bacterial communities can be used to distinguish between the ante- and postmortem injuries through an animal experiment. Our findings showed that the differences of bacterial community were increasingly apparent from the 6th to 9th day after the wound created when the types of wounds were unidentified by morphological examination due to decomposition. The biomarkers at the genus level could effectively distinguish between injury types, Among them, Enterococcus and Enterobacter were only observed in the antemortem injured group, while Staphylococcus and Acinetobacter were only in the postmortem injured group. It is possible to tell whether cadaveric injuries developed before or after death by detecting differences in the bacterial communities of putrefying wounds. This study provides a new perspective for the differences between ante- and postmortem injuries and provides a promising method for us to identify the ante- and postmortem wounds, especially in decomposed cadavers.
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Affiliation(s)
- Qingqing Xiang
- School of Forensic Medicine, Kunming Medical University, Chunrong Road West 1168, Chenggong District, Kunming, 650500, China
| | - Qin Su
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University & Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan 2nd Road 74, Yuexiu District, Guangzhou, 510275, PR China; Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China
| | - Qi Li
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University & Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan 2nd Road 74, Yuexiu District, Guangzhou, 510275, PR China
| | - Jingjian Liu
- Department of Anatomy, North Sichuan Medical College, Nanchong, 637000, China
| | - Yukun Du
- School of Forensic Medicine, Southern Medical University, Shaitai Road South 1023-1063, Baiyun District, Guangzhou, 510515, China
| | - He Shi
- Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China
| | - Zhigang Li
- Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China
| | - Yanbin Ma
- Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China
| | - Yong Niu
- Section of Forensic Sciences, Criminal Investigation Department, Ministry of Public Security, Chang' an Avenue 14, Dongcheng District, Beijing, 100741, China
| | - Lifang Chen
- School of Forensic Medicine, Kunming Medical University, Chunrong Road West 1168, Chenggong District, Kunming, 650500, China.
| | - Chao Liu
- Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China.
| | - Jian Zhao
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University & Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan 2nd Road 74, Yuexiu District, Guangzhou, 510275, PR China; Guangzhou Forensic Science Institute & Key Laboratory of Forensic Pathology, Ministry of Public Security, Baiyun Avenue 1708, Baiyun District, Guangzhou, 510442, PR China.
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Wang Z, Zhang F, Wang L, Yuan H, Guan D, Zhao R. Advances in artificial intelligence-based microbiome for PMI estimation. Front Microbiol 2022; 13:1034051. [PMID: 36267183 PMCID: PMC9577360 DOI: 10.3389/fmicb.2022.1034051] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/15/2022] [Indexed: 11/13/2022] Open
Abstract
Postmortem interval (PMI) estimation has always been a major challenge in forensic science. Conventional methods for predicting PMI are based on postmortem phenomena, metabolite or biochemical changes, and insect succession. Because postmortem microbial succession follows a certain temporal regularity, the microbiome has been shown to be a potentially effective tool for PMI estimation in the last decade. Recently, artificial intelligence (AI) technologies shed new lights on forensic medicine through analyzing big data, establishing prediction models, assisting in decision-making, etc. With the application of next-generation sequencing (NGS) and AI techniques, it is possible for forensic practitioners to improve the dataset of microbial communities and obtain detailed information on the inventory of specific ecosystems, quantifications of community diversity, descriptions of their ecological function, and even their application in legal medicine. This review describes the postmortem succession of the microbiome in cadavers and their surroundings, and summarizes the application, advantages, problems, and future strategies of AI-based microbiome analysis for PMI estimation.
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Affiliation(s)
- Ziwei Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Fuyuan Zhang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
| | - Linlin Wang
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Huiya Yuan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Dawei Guan
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
| | - Rui Zhao
- Department of Forensic Pathology, China Medical University School of Forensic Medicine, Shenyang, China
- Liaoning Province Key Laboratory of Forensic Bio-evidence Science, Shenyang, China
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Hu L, Xing Y, Jiang P, Gan L, Zhao F, Peng W, Li W, Tong Y, Deng S. Predicting the postmortem interval using human intestinal microbiome data and random forest algorithm. Sci Justice 2021; 61:516-527. [PMID: 34482931 DOI: 10.1016/j.scijus.2021.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 05/20/2021] [Accepted: 06/22/2021] [Indexed: 01/04/2023]
Abstract
Gradual changes in microbial communities in a human body after death can be used to determine postmortem interval (PMI). In this study, gut microflora samples were collected from the vermiform appendix and the transverse colon of human cadavers with PMIs between 5 and 192 h. The results revealed that the appendix might be an excellent intestinal sampling site and the appendix flora had an inferred succession rule during human body decomposition. Firmicutes, Bacteroidetes, and their respective subclasses showed a predictable successionrule in relative abundance over time. A Random Forest regression model was developed to correlate human gut microbiota with PMI. We believe that our findings have increased the knowledge of the composition and abundance of the gut microbiota in human corpses, and suggest that the use of the human appendix microbial succession may be a potential method for forensic estimation of the time of death.
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Affiliation(s)
- Lai Hu
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Yu Xing
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Pu Jiang
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Li Gan
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Fan Zhao
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Wenli Peng
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Weihan Li
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China
| | - Yanqiu Tong
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China; School of Humanities, Chongqing Jiaotong University, #66 Xuefu Road, Chongqing 400016, China
| | - Shixiong Deng
- Department of Forensic Medicine, Chongqing Medical University, #1 Yixueyuan Road, Chongqing 400016, China.
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Yu Z, Xie Q, Zhao Y, Duan L, Qiu P, Fan H. NGS plus bacterial culture: A more accurate method for diagnosing forensic-related nosocomial infections. Leg Med (Tokyo) 2021; 52:101910. [PMID: 34052680 DOI: 10.1016/j.legalmed.2021.101910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/19/2021] [Accepted: 05/20/2021] [Indexed: 11/30/2022]
Abstract
Traditional autopsy and microscopic examination of pathological sections are the "gold standard" for the cause of death diagnosis. However, in some special cases, such as the deaths caused by bacterial infections, pathological sections are not always sufficient to provide convincing evidences for determining the causes of death. In recent years, with the development of Next Generation Sequencing (NGS), clinical medicine has already introduced it into the diagnosis of difficult diseases, which is rare in forensic pathological diagnoses. Here, we applied an NGS-based method combined with bacterial culture to examine a special case in which the deceased was suspected of having suffered from nosocomial infections. Results of the NGS and bacterial culture showed that Enterococcus and Acinetobacter baumannii, which are the most common bacteria causing nosocomial infections, were abundant in blood and hydropericardium of the deceased. Combining medical records and the results of the dissections, we proved that the death was actually caused by MODS which was the adverse consequence of nosocomial infections. In this case, the combination of NGS and bacterial culture was used to identify the pathogen which had caused the death. The results of NGS not only shorten the period of diagnosis, but also greatly increase the credibility of traditional anatomy and results of bacterial culture, which is expected to be further applied for forensic practices in the near future.
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Affiliation(s)
- Zhonghao Yu
- School of Forensic Medicine, Southern Medical University, Guangzhou, 510515 Guangdong, China
| | - Qiqian Xie
- School of Forensic Medicine, Southern Medical University, Guangzhou, 510515 Guangdong, China
| | - Yifeng Zhao
- Nanjing Zhenghong Judicial Identification Institute, Nanjing, 211800 Jiangsu, China
| | - Lizhong Duan
- Beijing Municipal Public Security Bureau, 102600 Beijing, China
| | - Pingming Qiu
- School of Forensic Medicine, Southern Medical University, Guangzhou, 510515 Guangdong, China.
| | - Haoliang Fan
- School of Forensic Medicine, Southern Medical University, Guangzhou, 510515 Guangdong, China; School of Basic Medicine and Life Science, Hainan Medical University, Haikou, 571199 Hainan, China.
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