Forensic Microbiology

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