Edited by
David O. Carter
Forensic Sciences Unit, Chaminade University of Honolulu, USA

Jeffery K. Tomberlin
Department of Entomology, Texas A&M University, USA

M. Eric Benbow
Department of Entomology, Michigan State University, USA

Jessica L. Metcalf
Department of Animal Sciences, Colorado State University, USA

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