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      Thanatomicrobiome composition profiling as a tool for forensic investigation

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          ABSTRACT

          Thanatomicrobiome, or the postmortem microbiome, has been recognized as a useful microbial marker of the time and location of host death. In this mini-review, we compare the experimental methods commonly applied to thanatomicrobiome studies to the state-of-the-art methodologies in the microbiome field. Then, we review present findings in thanatomicrobiome studies, focusing on the diversity of the thanatomicrobiome composition and prediction models that have been proposed. Finally, we discuss potential improvements and future directions of the field.

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          Most cited references29

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          The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota.

          Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.
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            The skin microbiome

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              An introduction to the analysis of shotgun metagenomic data

              Environmental DNA sequencing has revealed the expansive biodiversity of microorganisms and clarified the relationship between host-associated microbial communities and host phenotype. Shotgun metagenomic DNA sequencing is a relatively new and powerful environmental sequencing approach that provides insight into community biodiversity and function. But, the analysis of metagenomic sequences is complicated due to the complex structure of the data. Fortunately, new tools and data resources have been developed to circumvent these complexities and allow researchers to determine which microbes are present in the community and what they might be doing. This review describes the analytical strategies and specific tools that can be applied to metagenomic data and the considerations and caveats associated with their use. Specifically, it documents how metagenomes can be analyzed to quantify community structure and diversity, assemble novel genomes, identify new taxa and genes, and determine which metabolic pathways are encoded in the community. It also discusses several methods that can be used compare metagenomes to identify taxa and functions that differentiate communities.
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                Author and article information

                Journal
                Forensic Sci Res
                Forensic Sci Res
                TFSR
                tfsr20
                Forensic sciences research
                Taylor & Francis
                2096-1790
                2471-1411
                2018
                31 May 2018
                : 3
                : 2
                : 105-110
                Affiliations
                [a ]The Jackson Laboratory for Genomic Medicine , Farmington, CT, USA
                [b ]Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science , Shanghai, China
                Author notes
                Article
                1466430
                10.1080/20961790.2018.1466430
                6197100
                30483658
                dbd91ce4-63c0-4049-b8d3-677b8d91b387
                © 2018 The Author(s). Published by Taylor & Francis Group on behalf of the Academy of Forensic Science.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 15 November 2017
                : 29 March 2018
                Page count
                Figures: 0, Tables: 0, References: 68, Pages: 6
                Funding
                Funded by: National Natural Science Foundation of China 10.13039/501100001809
                Award ID: 81601651 and 81625013
                Funded by: Science and Technology Committee of Shanghai Municipality 10.13039/501100003399
                Award ID: 16dz1205500, 16DZ2290900 and 17DZ2273200
                Funded by: National Key R&D Program of China
                Award ID: 2016YFC0800703
                Funded by: Ministry of Finance of China
                Award ID: GY2016D1
                This study is supported by the National Natural Science Foundation of China [grant numbers 81601651 and 81625013]; the Science and Technology Committee of Shanghai Municipality [grant numbers 16dz1205500, 16DZ2290900 and 17DZ2273200]; the National Key R&D Program of China [grant number 2016YFC0800703]; the Ministry of Finance of China [grant number GY2016D1].
                Categories
                Review

                forensic science,forensic genetics,thanatomicrobiome,microbiome,postmortem microbiome,pmi,prediction model

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