Microbial Forensics: A Present to Future Perspective on Genomic Targets, Bioinformatic Challenges, and Applications

Shadoff, Rachel; Panoyan, Mary Anne; Novroski, Nicole M.M.

doi:10.1089/forensic.2022.0007

Cited by 5 publications

(6 citation statements)

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“…or the total microbial load (which would require quantitative sequencing methods) [ 77 ]. The number of OTUs generated for a sample is also significantly affected by which variable region is selected for targeted sequencing, thus, as a new standard, full 16S rRNA gene sequencing was proposed [ 78 ]; still, despite that full sequencing is becoming more and more popular, the targeted sequencing of 16S rRNA variable region remains the more widespread method applied [ 40 ].…”

Section: Discussionmentioning

confidence: 99%

“…Examination of human microbiomes through directed sequencing of 16S ribosomes (rRNA genes) allows for an estimation of the taxonomic diversity and the distribution of the contributory bacterial species, since the targeted 16S rRNA sequencing can be analysed bioinformatically, having the advantage of high-quality databases, reliable classification pipelines for sequencing data and the possibility of a greater read depth and a reduced cost when compared with metagenomic sequencing [ 40 ]. The 16S ribosomal RNA (or 16S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome (SSU rRNA- Small subunit ribosomal ribonucleic acid).…”

Section: Introductionmentioning

confidence: 99%

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Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review

et al. 2022

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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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review

et al. 2022

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“…Contamination is a primary concern, since even small traces coming from environmental sources or handling can obscure exogenous microbial signals [108,109]. Mitigating contamination requires meticulous sample collection, processing and stringent bioinformatic protocols to differentiate true microbial signatures from background noise [110]. Additionally, forensic samples often exhibit low biomass, making it challenging to obtain sufficient genetic material for analysis.…”

Section: Next-generation Sequencing (Ngs) For Microbiological Post-mo...mentioning

confidence: 99%

Forensic Microbiology: When, Where and How

Nodari,

Arghittu,

Bailo

et al. 2024

Microorganisms

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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.

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“…Microbiome samples are employed for several purposes, including human identification, measuring postmortem intervals, and determining geolocation. By utilising advanced technologies such as MPS and long-read sequencing, in conjunction with BI tools and machine learning models, it becomes possible to analyse and describe individual samples of the human microbiome efficiently and accurately [33]. Metagenomics Analysis Software (MEGAN) allows visual and quantitative exploration of microbiomes on a desktop computer.…”

Section: The Field Of Microbial Forensics and Bimentioning

confidence: 99%

Untitled

2024

IJNSA

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Bioinformatics (BI) is a diverse and interdisciplinary domain that studies biological data through computational techniques. Its rapid technological progress has led to a significant increase in biological data production, sparking a notable expansion in BI research and application. In recent years, the convergence between BI and forensic science has become increasingly evident, with the growing use of BI tools and techniques in forensic investigations. BI is not only extensively used in biomedical research to analyse biological data and forecast gene regulation but also in the development of drugs targeting disorders linked to epigenetic alterations. It merges principles from various fields like biology, computer science, and statistics to process extensive omics data, create databases, predict structures, and model metabolic processes. The impact of BI on biomedical research is substantial, aiding in data processing, prediction, and visualisation. Moreover, BI is increasingly important in analysing data generated through Sanger-based electrophoresis methods and massively parallel sequencing in forensic DNA analysis, demonstrating its practical application in the field. Therefore, BI plays a critical role in forensic identification, searching databases side by side, forensic DNA phenotyping and biographic ancestry, forensic genetic genealogy, and forensic epigenomics. An overview of different bioinformatic methodologies employed in forensic applications, exploring approaches for managing data and investigating trend analysis strategies within forensic contexts, is discussed. Additionally, it investigates data management strategies. The primary objective was to explore how BI facilitates forensic BI's use, integration, and impact. Utilising a systematic literature review and content analysis, the study examined peer-reviewed articles, conference proceedings, and reports from critical databases like Google Scholar and Scopus, focusing on publications from 2010 to 2024. Key findings highlight the significant advancements in genomic sequencing technologies and their application in personalised therapeutics. Forensic scientists can improve forensic exams' accuracy, reliability, and efficiency by using BI tools, metrics, and efficient data management procedures.

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Microbial Forensics: A Present to Future Perspective on Genomic Targets, Bioinformatic Challenges, and Applications

Cited by 5 publications

References 176 publications

Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review

Post-Mortem Interval and Microbiome Analysis through 16S rRNA Analysis: A Systematic Review

Forensic Microbiology: When, Where and How

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