Abstract
Decomposing remains are a nutrient-rich ecosystem undergoing constant change due to cell breakdown and abiotic fluxes, such as pH level and oxygen availability. These environmental fluxes affect bacterial communities who respond in a predictive manner associated with the time since organismal death, or the postmortem interval (PMI). Profiles of microbial taxonomic turnover and transmigration are currently being studied in decomposition ecology, and in the field of forensic microbiology as indicators of the PMI. We monitored bacterial community structural and functional changes taking place during decomposition of the intestines, bone marrow, lungs, and heart in a highly controlled murine model. We found that organs presumed to be sterile during life are colonized by Clostridium during later decomposition as the fluids from internal organs begin to emulsify within the body cavity. During colonization of previously sterile sites, gene transcripts for multiple metabolism pathways were highly abundant, while transcripts associated with stress response and dormancy increased as decomposition progressed. We found our model strengthens known bacterial taxonomic succession data after host death. This study is one of the first to provide data of expressed bacterial community genes, alongside transmigration and structural changes of microbial species during laboratory controlled vertebrate decomposition. This is an important dataset for studying the effects of the environment on bacterial communities in an effort to determine which bacterial species and which bacterial functional pathways, such as amino acid metabolism, provide key changes during stages of decomposition that relate to the PMI. Finding unique PMI species or functions can be useful for determining time since death in forensic investigations.
Highlights
Decomposing remains are a continuously shifting ecological system leading to changes in nutrient availability and microhabitat conditions, yielding a microbial consortium under constant selective pressures (Carter et al, 2007; Janaway et al, 2009; Hyde et al, 2013; Metcalf et al, 2016)
Sixty-four 1 mL cultures obtained from the original culture were pelleted and S. aureus KUB7 was resuspended in 7 μL tryptic soy broth (TSB) while C. perfringens was resuspended in 7 μL of reinforced clostridial medium (RCM) supplemented with 60 g/L sucrose
The S. aureus KUB7 mean log genomic units in the lungs decreased from 6.91 ± 2.32 logGU to 4.21 ± 2.74 logGU to 0 ± 0 logGU from 1 to 3 5 h after death, respectively
Summary
Decomposing remains are a continuously shifting ecological system leading to changes in nutrient availability and microhabitat conditions, yielding a microbial consortium under constant selective pressures (Carter et al, 2007; Janaway et al, 2009; Hyde et al, 2013; Metcalf et al, 2016). After an initial lag phase immediately following organismal death, bacterial communities begin to exponentially proliferate, transmigrate, and create specialized proteins that digest host tissues during putrefaction (Can et al, 2014; Pozhitkov et al, 2017). These metabolic changes drive the transformation of the environmental decomposing landscape through the release of waste products, nutrient depletion, oxygen availability, and pH cycles which further facilitates host tissue breakdown. Bacterial communities involved in the decomposition process are highly dynamic and constantly competing for survival, nutrient acquisition, and habitat space
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