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An Elemental Diet Enriched in Amino Acids Alters the Gut Microbial Community and Prevents Colonic Mucus Degradation in Mice with Colitis. mSystems 2022; 7:e0088322. [PMID: 36468853 PMCID: PMC9765100 DOI: 10.1128/msystems.00883-22] [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] [Indexed: 12/07/2022] Open
Abstract
The role of dietary amino acids or intact proteins in the progression of colitis remains controversial, and the mechanism involving gut microbes is unclear. Here, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of dextran sulfate sodium (DSS)-induced colitis in mice. Our results showed that the ED induced remission of colitis in mice. Notably, ED treatment reduced the abundance of the mucolytic bacteria Akkermansia and Bacteroides, which was attributed to decreased colonic protein fermentation. Consistently, the activities of mucolytic enzymes were decreased, leading to protection against mucus layer degradation and microbial invasion. Fecal microbiota transplantation from ED-fed mice reshaped microbial ecology and alleviated intestinal inflammation in recipient mice. The ED failed to induce remission of colitis in pseudogermfree mice. Together, our results demonstrate the critical role of the gut microbiota in the prevention of colitis by an ED. IMPORTANCE The prevalence of inflammatory bowel disease is rapidly increasing and has become a global burden. Several specific amino acids have been shown to benefit mucosal healing and colitis remission. However, the role of amino acids or intact proteins in diets and enteral nutrition formulas is controversial, and the mechanisms involving gut microbes remain unclear. In this study, we investigated the effects of an elemental diet (ED) enriched in amino acids and a polymeric diet enriched in intact protein on the pathogenesis of colitis in mice. The underlying mechanisms were explored by utilizing fecal microbiota transplantation and pseudogermfree mice. ED treatment reduced the abundance of mucolytic bacteria, thereby protecting the mucus layer from microbial invasion and degradation. For the first time, we convincingly demonstrated the critical role of gut microbiota in the effects of the ED. This study may provide new insights into the gut microbiota-diet interaction and its role in human health.
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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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Bamberg M, Dierig L, Kulstein G, Kunz SN, Schmidt M, Hadrys T, Wiegand P. Development and validation of an mRNA-based multiplex body fluid identification workflow and a rectal mucosa marker pilot study. Forensic Sci Int Genet 2021; 54:102542. [PMID: 34098418 DOI: 10.1016/j.fsigen.2021.102542] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 05/26/2021] [Indexed: 01/26/2023]
Abstract
Molecular identification of body fluids and tissues is crucial in order to understand the circumstances of crimes. For that reason, molecular investigations used to identify body fluids/tissues have increasingly been examined recently. Various studies have proved that messenger RNA (mRNA) profiling is a sensitive and robust method for body fluid/tissue identification. The forensically relevant body fluids/tissues blood, semen, saliva, vaginal secretion, menstrual blood and skin have all been detected successfully by applying suitable mRNA assay. However, rectal mucosa, which can be found as evidence in sexual assault cases, has been neglected in forensic investigations. So far there is no mRNA marker to detect rectal mucosa, although anal penetration occurs in a large number of sexual assaults (23.2% of female victims and 50% of male victims). In this study, specific and sensitive mRNA markers for forensically relevant body fluids were adapted and validated in an mRNA multiplex assay for routine casework. This included the implementation of a DNA/RNA re-extraction method for automated extraction that can be integrated into casework without loss of DNA. This re-extraction method and the mRNA multiplex assay were tested using casework samples. PCR-primers were designed for the identification of rectal mucosa and the more effective marker MUC12 was integrated into an extended multiplex assay. The result of our study is a highly specific and sensitive mRNA multiplex assay plus an automated DNA/RNA re-extraction method, that can be integrated into casework and identify rectal mucosa for the first time.
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Affiliation(s)
- Malte Bamberg
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
| | - Lisa Dierig
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | | | - Sebastian N Kunz
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Max Schmidt
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Thorsten Hadrys
- Bavarian State Criminal Police Office, Institute of Forensic Sciences, DNA Department, Maillingerstr. 15, 80636 Munich, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
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Salzmann AP, Arora N, Russo G, Kreutzer S, Snipen L, Haas C. Assessing time dependent changes in microbial composition of biological crime scene traces using microbial RNA markers. Forensic Sci Int Genet 2021; 53:102537. [PMID: 34090061 DOI: 10.1016/j.fsigen.2021.102537] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 01/16/2023]
Abstract
Current body fluid identification methods do not reveal any information about the time since deposition (TsD) of biological traces, even though determining the age of traces could be crucial for the investigative process. To determine the utility of microbial RNA markers for TsD estimation, we examined RNA sequencing data from five forensically relevant body fluids (blood, menstrual blood, saliva, semen, and vaginal secretion) over seven time points, ranging from fresh to 1.5 years. One set of samples was stored indoors while another was exposed to outdoor conditions. In outdoor samples, we observed a consistent compositional shift, occurring after 4 weeks: this shift was characterized by an overall increase in non-human eukaryotic RNA and an overall decrease in prokaryotic RNA. In depth analyses showed a high fraction of tree, grass and fungal signatures, which are characteristic for the environment the samples were exposed to. When examining the prokaryotic fraction in more detail, three bacterial phyla were found to exhibit the largest changes in abundance, namely Actinobacteria, Proteobacteria and Firmicutes. More detailed analyses at the order level were done using a Lasso regression analysis to find a predictive subset of bacterial taxa. We found 26 bacterial orders to be indicative of sample age. Indoor samples did not reveal such a clear compositional change at the domain level: eukaryotic and prokaryotic abundance remained relatively stable across the assessed time period. Nonetheless, a Lasso regression analysis identified 32 bacterial orders exhibiting clear changes over time, enabling the prediction of TsD. For both indoor and outdoor samples, a larger number (around 60%) of the bacterial orders identified as indicative of TsD are part of the Actinobacteria, Proteobacteria and Firmicutes. In summary, we found that the observed changes across time are not primarily due to changes associated with body fluid specific bacteria but mostly due to accumulation of bacteria from the environment. Orders of these environmental bacteria could be evaluated for TsD prediction, considering the location and environment of the crime scene. However, further studies are needed to verify these findings, determine the applicability across samples, replicates, donors, and other variables, and also to further assess the effect of different seasons and locations on the samples.
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Affiliation(s)
| | - Natasha Arora
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland
| | - Giancarlo Russo
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Susanne Kreutzer
- Functional Genomics Centre Zurich (FGCZ), University of Zurich/ETH Zurich, Switzerland
| | - Lars Snipen
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Cordula Haas
- Zurich Institute of Forensic Medicine, University of Zurich, Switzerland.
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Akçan R, Taştekin B, Yildirim MŞ, Aydogan HC, Sağlam N. Omics era in forensic medicine: towards a new age. Turk J Med Sci 2020; 50:1480-1490. [PMID: 32283897 PMCID: PMC7491271 DOI: 10.3906/sag-1912-197] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 04/11/2020] [Indexed: 02/06/2023] Open
Abstract
Background/aim Forensic medicine and sciences is a multidisciplinary branch of science, which frequently benefit from novel technologies. State of the art omics technologies have begun to be performed in forensic medicine and sciences, particularly in postmortem interval, intoxication, drugs of abuse, diagnosis of diseases and cause of death. This review aims to discuss the role and use of great omics (metabolomics, proteomics, genomics and transcriptomics) in forensic sciences, in detail. Materials and methods A detailed review of related literature was performed, and studies were subdivided as per the type of omics. Results and conclusion Omics seems as a revolutionary step in forensic science and sure carries it towards a new age. The number of forensic studies utilizing omics steadily increases in last years. Omics strategies should be used together in order to gather more accurate and certain data. Additional studies need to be performed to incorporate omics into routine forensic methodology.
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Affiliation(s)
- Ramazan Akçan
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Burak Taştekin
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Mahmut Şerif Yildirim
- Department of Forensic Medicine, Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar, Turkey
| | - Halit Canberk Aydogan
- Department of Forensic Medicine, Faculty of Medicine, Hacettepe University, Ankara, Turkey
| | - Necdet Sağlam
- Department of Nanotechnology and Nanomedicine, Graduate School of Science and Engineering, Hacettepe University, Ankara, Turkey
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Bishop AH. The signatures of microorganisms and of human and environmental biomes can now be used to provide evidence in legal cases. FEMS Microbiol Lett 2019; 366:5303725. [PMID: 30689874 DOI: 10.1093/femsle/fnz021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/26/2019] [Indexed: 12/28/2022] Open
Abstract
The microorganisms with which we share our world go largely unnoticed. We are, however, beginning to be able to exploit their apparently silent presence as witnesses to events that are of legal concern. This information can be used to link forensic samples to criminal events and even perpetrators. Once dead, our bodies are rapidly colonised, internally and externally. The progress of these events can be charted to inform how long and even by what means a person has died. A small number of microbial species could actually be the cause of such deaths as a result of biocrime or bioterrorism. The procedures and techniques to respond to such attacks have matured in the last 20 years. The capability now exists to identify malicious intent, characterise the threat agent to isolate level and potentially link it to perpetrators with a high level of confidence.
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Affiliation(s)
- A H Bishop
- School of Biological and Marine Sciences, University of Plymouth, Drake Circus, Devon, PL4 8AA, UK
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7
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Quaak FC, van de Wal Y, Maaskant-van Wijk PA, Kuiper I. Combining human STR and microbial population profiling: Two case reports. Forensic Sci Int Genet 2018; 37:196-199. [DOI: 10.1016/j.fsigen.2018.08.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 12/14/2022]
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8
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Human-associated microbial populations as evidence in forensic casework. Forensic Sci Int Genet 2018; 36:176-185. [PMID: 30036744 DOI: 10.1016/j.fsigen.2018.06.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 06/01/2018] [Accepted: 06/28/2018] [Indexed: 01/26/2023]
Abstract
In forensic investigations involving human biological traces, cell type identification is often required. Identifying the cell type from which a human STR profile has originated can assist in verifying scenarios. Several techniques have been developed for this purpose, most of which focus on molecular characteristics of human cells. Here we present a microarray method focusing on the microbial populations that are associated with human cell material. A microarray with 863 probes targeting (sets of) species, specific genera, groups of genera or families was designed for this study and evaluated with samples from different body sites: hand, foot, groin, penis, vagina, mouth and faeces. In total 175 samples from healthy individuals were analysed. Next to human faeces, 15 feline and 15 canine faeces samples were also included. Both clustering and classification analysis were used for data analysis. Faecal and oral samples could clearly be distinguished from vaginal and skin samples, and also canine and feline faeces could be differentiated from human faeces. Some penis samples showed high similarity to vaginal samples, others to skin samples. Discriminating between skin samples from different skin sites proved to be challenging. As a proof of principle, twenty-one mock case samples were analysed with the microarray method. All mock case samples were clustered or classified within the correct main cluster/group. Only two of the mock case samples were assigned to the wrong sub-cluster/class; with classification one additional sample was classified within the wrong sub-class. Overall, the microarray method is a valuable addition to already existing cell typing techniques. Combining the results of microbial population analysis with for instance mRNA typing can increase the evidential value of a trace, since both techniques focus on independent targets within a sample.
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Zou KN, Ren LJ, Ping Y, Ma K, Li H, Cao Y, Zhou HG, Wei YL. Identification of vaginal fluid, saliva, and feces using microbial signatures in a Han Chinese population. J Forensic Leg Med 2016; 43:126-131. [PMID: 27570236 DOI: 10.1016/j.jflm.2016.08.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 07/14/2016] [Accepted: 08/11/2016] [Indexed: 10/21/2022]
Abstract
In recent years, forensic scientists have focused on the discrimination of body fluids using microbial signatures. In this study, we performed PCR-based detection of microbial signatures of vaginal fluid, saliva, and feces in a Han Chinese population. We investigated the 16S rRNA genes of Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus iners, and Atopobium vaginae in vaginal fluid, the 16S rRNA and the glucosyltransferase enzyme genes of Streptococcus salivarius and Streptococcus mutans in saliva, and the 16S rRNA genes of Enterococcus species, the RNA polymerase β-subunit gene of Bacteroides uniformis and Bacteroides vulgatus, and the α-1-6 mannanase gene of Bacteroides thetaiotaomicron in feces. As a result, the detection proportions of L. crispatus, L. gasseri, L. jensenii, L. iners, and A. vaginae were 15/16, 5/16, 8/16, 14/16, and 3/16 in 16 vaginal fluid donors, respectively. L. crispatus and L. jensenii were specifically detected in vaginal fluid; L. gasseri, L. iners, and A. vaginae were also detected in non-vaginal fluid. S. salivarius and S. mutans were not specifically detected in saliva. The detection proportions of Enterococcus species, B. uniformis, B. vulgatus, and B. thetaiotaomicron in 16 feces samples were 16/16, 12/16, 15/16, and 11/16, respectively. B. uniformis and B. thetaiotaomicron were specifically detected in feces. In addition, DNA samples prepared for the identification of body fluid can also be used for individual identification by short tandem repeat typing. The mean detection sensitivities of L. crispatus and L. jensenii were 0.362 and 0.249 pg/uL, respectively. In conclusion, L. crispatus, L. jensenii, B. uniformis, and B. thetaiotaomicron can be used as effective markers for forensic identification of vaginal fluid and feces.
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Affiliation(s)
- Kai-Nan Zou
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, 200083, People's Republic of China; Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, 300070, People's Republic of China; Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, People's Republic of China
| | - Li-Jie Ren
- The 519th Hospital of the People's Liberation Army, Wenchang, 300457, Hainan, People's Republic of China
| | - Yuan Ping
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, 200083, People's Republic of China
| | - Ke Ma
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, 200083, People's Republic of China
| | - Hui Li
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, 200083, People's Republic of China
| | - Yu Cao
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, 200083, People's Republic of China
| | - Huai-Gu Zhou
- Key Laboratory of Forensic Evidence and Science Technology, Ministry of Public Security, Institute of Forensic Science, Shanghai Public Security Bureau, Shanghai, 200083, People's Republic of China.
| | - Yi-Liang Wei
- Department of Immunology, Biochemistry and Molecular Biology, 2011 Collaborative Innovation Center of Tianjin for Medical Epigenetics, Tianjin Key Laboratory of Medical Epigenetics, Tianjin Medical University, Tianjin, 300070, People's Republic of China; Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, People's Republic of China.
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10
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Nakanishi H, Ohmori T, Hara M, Takahashi S, Kurosu A, Takada A, Saito K. Screening Test for Shed Skin Cells by Measuring the Ratio of Human DNA to Staphylococcus epidermidis DNA. J Forensic Sci 2016; 61:618-22. [PMID: 27122397 DOI: 10.1111/1556-4029.13028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2014] [Revised: 06/22/2015] [Accepted: 07/03/2015] [Indexed: 11/28/2022]
Abstract
A novel screening method for shed skin cells by detecting Staphylococcus epidermidis (S. epidermidis), which is a resident bacterium on skin, was developed. Staphylococcus epidermidis was detected using real-time PCR. Staphylococcus epidermidis was detected in all 20 human skin surface samples. Although not present in blood and urine samples, S. epidermidis was detected in 6 of 20 saliva samples, and 5 of 18 semen samples. The ratio of human DNA to S. epidermidisDNA was significantly smaller in human skin surface samples than in saliva and semen samples in which S. epidermidis was detected. Therefore, although skin cells could not be identified by detecting only S. epidermidis, they could be distinguished by measuring the S. epidermidis to human DNA ratio. This method could be applied to casework touch samples, which suggests that it is useful for screening whether skin cells and human DNA are present on potential evidentiary touch samples.
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Affiliation(s)
- Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
| | - Takeshi Ohmori
- National Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba, 277-0882, Japan
| | - Masaaki Hara
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Shirushi Takahashi
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Akira Kurosu
- Department of Legal Medicine, Dokkyo Medical University School of Medicine, 880 Kitakobayashi, Mibu, Tochigi, 321-0293, Japan
| | - Aya Takada
- Department of Forensic Medicine, Saitama Medical University, 38 Morohongo, Moroyama, Saitama, 350-0495, Japan
| | - Kazuyuki Saito
- Department of Forensic Medicine, Juntendo University School of Medicine, 2-1-1, Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
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Castillo-Peinado LS, Luque de Castro MD. Present and foreseeable future of metabolomics in forensic analysis. Anal Chim Acta 2016; 925:1-15. [PMID: 27188312 DOI: 10.1016/j.aca.2016.04.040] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 04/12/2016] [Accepted: 04/17/2016] [Indexed: 01/24/2023]
Abstract
The revulsive publications during the last years on the precariousness of forensic sciences worldwide have promoted the move of major steps towards improvement of this science. One of the steps (viz. a higher involvement of metabolomics in the new era of forensic analysis) deserves to be discussed under different angles. Thus, the characteristics of metabolomics that make it a useful tool in forensic analysis, the aspects in which this omics is so far implicit, but not mentioned in forensic analyses, and how typical forensic parameters such as the post-mortem interval or fingerprints take benefits from metabolomics are critically discussed in this review. The way in which the metabolomics-forensic binomial succeeds when either conventional or less frequent samples are used is highlighted here. Finally, the pillars that should support future developments involving metabolomics and forensic analysis, and the research required for a fruitful in-depth involvement of metabolomics in forensic analysis are critically discussed.
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Affiliation(s)
- L S Castillo-Peinado
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; University of Córdoba, Agrifood Excellence Campus, ceiA3, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, E-14071, Córdoba, Spain
| | - M D Luque de Castro
- Department of Analytical Chemistry, Annex Marie Curie Building, Campus of Rabanales, University of Córdoba, Córdoba, Spain; University of Córdoba, Agrifood Excellence Campus, ceiA3, Spain; Maimónides Institute of Biomedical Research (IMIBIC), Reina Sofía University Hospital, University of Córdoba, E-14071, Córdoba, Spain.
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12
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Mayorga Reyes L, González Vázquez R, Cruz Arroyo SM, Melendez Avalos A, Reyes Castillo PA, Chavaro Pérez DA, Ramos Terrones I, Ramos Ibáñez N, Rodríguez Magallanes MM, Langella P, Bermúdez Humarán L, Azaola Espinosa A. Correlation between diet and gut bacteria in a population of young adults. Int J Food Sci Nutr 2016; 67:470-8. [DOI: 10.3109/09637486.2016.1162770] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Lino Mayorga Reyes
- Laboratory of Biotechnology, Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, México City
| | - Raquel González Vázquez
- Laboratory of Biotechnology, Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, México City
| | - Schahrasad M. Cruz Arroyo
- Laboratory of Biotechnology, Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, México City
| | - Araceli Melendez Avalos
- Laboratory of Biotechnology, Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, México City
| | - Pedro A. Reyes Castillo
- Laboratory of Biotechnology, Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, México City
| | - David A. Chavaro Pérez
- Laboratory of Biotechnology, Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, México City
| | - Idalia Ramos Terrones
- Laboratory of Nutrition, Body Composition and Energy Expenditure, Universidad Autónoma Metropolitana-Xochimilco, Atención a la Salud, Coyoacán, México City
| | - Norma Ramos Ibáñez
- Laboratory of Nutrition, Body Composition and Energy Expenditure, Universidad Autónoma Metropolitana-Xochimilco, Atención a la Salud, Coyoacán, México City
| | - Magdalena M. Rodríguez Magallanes
- Laboratory of Nutrition, Body Composition and Energy Expenditure, Universidad Autónoma Metropolitana-Xochimilco, Atención a la Salud, Coyoacán, México City
| | - Philippe Langella
- Laboratory of Commensal and Probiotics-Host Interactions, INRA, Jouy-en-Josas, France
- AgroParisTech, Jouy-en-Josas, France
| | - Luis Bermúdez Humarán
- Laboratory of Commensal and Probiotics-Host Interactions, INRA, Jouy-en-Josas, France
| | - Alejandro Azaola Espinosa
- Laboratory of Biotechnology, Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Coyoacán, México City
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13
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Molecular approaches for forensic cell type identification: On mRNA, miRNA, DNA methylation and microbial markers. Forensic Sci Int Genet 2015; 18:21-32. [DOI: 10.1016/j.fsigen.2014.11.015] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 11/15/2014] [Accepted: 11/17/2014] [Indexed: 02/06/2023]
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14
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Doi M, Gamo S, Okiura T, Nishimukai H, Asano M. A simple identification method for vaginal secretions using relative quantification of Lactobacillus DNA. Forensic Sci Int Genet 2014; 12:93-9. [PMID: 24905338 DOI: 10.1016/j.fsigen.2014.05.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 05/07/2014] [Accepted: 05/08/2014] [Indexed: 01/02/2023]
Abstract
In criminal investigations there are some cases in which identifying the presence of vaginal secretions provides crucial evidence in proving sexual assault. However, there are no methods for definitively identifying vaginal secretions. In the present study, we focused on Lactobacillus levels in vaginal secretions and developed a novel identification method for vaginal secretions by relative quantification based on real time PCR. We designed a Lactobacillus conserved region primer pair (LCP) by aligning 16S rRNA gene sequences from major vaginal Lactobacillus species (Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners and Lactobacillus jensenii), and selected the human specific primer pair (HSP) as an endogenous control for relative quantification. As a result, the ΔCt (ΔCt=Ct[LCP]-Ct[HSP]) values of vaginal secretions (11 out of 12 samples) were significantly lower than those of saliva, semen and skin surface samples, and it was possible to discriminate between vaginal secretions and other body fluids. For the one remaining sample, it was confirmed that the predominant species in the microflora was not of the Lactobacillus genus. The ΔCt values in this study were calculated when the total DNA input used from the vaginal secretions was 10pg or more. Additionally, the ΔCt values of samples up to 6-months-old, which were kept at room temperature, remained unchanged. Thus, we concluded in this study that the simple ΔCt method by real time PCR is a useful tool for detecting the presence of vaginal secretions.
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Affiliation(s)
- Masanori Doi
- Forensic Science Laboratory, Ehime Prefectural Police Headquarters, 2-2 Minamihoribatacho, Matsuyama, Ehime 790-8573, Japan.
| | - Shinsuke Gamo
- Forensic Science Laboratory, Ehime Prefectural Police Headquarters, 2-2 Minamihoribatacho, Matsuyama, Ehime 790-8573, Japan
| | - Tatsuyuki Okiura
- Forensic Science Laboratory, Ehime Prefectural Police Headquarters, 2-2 Minamihoribatacho, Matsuyama, Ehime 790-8573, Japan; Department of Legal Medicine, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Hiroaki Nishimukai
- Department of Legal Medicine, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Migiwa Asano
- Department of Legal Medicine, Ehime University Graduate School of Medicine, Shitsukawa, Toon, Ehime 791-0295, Japan
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15
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Li M, Li G, Zhu L, Yin Y, Zhao X, Xiang C, Yu G, Wang X. Isolation and characterization of an agaro-oligosaccharide (AO)-hydrolyzing bacterium from the gut microflora of Chinese individuals. PLoS One 2014; 9:e91106. [PMID: 24622338 PMCID: PMC3951304 DOI: 10.1371/journal.pone.0091106] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Accepted: 02/07/2014] [Indexed: 12/28/2022] Open
Abstract
Agarose (AP) from red algae has a long history as food ingredients in East Asia. Agaro-oligosaccharides (AO) derived from AP have shown potential prebiotic effects. However, the human gut microbes responsible for the degradation of AO and AP have not yet been fully investigated. Here, we reported that AO and AP can be degraded and utilized at various rates by fecal microbiota obtained from different individuals. Bacteroides uniformis L8 isolated from human feces showed a pronounced ability to degrade AO and generate D-galactose as its final end product. PCR-DGGE analysis showed B. uniformis to be common in the fecal samples, but only B. uniformis L8 had the ability to degrade AO. A synergistic strain, here classified as Escherichia coli B2, was also identified because it could utilize the D-galactose as the growth substrate. The cross-feeding interaction between B. uniformis L8 and E. coli B2 led to exhaustion of the AO supply. Bifidobacterium infantis and Bifidobacterium adolescentis can utilize one of the intermediates of AO hydrolysis, agarotriose. Growth curves indicated that AO was the substrate that most favorably sustained the growth of B. uniformis L8. In contrast, κ-carrageenan oligosaccharides (KCO), guluronic acid oligosaccharides (GO), and mannuronic acid oligosaccharides (MO) were found to be unusable to B. uniformis L8. Current results indicate that B. uniformis L8 is a special degrader of AO in the gut microbiota. Because B. uniformis can mitigate high-fat-diet-induced metabolic disorders, further study is required to determine the potential applications of AO.
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Affiliation(s)
- Miaomiao Li
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, and Key Laboratory of Marine Drugs of Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Guangsheng Li
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, and Key Laboratory of Marine Drugs of Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Liying Zhu
- State Key Laboratory of Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- Key laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Yeshi Yin
- State Key Laboratory of Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- Key laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Xiaoliang Zhao
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, and Key Laboratory of Marine Drugs of Ministry of Education, Ocean University of China, Qingdao, Shandong, China
| | - Charlie Xiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Guangli Yu
- Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, and Key Laboratory of Marine Drugs of Ministry of Education, Ocean University of China, Qingdao, Shandong, China
- * E-mail: (GY); (XW)
| | - Xin Wang
- State Key Laboratory of Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- Key laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
- * E-mail: (GY); (XW)
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16
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Assessment of viable bacteria and bacterial DNA in blood and bloodstain specimens stored under various conditions. J Forensic Leg Med 2013; 20:1035-40. [PMID: 24237815 DOI: 10.1016/j.jflm.2013.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 09/23/2013] [Accepted: 09/28/2013] [Indexed: 11/24/2022]
Abstract
Microbial forensic specimens that are collected at biocrime and bioterrorism scenes include blood, tissue, cloths containing biological fluids, swabs, water, soil, and aerosols. It is preferable that pathogens in such specimens are alive and kept in a steady state. Specimens may be stored for a prolonged period before analysis; therefore, it is important to understand the effect of the storage conditions on the pathogens contained within the specimens. In this study, we prepared blood and bloodstain specimens containing Gram-negative or -positive bacteria, stored the samples for 482 days under various conditions, and measured viable bacterial counts and total bacterial contents in the samples. Viable bacteria were preserved well in the samples stored at -30 and -80 °C, but were diminished or undetectable in the samples stored at 4 °C and room temperature. The total bacterial content was maintained in the blood samples stored at -30 and -80 °C and in the bloodstain samples stored under all temperature conditions, but decreased in the blood samples stored at 4 °C and room temperature. This study showed that the storage conditions affected viable bacteria and bacterial DNA and that freezing and drying were significant for their long-term storage. We provide important information for the storage of microbial forensic specimens.
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