Potential applications of soil microbial ecology and next-generation sequencing in criminal investigations
Tài liệu tham khảo
Antony-Babu, 2013, An improved method compatible with metagenomic analyses to extract genomic DNA from soil in Tuber melanosporum orchards, J. Appl. Microbiol., 115, 163, 10.1111/jam.12205
Baldrian, 2012, Active total microbial communities in forest soil are largely different and highly stratified during decomposition, Int. Soc. Microb. Ecol. J., 6, 248
Benbow, 2013, Seasonal necrophagous insect community assembly during vertebrate carrion decomposition, J. Med. Entomol., 50, 440, 10.1603/ME12194
Benninger, 2008, The biochemical alteration of soil beneath a decomposing carcass, Forensic Sci. Int., 180, 70, 10.1016/j.forsciint.2008.07.001
Bunyard, 2004, Commentary on: Carter D O, Tibbett M.; Taphonomic mycota: fungi with forensic potential. J. Forensic Sci. 2003;48(1): 168–71, J. Forensic Sci., 49, 1134, 10.1520/JFS2003418
Burkepile, 2006, Chemically mediated competition between microbes and animals: microbes as consumers in food webs, Ecology, 87, 2821, 10.1890/0012-9658(2006)87[2821:CMCBMA]2.0.CO;2
Can, 2014, Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans, J. Microbiol. Methods, 106, 1, 10.1016/j.mimet.2014.07.026
Caporaso, 2012, Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms, Int. Soc. Microb. Ecol. J., 6, 1621
Carter, 2003, Taphonomic mycota: fungi with forensic potential, J. Forensic Sci., 48, 168, 10.1520/JFS2002169
Carter, 2007, Cadaver decomposition in terrestrial ecosystems, Naturwissenschaften, 94, 12, 10.1007/s00114-006-0159-1
Carter, 2008, Temperature affects microbial decomposition of cadavers (Rattus rattus) in contrasting soils, Appl. Soil Ecol., 40, 129, 10.1016/j.apsoil.2008.03.010
Carter, 2010, Moisture can be the dominant environmental parameter governing cadaver decomposition in soil, Forensic Sci. Int., 200, 60, 10.1016/j.forsciint.2010.03.031
Carvalhais, 2012, Application of metatranscriptomics to soil environments, J. Microbiol. Methods, 91, 246, 10.1016/j.mimet.2012.08.011
Chandra, 1968, Determination of time since death from a study of various postmortem changes, J. Indian Med. Assoc., 51, 336
Concheri, 2011, Chemical elemental distribution and soil DNA fingerprints provide the critical evidence in murder case investigation, PLoS ONE, 6, e20222, 10.1371/journal.pone.0020222
Delmont, 2011, Metagenomic comparison of direct and indirect soil DNA extraction approaches, J. Microbiol. Methods, 86, 397, 10.1016/j.mimet.2011.06.013
Drancourt, 2000, 16S ribosomal DNA sequence analysis of a large collection of environmental and clinical unidentifiable bacterial isolates, J. Clin. Microbiol., 38, 3623, 10.1128/JCM.38.10.3623-3630.2000
El-Metwally, 2013, Next-generation sequence assembly: four stages of data processing and computational challenges, PLos Comput. Biol., 9, e1003345, 10.1371/journal.pcbi.1003345
Fiedler, 2003, Decomposition of buried corpses, with special reference to the formation of adipocere, Naturwissenschaften, 90, 291, 10.1007/s00114-003-0437-0
Fierer, 2010, Forensic identification using skin bacterial communities, Proc. Natl. Acad. Sci., 107, 6477, 10.1073/pnas.1000162107
Finley, 2014, Microbial communities associated with human decomposition and their potential use as postmortem clocks, Int. J. Legal Med., 1
Fitzpatrick, 2008, Nature, distibution, and origin of soil materials in forensic comparison of soils, 1
Gilbert, 2010, Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project, Stand. Genomic Sci., 3, 243, 10.4056/sigs.1433550
Gilbert, 2012, Defining seasonal marine microbial community dynamics, Int. Soc. Microb. Ecol. J., 6, 298
Girvan, 2003, Soil type is the primary determinant of the composition of the total and active bacterial communitiies in arable soils, Appl. Environ. Microbiol., 69, 1800, 10.1128/AEM.69.3.1800-1809.2003
Haas, 2011, Chimeric 16éS rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons, Genome Res., 21, 494, 10.1101/gr.112730.110
Haslam, 2009, Soils of contrasting pH affect the decomposition of buried mammalian (Ovis aries) skeletal muscle tissue, J. Forensic Sci., 54, 900, 10.1111/j.1556-4029.2009.01070.x
Hawksworth, 2011, Forensic mycology: the use of fungi in criminal investigations, Forensic Sci. Int., 106, 1, 10.1016/j.forsciint.2010.06.012
Heath, 2009, Assessing the potential of bacterial DNA profiling for forensic soil comparisons, J. Forensic Sci., 51, 1061
Hewadikaram, 1991, Effect of carcass size on rate of decomposition and arthropod succession patterns, Am. J. Forensic Med. Pathol., 12, 235, 10.1097/00000433-199109000-00013
Hill, 2000, Methods for assessing the composition and diversity of soil microbial communities, Appl. Soil Ecol., 15, 25, 10.1016/S0929-1393(00)00069-X
Hopkins, 2000, Microbial characteristics of soils from graves: an investigation at the interface of soil microbiology and forensic science, Appl. Soil Ecol., 14, 283, 10.1016/S0929-1393(00)00063-9
Howard, 2010, Characterization of the soil microbial community associated with the decomposition of a swine carcass, Int. Biodeterior. Biodegred., 64, 300, 10.1016/j.ibiod.2010.02.006
Hyde, 2014, Initial insights into bacterial succession during human decomposition, Int. J. Legal Med., 10.1007/s00414-014-1128-4
Hyde, 2013, The living dead: bacterial community structure of a cadaver at the onset and end of the bloat stage of decomposition, PLoS ONE, 8, e0077733, 10.1371/journal.pone.0077733
Janda, 2007, 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls, J. Clin. Microbiol., 45, 2761, 10.1128/JCM.01228-07
Killiam, 2004
Killham, 1994
Knauth, 2012, Comparison of commercial kits for the extraction of DNA from paddy soils, Lett. Appl. Microbiol., 56, 222, 10.1111/lam.12038
Kosugi, 2013, Coval: improving alignment quality and variant calling accurancy for next-generation sequencing data, PLoS ONE, 8, e75402, 10.1371/journal.pone.0075402
Lauber, 2014, Vertebrate decomposition is accelerated by soil microbes, Appl. Environ. Microbiol., 80, 4920, 10.1128/AEM.00957-14
Lennon, 2012, Mapping the niche space of soil microorganisms using taxonomy and traits, Ecology, 93, 1867, 10.1890/11-1745.1
Lenz, 2010, Bacterial profiling of soil using genus-specific markers and multidimensional scaling, J. Forensic Sci., 55, 1437, 10.1111/j.1556-4029.2010.01464.x
Logares, 2012, Environmental microbiology through the lens of high-throughput DNA sequencing: synopsis of current platforms and bioinformatics approaches, J. Microbiol. Methods, 91, 106, 10.1016/j.mimet.2012.07.017
Loman, 2012, High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity, Nat. Rev. Microbiol., 10, 599, 10.1038/nrmicro2850
Lv, 2014, A time course study demonstrating mRNA, microRNA, 18S rRNA, and U6 snRNA changes to estimate PMI in decreased rat’s spleen, J. Forensic Sci., 59, 1286, 10.1111/1556-4029.12447
Mann, 1990, Time since death and decomposition of the human body: variables and observations in case and experimental field studies, J. Forensic Sci., 35, 103, 10.1520/JFS12806J
Manzoni, 2012, Responses of soil microbial communities to water stress: results from a meta-analysis, Ecology, 93, 930, 10.1890/11-0026.1
Margulies, 2005, Genome sequencing in microfabricated high-denisity picoliter reactors, Nature, 437, 376, 10.1038/nature03959
Maron, 2011, Soil microbial diversity: methodological strategy, spatial overview and functional interest, C. R. Biol., 334, 403, 10.1016/j.crvi.2010.12.003
Matuszewski, 2010, Insect succession and carrion decomposition in selected forests of central Europe. Part 1: pattern and rate of decomposition, Forensic Sci. Int., 194, 85, 10.1016/j.forsciint.2009.10.016
Megyesi, 2005, Using accumulated degree-days to estimate the postmortem interval from decomposed human remains, J. Forensic Sci., 50, 618, 10.1520/JFS2004017
Metcalf, 2013, A microbial clock provides an accurate estimate of the postmortem interal in a mouse model system, eLife, 2, e01104, 10.7554/eLife.01104
Moreira, 1998, Efficient removal of PCR inhibitors using agarose-embedded DNA preparations, Nucleic Acids Res., 26, 3309, 10.1093/nar/26.13.3309
Moreno, 2006, Microbial metagenome profiling using amplicon length heterogeneity-polymerase chain reaction proves more effective than elemental analysis in discriminating soil specimens, J. Forensic Sci., 51, 1315, 10.1111/j.1556-4029.2006.00264.x
Moreno, 2011, The application of amplicon length heterogeneity PCR (LH-PCR) for monitoring the dynamics of soil microbial communities associated with cadaver decomposition, J. Microbiol. Methods, 84, 388, 10.1016/j.mimet.2010.11.023
Muyzer, 1993, Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA, Appl. Environ. Microbiol., 59, 695, 10.1128/AEM.59.3.695-700.1993
Osborne, 2006, New threshold and confidence estimates for terminal restriction fragment length polymorphism analysis of complex bacterial communities, Appl. Environ. Microbiol., 72, 1270, 10.1128/AEM.72.2.1270-1278.2006
Parkinson, 2009, Microbial community analysis of human decomposition on soil, 379
Payne, 1965, A summer carrion study of the baby pig Sus Scrofa Linnaeus, Ecology, 46, 592, 10.2307/1934999
Pechal, 2014, The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing, Int. J. Legal Med., 128, 193, 10.1007/s00414-013-0872-1
Pechal, 2013, Microbial community functional change during vertebrate carrion decomposition, PLoS ONE, 8, e79035, 10.1371/journal.pone.0079035
Pfeiffer, 1998, The natural decomposition of adipocere, J. Forensic Sci., 43, 368, 10.1520/JFS16147J
Pietikainen, 2005, Comparison of temperature effects on soil respiration and bacterial and fungal growth rates, FEMS Microbiol. Ecol., 52, 49, 10.1016/j.femsec.2004.10.002
Ranjard, 2001, Quantitative and qualitative microscale distribution of bacteria in soil, Res. Microbiol., 152, 707, 10.1016/S0923-2508(01)01251-7
Redford, 2009, Bacterial succession of the leaf surface: a novel system for studying successional dynamics, Microb. Ecol., 58, 189, 10.1007/s00248-009-9495-y
Ritchie, 2000, Use of length heterogeneity PCR and fatty acid methyl ester profiles to characterize microbial communities in soil, Appl. Environ. Microbiol., 66, 1668, 10.1128/AEM.66.4.1668-1675.2000
Roesch, 2007, Pyrosequencing enumerates and contrasts soil microbial diversity, Int. Soc. Microb. Ecol., 1, 283
Sagara, 2008, Soil fungi associated with graves and latrines: toward a forensic mycology, 67
Sagova-Mareckova, 2008, Innovative methods of soil DNA purification tested in soils with widely differing characteristics, Appl. Environ. Microbiol., 74, 2902, 10.1128/AEM.02161-07
Schloss, 2011, Reducing the effects of PCR amplification and sequencing artifacts on 16S rRNA-based studies, PLoS ONE, 6, e27310, 10.1371/journal.pone.0027310
Schoch, 2012, Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for fungi, Proc. Natl. Acad. Sci. U. S. A., 109, 6241, 10.1073/pnas.1117018109
Schoenly, 1987, Dynamics of heterotrophic succession in carrion arthropod assemblages: discrete seres of a continuum of change?, Oecologia, 73, 192, 10.1007/BF00377507
Scholz, 2012, Next generation sequencing and bioinformatic bottlenecks: the current state of metagenomic data analysis, Curr. Opin. Biotechnol., 23, 9, 10.1016/j.copbio.2011.11.013
Seo, 2013, Improvement of short tandem repeat analysis of samples highly contaminated by humic acid, J. Forensic Legal Med., 20, 922, 10.1016/j.jflm.2013.08.001
Shade, 2013, A meta-analysis of changes in bacterial and archaeal communities with time, ISME J., 7, 1493, 10.1038/ismej.2013.54
Shokralla, 2012, Next-generation sequencing technologies for environmental DNA research, Mol. Ecol., 21, 1794, 10.1111/j.1365-294X.2012.05538.x
Solomon, 2014, Extracting data from the muck: deriving biological insight from complex microbial communities and non-model organisms with next generation sequencing, Curr. Opin. Biotechnol., 28, 103, 10.1016/j.copbio.2014.01.007
Stotzky, 1997, Soil as an Environment for microbial life, 1
Strickland, 2010, Considering fungal: bacterial dominance in soil – methods, controls, and ecosystem implications, Soil Biol. Biochem., 42, 1385, 10.1016/j.soilbio.2010.05.007
Swindles, 2009, A preliminary investigation into the use of testate amoebae for the discrimination of forensic soil samples, Sci. Justice, 49, 182, 10.1016/j.scijus.2008.11.002
Szelecz, 2014, Can soil testate amoebae be used for estimating the time since death? A field experiment in a deciduous forest, Forensic Sci. Int., 236, 90, 10.1016/j.forsciint.2013.12.030
Tabaac, 2013, Bacteria detected on surfaces of formalin fixed anatomy cadavers, Ital. J. Anat. Embryol., 118, 1
Teeling, 2012, Current opportunities and challenges in microbial metagenome analysis – a bioinformatic perspective, Brief. Bioinform., 13, 728, 10.1093/bib/bbs039
Teo, 2013, Post mortem changes in relation to different types of clothing, Malays. J. Pathol., 35, 77
Tomberlin, 2011, A roadmap for bridging basic and applied research in forensic entomology, Annu. Rev. Entomol., 56, 401, 10.1146/annurev-ento-051710-103143
Tranchida, 2014, Soil fungi: their potential use as a forensic tool, J. Forensic Sci., 59, 785, 10.1111/1556-4029.12391
Tumer, 2013, Effects of different types of soil on decomposition: an experimental study, Legal Med. (Tokyo, Japan), 15, 149, 10.1016/j.legalmed.2012.11.003
Tuomisto, 2013, Evaluation of postmortem bacterial migration using culturing and real-time quantitative PCR, J. Forensic Sci., 58, 910, 10.1111/1556-4029.12124
Turbé, 2010
Turnbaugh, 2007, The human microbiome project, Nature, 449, 804, 10.1038/nature06244
VanLaerhoven, 2010, Ecological theory and its application for forensic entomology, 493
Vanwonterghem, 2014, Linking microbial community structure, interactions and function in anaerobic digesters using new molecular techniques, Curr. Opin. Biotechnol., 27, 55, 10.1016/j.copbio.2013.11.004
Wilson-Taylor, 2012, Time since death estimation and bone weathering, 340
Wooley, 2010, A primer on metagenomics, PLoS Comput. Biol., 6, e1000667, 10.1371/journal.pcbi.1000667
