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Üstüntürk-Onan M, Tüccar T, Ilhan-Sungur E. Occurrence of sulfate-reducing bacteria in well water: identification of anaerobic sulfidogenic bacterial enrichment cultures. JOURNAL OF WATER AND HEALTH 2024; 22:746-756. [PMID: 38678427 DOI: 10.2166/wh.2024.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 03/15/2024] [Indexed: 04/30/2024]
Abstract
Bacteriological studies of well water mainly focus on aerobic and facultative aerobic coliform bacteria. However, the presence of obligate anaerobic bacteria in well water, especially sulfate-reducing bacteria (SRB), possible causative agents of some diseases, is often ignored. In this study, the presence of SRB and coexisting anaerobic bacteria with SRB in sulfate-reducing enrichment cultures obtained from 10 well water samples in Istanbul was investigated. A nested polymerase chain reaction-denaturing gradient gel electrophoresis strategy was performed to characterize the bacterial community structure of the enrichments. The most probable number method was used to determine SRB number. Out of 10, SRB growth was observed in only one (10%) enrichment culture and the SRB number was low (<10 cells/mL). Community members were identified as Desulfolutivibrio sulfodismutans and Anaerosinus sp. The results show that SRB coexist with Anaerosinus sp., and this may indicate poor water quality, posing a risk to public health. Furthermore, Anaerosinus sp., found in the human intestinal tract, may be used as an alternative anaerobic fecal indicator. It is worth noting that the detection of bacteria using molecular analyzes following enrichment culture techniques can bring new perspectives to determine the possible origin and presence of alternative microbial indicators in aquatic environments.
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Affiliation(s)
- Miray Üstüntürk-Onan
- Department of Biology, Faculty of Science, Istanbul University, Vezneciler, Istanbul 34134, Türkiye
| | - Tuğçe Tüccar
- Medical Laboratory Techniques Program, Vocational School, Istanbul Arel University, Cevizlibağ, Istanbul 34010, Türkiye E-mail:
| | - Esra Ilhan-Sungur
- Department of Biology, Faculty of Science, Istanbul University, Vezneciler, Istanbul 34134, Türkiye
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2
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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.
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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
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Gouello A, Henry L, Chadli D, Salipante F, Gibert J, Boutet-Dubois A, Lavigne JP. Evaluation of the Microbiome Identification of Forensically Relevant Biological Fluids: A Pilot Study. Diagnostics (Basel) 2024; 14:187. [PMID: 38248064 PMCID: PMC10814007 DOI: 10.3390/diagnostics14020187] [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: 11/19/2023] [Revised: 01/04/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
In forensic sciences, body fluids, or biological traces, are a major source of information, and their identification can play a decisive role in criminal investigations. Currently, the nature of biological fluids is assessed using immunological, physico-chemical, mRNA and epigenetic methods, but these have limits in terms of sensitivity and specificity. The emergence of next-generation sequencing technologies offers new opportunities to identify the nature of body fluids by determining bacterial communities. The aim of this pilot study was to assess whether analysis of the bacterial communities in isolated and mixed biological fluids could reflect the situation observed in real forensics labs. Several samples commonly encountered in forensic sciences were tested from healthy volunteers: saliva, vaginal fluid, blood, semen and skin swabs. These samples were analyzed alone or in combination in a ratio of 1:1. Sequencing was performed on the Ion Gene StudioTM S5 automated sequencer. Fluids tested alone revealed a typical bacterial signature with specific bacterial orders, enabling formal identification of the fluid of interest, despite inter-individual variations. However, in biological fluid mixtures, the predominance of some bacterial microbiomes inhibited interpretation. Oral and vaginal microbiomes were clearly preponderant, and the relative abundance of their bacterial communities and/or the presence of common species between samples made it impossible to detect bacterial orders or genera from other fluids, although they were distinguishable from one another. However, using the beta diversity, salivary fluids were identified and could be distinguished from fluids in combination. While this method of fluid identification is promising, further analyses are required to consolidate the protocol and ensure reliability.
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Affiliation(s)
- Audrey Gouello
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95000 Cergy-Pontoise, France; (A.G.); (L.H.); (D.C.); (J.G.)
- VBIC, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France;
| | - Laura Henry
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95000 Cergy-Pontoise, France; (A.G.); (L.H.); (D.C.); (J.G.)
- Sciences Sorbonne Universtity, 75005 Paris, France
| | - Djamel Chadli
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95000 Cergy-Pontoise, France; (A.G.); (L.H.); (D.C.); (J.G.)
- Aix-Marseille University, 13005 Marseille, France
| | - Florian Salipante
- Service de Biostatistiques, Epidémiologie, Santé Publique et Innovation en Méthodologie, Université Montpellier, CHU Nîmes, 30029 Nîmes, France;
| | - Joséphine Gibert
- Institut de Recherche Criminelle de la Gendarmerie Nationale, 95000 Cergy-Pontoise, France; (A.G.); (L.H.); (D.C.); (J.G.)
| | - Adeline Boutet-Dubois
- VBIC, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France;
| | - Jean-Philippe Lavigne
- VBIC, INSERM U1047, Université Montpellier, Service de Microbiologie et Hygiène Hospitalière, CHU Nîmes, 30908 Nîmes, France;
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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.
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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.
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Locci E, Stocchero M, Gottardo R, Chighine A, De-Giorgio F, Ferino G, Nioi M, Demontis R, Tagliaro F, d'Aloja E. PMI estimation through metabolomics and potassium analysis on animal vitreous humour. Int J Legal Med 2023; 137:887-895. [PMID: 36799966 PMCID: PMC10085955 DOI: 10.1007/s00414-023-02975-6] [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: 10/23/2022] [Accepted: 02/08/2023] [Indexed: 02/18/2023]
Abstract
INTRODUCTION The estimation of post-mortem interval (PMI) remains a major challenge in forensic science. Most of the proposed approaches lack the reliability required to meet the rigorous forensic standards. OBJECTIVES We applied 1H NMR metabolomics to estimate PMI on ovine vitreous humour comparing the results with the actual scientific gold standard, namely vitreous potassium concentrations. METHODS Vitreous humour samples were collected in a time frame ranging from 6 to 86 h after death. Experiments were performed by using 1H NMR metabolomics and ion capillary analysis. Data were submitted to multivariate statistical data analysis. RESULTS A multivariate calibration model was built to estimate PMI based on 47 vitreous humour samples. The model was validated with an independent test set of 24 samples, obtaining a prediction error on the entire range of 6.9 h for PMI < 24 h, 7.4 h for PMI between 24 and 48 h, and 10.3 h for PMI > 48 h. Time-related modifications of the 1H NMR vitreous metabolomic profile could predict PMI better than potassium up to 48 h after death, whilst a combination of the two is better than the single approach for higher PMI estimation. CONCLUSION The present study, although in a proof-of-concept animal model, shows that vitreous metabolomics can be a powerful tool to predict PMI providing a more accurate estimation compared to the widely studied approach based on vitreous potassium concentrations.
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Affiliation(s)
- Emanuela Locci
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Matteo Stocchero
- Department of Women's and Children's Health, University of Padova, Padua, Italy
| | - Rossella Gottardo
- Department of Diagnostics and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
| | - Alberto Chighine
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy.
| | - Fabio De-Giorgio
- Department of Health Surveillance and Bioethics, Section of Legal Medicine, Catholic University of Rome, Rome, Italy.,Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giulio Ferino
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Matteo Nioi
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Roberto Demontis
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
| | - Franco Tagliaro
- Department of Diagnostics and Public Health, Unit of Forensic Medicine, University of Verona, Verona, Italy
| | - Ernesto d'Aloja
- Department of Medical Sciences and Public Health, Section of Legal Medicine, University of Cagliari, Cittadella Universitaria di Monserrato, 09042, Monserrato, Cagliari, Italy
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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.
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Tozzo P, Amico I, Delicati A, Toselli F, Caenazzo L. Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review. Diagnostics (Basel) 2022; 12:2641. [PMID: 36359484 PMCID: PMC9689864 DOI: 10.3390/diagnostics12112641] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 08/12/2023] Open
Abstract
The determination of the Post-Mortem Interval (PMI) is an issue that has always represented a challenge in the field of forensic science. Different innovative approaches, compared to the more traditional ones, have been tried over the years, without succeeding in being validated as successful methods for PMI estimation. In the last two decades, innovations in sequencing technologies have made it possible to generate large volumes of data, allowing all members of a bacterial community to be sequenced. The aim of this manuscript is to provide a review regarding new advances in PMI estimation through cadaveric microbiota identification using 16S rRNA sequencing, in order to correlate specific microbiome profiles obtained from different body sites to PMI. The systematic review was performed according to PRISMA guidelines. For this purpose, 800 studies were identified through database searching (Pubmed). Articles that dealt with PMI estimation in correlation with microbiome composition and contained data about species, body site of sampling, monitoring time and sequencing method were selected and ultimately a total of 25 studies were considered. The selected studies evaluated the contribution of the various body sites to determine PMI, based on microbiome sequencing, in human and animal models. The results of this systematic review highlighted that studies conducted on both animals and humans yielded results that were promising. In order to fully exploit the potential of the microbiome in the estimation of PMI, it would be desirable to identify standardized body sampling sites and specific sampling methods in order to align data obtained by different research groups.
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Affiliation(s)
- Pamela Tozzo
- Department of Cardiac, Thoracic, Vascular Sciences and Public Health, University of Padova, 35121 Padova, Italy
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Carratto TMT, Moraes VMS, Recalde TSF, Oliveira MLGD, Teixeira Mendes-Junior C. Applications of massively parallel sequencing in forensic genetics. Genet Mol Biol 2022; 45:e20220077. [PMID: 36121926 PMCID: PMC9514793 DOI: 10.1590/1678-4685-gmb-2022-0077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/22/2022] Open
Abstract
Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.
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Affiliation(s)
- Thássia Mayra Telles Carratto
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | - Vitor Matheus Soares Moraes
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
| | | | | | - Celso Teixeira Mendes-Junior
- Universidade de São Paulo, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Departamento de Química, Laboratório de Pesquisas Forenses e Genômicas, Ribeirão Preto, SP, Brazil
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Lovisolo F, Ogbanga N, Sguazzi G, Renò F, Migliario M, Nelson A, Procopio N, Gino S. ORAL AND SKIN MICROBIOME AS POTENTIAL TOOLS IN FORENSIC FIELD. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2022. [DOI: 10.1016/j.fsigss.2022.09.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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10
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Sguazzi G, Mickleburgh HL, Ghignone S, Voyron S, Renò F, Migliario M, Sellitto F, Lovisolo F, Camurani G, Ogbanga N, Gino S, Procopio N. Microbial DNA in human nucleic acid extracts: Recoverability of the microbiome in DNA extracts stored frozen long-term and its potential and ethical implications for forensic investigation. Forensic Sci Int Genet 2022; 59:102686. [PMID: 35338895 DOI: 10.1016/j.fsigen.2022.102686] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 11/28/2022]
Abstract
Human DNA samples can remain unaltered for years and preserve important genetic information for forensic investigations. In fact, besides human genetic information, these extracts potentially contain additional valuable information: microbiome signatures. Forensic microbiology is rapidly becoming a significant tool for estimating post-mortem interval (PMI), and establishing cause of death and personal identity. To date, the possibility to recover unaltered microbiome signatures from human DNA extracts has not been proven. This study examines the microbiome signatures within human DNA extracts obtained from six cadavers with different PMIs, which were stored frozen for 5-16 years. Results demonstrated that the microbiome can be co-extracted with human DNA using forensic kits designed to extract the human host's DNA from different tissues and fluids during decomposition. We compared the microbial communities identified in these samples with microbial DNA recovered from two human cadavers donated to the Forensic Anthropology Center at Texas State University (FACTS) during multiple decomposition stages, to examine whether the microbial signatures recovered from "old" (up to 16 years) extracts are consistent with those identified in recently extracted microbial DNA samples. The V4 region of 16 S rRNA gene was amplified and sequenced using Illumina MiSeq for all DNA extracts. The results obtained from the human DNA extracts were compared with each other and with the microbial DNA from the FACTS samples. Overall, we found that the presence of specific microbial taxa depends on the decomposition stage, the type of tissue, and the depositional environment. We found no indications of contamination in the microbial signatures, or any alterations attributable to the long-term frozen storage of the extracts, demonstrating that older human DNA extracts are a reliable source of such microbial signatures. No shared Core Microbiome (CM) was identified amongst the total 18 samples, but we identified certain species in association with the different decomposition stages, offering potential for the use of microbial signatures co-extracted with human DNA samples for PMI estimation in future. Unveiling the new significance of older human DNA extracts brings with it important ethical-legal considerations. Currently, there are no shared legal frameworks governing the long-term storage and use of human DNA extracts obtained from crime scene evidence for additional research purposes. It is therefore important to create common protocols on the storage of biological material collected at crime scenes. We review existing legislation and guidelines, and identify some important limitations for the further development and application of forensic microbiomics.
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Affiliation(s)
- Giulia Sguazzi
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy; CRIMEDIM - Center for Research and Training in Disaster Medicine, Humanitarian Aid and Global Health, Università del Piemonte Orientale, Via Lanino, 1-28100 Novara, Italy
| | - Hayley L Mickleburgh
- Department of Cultural Sciences, Linnaeus University, Växjö, Sweden; Forensic Anthropology Center, Texas State University, San Marcos, TX, USA
| | - Stefano Ghignone
- Institute for Sustainable Plant Protection (IPSP) - Turin Unit - National Research Council (CNR), 1-10125 Turin, Italy
| | - Samuele Voyron
- Institute for Sustainable Plant Protection (IPSP) - Turin Unit - National Research Council (CNR), 1-10125 Turin, Italy; Department of Life Sciences and Systems Biology, University of Torino, V.le P.A. Mattioli 25, 10125 Turin, Italy
| | - Filippo Renò
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Mario Migliario
- Department of Translational Medicine, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Federica Sellitto
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST, Newcastle Upon Tyne, UK
| | - Flavia Lovisolo
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Giulia Camurani
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Nengi Ogbanga
- Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST, Newcastle Upon Tyne, UK
| | - Sarah Gino
- Department of Health Science, University of Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy
| | - Noemi Procopio
- Forensic Anthropology Center, Texas State University, San Marcos, TX, USA; Forensic Science Research Group, Faculty of Health and Life Sciences, Applied Sciences, Northumbria University, NE1 8ST, Newcastle Upon Tyne, UK.
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11
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Caenazzo L, Tozzo P. Microbiome Forensic Biobanking: A Step toward Microbial Profiling for Forensic Human Identification. Healthcare (Basel) 2021; 9:1371. [PMID: 34683051 PMCID: PMC8544459 DOI: 10.3390/healthcare9101371] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/04/2021] [Accepted: 10/11/2021] [Indexed: 11/16/2022] Open
Abstract
In recent years many studies have highlighted the great potential of microbial analysis in human identification for forensic purposes, with important differences in microbial community composition and function across different people and locations, showing a certain degree of uncertainty. Therefore, further studies are necessary to enable forensic scientists to evaluate the risk of microbial transfer and recovery from various items and to further critically evaluate the suitability of current human DNA recovery protocols for human microbial profiling for identification purposes. While the establishment and development of microbiome research biobanks for clinical applications is already very structured, the development of studies on the applicability of microbiome biobanks for forensic purposes is still in its infancy. The creation of large population microbiome biobanks, specifically dedicated to forensic human identification, could be worthwhile. This could also be useful to increase the practical applications of forensic microbiology for identification purposes, given that this type of evidence is currently absent from most real casework investigations and judicial proceedings in courts.
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Affiliation(s)
| | - Pamela Tozzo
- Laboratory of Forensic Genetics, Department of Molecular Medicine, University of Padova, 35121 Padova, Italy;
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