Forensic Microbiology
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About the editors, xvi
List of contributors, xix
Foreword, xxii
Series preface, xxiv
Preface, xxv
1 A primer on microbiology, 1
David O. Carter, Emily N. Junkins and Whitney A. Kodama
1.1 Introduction, 1
1.2 Microbial characteristics, 2
1.3 Microorganisms and their habitats, 7
1.4 Competition for resources, 10
1.5 The ecology of some forensically relevant bacteria, 11
1.6 Archaea and microbial eukaryotes, 20
1.7 Conclusions, 21
2 History, current, and future use of microorganisms as physical evidence, 25
Zachary M. Burcham and Heather R. Jordan
2.1 Introduction, 25
2.2 Methods for identification, 26
2.3 Estimating PMI, 30
2.4 Cause of death, 36
2.5 Trace evidence, 40
2.6 Other medicolegal aspects, 43
2.7 Needs that must be met for use in chain of custody, 48
2.8 Summary, 49
3 Approaches and considerations for forensic microbiology decomposition research, 56
M. Eric Benbow and Jennifer L. Pechal
3.1 Introduction, 56
3.2 Challenges of human remains research, 57
3.3 Human remains research during death investigations, 58
3.4 Human surrogates in research, 60
3.5 Considerations for field studies, 61
3.6 Descriptive and hypothesis?]driven research, 62
3.7 Experiment design, 65
3.8 Validation studies, 69
4 Sampling methods and data generation, 72
Jennifer L. Pechal, M. Eric Benbow and Tawni L. Crippen
4.1 Introduction, 72
4.2 Materials, 73
4.3 Sample collection techniques, 79
4.4 Sample preservation, storage, and handling techniques, 80
4.5 Data considerations, 86
4.6 Conclusions, 90
5 An introduction to metagenomic data generation, analysis, visualization, and interpretation, 94
Baneshwar Singh, Tawni L. Crippen and Jeffery K. Tomberlin
5.1 Introduction, 94
5.2 DNA extraction, 96
5.3 DNA sequencing, 99
5.4 Marker gene data analysis, visualization, and interpretation, 107
5.5 Multi?]omics data analysis, visualization, and interpretation, 114
5.6 Statistical analysis, 117
5.7 Major challenges and future directions, 118
6 Culture and long?]term storage of microorganisms for forensic science, 127
Emily N. Junkins, Embriette R. Hyde and David O. Carter
6.1 Introduction, 127
6.2 The value of culturing microorganisms, 128
6.3 Collection and handling of samples, 132
6.4 Protocols, 134
6.5 Conclusions, 143
7 Clinical microbiology and virology in the context of the autopsy, 146
Elisabeth J. Ridgway, Bala M. Subramanian and Mohammad Raza
7.1 Introduction, 146
7.2 The historical view of autopsy microbiology, 147
7.3 Which samples should you collect and how?, 149
7.4 Which methods are available for the diagnosis of infection?, 154
7.5 How do you put the results into context?, 156
7.6 What are the risks of transmission of infection in the postmortem room?, 163
7.7 How does autopsy microbiology contribute to the diagnosis of specific conditions?, 164
8 Postmortem bacterial translocation, 192
Vadim Mesli, Christel Neut and Valery Hedouin
8.1 Introduction, 192
8.2 Bacterial translocation in health and disease, 195
8.3 Bacterial translocation in humans, 198
8.4 Physiological changes after death influencing the selection of commensal bacteria, 200
8.5 Consequences of bacterial translocation, 204
9 Microbial impacts in postmortem toxicology, 212
Jared W. Castle, Danielle M. Butzbach, G. Stewart Walker, Claire E. Lenehan, Frank Reith and K. Paul Kirkbride
9.1 Introduction, 212
9.2 Microbial factors complicating postmortem toxicological analyses, 213
9.3 Precautions taken to limit microbial impacts, 214
9.4 Experimental protocols used to investigate postmortem drug and metabolite degradation due to microbial activity, 218
9.5 Examples of microbially mediated drug degradation, 219
10 Microbial communities associated with decomposing corpses, 245
Embriette R. Hyde, Jessica L. Metcalf, Sibyl R. Bucheli, Aaron M. Lynne and Rob Knight
10.1 Introduction, 245
10.2 The soil microbiology of decomposition, 248
10.3 Freshwater and marine decomposition, 252
10.4 The microbiology of nonhuman models of terrestrial decomposition, 255
10.5 The microbiology of terrestrial human decomposition, 258
10.6 Is there a universal decomposition signature?, 263
10.7 Using microbial signatures to estimate PMI, 264
11 Arthropod-microbe interactions on vertebrate remains: Potential applications in the forensic sciences, 274
Jeffery K. Tomberlin, M. Eric Benbow, Kate M. Barnes and Heather R. Jordan
11.1 Introduction, 274
11.2 Framework for understanding microbe-arthropod interactions on vertebrate remains, 282
11.3 Postcolonization interval, 287
11.4 Future directions and conclusion, 297
11.5 Acknowledgments, 298
12 Microbes, anthropology, and bones, 312
Franklin E. Damann and Miranda M.E. Jans
12.1 Introduction, 312
12.2 Bone microstructure, 313
12.3 Microbially mediated decomposition, 315
12.4 Bone bioerosion, 317
12.5 Reconstructing postmortem histories, 322
13 Forensic microbiology in built environments, 328
Simon Lax and Jack A. Gilbert
13.1 Introduction, 328
13.2 The human skin microbiome, 328
13.3 The microbiota of the built environment, 329
13.4 Tools for the forensic classification of the built environment microbiome, 332
13.5 Forensic microbiology of the built environment, 335
14 Soil bacteria as trace evidence, 339
David R. Foran, Ellen M. Jesmok and James M. Hopkins
14.1 The forensic analysis of soil, 339
14.2 Assessing the biological components of soil, 340
14.3 Bacteria in soil, 341
14.4 Molecular techniques for the forensic analysis of soil, 342
14.5 Soil microbial profile data analysis methods, 345
14.6 Feasibility of next?]generation sequencing for forensic soil analysis, 350
14.7 Consensus on methodologies for soil collection and analysis, 353
15 DNA profiling of bacteria from human hair: Potential and pitfalls, 358
Silvana R. Tridico, Dáithí C. Murray, Michael Bunce and K. Paul Kirkbride
15.1 An introduction to human hair as a forensic substrate, 358
15.2 Current research into hair microbiomes, 361
15.3 Importance of hair sample collection, storage, and isolation of microbial DNA, 365
15.4 DNA sequencing of hair microbiomes, 367
15.5 Conclusions and future directions, 369
Perspectives on the future of forensic microbiology, 376
David O. Carter, Jeffery K. Tomberlin, M. Eric Benbow and Jessica L. Metcalf
Index, 379
