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Environmental Microbial Forensics

Editors: Raúl J. Cano1, Gary A. Toranzos2
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Affiliations: 1: Department of Biology, Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California; 2: Environmental Microbiology Laboratory, Department of Biology, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico
Content Type: Monograph
Format: Electronic
Publication Year: 2018

Category: Environmental Microbiology; Applied and Industrial Microbiology

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Forensic scientists use tools from the natural sciences and engineering to analyze physical evidence. Such evidence might be at a crime scene, a bioterrorism event, at the site of an oil spill or chemical discharge, or when in pursuit of a foodborne infectious disease. Increasingly, microbes are serving as some of that physical evidence. The DNA of isolated microorganisms is being subjected to whole-genome sequencing, while the metagenomes of microbiomes found in the environment are now routinely sequenced and analyzed. Databases of microbial genomes are growing rapidly, and probing those databases with powerful bioinformatics tools and other analytical techniques enables comparative microbial genomics to be applied to forensic analysis.

The powerful genomics tools available today are being applied to forensic analysis of microorganisms in a diverse array of situations. Many of these methods and applications are presented in , edited by Gary Toranzos and Raúl Cano. This fascinating book includes detailed discussions on

  • Soil microbiomes are being analyzed to evaluate cadaver decomposition, identify clandestine graves, and serve as trace evidence. Plant pathogens are monitored as potential agroterrorism agents, have been used as herbicides sprayed on drug crops, and been sequenced and identified when determining liability for the unintentional spread of phytopathogens. Bioterrorism attacks are often solved by using genomics analysis of the pathogen to trace it to its source, as was done in solving the Bacillus anthracis United States mail attacks in 2001.
  • Paleomicrobiology, or the study of ancient microbes (and especially of their DNA), is revealing the epidemiology of ancient infectious diseases, tracing ancient disease migration patterns, and using coprolites (petrified feces) as a window into the gut microbiomes—and by extension, the dietary habits—of our human ancestors. Victims of epidemics, such as the major plague outbreaks in Europe and Asia, who were buried in “catastrophe cemeteries,” are telling tales about the strains of Yersinia pestis responsible for their demise.
  • Source tracking outbreaks of foodborne diseases, monitoring water quality, and expanding our knowledge of host-pathogen interactions are all benefiting from molecular forensic analyses. Molecular microbial forensics provides insights into the evolutionary changes of host-pathogen interactions. To maintain water quality and minimize the impacts of foodborne diseases, methods like qPCR, microarray analysis, and high-throughput sequencing allow scientists to subtype microbial culprits and track them to their source.
  • Microbial forensic methods require stringent quality control procedures from sample collection through data collection. The Microbiome Quality Control project, for example, is a recent effort to evaluate methods for probing microbiomes. Bioinformatics programs are now available that accept multiple microbial genome datasets as input and assist in reconstructing transmission pathways of an outbreak. In microbial forensic situations, likelihood and Bayesian approaches are perhaps the better statistical methods to choose when it comes time to analyze the data.

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