Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model

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.

Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data

“…Research on ecological succession is key to advance our understanding of how communities are assembled and affect ecosystem functioning and dynamics. In accordance with classical studies on plant community succession, the relatively recent advances in high-throughput sequencing technologies and microbiome profiling have revealed that microbial communities across a broad range of habitats also undergo sequential changes through different time scales [1][2][3].…”

Total RNA Analysis of Bacterial Community Structural and Functional Shifts Throughout Vertebrate Decomposition

“…The lack of diversity differences between sterilization treatments suggests that internal antemortem microbial communities give rise to the dominating internal postmortem communities during decomposition. In a previous model, we detected a similar trend where the internal microbial profile was consistent across surface sterilization techniques further strengthening the hypothesis that internal microbes are the main contributors to internal host tissue breakdown and may serve as reliable PMI biomarkers . Additionally, we believe the introduction of S. aureus KUB7 and C. perfringens + pZMB2 did not greatly alter the existing community structure due to the low detection by highly sensitive DNA techniques.…”

“…C. perfringens + pZMB2 was essentially absent, apart from a few outliers, in all organs except the intestines and one instance of a 14‐day heart sample. Introduced species in a previous model were shown to significantly die off past 30 days postmortem . The low colonization abundances and inconsistencies across mice inhibited reliable translocation tracking of S. aureus KUB7 and C. perfringens + pZMB2; therefore, further analyses focused on the bacterial community structural and functional turnover across postmortem time through high‐throughput sequencing.…”

“…These two bacterial species have been found in mice and shown to colonize living humans, albeit in separate niches, and have been shown to translocate and produce enzymes that break down tissues during decomposition. Additionally, mouse models have shown to contain microbial trends similar in human decomposition and provide an opportunity to easily obtain statistically relevant study sizes along with controlled laboratory conditions . We describe here the colonization of mice orally with chromosomally tagged red fluorescent S. aureus and nonfluorescent plasmid tagged C. perfringens .…”

“…Further, we are among the first to utilize postmortem microbial metatranscriptomic analyses, determining both community structure and function from single samples. However, it is important to note that multiple studies have shown functional potential is predicted to change with the PMI or have focused on select sole‐carbon source utilization, even fewer studies have studied the full microbial functional profile of RNA transcripts . Until recently, postmortem transcriptome analyses have focused on the host transcriptome changes instead of the bacterial communities associated with the host.…”