Human Thanatomicrobiome Succession and Time Since Death

Human Microbiome Project (HMP) metagenomic sequencing studies characterized the complexity of the human microbiome at numerous body sites, highlighting significant differences between microbial communities within and among individuals1. In a healthy adult, a ratio of 10:1 of the cells in a body are microbial1,2. Sender et al.3 have challenged this estimate and suggested that the ratio is much closer to 1:1. The thanatomicrobiome is the postmortem microbial community of the human body, which involves a successional process where trillions of microbes inhabit, proliferate, and die internally and externally throughout the dead body, resulting in temporal shifts in community composition over time4,5. Upon death, the host environment changes due to the decomposition of cells and subsequent release of cellular components to the surrounding tissues. There are several sequential events that occur after a person dies that lead to uninhibited reproduction of certain types of microbial cells and the quiescence or death of other cells6,7,8,9,10. The study of the thanatomicrobiome of internal organs and blood is not directly influenced by the same environmental abiotic factors (i.e., pH and temperature) and biotic factors (i.e., insects and scavenger activities)11 that are encountered by the necrobiome12. Additionally, it is presumed that the thanatomicrobiome of certain organs is not immediately affected by gut-associated microorganisms that proliferate rapidly after human death13. It was once a long held belief that human internal organs were sterile in living hosts14,15. However, there is sufficient evidence demonstrated by HMP data that some internal organs (i.e., lungs and gut) provide distinct niches for commensal opportunistic and pathogenic microorganisms to colonize microbiomes1. The microbes discovered in the internal organs of cadavers could represent those directly associated with human decomposition. Tuomisto et al.13 demonstrated that internal organs such as the liver remain sterile up to five days after death. As a human body decays, microbes proliferate in the blood, liver, spleen, heart and brain in a time-dependent manner; therefore, the relative abundances of microbes will vary by respective body organ and postmortem interval (PMI)5. In order to address the dearth of knowledge regarding the internal thanatomicrobiome, we describe here results of the largest study thus far of the postmortem microbial communities of internal organs. We hypothesized that as a human body decomposes, the thanatomicrobiome within internal organs shifts in microbial community structure as time progresses. To assess this hypothesis, we sampled 27 corpses with varying times of death (range 3.5–240 hours), across multiple causes of death, using 16S rRNA amplicon sequencing technologies to classify the microbial taxa associated with the organs of cadavers. Further, we demonstrated a significant correlation in the thanatomicrobiome signatures, which corresponded with PMI. Thus, we produced a microbial catalogue of the thanatomicrobiome, which may establish a useful forensic tool and provide constructive information to those who study human remains.