1
|
Nodari R, Arghittu M, Bailo P, Cattaneo C, Creti R, D’Aleo F, Saegeman V, Franceschetti L, Novati S, Fernández-Rodríguez A, Verzeletti A, Farina C, Bandi C. Forensic Microbiology: When, Where and How. Microorganisms 2024; 12:988. [PMID: 38792818 PMCID: PMC11123702 DOI: 10.3390/microorganisms12050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 04/30/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Forensic microbiology is a relatively new discipline, born in part thanks to the development of advanced methodologies for the detection, identification and characterization of microorganisms, and also in relation to the growing impact of infectious diseases of iatrogenic origin. Indeed, the increased application of medical practices, such as transplants, which require immunosuppressive treatments, and the growing demand for prosthetic installations, associated with an increasing threat of antimicrobial resistance, have led to a rise in the number of infections of iatrogenic origin, which entails important medico-legal issues. On the other hand, the possibility of detecting minimal amounts of microorganisms, even in the form of residual traces (e.g., their nucleic acids), and of obtaining gene and genomic sequences at contained costs, has made it possible to ask new questions of whether cases of death or illness might have a microbiological origin, with the possibility of also tracing the origin of the microorganisms involved and reconstructing the chain of contagion. In addition to the more obvious applications, such as those mentioned above related to the origin of iatrogenic infections, or to possible cases of infections not properly diagnosed and treated, a less obvious application of forensic microbiology concerns its use in cases of violence or violent death, where the characterization of the microorganisms can contribute to the reconstruction of the case. Finally, paleomicrobiology, e.g., the reconstruction and characterization of microorganisms in historical or even archaeological remnants, can be considered as a sister discipline of forensic microbiology. In this article, we will review these different aspects and applications of forensic microbiology.
Collapse
Affiliation(s)
- Riccardo Nodari
- Department of Pharmacological and Biomolecular Sciences (DiSFeB), University of Milan, 20133 Milan, Italy
| | - Milena Arghittu
- Analysis Laboratory, ASST Melegnano e Martesana, 20077 Vizzolo Predabissi, Italy
| | - Paolo Bailo
- Section of Legal Medicine, School of Law, University of Camerino, 62032 Camerino, Italy
| | - Cristina Cattaneo
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Roberta Creti
- Antibiotic Resistance and Special Pathogens Unit, Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Francesco D’Aleo
- Microbiology and Virology Laboratory, GOM—Grande Ospedale Metropolitano, 89124 Reggio Calabria, Italy
| | - Veroniek Saegeman
- Microbiology and Infection Control, Vitaz Hospital, 9100 Sint-Niklaas, Belgium
| | - Lorenzo Franceschetti
- LABANOF, Laboratory of Forensic Anthropology and Odontology, Section of Forensic Medicine, Department of Biomedical Sciences for Health, University of Milan, 20133 Milan, Italy
| | - Stefano Novati
- Department of Infectious Diseases, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy
| | - Amparo Fernández-Rodríguez
- Microbiology Department, Biology Service, Instituto Nacional de Toxicología y Ciencias Forenses, 41009 Madrid, Spain
| | - Andrea Verzeletti
- Department of Medical and Surgical Specialties, Radiological Sciences and Public Health University of Brescia, 25123 Brescia, Italy
| | - Claudio Farina
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, 24127 Bergamo, Italy
| | - Claudio Bandi
- Romeo ed Enrica Invernizzi Paediatric Research Centre, Department of Biosciences, University of Milan, 20133 Milan, Italy
| |
Collapse
|
2
|
Tang X, Wen D, Jin X, Wang C, Xu W, Qu W, Xu R, Jia H, Liu Y, Li X, Chen S, Fu X, Liang B, Li J, Liu Y, Zha L. A preliminary study on identification of the blood donor in a body fluid mixture using a novel compound genetic marker blood-specific methylation-microhaplotype. Forensic Sci Int Genet 2024; 70:103031. [PMID: 38493735 DOI: 10.1016/j.fsigen.2024.103031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
Blood-containing mixtures are frequently encountered at crime scenes involving violence and murder. However, the presence of blood, and the association of blood with a specific donor within these mixtures present significant challenges in forensic analysis. In light of these challenges, this study sought to address these issues by leveraging blood-specific methylation sites and closely linked microhaplotype sites, proposing a novel composite genetic marker known as "blood-specific methylation-microhaplotype". This marker was designed to the detection of blood and the determination of blood donor within blood-containing mixtures. According to the selection criteria mentioned in the Materials and Methods section, we selected 10 blood-specific methylation-microhaplotype loci for inclusion in this study. Among these loci, eight exhibited blood-specific hypomethylation, while the remaining two displayed blood-specific hypermethylation. Based on data obtained from 124 individual samples in our study, the combined discrimination power (CPD) of these 10 successfully sequenced loci was 0.999999298. The sample allele methylation rate (Ram) was obtained from massive parallel sequencing (MPS), which was defined as the proportion of methylated reads to the total clustered reads that were genotyped to a specific allele. To develop an allele type classification model capable of identifying the presence of blood and the blood donor, we used the Random Forest algorithm. This model was trained and evaluated using the Ram distribution of individual samples and the Ram distribution of simulated shared alleles. Subsequently, we applied the developed allele type classification model to predict alleles within actual mixtures, trying to exclude non-blood-specific alleles, ultimately allowing us to identify the presence of blood and the blood donor in the blood-containing mixtures. Our findings demonstrate that these blood-specific methylation-microhaplotype loci have the capability to not only detect the presence of blood but also accurately associate blood with the true donor in blood-containing mixtures with the mixing ratios of 1:29, 1:19, 1:9, 1:4, 1:2, 2:1, 7:1, 8:1, 31:1 and 36:1 (blood:non-blood) by DNA mixture interpretation methods. In addition, the presence of blood and the true blood donor could be identified in a mixture containing four body fluids (blood:vaginal fluid:semen:saliva = 1:1:1:1). It is important to note that while these loci exhibit great potential, the impact of allele dropouts and alleles misidentification must be considered when interpreting the results. This is a preliminary study utilising blood-specific methylation-microhaplotype as a complementary tool to other well-established genetic markers (STR, SNP, microhaplotype, etc.) for the analysis in blood-containing mixtures.
Collapse
Affiliation(s)
- Xuan Tang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Xin Jin
- Department of Public Security of Hainan Province, Haikou, Hainan Province, PR China
| | - Chudong Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Wei Xu
- Central Laboratory, Hunan Provincal People's Hospital (The First Affiliated Hospitak of Hunan Normal University), Changsha, Hunan Province 410000, PR China
| | - Weifeng Qu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Ruyi Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Hongtao Jia
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Yi Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Xue Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830017, PR China
| | - Siqi Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Xiaoyi Fu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Bin Liang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Ying Liu
- Xiangya Stomatological Collage, Central South University, No72. Xiangya Road, Changsha, Hunan 410013, PR China.
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China; Hebei Key Laboratory of Forensic Medicine, School of Forensic Medicine, Hebei Medical University, Shijiazhuang, PR China.
| |
Collapse
|
3
|
Huang L, Liang X, Xiao G, Du J, Ye L, Su Q, Liu C, Chen L. Response of salivary microbiome to temporal, environmental, and surface characteristics under in vitro exposure. Forensic Sci Int Genet 2024; 70:103020. [PMID: 38286081 DOI: 10.1016/j.fsigen.2024.103020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/22/2023] [Accepted: 01/21/2024] [Indexed: 01/31/2024]
Abstract
The microbiome of saliva stains deposited at crime scenes and in everyday settings is valuable for forensic investigations and environmental ecology. However, the dynamics and applications of microbial communities in these saliva stains have not been fully explored. In this study, we analyzed saliva samples that were exposed to indoor conditions for up to 1 year and to different carriers (cotton, sterile absorbent cotton swab, woolen, dacron) in both indoor and outdoor environments for 1 month using high-throughput sequencing. The analysis of microbial composition and Mfuzz clustering showed that the salivary flora, specifically Streptococcus (cluster7), which was associated with microbial contamination, remained stable over short periods of time. However, prolonged exposure led to significant differences due to the invasion of environmental bacteria such as Pseudomonas and Achromobacter. The growth and colonization of environmental flora were promoted by humidity. The neutral model predictions indicated that the assembly of salivary microbial communities in outdoor environments was significantly influenced by stochastic processes, with environmental characteristics having a greater impact on community change compared to surface characteristics. By incorporating data from previous studies on fecal and vaginal secretion microbiology, we developed RF and XGBoost classification models that achieved high accuracy (>98 %) and AUC (>0.8). Additionally, a RF regression model was created to determine the time since deposition (TsD) of the stains. Time inference models yielded a mean absolute error (MAE) of 7.1 days for stains exposed for 1 year and 14.2 h for stains exposed for 14 days. These findings enhance our understanding of the changes in the microbiome of saliva stains over time, in different environments, and on different surfaces. They also have potential applications in assessing potential microbial contamination, identifying body fluids, and inferring the time of deposition.
Collapse
Affiliation(s)
- Litao Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Xiaomin Liang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Guichao Xiao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Jieyu Du
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Linying Ye
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Qin Su
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China; National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, China.
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China.
| |
Collapse
|
4
|
Wang S, Song F, Song M, Wei X, Zhou Y, Jiang L, Wang Z, Sun C, Yao H, Liang W, Luo H. Explore variation of salivary bacteria across time and geolocations. Int J Legal Med 2024; 138:547-554. [PMID: 37353677 DOI: 10.1007/s00414-023-03045-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/13/2023] [Indexed: 06/25/2023]
Abstract
Saliva is an informative body fluid that can be found at various crime scenes, and the salivary bacterial community has been revealed it is a potential auxiliary target for forensic identification. However, the variation of salivary bacterial community composition across time and geolocation needs to be explored. The study was designed to be carried out during the winter vacation that was across about 50 days and eight geographic locations. The high throughput sequencing was performed with the V3-V4 region of the16S rRNA gene to explore salivary bacterial community composition. An overall slight fluctuation of the salivary bacteria was observed, which primarily occurred in the relative abundance of the salivary bacterial taxa. The results of principal coordinate analysis and hierarchical clustering showed samples were clustered by the individuals. All individuals could be correctly identified with the random forest model. In summation, although the relative abundance of salivary bacteria varied across the changes of time and geolocation, the individualized characteristic of salivary bacteria remained steady, which is beneficial for the salivary bacterial application in personal identification.
Collapse
Affiliation(s)
- Shuangshuang Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaowen Wei
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Zefei Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Chaoran Sun
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, China.
| |
Collapse
|
5
|
Daniels BN, Nurge J, De Smet C, Sleeper O, White C, Davidson JM, Fidopiastis P. Microbiome composition and function within the Kellet's whelk perivitelline fluid. Microbiol Spectr 2024; 12:e0351423. [PMID: 38334378 PMCID: PMC10913743 DOI: 10.1128/spectrum.03514-23] [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: 10/02/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
Microbiomes have gained significant attention in ecological research, owing to their diverse interactions and essential roles within different organismal ecosystems. Microorganisms, such as bacteria, archaea, and viruses, have profound impact on host health, influencing digestion, metabolism, immune function, tissue development, and behavior. This study investigates the microbiome diversity and function of Kellet's whelk (Kelletia kelletii) perivitelline fluid (PVF), which sustains thousands of developing K. kelletii embryos within a polysaccharide and protein matrix. Our core microbiome analysis reveals a diverse range of bacteria, with the Roseobacter genus being the most abundant. Additionally, genes related to host-microbe interactions, symbiosis, and quorum sensing were detected, indicating a potential symbiotic relationship between the microbiome and Kellet's whelk embryos. Furthermore, the microbiome exhibits gene expression related to antibiotic biosynthesis, suggesting a defensive role against pathogenic bacteria and potential discovery of novel antibiotics. Overall, this study sheds light on the microbiome's role in Kellet's whelk development, emphasizing the significance of host-microbe interactions in vulnerable life history stages. To our knowledge, ours is the first study to use 16S sequencing coupled with RNA sequencing (RNA-seq) to profile the microbiome of an invertebrate PVF.IMPORTANCEThis study provides novel insight to an encapsulated system with strong evidence of symbiosis between the microbial inhabitants and developing host embryos. The Kellet's whelk perivitelline fluid (PVF) contains microbial organisms of interest that may be providing symbiotic functions and potential antimicrobial properties during this vulnerable life history stage. This study, the first to utilize a comprehensive approach to investigating Kellet's whelk PVF microbiome, couples 16S rRNA gene long-read sequencing with RNA-seq. This research contributes to and expands our knowledge on the roles of beneficial host-associated microbes.
Collapse
Affiliation(s)
- Benjamin N. Daniels
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Jenna Nurge
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Chanel De Smet
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Olivia Sleeper
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Crow White
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Jean M. Davidson
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| | - Pat Fidopiastis
- Department of Biological Sciences, California Polytechnic State University, San Luis Obispo, California, USA
| |
Collapse
|
6
|
Yang MQ, Wang ZJ, Zhai CB, Chen LQ. Research progress on the application of 16S rRNA gene sequencing and machine learning in forensic microbiome individual identification. Front Microbiol 2024; 15:1360457. [PMID: 38371926 PMCID: PMC10869621 DOI: 10.3389/fmicb.2024.1360457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 01/23/2024] [Indexed: 02/20/2024] Open
Abstract
Forensic microbiome research is a field with a wide range of applications and a number of protocols have been developed for its use in this area of research. As individuals host radically different microbiota, the human microbiome is expected to become a new biomarker for forensic identification. To achieve an effective use of this procedure an understanding of factors which can alter the human microbiome and determinations of stable and changing elements will be critical in selecting appropriate targets for investigation. The 16S rRNA gene, which is notable for its conservation and specificity, represents a potentially ideal marker for forensic microbiome identification. Gene sequencing involving 16S rRNA is currently the method of choice for use in investigating microbiomes. While the sequencing involved with microbiome determinations can generate large multi-dimensional datasets that can be difficult to analyze and interpret, machine learning methods can be useful in surmounting this analytical challenge. In this review, we describe the research methods and related sequencing technologies currently available for application of 16S rRNA gene sequencing and machine learning in the field of forensic identification. In addition, we assess the potential value of 16S rRNA and machine learning in forensic microbiome science.
Collapse
Affiliation(s)
- Mai-Qing Yang
- Department of Pathology, Weifang People's Hospital (First Affiliated Hospital of Shandong Second Medical University), Weifang, China
| | - Zheng-Jiang Wang
- Department of Pathology, Weifang People's Hospital (First Affiliated Hospital of Shandong Second Medical University), Weifang, China
| | - Chun-Bo Zhai
- Department of Second Ward of Thoracic Surgery, Weifang People's Hospital (First Affiliated Hospital of Shandong Second Medical University), Weifang, China
| | - Li-Qian Chen
- Department of Pathology, Weifang People's Hospital (First Affiliated Hospital of Shandong Second Medical University), Weifang, China
| |
Collapse
|
7
|
Ferenc K, Sokal-Dembowska A, Helma K, Motyka E, Jarmakiewicz-Czaja S, Filip R. Modulation of the Gut Microbiota by Nutrition and Its Relationship to Epigenetics. Int J Mol Sci 2024; 25:1228. [PMID: 38279228 PMCID: PMC10816208 DOI: 10.3390/ijms25021228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/28/2024] Open
Abstract
The intestinal microbiota is a community of microorganisms inhabiting the human intestines, potentially influencing both physiological and pathophysiological processes in the human body. Existing evidence suggests that nutrients can influence the modulation of the gut microbiota. However, there is still limited evidence regarding the effects of vitamin and mineral supplementation on the human gut microbiota through epigenetic modification. It is plausible that maintaining an adequate dietary intake of vitamin D, iron, fibre, zinc and magnesium may have a beneficial effect on alleviating inflammation in the body, reducing oxidative stress, and improving the condition of the intestinal microbiota through various epigenetic mechanisms. Moreover, epigenetics involves alterations in the phenotype of a cell without changing its fundamental DNA sequence. It appears that the modulation of the microbiota by various nutrients may lead to epigenetic regulation. The correlations between microbiota and epigenetics are potentially interdependent. Therefore, the primary objective of this review is to identify the complex relationships between diet, gut microbiota, and epigenetic regulation. These interactions could play a crucial role in systemic health.
Collapse
Affiliation(s)
- Katarzyna Ferenc
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Aneta Sokal-Dembowska
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Kacper Helma
- Institute of Health Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | - Elżbieta Motyka
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
| | | | - Rafał Filip
- Institute of Medicine, Medical College of Rzeszow University, 35-959 Rzeszow, Poland
- Department of Gastroenterology with IBD Unit, Clinical Hospital No. 2, 35-301 Rzeszow, Poland
| |
Collapse
|
8
|
Palm KM, Abrams MK, Sears SB, Wherley SD, Alfahmy AM, Kamumbu SA, Chakraborty NN, Mahajan ST, El-Nashar SA, Henderson JW, Hijaz AK, Mangel JM, Pollard RR, Al-Shakhshir H, Retuerto MA, Steller KM, Elshaer M, Ghannoum MA, Sheyn D. The Response of the Urinary Microbiome to Botox. Int Urogynecol J 2024; 35:237-251. [PMID: 38165444 DOI: 10.1007/s00192-023-05703-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/15/2023] [Indexed: 01/03/2024]
Abstract
INTRODUCTION AND HYPOTHESIS Our objective was to evaluate if botox alters the urinary microbiome of patients with overactive bladder and whether this alteration is predictive of treatment response. METHODS This multicenter prospective cohort study included 18-89-year-old patients undergoing treatment for overactive bladder with 100 units of botox. Urine samples were collected by straight catheterization on the day of the procedure (S1) and again 4 weeks later (S2). Participants completed the Patient Global Impression of Improvement form at their second visit for dichotomization into responders and nonresponders. The microbiome was sequenced using 16s rRNA sequencing. Wilcoxon signed rank and Wilcoxon rank sum were used to compare the microbiome, whereas chi-square, Wilcoxon rank sum, and the independent t-test were utilized for clinical data. RESULTS Sixty-eight participants were included in the analysis. The mean relative abundance and prevalence of Beauveria bassiana, Xerocomus chrysenteron, Crinipellis zonata, and Micrococcus luteus were all found to increase between S1 and S2 in responders; whereas in nonresponders the mean relative abundance and prevalence of Pseudomonas fragi were found to decrease. The MRA and prevalence of Weissella cibaria, Acinetobacter johnsonii, and Acinetobacter schindleri were found to be greater in responders than nonresponders at the time of S1. Significant UM differences in the S1 of patients who did (n = 5) and did not go on to develop a post-treatment UTI were noted. CONCLUSIONS Longitudinal urobiome differences may exist between patients who do and do not respond to botox.
Collapse
Affiliation(s)
- Kasey M Palm
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA.
| | - Megan K Abrams
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sarah B Sears
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Susan D Wherley
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Anood M Alfahmy
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Stacy A Kamumbu
- Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Natalie N Chakraborty
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sangeeta T Mahajan
- Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics and Gynecology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Sherif A El-Nashar
- Division of Female Pelvic Medicine and Reconstructive Surgery, Department of Obstetrics and Gynecology, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Joseph W Henderson
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Adonis K Hijaz
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| | - Jeffrey M Mangel
- Division of Female Pelvic Medicine and Reconstructive Surgery, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Robert R Pollard
- Division of Female Pelvic Medicine and Reconstructive Surgery, MetroHealth Medical Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Hilmi Al-Shakhshir
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Martin A Retuerto
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Kelly M Steller
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - Mohammed Elshaer
- Clinical Pathology Department, Mansoura Faculty of Medicine, Mansoura, Egypt
| | - Mahmoud A Ghannoum
- Center for Medical Mycology, Department of Dermatology, Case Western Reserve University, Cleveland, OH, USA
| | - David Sheyn
- Division of Female Pelvic Medicine and Reconstructive Surgery, Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH, USA
| |
Collapse
|
9
|
Mir TUG, Manhas S, Khurshid Wani A, Akhtar N, Shukla S, Prakash A. Alterations in microbiome of COVID-19 patients and its impact on forensic investigations. Sci Justice 2024; 64:81-94. [PMID: 38182316 DOI: 10.1016/j.scijus.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 11/12/2023] [Accepted: 12/11/2023] [Indexed: 01/07/2024]
Abstract
The human microbiome is vital for maintaining human health and has garnered substantial attention in recent years, particularly in the context of the coronavirus disease 2019 (COVID-19) outbreak. Studies have underscored significant alterations in the microbiome of COVID-19 patients across various body niches, including the gut, respiratory tract, oral cavity, skin, and vagina. These changes manifest as shifts in microbiota composition, characterized by an increase in opportunistic pathogens and a decrease in beneficial commensal bacteria. Such microbiome transformations may play a pivotal role in influencing the course and severity of COVID-19, potentially contributing to the inflammatory response. This ongoing relationship between COVID-19 and the human microbiome serves as a compelling subject of research, underscoring the necessity for further investigations into the underlying mechanisms and their implications for patient health. Additionally, these alterations in the microbiome may have significant ramifications for forensic investigations, given the microbiome's potential in establishing individual characteristics. Consequently, changes in the microbiome could introduce a level of complexity into forensic determinations. As research progresses, a more profound understanding of the human microbiome within the context of COVID-19 may offer valuable insights into disease prevention, treatment strategies, and its potential applications in forensic science. Consequently, this paper aims to provide an overarching review of microbiome alterations due to COVID-19 and the associated impact on forensic applications, bridging the gap between the altered microbiome of COVID-19 patients and the challenges forensic investigations may encounter when analyzing this microbiome as a forensic biomarker.
Collapse
Affiliation(s)
- Tahir Ul Gani Mir
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India; State Forensic Science Laboratory, Srinagar, Jammu and Kashmir 190001, India.
| | - Sakshi Manhas
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India
| | - Saurabh Shukla
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara 144411, Punjab, India.
| | - Ajit Prakash
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| |
Collapse
|
10
|
Liu Z, Liu J, Geng J, Wu E, Zhu J, Cong B, Wu R, Sun H. Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study. Forensic Sci Int Genet 2024; 68:102978. [PMID: 37995518 DOI: 10.1016/j.fsigen.2023.102978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/21/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023]
Abstract
Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the "core microbiome," which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.
Collapse
Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Enlin Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jianzhang Zhu
- Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou 510080, China
| | - Bin Cong
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Shijiazhuang 050017, China.
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China; Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China.
| |
Collapse
|
11
|
Xu G, Teng X, Gao XH, Zhang L, Yan H, Qi RQ. Advances in machine learning-based bacteria analysis for forensic identification: identity, ethnicity, and site of occurrence. Front Microbiol 2023; 14:1332857. [PMID: 38179452 PMCID: PMC10764511 DOI: 10.3389/fmicb.2023.1332857] [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: 11/03/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
When faced with an unidentified body, identifying the victim can be challenging, particularly if physical characteristics are obscured or masked. In recent years, microbiological analysis in forensic science has emerged as a cutting-edge technology. It not only exhibits individual specificity, distinguishing different human biotraces from various sites of occurrence (e.g., gastrointestinal, oral, skin, respiratory, and genitourinary tracts), each hosting distinct bacterial species, but also offers insights into the accident's location and the surrounding environment. The integration of machine learning with microbiomics provides a substantial improvement in classifying bacterial species compares to traditional sequencing techniques. This review discusses the use of machine learning algorithms such as RF, SVM, ANN, DNN, regression, and BN for the detection and identification of various bacteria, including Bacillus anthracis, Acetobacter aceti, Staphylococcus aureus, and Streptococcus, among others. Deep leaning techniques, such as Convolutional Neural Networks (CNN) models and derivatives, are also employed to predict the victim's age, gender, lifestyle, and racial characteristics. It is anticipated that big data analytics and artificial intelligence will play a pivotal role in advancing forensic microbiology in the future.
Collapse
Affiliation(s)
- Geyao Xu
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Xianzhuo Teng
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xing-Hua Gao
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Li Zhang
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Hongwei Yan
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| | - Rui-Qun Qi
- Department of Dermatology, The First Hospital of China Medical University, Shenyang, China
- Key Laboratory of Immunodermatology, Ministry of Education and NHC, National Joint Engineering Research Center for Theranostics of Immunological Skin Diseases, Shenyang, China
| |
Collapse
|
12
|
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.
Collapse
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.)
| |
Collapse
|
13
|
Liao L, Sun Y, Huang L, Ye L, Chen L, Shen M. A novel approach for exploring the regional features of vaginal fluids based on microbial relative abundance and alpha diversity. J Forensic Leg Med 2023; 100:102615. [PMID: 37995431 DOI: 10.1016/j.jflm.2023.102615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 09/14/2023] [Accepted: 11/05/2023] [Indexed: 11/25/2023]
Abstract
Vaginal fluids are one of the most common biological samples in forensic sexual assault cases, and their characterization is vital to narrow the scope of investigation. Presently, approaches for identifying vaginal fluids in different regions are not only rare but also have certain limitations. However, the microbiome has shown the potential to identify the source of body fluids and reveal the characteristics of individuals. In this study, 16S rRNA gene high-throughput sequencing was used to characterize the vaginal microbial community from three regions, Sichuan, Hainan and Hunan. In addition, data on relative abundance and alpha diversity were used to construct a random forest model. The results revealed that the dominant genera in the three regions were Lactobacillus, followed by Gardnerella. In addition, Ureaplasma, Nitrospira, Nocardiodes, Veillonella and g-norank-f-Vicinamibacteraceae were significantly enriched genera in Sichuan, llumatobacter was enriched in Hainan, and Pseudomonas was enriched in Hunan. The random forest classifier based on combined data on relative abundance and alpha diversity had a good ability to distinguish vaginal fluids with similar dominant microbial compositions in the three regions. The study suggests that combining high-throughput sequencing data with machine learning models has good potential for application in the biogeographic inference of vaginal fluids.
Collapse
Affiliation(s)
- Lili Liao
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China; Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Yunxia Sun
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China
| | - Litao Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Linying Ye
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China.
| | - Mei Shen
- Department of Hygiene Inspection & Quarantine Science, Guangdong Provincial Key Laboratory of Tropical Disease Research, School of Public Health, Southern Medical University, Guangzhou, 510515, China.
| |
Collapse
|
14
|
Yu D, Zhang J, Gao N, Huo Y, Li W, Wang T, Zhang X, Simayijiang H, Yan J. Rapid and visual detection of specific bacteria for saliva and vaginal fluid identification with the lateral flow dipstick strategy. Int J Legal Med 2023; 137:1853-1863. [PMID: 37358650 DOI: 10.1007/s00414-023-03051-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/19/2023] [Indexed: 06/27/2023]
Abstract
Identification of body fluids is critical for crime scene reconstruction, and a source of investigation source of investigative leads. In recent years, microbial DNA analysis using sequencing and quantitative real-time polymerase chain reaction have been used to identify body fluids. However, these techniques are time-consuming, expensive, and require complex workflows. In this study, a new method for simultaneous detection of Streptococcus salivarius and Lactobacillus crispatus using polymerase chain reaction (PCR) in combination with a lateral flow dipstick (LFD) was developed to identify saliva and vaginal fluid in forensic samples. LFD results can be observed with the naked eye within 3 min with a sensitivity of 0.001 ng/µL DNA. The PCR-LFD assay was successfully used to detect S. salivarius and L. crispatus in saliva and vaginal fluid respectively, and showed negative results in blood, semen, nasal fluid, and skin. Moreover, saliva and vaginal fluid were detectable even at an extremely high mixing ratio of sample DNA (1:999). Saliva and vaginal fluid were identified in various mock forensic samples. These results indicate that saliva and vaginal fluid can be effectively detected by identifying S. salivarius and L. crispatus, respectively. Furthermore, we have shown that DNA samples used to identify saliva and vaginal fluid can also provide a complete short tandem repeat (STR) profile when used as source material for forensic STR profiling. In summary, our results suggest that PCR-LFD is a promising assay for rapid, simple, reliable, and efficient identification of body fluids.
Collapse
Affiliation(s)
- Daijing Yu
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Jun Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Niu Gao
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Yumei Huo
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Wanting Li
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Tian Wang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Xiaomeng Zhang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China.
- Shanxi Key Laboratory of Forensic Medicine, Jinzhong, 030600, Shanxi, People's Republic of China.
| |
Collapse
|
15
|
Tambuzzi S, Maciocco F, Gentile G, Boracchi M, Bailo P, Marchesi M, Zoja R. Applications of microbiology to different forensic scenarios - A narrative review. J Forensic Leg Med 2023; 98:102560. [PMID: 37451142 DOI: 10.1016/j.jflm.2023.102560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 07/09/2023] [Indexed: 07/18/2023]
Abstract
In contrast to other forensic disciplines, forensic microbiology is still too often considered a "side activity" and is not able to make a real and concrete contribution to forensic investigations. Indeed, the various application aspects of this discipline still remain a niche activity and, as a result, microbiological investigations are often omitted or only approximated, in part due to poor report in the literature. However, in certain situations, forensic microbiology can prove to be extremely effective, if not crucial, when all other disciplines fail. Precisely because microorganisms can represent forensic evidence, in this narrative review all the major pathological forensic applications described in the literature have been presented. The goal of our review is to highlight the versatility and transversality of microbiology in forensic science and to provide a comprehensive source of literature to refer to when needed.
Collapse
Affiliation(s)
- Stefano Tambuzzi
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| | - Francesca Maciocco
- Azienda Ospedaliera "San Carlo Borromeo", Servizio di Immunoematologia e Medicina Trasfusionale (SIMT), Via Pio II°, n. 3, Milano, Italy
| | - Guendalina Gentile
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy.
| | - Michele Boracchi
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| | | | - Matteo Marchesi
- ASST Papa Giovanni XXIII, Piazza OMS 1, 24127, Bergamo, Italy
| | - Riccardo Zoja
- Dipartimento di Scienze Biomediche per la Salute, Sezione di Medicina Legale e delle Assicurazioni, Università degli Studi di Milano, Via Luigi Mangiagalli, 37, 20133, Milano, Italy
| |
Collapse
|
16
|
Kaesler T, Kirkbride KP, Linacre A. Persistence of touch DNA on commonly encountered substrates in different storage conditions. Forensic Sci Int 2023; 348:111728. [PMID: 37209547 DOI: 10.1016/j.forsciint.2023.111728] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/29/2023] [Accepted: 05/08/2023] [Indexed: 05/22/2023]
Abstract
The persistence of touch DNA deposited after realistic handling of items typically encountered in forensic investigations has been the subject of few studies. Understanding the long-term persistence of touch DNA on different substrates in varying conditions can be central to the effective triage of samples for further processing. As the time between an alleged incident and collection of evidence may vary from a few days to years after an alleged event, this study assessed three different common substrates for the persistence of touch DNA over a time span up to 9 months. These substrates included fabric, steel, and rubber, each of which were handled in a way to imitate what may happen during a criminal act. The three substrates were exposed to two different environments for up to 9 months: inside a dark cupboard with no traffic to act as a control and an outside semi-exposed environment. Ten replicates from each of the 3 substrates were tested at 5 time points to create 300 samples. All samples were processed using a standard operating workflow to provide genotype data after exposure to different environments. It was found that the fabric samples produced informative STR profiles (defined here as 12 or more alleles) up to the 9 month timepoint for either environment. The rubber and steel substrates for the inside condition produced informative STR profiles up to the 9 month timepoint, but only generated informative STR profiles for the outside condition up to 3 and 6 months, respectively. These data add to our understanding of the external factors that affect DNA persistence.
Collapse
Affiliation(s)
- Todd Kaesler
- College of Science & Engineering, Flinders University, Adelaide 5042, South Australia.
| | - K Paul Kirkbride
- College of Science & Engineering, Flinders University, Adelaide 5042, South Australia
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide 5042, South Australia
| |
Collapse
|
17
|
Santiago-Rodriguez TM, Le François B, Macklaim JM, Doukhanine E, Hollister EB. The Skin Microbiome: Current Techniques, Challenges, and Future Directions. Microorganisms 2023; 11:1222. [PMID: 37317196 DOI: 10.3390/microorganisms11051222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 06/16/2023] Open
Abstract
Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the skin microbiome, offers protection against pathogens while actively interacting with the host's immune system. Some members of the skin microbiome can also act as opportunistic pathogens. The skin microbiome is influenced by factors such as skin site, birth mode, genetics, environment, skin products, and skin conditions. The association(s) of the skin microbiome with health and disease has (have) been identified and characterized via culture-dependent and culture-independent methods. Culture-independent methods (such as high-throughput sequencing), in particular, have expanded our understanding of the skin microbiome's role in maintaining health or promoting disease. However, the intrinsic challenges associated with the low microbial biomass and high host content of skin microbiome samples have hindered advancements in the field. In addition, the limitations of current collection and extraction methods and biases derived from sample preparation and analysis have significantly influenced the results and conclusions of many skin microbiome studies. Therefore, the present review discusses the technical challenges associated with the collection and processing of skin microbiome samples, the advantages and disadvantages of current sequencing approaches, and potential future areas of focus for the field.
Collapse
|
18
|
Liang X, Liu X, Ye L, Du W, Huang L, Liu C, Xiao G, Huang M, Zheng Y, Shi M, Liu C, Chen L. Development and application of a multiplex PCR system for forensic salivary identification. Int J Legal Med 2023:10.1007/s00414-023-03004-2. [PMID: 37127761 DOI: 10.1007/s00414-023-03004-2] [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: 11/15/2022] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
In forensics, accurate identification of the origin of body fluids is essential for reconstructing a crime scene or presenting strong evidence in court. Microorganisms have demonstrated great potential in body fluid identification. We developed a multiplex PCR system for forensic salivary identification, which contains five types of bacteria:Streptococcus salivarius, Neisseria subflava, Streptococcus. mutans, Bacteroides thetaiotaomicron, and Bacteroides. uniformis. And the validated studies were carried out following the validation guidelines for DNA analysis methods developed by the Scientific Working Group on DNA Analysis Methods (SWGDAM), which included tests for sensitivity, species specificity, repeatability, stability, and mixed samples, trace samples, case samples, and a population study. Our result depicted that the lowest detection limit of the system was 0.01 ng template DNA. Moreover, the corresponding bacteria can still be detected when the amount of saliva input is low to 0.1 μL for DNA extraction. In addition, the target bacteria were not detected in the DNA of human, seven common animals, and seven bacteria DNA and in nine other body fluid samples (skin, semen, blood, menstrual blood, nasal mucus, sweat, tears, urine, and vaginal secretions). Six common inhibitors such as indigo, EDTA, hemoglobin, calcium ions, alcohol and humic acid were well tolerated by the system. What is more, the salivary identification system recognized the saliva component in all mixed samples and simulated case samples. Among 400 unrelated individuals from the Chinese Han population analyzed by this novel system, the detection rates of N. subflava, S. salivarius, and S. mutans were 97.75%, 70.75%, and 19.75%, respectively, with 100% identification of saliva. In conclusion, the salivary identification system has good sensitivity, specificity, stability, and accuracy, which can be a new effective tool for saliva identification.
Collapse
Affiliation(s)
- Xiaomin Liang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, China
| | - Linying Ye
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Weian Du
- Guangdong Homy Genetics Ltd, Foshan, 528000, China
| | - Litao Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Changhui Liu
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, China
| | - Guichao Xiao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Manling Huang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | | | - Meisen Shi
- Criminal Justice College of China University of Political Science and Law, Beijing, 100088, People's Republic of China.
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
- Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou Forensic Science Institute, Guangzhou, 510030, China.
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| |
Collapse
|
19
|
Ogbanga N, Nelson A, Ghignone S, Voyron S, Lovisolo F, Sguazzi G, Renò F, Migliario M, Gino S, Procopio N. The Oral Microbiome for Geographic Origin: An Italian Study. Forensic Sci Int Genet 2023; 64:102841. [PMID: 36774834 DOI: 10.1016/j.fsigen.2023.102841] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/30/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023]
Abstract
The human oral microbiome has primarily been studied in clinical settings and for medical purposes. More recently, oral microbial research has been incorporated into other areas of study. In forensics, research has aimed to exploit the variation in composition of the oral microbiome to answer forensic relevant topics, such as human identification and geographical provenience. Several studies have focused on the use of microbiome for continental, national, or ethnic origin evaluations. However, it is not clear how the microbiome varies between similar ethnic populations across different regions in a country. We report here a comparison of the oral microbiomes of individuals living in two regions of Italy - Lombardy and Piedmont. Oral samples were obtained by swabbing the donors' oral mucosa, and the V4 region of the 16S rRNA gene was sequenced from the extracted microbial DNA. Additionally, we compared the oral and the skin microbiome from a subset of these individuals, to provide an understanding of which anatomical region may provide more robust results that can be useful for forensic human identification. Initial analysis of the oral microbiota revealed the presence of a core oral microbiome, consisting of nine taxa shared across all oral samples, as well as unique donor characterising taxa in 31 out of 50 samples. We also identified a trend between the abundance of Proteobacteria and Bacteroidota and the smoking habits, and of Spirochaetota and Synergistota and the age of the enrolled participants. Whilst no significant differences were observed in the oral microbial diversity of individuals from Lombardy or Piedmont, we identified two bacterial families - Corynebacteriaceae and Actinomycetaceae - that showed abundance trends between the two regions. Comparative analysis of the skin and oral microbiota showed significant differences in the alpha (p = 0.0011) and beta (Pr(>F)= 9.999e-05) diversities. Analysis of skin and oral samples from the same donor further revealed that the skin microbiome contained more unique donor characterising taxa than the oral one. Overall, this study demonstrates that whilst the oral microbiome of individuals from the same country and of similar ethnicity are largely similar, there may be donor characterising taxa that might be useful for identification purposes. Furthermore, the bacterial signatures associated with certain lifestyles could provide useful information for investigative purposes. Finally, additional studies are required, the skin microbiome may be a better discriminant for human identification than the oral one.
Collapse
Affiliation(s)
- Nengi Ogbanga
- Faculty of Health and Life Sciences - Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK
| | - Andrew Nelson
- Faculty of Health and Life Sciences - Applied Sciences, Northumbria University, Newcastle Upon Tyne NE1 8ST, UK
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection (IPSP) - Turin Unit - National Research Council (CNR), 10125 Turin, Italy
| | - Samuele Voyron
- Institute for Sustainable Plant Protection (IPSP) - Turin Unit - National Research Council (CNR), 10125 Turin, Italy; Department of Life Sciences and Systems Biology, University of Torino, V.le P.A. Mattioli 25, 10125 Turin, Italy
| | - Flavia Lovisolo
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - 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
| | - 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
| | - Sarah Gino
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Noemi Procopio
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy; School of Natural Sciences, University of Central Lancashire, PR1 2HE Preston, UK.
| |
Collapse
|
20
|
The dynamic balance of the skin microbiome across the lifespan. Biochem Soc Trans 2023; 51:71-86. [PMID: 36606709 PMCID: PMC9988004 DOI: 10.1042/bst20220216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/07/2023]
Abstract
For decades research has centered on identifying the ideal balanced skin microbiome that prevents disease and on developing therapeutics to foster this balance. However, this single idealized balance may not exist. The skin microbiome changes across the lifespan. This is reflected in the dynamic shifts of the skin microbiome's diverse, inter-connected community of microorganisms with age. While there are core skin microbial taxa, the precise community composition for any individual person is determined by local skin physiology, genetics, microbe-host interactions, and microbe-microbe interactions. As a key interface with the environment, the skin surface and its appendages are also constantly exchanging microbes with close personal contacts and the environment. Hormone fluctuations and immune system maturation also drive age-dependent changes in skin physiology that support different microbial community structures over time. Here, we review recent insights into the factors that shape the skin microbiome throughout life. Collectively, the works summarized within this review highlight how, depending on where we are in lifespan, our skin supports robust microbial communities, while still maintaining microbial features unique to us. This review will also highlight how disruptions to this dynamic microbial balance can influence risk for dermatological diseases as well as impact lifelong health.
Collapse
|
21
|
Influence of Hormonal Contraceptive Use and HIV on Cervicovaginal Cytokines and Microbiota in Malawi. mSphere 2023; 8:e0058522. [PMID: 36622252 PMCID: PMC9942570 DOI: 10.1128/msphere.00585-22] [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: 01/10/2023] Open
Abstract
Important questions remain on how hormonal contraceptives alter the local immune environment and the microbiota in the female genital tract and how such effects may impact susceptibility to HIV infection. We leveraged samples from a previously conducted clinical trial of Malawian women with (n = 73) and without (n = 24) HIV infection randomized to depot medroxyprogesterone acetate (DMPA) or the levonogestrel implant in equal numbers within each group and determined the effects of these hormonal contraceptives (HCs) on the vaginal immune milieu and the composition of the vaginal microbiota. Longitudinal data for soluble immune mediators, measured by multiplex bead arrays and enzyme-linked immunosorbent assays (ELISAs), and vaginal microbiota, assessed by 16S rRNA gene amplicon, were collected prior to and over a period of 180 days post-HC initiation. DMPA and levonogestrel had only minimal effects on the vaginal immune milieu and microbiota. In women with HIV, with the caveat of a small sample size, there was an association between the median log10 change in the interleukin-12 (IL-12)/IL-10 ratio in vaginal fluid at day 180 post-HC compared to baseline when these women were classified as having a community state type (CST) IV vaginal microbiota and were randomized to DMPA. Long-lasting alterations in soluble immune markers or shifts in microbiota composition were not observed. Furthermore, women with HIV did not exhibit increased viral shedding in the genital tract after HC initiation. Consistent with the results of the ECHO (Evidence for Contraceptive Options and HIV Outcomes) trial, our data imply that the progestin-based HC DMPA and levonorgestrel are associated with minimal risk for women with HIV. (This study has been registered at ClinicalTrials.gov under registration no. NCT02103660). IMPORTANCE The results of the Evidence for Contraceptive Options and HIV Outcomes (ECHO) trial, the first large randomized controlled clinical trial comparing the HIV acquisition risk of women receiving DMPA, the levonorgestrel (LNG) implant, or the copper intrauterine device (IUD), did not reveal an increased risk of HIV acquisition for women on any of these three contraceptives. Our study results confirm that the two different progestin-based hormonal contraceptives DMPA and levonogestrel will not increase the risk for HIV infection. Furthermore, DMPA and levonogestrel have only minimal effects on the immune milieu and the microbiota in the vaginal tract, attesting to the safety of these hormonal contraceptives.
Collapse
|
22
|
Yu KM, Lee AM, Cho HS, Lee JW, Lim SK. Optimization of DNA extraction and sampling methods for successful forensic microbiome analyses of the skin and saliva. Int J Legal Med 2023; 137:63-77. [PMID: 36416962 DOI: 10.1007/s00414-022-02919-6] [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: 07/15/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022]
Abstract
Microbiome studies have contributed to many fields, such as healthcare and medicine; however, these studies are relatively limited in forensics. Microbiome analyses can provide information, such as geolocation and ancestry information, when short tandem repeat (STR) profiling fails. In this study, methods for DNA extraction and sampling from the skin and saliva were optimized for the construction of a Korean Forensic Microbiome Database (KFMD). DNA yields were estimated using four DNA extraction kits, including two automated kits (Maxwell® FSC DNA IQ™ Casework Kit and PrepFiler™ Forensic DNA Extraction Kit, updated) and two manual kits (QIAamp DNA Mini Kit and QIAamp DNA Micro Kit) commonly used in forensic DNA profiling laboratories. Next-generation sequencing of the 16S rRNA V4 region was performed to analyze microbial communities in samples. The Bacterial Transport Swab with Liquid Media (NobleBio), two cotton swabs (PoongSung and Puritan), and nylon-flocked swabs (NobleBio and COPAN) were tested for DNA recovery. The PrepFiler and Maxwell kits showed the highest yields of 3.884 ng/μL and 23.767 ng/μL from the scalp and saliva, respectively. With respect to DNA recovery, nylon-flocked swabs performed better than cotton swabs. The relative abundances of taxa sorted by DNA extraction kits were similar contributions; however, with significant differences in community composition between scalp and saliva samples. Lawsonella and Veillonella were the most abundant genera in the two sample types. Thus, the Maxwell® FSC DNA IQ™ Casework Kit and nylon-flocked swab (NobleBio) were optimal for DNA extraction and collection in microbiome analyses.
Collapse
Affiliation(s)
- Kyeong-Min Yu
- Department of Forensic Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - A-Mi Lee
- Department of Forensic Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Hye-Seon Cho
- Department of Forensic Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Ji-Woo Lee
- Department of Forensic Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea
| | - Si-Keun Lim
- Department of Forensic Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| |
Collapse
|
23
|
Abstract
This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.
Collapse
|
24
|
Hu X, Haas JG, Lathe R. The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data. BMC Microbiol 2022; 22:317. [PMID: 36550399 PMCID: PMC9773549 DOI: 10.1186/s12866-022-02671-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 10/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life. RESULTS We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved. CONCLUSIONS This generic methodology is likely to find wide application in microbiome analysis including diagnostics.
Collapse
Affiliation(s)
- Xinyue Hu
- Program in Bioinformatics, School of Biological Sciences, King's Buildings, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Jürgen G Haas
- Division of Infection Medicine, University of Edinburgh, Little France, Edinburgh, EH16 4SB, UK
| | - Richard Lathe
- Division of Infection Medicine, University of Edinburgh, Little France, Edinburgh, EH16 4SB, UK.
| |
Collapse
|
25
|
Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes. Sci Rep 2022; 12:18547. [PMID: 36329122 PMCID: PMC9633824 DOI: 10.1038/s41598-022-21779-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/04/2022] [Indexed: 11/06/2022] Open
Abstract
Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals. As such, significant forensic information could be obtained from high throughput sequencing of the human microbiome. This approach, combined with multiple analytical techniques demonstrates that bacterial DNA can be used to uniquely identify an individual and to provide information about their life and behavioral patterns. However, the transformation of these findings into actionable forensic information, including the geolocation of the samples, remains limited by incomplete understanding of the effects of confounding factors and the paucity of diverse sequences. We obtained 16S rRNA sequences of stool and oral microbiomes collected from 206 young and healthy females from four globally diverse populations, in addition to supporting metadata, including dietary and medical information. Analysis of these microbiomes revealed detectable geolocation signals between the populations, even for populations living within the same city. Accounting for other lifestyle variables, such as diet and smoking, lessened but does not remove the geolocation signal.
Collapse
|
26
|
Ruuskanen MO, Vats D, Potbhare R, RaviKumar A, Munukka E, Ashma R, Lahti L. Towards standardized and reproducible research in skin microbiomes. Environ Microbiol 2022; 24:3840-3860. [PMID: 35229437 PMCID: PMC9790573 DOI: 10.1111/1462-2920.15945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 12/30/2022]
Abstract
Skin is a complex organ serving a critical role as a barrier and mediator of interactions between the human body and its environment. Recent studies have uncovered how resident microbial communities play a significant role in maintaining the normal healthy function of the skin and the immune system. In turn, numerous host-associated and environmental factors influence these communities' composition and diversity across the cutaneous surface. In addition, specific compositional changes in skin microbiota have also been connected to the development of several chronic diseases. The current era of microbiome research is characterized by its reliance on large data sets of nucleotide sequences produced with high-throughput sequencing of sample-extracted DNA. These approaches have yielded new insights into many previously uncharacterized microbial communities. Application of standardized practices in the study of skin microbial communities could help us understand their complex structures, functional capacities, and health associations and increase the reproducibility of the research. Here, we overview the current research in human skin microbiomes and outline challenges specific to their study. Furthermore, we provide perspectives on recent advances in methods, analytical tools and applications of skin microbiomes in medicine and forensics.
Collapse
Affiliation(s)
- Matti O. Ruuskanen
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| | - Deepti Vats
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Renuka Potbhare
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Ameeta RaviKumar
- Institute of Bioinformatics and BiotechnologySavitribai Phule Pune UniversityPuneIndia
| | - Eveliina Munukka
- Microbiome Biobank, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Richa Ashma
- Department of Zoology, Centre of Advanced StudySavitribai Phule Pune UniversityPuneIndia
| | - Leo Lahti
- Department of Computing, Faculty of TechnologyUniversity of TurkuTurkuFinland
| |
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Abstract
The failure of animal models to predict therapeutic responses in humans is a major problem that also brings into question their use for basic research. Organ-on-a-chip (organ chip) microfluidic devices lined with living cells cultured under fluid flow can recapitulate organ-level physiology and pathophysiology with high fidelity. Here, I review how single and multiple human organ chip systems have been used to model complex diseases and rare genetic disorders, to study host-microbiome interactions, to recapitulate whole-body inter-organ physiology and to reproduce human clinical responses to drugs, radiation, toxins and infectious pathogens. I also address the challenges that must be overcome for organ chips to be accepted by the pharmaceutical industry and regulatory agencies, as well as discuss recent advances in the field. It is evident that the use of human organ chips instead of animal models for drug development and as living avatars for personalized medicine is ever closer to realization.
Collapse
Affiliation(s)
- Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering at Harvard University, Boston, MA, USA.
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA.
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, USA.
| |
Collapse
|
29
|
Effect of β-Estradiol on Mono- and Mixed-Species Biofilms of Human Commensal Bacteria Lactobacillus paracasei AK508 and Micrococcus luteus C01 on Different Model Surfaces. COATINGS 2022. [DOI: 10.3390/coatings12040436] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The impact of steroid hormones, and particularly estradiol, on human microbiota could be recognized as a substantial part of human-microbiota interactions. However, an area that remains poorly investigated is that of the skin and vaginal microbial communities and biofilms, which contain non-pathogenic bacteria of phyla Firmicutes and Actinobacteria, especially probiotic bacteria of the genus Lactobacillus and the widespread, safe skin genus, Micrococcus. Experiments with Lactobacillus paracasei AK508 and Micrococcus luteus C01 biofilms on PTFE cubes showed dose-dependent effects of estradiol at concentrations of 0.22 nM and 22 nM. The hormone mostly inhibits L. paracasei growth and stimulates M. luteus. The presented studies of colony-forming unit (CFU) amountsand cell aggregation in biofilms on glass fiber filters showed the same general tendencies. Estradiol generally increased the aggregation of cells in monospecies communities and potentially changed the synthesis of antibacterial metabolites in L. paracasei. The balance between two bacteria in mixed-species biofilms depended on the initial adhesion stage, and when this stage was reduced, micrococci were more resistant to the antagonistic action of L. paracasei. Moreover, in mixed-species biofilms, the effect of estradiol on lactobacilli altered from inhibition to stimulation, potentially due to the presence of M. luteus. At the same time, ethanol as a solvent for estradiol at the concentration 0.6% acted mostly as an antagonist of the hormone and had an opposite effect on bacteria; nevertheless, the overlapping of ethanol and estradiol effects was shown to be minimal. The data obtained prove the complexity of microbial interactions and the regulatory effect of estradiol on commensal bacteria biofilms.
Collapse
|
30
|
Poetsch M, Markwerth P, Konrad H, Bajanowski T, Helmus J. About the influence of environmental factors on the persistence of DNA - a long-term study. Int J Legal Med 2022; 136:687-693. [PMID: 35195781 PMCID: PMC9005405 DOI: 10.1007/s00414-022-02800-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/09/2022] [Indexed: 11/05/2022]
Abstract
DNA persistence and DNA transfer are important features in the assessment of a crime scene. The question how long DNA may persist at a certain location is similarly important as the one how the DNA has been transferred to this location. Depending on the source of the DNA as well as the conditions at the crime scene, the answer to this question is quite difficult. In this study, persistence of DNA from epithelial abrasions, blood cells, and saliva cells in indoor and outdoor scenarios has been investigated with regard to exposure time and exposure conditions including sunlight, temperature, and humidity in summer and winter scenarios. Overall, we generated 338 epithelial samples, 572 blood samples, and 572 saliva samples. A complete profile of the cell/DNA donor after exposure could be obtained in 47%, 65%, and 58% of epithelial abrasions, blood samples, and saliva samples, respectively. Regarding blood samples, there were no differences between supporting materials cloth and plastic; however, the percentage of complete profiles was higher for saliva samples on plastic and for epithelial samples on cloth. In indoor scenarios, complete profiles could be recovered from nearly all blood and saliva samples up to 9 months, whereas the amount of epithelial complete profiles already started to decline after 3 months. In outdoor scenarios, we observed a tipping point at an exposure time of 3 months. Blood and saliva samples collected after this period displayed complete profiles in less than 25% of samples. After 12 months, no outdoor sample showed a complete profile. The results of this study facilitate decisions on the relevance of recovered DNA from crime scenes.
Collapse
Affiliation(s)
- Micaela Poetsch
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany.
| | - Philipp Markwerth
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Helen Konrad
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Thomas Bajanowski
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| | - Janine Helmus
- Institute of Legal Medicine, University Hospital Essen, Hufelandstr. 55, 45122, Essen, Germany
| |
Collapse
|
31
|
Sijen T, Harbison S. On the Identification of Body Fluids and Tissues: A Crucial Link in the Investigation and Solution of Crime. Genes (Basel) 2021; 12:1728. [PMID: 34828334 PMCID: PMC8617621 DOI: 10.3390/genes12111728] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 10/26/2021] [Accepted: 10/26/2021] [Indexed: 12/13/2022] Open
Abstract
Body fluid and body tissue identification are important in forensic science as they can provide key evidence in a criminal investigation and may assist the court in reaching conclusions. Establishing a link between identifying the fluid or tissue and the DNA profile adds further weight to this evidence. Many forensic laboratories retain techniques for the identification of biological fluids that have been widely used for some time. More recently, many different biomarkers and technologies have been proposed for identification of body fluids and tissues of forensic relevance some of which are now used in forensic casework. Here, we summarize the role of body fluid/ tissue identification in the evaluation of forensic evidence, describe how such evidence is detected at the crime scene and in the laboratory, elaborate different technologies available to do this, and reflect real life experiences. We explain how, by including this information, crucial links can be made to aid in the investigation and solution of crime.
Collapse
Affiliation(s)
- Titia Sijen
- Division Human Biological Traces, Netherlands Forensic Institute, Laan van Ypenburg 6, 2497 GB The Hague, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - SallyAnn Harbison
- Institute of Environmental Science and Research Limited, Private Bag 92021, Auckland 1142, New Zealand;
- Department of Statistics, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| |
Collapse
|