Edited byDavid O. CarterForensic Sciences Unit, Chaminade University of Honolulu, USAJeffery K. TomberlinDepartment of Entomology, Texas A&M University, USAM. Eric BenbowDepartment of Entomology, Michigan State University, USAJessica L. MetcalfDepartment of Animal Sciences, Colorado State University, USA

• About the editors, xviList of contributors, xixForeword, xxiiSeries preface, xxivPreface, xxv1 A primer on microbiology, 1David O. Carter, Emily N. Junkins and Whitney A. Kodama1.1 Introduction, 11.2 Microbial characteristics, 21.3 Microorganisms and their habitats, 71.4 Competition for resources, 101.5 The ecology of some forensically relevant bacteria, 111.6 Archaea and microbial eukaryotes, 201.7 Conclusions, 212 History, current, and future use of microorganisms as physical evidence, 25Zachary M. Burcham and Heather R. Jordan2.1 Introduction, 252.2 Methods for identification, 262.3 Estimating PMI, 302.4 Cause of death, 362.5 Trace evidence, 402.6 Other medicolegal aspects, 432.7 Needs that must be met for use in chain of custody, 482.8 Summary, 493 Approaches and considerations for forensic microbiology decomposition research, 56M. Eric Benbow and Jennifer L. Pechal3.1 Introduction, 563.2 Challenges of human remains research, 573.3 Human remains research during death investigations, 583.4 Human surrogates in research, 603.5 Considerations for field studies, 613.6 Descriptive and hypothesis]driven research, 623.7 Experiment design, 653.8 Validation studies, 694 Sampling methods and data generation, 72Jennifer L. Pechal, M. Eric Benbow and Tawni L. Crippen4.1 Introduction, 724.2 Materials, 734.3 Sample collection techniques, 794.4 Sample preservation, storage, and handling techniques, 804.5 Data considerations, 864.6 Conclusions, 905 An introduction to metagenomic data generation, analysis, visualization, and interpretation, 94Baneshwar Singh, Tawni L. Crippen and Jeffery K. Tomberlin5.1 Introduction, 945.2 DNA extraction, 965.3 DNA sequencing, 995.4 Marker gene data analysis, visualization, and interpretation, 1075.5 Multi]omics data analysis, visualization, and interpretation, 1145.6 Statistical analysis, 1175.7 Major challenges and future directions, 1186 Culture and long]term storage of microorganisms for forensic science, 127Emily N. Junkins, Embriette R. Hyde and David O. Carter6.1 Introduction, 1276.2 The value of culturing microorganisms, 1286.3 Collection and handling of samples, 1326.4 Protocols, 1346.5 Conclusions, 1437 Clinical microbiology and virology in the context of the autopsy, 146Elisabeth J. Ridgway, Bala M. Subramanian and Mohammad Raza7.1 Introduction, 1467.2 The historical view of autopsy microbiology, 1477.3 Which samples should you collect and how?, 1497.4 Which methods are available for the diagnosis of infection?, 1547.5 How do you put the results into context?, 1567.6 What are the risks of transmission of infection in the postmortem room?, 1637.7 How does autopsy microbiology contribute to the diagnosis of specific conditions?, 1648 Postmortem bacterial translocation, 192Vadim Mesli, Christel Neut and Valery Hedouin8.1 Introduction, 1928.2 Bacterial translocation in health and disease, 1958.3 Bacterial translocation in humans, 1988.4 Physiological changes after death influencing the selection of commensal bacteria, 2008.5 Consequences of bacterial translocation, 2049 Microbial impacts in postmortem toxicology, 212Jared W. Castle, Danielle M. Butzbach, G. Stewart Walker, Claire E. Lenehan, Frank Reith and K. Paul Kirkbride9.1 Introduction, 2129.2 Microbial factors complicating postmortem toxicological analyses, 2139.3 Precautions taken to limit microbial impacts, 2149.4 Experimental protocols used to investigate postmortem drug and metabolite degradation due to microbial activity, 2189.5 Examples of microbially mediated drug degradation, 21910 Microbial communities associated with decomposing corpses, 245Embriette R. Hyde, Jessica L. Metcalf, Sibyl R. Bucheli, Aaron M. Lynne and Rob Knight10.1 Introduction, 24510.2 The soil microbiology of decomposition, 24810.3 Freshwater and marine decomposition, 25210.4 The microbiology of nonhuman models of terrestrial decomposition, 25510.5 The microbiology of terrestrial human decomposition, 25810.6 Is there a universal decomposition signature?, 26310.7 Using microbial signatures to estimate PMI, 26411 Arthropod–microbe interactions on vertebrate remains: Potential applications in the forensic sciences, 274Jeffery K. Tomberlin, M. Eric Benbow, Kate M. Barnes and Heather R. Jordan11.1 Introduction, 27411.2 Framework for understanding microbe–arthropod interactions on vertebrate remains, 28211.3 Postcolonization interval, 28711.4 Future directions and conclusion, 29711.5 Acknowledgments, 29812 Microbes, anthropology, and bones, 312Franklin E. Damann and Miranda M.E. Jans12.1 Introduction, 31212.2 Bone microstructure, 31312.3 Microbially mediated decomposition, 31512.4 Bone bioerosion, 31712.5 Reconstructing postmortem histories, 32213 Forensic microbiology in built environments, 328Simon Lax and Jack A. Gilbert13.1 Introduction, 32813.2 The human skin microbiome, 32813.3 The microbiota of the built environment, 32913.4 Tools for the forensic classification of the built environment microbiome, 33213.5 Forensic microbiology of the built environment, 33514 Soil bacteria as trace evidence, 339David R. Foran, Ellen M. Jesmok and James M. Hopkins14.1 The forensic analysis of soil, 33914.2 Assessing the biological components of soil, 34014.3 Bacteria in soil, 34114.4 Molecular techniques for the forensic analysis of soil, 34214.5 Soil microbial profile data analysis methods, 34514.6 Feasibility of next]generation sequencing for forensic soil analysis, 35014.7 Consensus on methodologies for soil collection and analysis, 35315 DNA profiling of bacteria from human hair: Potential and pitfalls, 358Silvana R. Tridico, Dáithí C. Murray, Michael Bunce and K. Paul Kirkbride15.1 An introduction to human hair as a forensic substrate, 35815.2 Current research into hair microbiomes, 36115.3 Importance of hair sample collection, storage, and isolation of microbial DNA, 36515.4 DNA sequencing of hair microbiomes, 36715.5 Conclusions and future directions, 369Perspectives on the future of forensic microbiology, 376David O. Carter, Jeffery K. Tomberlin, M. Eric Benbow and Jessica L. MetcalfIndex, 379

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Edited byDavid O. CarterForensic Sciences Unit, Chaminade University of Honolulu, USAJeffery K. TomberlinDepartment of Entomology, Texas A&M University, USAM. Eric BenbowDepartment of Entomology, Michigan State University, USAJessica L. MetcalfDepartment of Animal Sciences, Colorado State University, USA

• About the editors, xviList of contributors, xixForeword, xxiiSeries preface, xxivPreface, xxv1 A primer on microbiology, 1David O. Carter, Emily N. Junkins and Whitney A. Kodama1.1 Introduction, 11.2 Microbial characteristics, 21.3 Microorganisms and their habitats, 71.4 Competition for resources, 101.5 The ecology of some forensically relevant bacteria, 111.6 Archaea and microbial eukaryotes, 201.7 Conclusions, 212 History, current, and future use of microorganisms as physical evidence, 25Zachary M. Burcham and Heather R. Jordan2.1 Introduction, 252.2 Methods for identification, 262.3 Estimating PMI, 302.4 Cause of death, 362.5 Trace evidence, 402.6 Other medicolegal aspects, 432.7 Needs that must be met for use in chain of custody, 482.8 Summary, 493 Approaches and considerations for forensic microbiology decomposition research, 56M. Eric Benbow and Jennifer L. Pechal3.1 Introduction, 563.2 Challenges of human remains research, 573.3 Human remains research during death investigations, 583.4 Human surrogates in research, 603.5 Considerations for field studies, 613.6 Descriptive and hypothesis]driven research, 623.7 Experiment design, 653.8 Validation studies, 694 Sampling methods and data generation, 72Jennifer L. Pechal, M. Eric Benbow and Tawni L. Crippen4.1 Introduction, 724.2 Materials, 734.3 Sample collection techniques, 794.4 Sample preservation, storage, and handling techniques, 804.5 Data considerations, 864.6 Conclusions, 905 An introduction to metagenomic data generation, analysis, visualization, and interpretation, 94Baneshwar Singh, Tawni L. Crippen and Jeffery K. Tomberlin5.1 Introduction, 945.2 DNA extraction, 965.3 DNA sequencing, 995.4 Marker gene data analysis, visualization, and interpretation, 1075.5 Multi]omics data analysis, visualization, and interpretation, 1145.6 Statistical analysis, 1175.7 Major challenges and future directions, 1186 Culture and long]term storage of microorganisms for forensic science, 127Emily N. Junkins, Embriette R. Hyde and David O. Carter6.1 Introduction, 1276.2 The value of culturing microorganisms, 1286.3 Collection and handling of samples, 1326.4 Protocols, 1346.5 Conclusions, 1437 Clinical microbiology and virology in the context of the autopsy, 146Elisabeth J. Ridgway, Bala M. Subramanian and Mohammad Raza7.1 Introduction, 1467.2 The historical view of autopsy microbiology, 1477.3 Which samples should you collect and how?, 1497.4 Which methods are available for the diagnosis of infection?, 1547.5 How do you put the results into context?, 1567.6 What are the risks of transmission of infection in the postmortem room?, 1637.7 How does autopsy microbiology contribute to the diagnosis of specific conditions?, 1648 Postmortem bacterial translocation, 192Vadim Mesli, Christel Neut and Valery Hedouin8.1 Introduction, 1928.2 Bacterial translocation in health and disease, 1958.3 Bacterial translocation in humans, 1988.4 Physiological changes after death influencing the selection of commensal bacteria, 2008.5 Consequences of bacterial translocation, 2049 Microbial impacts in postmortem toxicology, 212Jared W. Castle, Danielle M. Butzbach, G. Stewart Walker, Claire E. Lenehan, Frank Reith and K. Paul Kirkbride9.1 Introduction, 2129.2 Microbial factors complicating postmortem toxicological analyses, 2139.3 Precautions taken to limit microbial impacts, 2149.4 Experimental protocols used to investigate postmortem drug and metabolite degradation due to microbial activity, 2189.5 Examples of microbially mediated drug degradation, 21910 Microbial communities associated with decomposing corpses, 245Embriette R. Hyde, Jessica L. Metcalf, Sibyl R. Bucheli, Aaron M. Lynne and Rob Knight10.1 Introduction, 24510.2 The soil microbiology of decomposition, 24810.3 Freshwater and marine decomposition, 25210.4 The microbiology of nonhuman models of terrestrial decomposition, 25510.5 The microbiology of terrestrial human decomposition, 25810.6 Is there a universal decomposition signature?, 26310.7 Using microbial signatures to estimate PMI, 26411 Arthropod–microbe interactions on vertebrate remains: Potential applications in the forensic sciences, 274Jeffery K. Tomberlin, M. Eric Benbow, Kate M. Barnes and Heather R. Jordan11.1 Introduction, 27411.2 Framework for understanding microbe–arthropod interactions on vertebrate remains, 28211.3 Postcolonization interval, 28711.4 Future directions and conclusion, 29711.5 Acknowledgments, 29812 Microbes, anthropology, and bones, 312Franklin E. Damann and Miranda M.E. Jans12.1 Introduction, 31212.2 Bone microstructure, 31312.3 Microbially mediated decomposition, 31512.4 Bone bioerosion, 31712.5 Reconstructing postmortem histories, 32213 Forensic microbiology in built environments, 328Simon Lax and Jack A. Gilbert13.1 Introduction, 32813.2 The human skin microbiome, 32813.3 The microbiota of the built environment, 32913.4 Tools for the forensic classification of the built environment microbiome, 33213.5 Forensic microbiology of the built environment, 33514 Soil bacteria as trace evidence, 339David R. Foran, Ellen M. Jesmok and James M. Hopkins14.1 The forensic analysis of soil, 33914.2 Assessing the biological components of soil, 34014.3 Bacteria in soil, 34114.4 Molecular techniques for the forensic analysis of soil, 34214.5 Soil microbial profile data analysis methods, 34514.6 Feasibility of next]generation sequencing for forensic soil analysis, 35014.7 Consensus on methodologies for soil collection and analysis, 35315 DNA profiling of bacteria from human hair: Potential and pitfalls, 358Silvana R. Tridico, Dáithí C. Murray, Michael Bunce and K. Paul Kirkbride15.1 An introduction to human hair as a forensic substrate, 35815.2 Current research into hair microbiomes, 36115.3 Importance of hair sample collection, storage, and isolation of microbial DNA, 36515.4 DNA sequencing of hair microbiomes, 36715.5 Conclusions and future directions, 369Perspectives on the future of forensic microbiology, 376David O. Carter, Jeffery K. Tomberlin, M. Eric Benbow and Jessica L. MetcalfIndex, 379

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Edited byDavid O. CarterForensic Sciences Unit, Chaminade University of Honolulu, USAJeffery K. TomberlinDepartment of Entomology, Texas A&M University, USAM. Eric BenbowDepartment of Entomology, Michigan State University, USAJessica L. MetcalfDepartment of Animal Sciences, Colorado State University, USA

• About the editors, xviList of contributors, xixForeword, xxiiSeries preface, xxivPreface, xxv1 A primer on microbiology, 1David O. Carter, Emily N. Junkins and Whitney A. Kodama1.1 Introduction, 11.2 Microbial characteristics, 21.3 Microorganisms and their habitats, 71.4 Competition for resources, 101.5 The ecology of some forensically relevant bacteria, 111.6 Archaea and microbial eukaryotes, 201.7 Conclusions, 212 History, current, and future use of microorganisms as physical evidence, 25Zachary M. Burcham and Heather R. Jordan2.1 Introduction, 252.2 Methods for identification, 262.3 Estimating PMI, 302.4 Cause of death, 362.5 Trace evidence, 402.6 Other medicolegal aspects, 432.7 Needs that must be met for use in chain of custody, 482.8 Summary, 493 Approaches and considerations for forensic microbiology decomposition research, 56M. Eric Benbow and Jennifer L. Pechal3.1 Introduction, 563.2 Challenges of human remains research, 573.3 Human remains research during death investigations, 583.4 Human surrogates in research, 603.5 Considerations for field studies, 613.6 Descriptive and hypothesis]driven research, 623.7 Experiment design, 653.8 Validation studies, 694 Sampling methods and data generation, 72Jennifer L. Pechal, M. Eric Benbow and Tawni L. Crippen4.1 Introduction, 724.2 Materials, 734.3 Sample collection techniques, 794.4 Sample preservation, storage, and handling techniques, 804.5 Data considerations, 864.6 Conclusions, 905 An introduction to metagenomic data generation, analysis, visualization, and interpretation, 94Baneshwar Singh, Tawni L. Crippen and Jeffery K. Tomberlin5.1 Introduction, 945.2 DNA extraction, 965.3 DNA sequencing, 995.4 Marker gene data analysis, visualization, and interpretation, 1075.5 Multi]omics data analysis, visualization, and interpretation, 1145.6 Statistical analysis, 1175.7 Major challenges and future directions, 1186 Culture and long]term storage of microorganisms for forensic science, 127Emily N. Junkins, Embriette R. Hyde and David O. Carter6.1 Introduction, 1276.2 The value of culturing microorganisms, 1286.3 Collection and handling of samples, 1326.4 Protocols, 1346.5 Conclusions, 1437 Clinical microbiology and virology in the context of the autopsy, 146Elisabeth J. Ridgway, Bala M. Subramanian and Mohammad Raza7.1 Introduction, 1467.2 The historical view of autopsy microbiology, 1477.3 Which samples should you collect and how?, 1497.4 Which methods are available for the diagnosis of infection?, 1547.5 How do you put the results into context?, 1567.6 What are the risks of transmission of infection in the postmortem room?, 1637.7 How does autopsy microbiology contribute to the diagnosis of specific conditions?, 1648 Postmortem bacterial translocation, 192Vadim Mesli, Christel Neut and Valery Hedouin8.1 Introduction, 1928.2 Bacterial translocation in health and disease, 1958.3 Bacterial translocation in humans, 1988.4 Physiological changes after death influencing the selection of commensal bacteria, 2008.5 Consequences of bacterial translocation, 2049 Microbial impacts in postmortem toxicology, 212Jared W. Castle, Danielle M. Butzbach, G. Stewart Walker, Claire E. Lenehan, Frank Reith and K. Paul Kirkbride9.1 Introduction, 2129.2 Microbial factors complicating postmortem toxicological analyses, 2139.3 Precautions taken to limit microbial impacts, 2149.4 Experimental protocols used to investigate postmortem drug and metabolite degradation due to microbial activity, 2189.5 Examples of microbially mediated drug degradation, 21910 Microbial communities associated with decomposing corpses, 245Embriette R. Hyde, Jessica L. Metcalf, Sibyl R. Bucheli, Aaron M. Lynne and Rob Knight10.1 Introduction, 24510.2 The soil microbiology of decomposition, 24810.3 Freshwater and marine decomposition, 25210.4 The microbiology of nonhuman models of terrestrial decomposition, 25510.5 The microbiology of terrestrial human decomposition, 25810.6 Is there a universal decomposition signature?, 26310.7 Using microbial signatures to estimate PMI, 26411 Arthropod–microbe interactions on vertebrate remains: Potential applications in the forensic sciences, 274Jeffery K. Tomberlin, M. Eric Benbow, Kate M. Barnes and Heather R. Jordan11.1 Introduction, 27411.2 Framework for understanding microbe–arthropod interactions on vertebrate remains, 28211.3 Postcolonization interval, 28711.4 Future directions and conclusion, 29711.5 Acknowledgments, 29812 Microbes, anthropology, and bones, 312Franklin E. Damann and Miranda M.E. Jans12.1 Introduction, 31212.2 Bone microstructure, 31312.3 Microbially mediated decomposition, 31512.4 Bone bioerosion, 31712.5 Reconstructing postmortem histories, 32213 Forensic microbiology in built environments, 328Simon Lax and Jack A. Gilbert13.1 Introduction, 32813.2 The human skin microbiome, 32813.3 The microbiota of the built environment, 32913.4 Tools for the forensic classification of the built environment microbiome, 33213.5 Forensic microbiology of the built environment, 33514 Soil bacteria as trace evidence, 339David R. Foran, Ellen M. Jesmok and James M. Hopkins14.1 The forensic analysis of soil, 33914.2 Assessing the biological components of soil, 34014.3 Bacteria in soil, 34114.4 Molecular techniques for the forensic analysis of soil, 34214.5 Soil microbial profile data analysis methods, 34514.6 Feasibility of next]generation sequencing for forensic soil analysis, 35014.7 Consensus on methodologies for soil collection and analysis, 35315 DNA profiling of bacteria from human hair: Potential and pitfalls, 358Silvana R. Tridico, Dáithí C. Murray, Michael Bunce and K. Paul Kirkbride15.1 An introduction to human hair as a forensic substrate, 35815.2 Current research into hair microbiomes, 36115.3 Importance of hair sample collection, storage, and isolation of microbial DNA, 36515.4 DNA sequencing of hair microbiomes, 36715.5 Conclusions and future directions, 369Perspectives on the future of forensic microbiology, 376David O. Carter, Jeffery K. Tomberlin, M. Eric Benbow and Jessica L. MetcalfIndex, 379

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