Shotgun metagenomics of biological stains using ultra-deep DNA sequencing

Microbial Forensics☆

Biothreats are a high priority concern for public safety and national security. The field of microbial forensics was developed to analyze evidence associated with biological crimes in which microbes or their toxins are used as weapons. Microbial forensics is the scientific discipline dedicated to analyzing evidence from a bioterrorism act, biocrime, hoax, or inadvertent microorganism/toxin release for attribution purposes. Microbial forensics combines the practices of epidemiology with the characterization of microbial and microbial-related evidence to assist in determining the specific source of the sample, as individualizing as possible, and/or the methods, means, processes and locations involved to determine the identity of the perpetrator(s) of an attack.

Application of next-generation sequencing technology in forensic science

Next-generation sequencing (NGS) technology, with its high-throughput capacity and low cost, has developed rapidly in recent years and become an important analytical tool for many genomics researchers. New opportunities in the research domain of the forensic studies emerge by harnessing the power of NGS technology, which can be applied to simultaneously analyzing multiple loci of forensic interest in different genetic contexts, such as autosomes, mitochondrial and sex chromosomes. Furthermore, NGS technology can also have potential applications in many other aspects of research. These include DNA database construction, ancestry and phenotypic inference, monozygotic twin studies, body fluid and species identification, and forensic animal, plant and microbiological analyses. Here we review the application of NGS technology in the field of forensic science with the aim of providing a reference for future forensics studies and practice.

A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures

Species identification can be interesting in a wide range of areas, for example, in forensic applications, food monitoring and in archeology. The vast majority of existing DNA typing methods developed for species determination, mainly focuses on a single species source. There are, however, many instances where all species from mixed sources need to be determined, even when the species in minority constitutes less than 1 % of the sample. The introduction of next generation sequencing opens new possibilities for such challenging samples. In this study we present a universal deep sequencing method using 454 GS Junior sequencing of a target on the mitochondrial gene 16S rRNA. The method was designed through phylogenetic analyses of DNA reference sequences from more than 300 mammal species. Experiments were performed on artificial species-species mixture samples in order to verify the method's robustness and its ability to detect all species within a mixture. The method was also tested on samples from authentic forensic casework. The results showed to be promising, discriminating over 99.9 % of mammal species and the ability to detect multiple donors within a mixture and also to detect minor components as low as 1 % of a mixed sample.

Mutations that affect mitochondrial functions and their association with neurodegenerative diseases

Mitochondria are essential for mammalian and human cell function as they generate ATP via aerobic respiration. The proteins required in the electron transport chain are mainly encoded by the circular mitochondrial genome but other essential mitochondrial proteins such as DNA repair genes, are coded in the nuclear genome and require transport into the mitochondria. In this review we summarize current knowledge on the association of point mutations and deletions in the mitochondrial genome that are detrimental to mitochondrial function and are associated with accelerated ageing and neurological disorders including Alzheimer's, Parkinson's, Huntington's and Amyotrophic lateral sclerosis (ALS). Mutations in the nuclear encoded genes that disrupt mitochondrial functions are also discussed. It is evident that a greater understanding of the causes of mutations that adversely affect mitochondrial metabolism is required to develop preventive measures against accelerated ageing and neurological disorders caused by mitochondrial dysfunction.

A microbial profiling method for the human microbiota using high-throughput sequencing

Study of the human microbiota in relation to human health and disease is a rapidly expanding field. To fully understand the complex relationship between the human gut microbiota and disease risks, study designs that capture the variation within and between human subjects at the population level are required, but this has been hampered by the lack of cost-effective methods to characterize this variation. Illumina sequencing is inexpensive and produces millions of reads per run, but it is unclear whether short reads can adequately represent the microbial community of a human host. In this study, we examined the utility of a profiling method, microbial nucleotide signatures (MNS), focused on low-depth sampling of the human microbiota using Ilumina short reads. This method is intended to aid in human population-based studies where large sample sizes are required to adequately capture variation in disease or phenotype differences. We found that, by calculating the nucleotide diversities along the sequenced 16S rRNA gene region, which did not require assembly or phylogenetic identification, we were able to differentiate the gut microbial nucleotide signatures of 9 healthy individuals. When we further subsampled the reads down to 40,000 reads (51 bp long) per sample, the diversity profiles were relatively unchanged. Applying MNS to a public datasets showed that it could differentiate body site differences. The scalability of our approach offers rapid classification of study participants for studies with the sample sizes required for epidemiological studies. Using MNS to classify the microbiome associated with a disease state followed by targeted in-depth sequencing will give a comprehensive understanding of the role of the microbiome in human health.

Evaluating the performance of whole genome amplification for use in low template DNA typing

We report on the performance of two whole genome amplification methods, GenomiPhi™ amplification and modified-improved primer extension preamplification (mIPEP), when analysing low template DNA samples. Template as low as 10 pg treated with mIPEP generated more than 1 ng of DNA that could be used in STR typing. Initial templates of 100-10 pg, when treated with mIPEP, generated an increase in alleles compared with control samples. Partial profiles using the AmpFℓSTR(®) Identifiler™ Kit were produced from this suboptimal DNA template, with 70% of the possible alleles (21.7 ± 2.1 in 32 alleles) recorded, using the mIPEP amplified products with an initial template of 100 pg. Allelic imbalance decreased with samples treated with whole genome amplification method (WGA) compared with those without this initial treatment. Further methods for improvement were also analysed including altering the condition of electrokinetic injection, and the successful DNA typing rate was increased to about 80%. This report illustrates the potential use and limitations of WGA for low template samples.