ArticlePloS one2014
Random whole metagenomic sequencing for forensic discrimination of soils.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Evaluation of targeted Massively Parallel Sequencing methods for forensic metagenomics.Applied microbiology and biotechnology · 2026Article
- Forensic Microbiology: When, Where and How.Microorganisms · 2024Review
- Bacterial Community of Grana Padano PDO Cheese and Generical Hard Cheeses: DNA Metabarcoding and DNA Metafingerprinting Analysis to Assess Similarities and Differences.Foods (Basel, Switzerland) · 2021Article
- Mechanistic models of microbial community metabolism.Molecular omics · 2021Review
- Lampenflora in a Show Cave in the Great Basin Is Distinct from Communities on Naturally Lit Rock Surfaces in Nearby Wild Caves.Microorganisms · 2021Article
- Machine learning applications in microbial ecology, human microbiome studies, and environmental monitoring.Computational and structural biotechnology journal · 2021Review
- Unraveling City-Specific Microbial Signatures and Identifying Sample Origins for the Data From CAMDA 2020 Metagenomic Geolocation Challenge.Frontiers in genetics · 2021Article
- Biological Ingredient Analysis of Traditional Herbal Patent Medicine Fuke Desheng Wan Using the Shotgun Metabarcoding Approach.Frontiers in pharmacology · 2021Article
- What we can see from very small size sample of metagenomic sequences.BMC bioinformatics · 2018Article
- A protocol for obtaining DNA barcodes from plant and insect fragments isolated from forensic-type soils.International journal of legal medicine · 2018Article
- Bioinformatics Approach to Assess the Biogeographical Patterns of Soil Communities: The Utility for Soil Provenance.Journal of forensic sciences · 2018Article
- Resemblance profiles as clustering decision criteria: Estimating statistical power, error, and correspondence for a hypothesis test for multivariate structure.Ecology and evolution · 2017Article
- Microbial composition analyses by 16S rRNA sequencing: A proof of concept approach to provenance determination of archaeological ochre.PloS one · 2017Article
- Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond.Microbes and environments · 2016Review
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Here we assess the ability of random whole metagenomic sequencing approaches to discriminate between similar soils from two geographically distinct urban sites for application in forensic science. Repeat samples from two parklands in residential areas separated by approximately 3 km were collected and the DNA was extracted. Shotgun, whole genome amplification (WGA) and single arbitrarily primed DNA amplification (AP-PCR) based sequencing techniques were then used to generate soil metagenomic profiles. Full and subsampled metagenomic datasets were then annotated against M5NR/M5RNA (taxonomic classification) and SEED Subsystems (metabolic classification) databases. Further comparative analyses were performed using a number of statistical tools including: hierarchical agglomerative clustering (CLUSTER); similarity profile analysis (SIMPROF); non-metric multidimensional scaling (NMDS); and canonical analysis of principal coordinates (CAP) at all major levels of taxonomic and metabolic classification. Our data showed that shotgun and WGA-based approaches generated highly similar metagenomic profiles for the soil samples such that the soil samples could not be distinguished accurately. An AP-PCR based approach was shown to be successful at obtaining reproducible site-specific metagenomic DNA profiles, which in turn were employed for successful discrimination of visually similar soil samples collected from two different locations.
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