The Living Dead: Bacterial Community Structure of a Cadaver at the Onset and End of the Bloat Stage of Decomposition
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{"title"=>"The Living Dead: Bacterial Community Structure of a Cadaver at the Onset and End of the Bloat Stage of Decomposition", "type"=>"journal", "authors"=>[{"first_name"=>"Embriette R.", "last_name"=>"Hyde"}, {"first_name"=>"Daniel P.", "last_name"=>"Haarmann"}, {"first_name"=>"Aaron M.", "last_name"=>"Lynne"}, {"first_name"=>"Sibyl R.", "last_name"=>"Bucheli"}, {"first_name"=>"Joseph F.", "last_name"=>"Petrosino"}], "year"=>2013, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"1932-6203", "scopus"=>"2-s2.0-84896963128", "sgr"=>"84896963128", "pui"=>"563079832", "isbn"=>"1932-6203", "pmid"=>"24204941", "doi"=>"10.1371/journal.pone.0077733"}, "id"=>"c9b80429-91a3-3c7e-8c35-8dadc9f064cc", "abstract"=>"Human decomposition is a mosaic system with an intimate association between biotic and abiotic factors. Despite the integral role of bacteria in the decomposition process, few studies have catalogued bacterial biodiversity for terrestrial scenarios. To explore the microbiome of decomposition, two cadavers were placed at the Southeast Texas Applied Forensic Science facility and allowed to decompose under natural conditions. The bloat stage of decomposition, a stage easily identified in taphonomy and readily attributed to microbial physiology, was targeted. Each cadaver was sampled at two time points, at the onset and end of the bloat stage, from various body sites including internal locations. Bacterial samples were analyzed by pyrosequencing of the 16S rRNA gene. Our data show a shift from aerobic bacteria to anaerobic bacteria in all body sites sampled and demonstrate variation in community structure between bodies, between sample sites within a body, and between initial and end points of the bloat stage within a sample site. These data are best not viewed as points of comparison but rather additive data sets. While some species recovered are the same as those observed in culture-based studies, many are novel. Our results are preliminary and add to a larger emerging data set; a more comprehensive study is needed to further dissect the role of bacteria in human decomposition.", "link"=>"http://www.mendeley.com/research/living-dead-bacterial-community-structure-cadaver-onset-end-bloat-stage-decomposition", "reader_count"=>131, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Researcher"=>26, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>4, "Student > Master"=>15, "Other"=>7, "Student > Bachelor"=>30, "Lecturer > Senior Lecturer"=>2, "Professor"=>7}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>3, "Researcher"=>26, "Student > Doctoral Student"=>8, "Student > Ph. D. Student"=>26, "Student > Postgraduate"=>4, "Student > Master"=>15, "Other"=>7, "Student > Bachelor"=>30, "Lecturer > Senior Lecturer"=>2, "Professor"=>7}, "reader_count_by_subject_area"=>{"Unspecified"=>9, "Agricultural and Biological Sciences"=>72, "Arts and Humanities"=>3, "Chemistry"=>7, "Computer Science"=>1, "Engineering"=>1, "Environmental Science"=>2, "Biochemistry, Genetics and Molecular Biology"=>17, "Materials Science"=>1, "Mathematics"=>1, "Medicine and Dentistry"=>12, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Psychology"=>1, "Social Sciences"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>12}, "Social Sciences"=>{"Social Sciences"=>2}, "Psychology"=>{"Psychology"=>1}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>9}, "Environmental Science"=>{"Environmental Science"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>3}, "Engineering"=>{"Engineering"=>1}, "Chemistry"=>{"Chemistry"=>7}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>72}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>17}}, "reader_count_by_country"=>{"Colombia"=>1, "Sweden"=>1, "Hungary"=>1, "United States"=>5, "Luxembourg"=>1, "South Africa"=>1, "Germany"=>1, "India"=>1}, "group_count"=>6}

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  • {"files"=>["https://ndownloader.figshare.com/files/4440475"], "description"=>"<p>A rarefaction curve plotting the average number of OTUs over the average number of sequences sampled per body site sampled shows that microbiome richness differs widely among different body site samples. Error bars represent the standard error of the mean. The legend indicates the body site and body identification number for each sample.</p>", "links"=>[], "tags"=>["cadaver", "Southeast Texas Applied Forensic Science facility", "body sites", "bacteria", "16 S rRNA gene", "sample", "Decomposition Human decomposition", "role", "bloat stage", "additive data sets", "Bacterial Community Structure"], "article_id"=>837743, "categories"=>["Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Science Policy"], "users"=>["Embriette R. Hyde", "Daniel P. Haarmann", "Aaron M. Lynne", "Sibyl R. Bucheli", "Joseph F. Petrosino"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0077733.g003"], "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Microbiome_richness_varies_widely_across_cadaver_body_sites_/837743", "title"=>"Microbiome richness varies widely across cadaver body sites.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-30 15:28:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/4440478"], "description"=>"<p>The first two principal coordinates (PC) of Unweighted (A) and Weighted (B) UniFrac-based principal coordinate analysis are plotted, and the percent variance explained by each PC is indicated in parenthesis.</p>", "links"=>[], "tags"=>["cadaver", "Southeast Texas Applied Forensic Science facility", "body sites", "bacteria", "16 S rRNA gene", "sample", "Decomposition Human decomposition", "role", "bloat stage", "additive data sets", "Bacterial Community Structure"], "article_id"=>837744, "categories"=>["Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Science Policy"], "users"=>["Embriette R. Hyde", "Daniel P. Haarmann", "Aaron M. Lynne", "Sibyl R. Bucheli", "Joseph F. Petrosino"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0077733.g004"], "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Principal_coordinate_analysis_reveals_separation_of_communities_based_on_location_in_the_gastrointestinal_tract_/837744", "title"=>"Principal coordinate analysis reveals separation of communities based on location in the gastrointestinal tract.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-30 15:28:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/4440472"], "description"=>"<p>Bodies were samples at the start of decomposition and at a point determined to be almost the end of the bloat stage. DD =  ((Maximum Temperature + Minimum Temperature)/2)-base temperature; ADD =  (DDx+DDx+1).</p>", "links"=>[], "tags"=>["cadaver", "Southeast Texas Applied Forensic Science facility", "body sites", "bacteria", "16 S rRNA gene", "sample", "Decomposition Human decomposition", "role", "bloat stage", "additive data sets", "Bacterial Community Structure"], "article_id"=>837742, "categories"=>["Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Science Policy"], "users"=>["Embriette R. Hyde", "Daniel P. Haarmann", "Aaron M. Lynne", "Sibyl R. Bucheli", "Joseph F. Petrosino"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0077733.g002"], "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Accumulated_degree_hours_calculated_at_a_base_of_4oC_for_STAFS_2011_006_and_STAFS_2011_016_/837742", "title"=>"Accumulated degree hours calculated at a base of 4oC for STAFS 2011-006 and STAFS 2011-016.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-30 15:28:36"}
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  • {"files"=>["https://ndownloader.figshare.com/files/4440466"], "description"=>"<div><p>Human decomposition is a mosaic system with an intimate association between biotic and abiotic factors. Despite the integral role of bacteria in the decomposition process, few studies have catalogued bacterial biodiversity for terrestrial scenarios. To explore the microbiome of decomposition, two cadavers were placed at the Southeast Texas Applied Forensic Science facility and allowed to decompose under natural conditions. The bloat stage of decomposition, a stage easily identified in taphonomy and readily attributed to microbial physiology, was targeted. Each cadaver was sampled at two time points, at the onset and end of the bloat stage, from various body sites including internal locations. Bacterial samples were analyzed by pyrosequencing of the 16S rRNA gene. Our data show a shift from aerobic bacteria to anaerobic bacteria in all body sites sampled and demonstrate variation in community structure between bodies, between sample sites within a body, and between initial and end points of the bloat stage within a sample site. These data are best not viewed as points of comparison but rather additive data sets. While some species recovered are the same as those observed in culture-based studies, many are novel. Our results are preliminary and add to a larger emerging data set; a more comprehensive study is needed to further dissect the role of bacteria in human decomposition.</p></div>", "links"=>[], "tags"=>["cadaver", "Southeast Texas Applied Forensic Science facility", "body sites", "bacteria", "16 S rRNA gene", "sample", "Decomposition Human decomposition", "role", "bloat stage", "additive data sets", "Bacterial Community Structure"], "article_id"=>837747, "categories"=>["Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Science Policy"], "users"=>["Embriette R. Hyde", "Daniel P. Haarmann", "Aaron M. Lynne", "Sibyl R. Bucheli", "Joseph F. Petrosino"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0077733.s001"], "stats"=>{"downloads"=>5, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_Living_Dead_Bacterial_Community_Structure_of_a_Cadaver_at_the_Onset_and_End_of_the_Bloat_Stage_of_Decomposition_/837747", "title"=>"The Living Dead: Bacterial Community Structure of a Cadaver at the Onset and End of the Bloat Stage of Decomposition", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-30 15:28:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/4440484"], "description"=>"<p>Stacked bar charts illustrate the relative abundances of phyla present from each individual sample collected from STAFS 2011-016.</p>", "links"=>[], "tags"=>["cadaver", "Southeast Texas Applied Forensic Science facility", "body sites", "bacteria", "16 S rRNA gene", "sample", "Decomposition Human decomposition", "role", "bloat stage", "additive data sets", "Bacterial Community Structure"], "article_id"=>837746, "categories"=>["Microbiology", "Evolutionary Biology", "Environmental Sciences not elsewhere classified", "Ecology", "Biological Sciences not elsewhere classified", "Science Policy"], "users"=>["Embriette R. Hyde", "Daniel P. Haarmann", "Aaron M. Lynne", "Sibyl R. Bucheli", "Joseph F. Petrosino"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0077733.g006"], "stats"=>{"downloads"=>1, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_relative_abundances_of_phyla_present_differ_between_sample_sites_in_STAFS_2011_016_/837746", "title"=>"The relative abundances of phyla present differ between sample sites in STAFS 2011-016.", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-10-30 15:28:36"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"193", "full-text"=>"223", "pdf"=>"28", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"2", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"207", "full-text"=>"233", "pdf"=>"18", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"170", "full-text"=>"197", "pdf"=>"10", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}
  • {"unique-ip"=>"120", "full-text"=>"129", "pdf"=>"12", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2019", "month"=>"8"}
  • {"unique-ip"=>"136", "full-text"=>"149", "pdf"=>"13", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}

Relative Metric

{"start_date"=>"2013-01-01T00:00:00Z", "end_date"=>"2013-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Anatomy", "average_usage"=>[248, 440, 562, 666, 765, 856, 944, 1028, 1112, 1198, 1282, 1362, 1430]}, {"subject_area"=>"/Biology and life sciences/Organisms", "average_usage"=>[281, 484, 611, 728, 835, 934, 1030, 1123, 1214, 1299, 1383, 1464]}, {"subject_area"=>"/Ecology and environmental sciences", "average_usage"=>[284, 475, 603, 722, 826, 928, 1026, 1129, 1225, 1310, 1390, 1468, 1549]}, {"subject_area"=>"/Ecology and environmental sciences/Ecology", "average_usage"=>[298, 487, 610, 722, 827, 929, 1029, 1125, 1217, 1306, 1388, 1464, 1535]}, {"subject_area"=>"/Medicine and health sciences", "average_usage"=>[264, 460, 584, 692, 794, 887, 978, 1067, 1154, 1241, 1328, 1408, 1474]}, {"subject_area"=>"/Medicine and health sciences/Anatomy", "average_usage"=>[248, 441, 564, 668, 769, 859, 948, 1034, 1117, 1202, 1290, 1368, 1437]}, {"subject_area"=>"/Medicine and health sciences/Anatomy and physiology", "average_usage"=>[253, 430]}, {"subject_area"=>"/Medicine and health sciences/Diagnostic medicine", "average_usage"=>[244, 425, 535, 636, 728, 814, 900, 982, 1063, 1139, 1221, 1296, 1361]}]}
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