Microbiome of Human Decomposition

A cadaver is far from dead when viewed as an ecosystem for a suite of bacteria, insects, and fungi. Decomposition is a mosaic system with an intimate association between biotic factors (i.e., the individuality of the cadaver, intrinsic and extrinsic bacteria and other microbes, and insects) and abiotic factors (i.e., weather, climate, and humidity) and therefore a function of a specific ecological scenario.

Along with Sibyl Bucheli, I have been investigating the microbiome of human cadavers for the last 10 years.  We are primarily interested in using microbial data (microbial community structure) to develop models to predict the post-mortem interval.  

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Our initial work has been funded by the National Institute of Justice and has involved looking at the change in microbial community structure of a cadaver.  Through the Southeast Texas Applied Forensic Science (STAFS) facility, we are able to place donated human cadavers outside to decompose in a natural setting and then collect a variety of samples as the body decomposes, which allows us to study decomposition in a very systematic manner.  In our study, we swabbed various body locations to collect bacteria which will be analyzed by metagenomic techniques using next-generation sequencing technology in collaboration with Dr. Joseph Petrosino (Director of the Alkek Center for Metagenomic and Microbiome Research Center at Baylor College of Medicine).

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We have been collaborating with Dr. Jessica Metcalf from Colorado State University and Rob Knight from University of California San Diego to build Random Forrest regression models for prediction of PMI by testing models built on different sample types (gravesoil, skin of the torso, skin of the head), gene markers (16S ribosomal RNA (rRNA), 18S rRNA, internal transcribed spacer regions (ITS)), and taxonomic levels (sequence variants, species, genus, etc.).  

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Finally, we have recently had two projects funded by the National Institute of Justice. The first is to compare the microbiome of cadavers decomposing indoors to cadaver decomposing outdoors.  If an indoor environment can alter the tempo and mode of decomposition by impacting scavenger activity, insect succession, and microbial succession, approximations of the PMI based off models developed for outdoor studies may lead to erroneous estimations.  The second study aims to investigate the use of microbes inside bones as a way to estimate the PMI for cadaver in advanced stages of decomposition.  The results on these ongoing studies will help us build more accurate models for estimating PMI