Changes in Microbial Communities Using Pigs as a Model for Postmortem Interval Estimation

Abstract

Microbial communities can undergo significant successional changes during decay and decomposition, potentially providing valuable insights for determining the postmortem interval (PMI). The microbiota produce various gases that cause cadaver bloating, and rupture releases nutrient-rich bodily fluids into the environment, altering the soil microbiota around the carcasses. In this study, we aimed to investigate the underlying principles governing the succession of microbial communities during the decomposition of pig carcasses and the soil beneath the carcasses. At early decay, the phylum Firmicutes and Bacteroidota were the most abundant in both the winter and summer pig rectum. However, Proteobacteria became the most abundant in the winter pig rectum in late decay. Using genus as a biomarker to estimate the PMI could get the MAE from 1.375 days to 2.478 days based on the RF model. The abundance of bacterial communities showed a decreasing trend with prolonged decomposition time. There were statistically significant differences in microbial diversity in the two periods (pre-rupture and post-rupture) of the four groups (WPG 0-8Dvs. WPG 16-40D, p < 0.0001; WPS 0-16Dvs. WPS 24-40D, p = 0.003; SPG 0D vs. SPG 8-40D, p = 0.0005; and SPS 0D vs. SPS 8-40D, p = 0.0208). Most of the biomarkers in the pre-rupture period belong to obligate anaerobes. In contrast, the biomarkers in the post-rupture period belong to aerobic bacteria. Furthermore, the genus Vagococcus shows a similar increase trend, whether in winter or summer. Together, these results suggest that microbial succession was predictable and can be developed into a forensic tool for estimating the PMI.

Keywords: forensic science; microbial community; postmortem interval estimation; rupture.

Figure 1

Morphological changes of pigs buried in different seasons.

Figure 2

An overview of the differences between groups. (a) Venn of OTUs in different groups; green for WPG, blue for WPS, pink for SPG, and yellow for SPS; WPG: winter pig rectal sample; WPS: winter pig soil sample; SPG: summer pig rectal sample; SPS: summer pig soil sample. (b) The Shannon index of different groups. (c) The Shannon index tendency over time as the corpse decomposed. (d) The difference between groups when dividing the sample into two stages. *: p < 0.05, ***: p < 0.001, ****: p < 0.0001.

Figure 3

OPLS-DA using the genus abundance. (a) The score scatter plot of rectum samples; (b) The score scatter plot of soil samples. WPG: winter pig rectal sample; WPS: winter pig soil sample; SPG: summer pig rectal sample; SPS: summer pig soil sample.

Figure 4

The relative abundance of bacteria in different groups changes with decomposition. (a) The phylum level of WPG; (b) the genus level of WPG; (c) the phylum level of WPS; (d) the genus level of WPS; (e) the phylum level of SPG; (f) the genus level of SPG; (g) the phylum level of SPS; and (h) the genus level of SPS. WPG: winter pig rectal sample; WPS: winter pig soil sample; SPG: summer pig rectal sample; SPS: summer pig soil sample.

Figure 5

The biomarkers and RF model based on genus. (a–d) The top biomarker bacterial genera were identified by applying a random forest model of their relative abundances in each group against PMIs. Biomarker taxa are ranked in descending order of importance to the accuracy of the model. The inset represents a 10-fold cross-validation error as a function of the number of input genera used to regress against the PMI. (a) WPG; (b) WPS; (c) SPG; (d) SPS; (e–h) RF model based on genus. (e) WPG; (f) WPS; (g) SPG; (h) SPS.

Figure 6

The biomarkers obtained using LEfSe analysis with an LDA > 4 in the rectum, including the genus Vagococcus and family Vagococcaceae with an LDA score of 3.96. The purple dotted line means LDA = 4.

Figure 7

The biomarkers obtained using LEfSe analysis with an LDA > 4 in the soil. The purple dotted line means LDA = 4.