A eukaryotic community succession based method for postmortem interval (PMI) estimation of decomposing porcine remains

• Published in: Forensic science international 2019-09, Vol.302, p.109838-109838, Article 109838
• Main Authors: Forger, Luisa V., Woolf, Michael S., Simmons, Tal L., Swall, Jenise L., Singh, Baneshwar
• Format: Article
• Language: English
• Subjects: 18S rDNA; Abdomen; Animal models; Animals; Biodiversity; Bloat; Communities; Decay; Decomposition; Decomposition ecology; DNA sequencing; Ecological succession; Eukaryota - genetics; Eukaryota - physiology; Forensic Pathology; Forensic science; Forensic sciences; Funding; High-Throughput Nucleotide Sequencing; Human remains; Microbial ecology; Microorganisms; Necrobiome; Next-generation sequencing; Postmortem Changes; Postmortem interval; Relative abundance; Rhabditida; RNA, Ribosomal, 18S; Root-mean-square errors; Statistical methods; Swine; Taxa; Torso; Variance analysis
• ISSN: 0379-0738; 1872-6283
• DOI: 10.1016/j.forsciint.2019.05.054

•Strong linear relationship exists between total body score (TBS) and log10 of accumulated degree days (ADD).•Eukaryotic community diversity of vertebrate carrion decreases with time or ADD.•Eukaryotic community structure changes significantly with time/ADD.•Random forest model predicted postmortem interval (PMI) with a root mean square error (RMSE) of 177.55 ADD or ≈6 days. Recent, short-term studies on porcine and human models (albeit with few replicates) demonstrated that the succession of the microbial community of remains may be used to estimate time since death. Using a porcine model (N=6) over an extended period of time (1703 ADD, or two months), this study characterized the eukaryote community of decomposing remains. Skin microbial samples were collected from the torso of each set of remains every day during the first week, on alternate days during the second week, and once a week for the remainder of the 60-day period; all collection intervals were recorded in accumulated degree days (ADD). The eukaryote community of each sample was determined using 18S ribosomal DNA (rDNA) MiSeq high throughput sequencing; data were analyzed in the Mothur pipeline (v1.39.5) and in IBM SPSS and R statistical packages. The relative abundance of eukaryote taxa across ADD/Days and an Analysis of Molecular Variance (AMOVA) indicated similarities between sequential ADD/Days, but significant differences in the eukaryote communities as broad stage ‘milestones’ of decomposition were reached. Fresh remains (0–57 ADD/0–2 Days; exhibiting a total body score (TBS) of 0–10) were characterized by the combined presence of Saccharomycetaceae, Debaryomycetaceae, Trichosporonaceae, Rhabditida, and Trichostomatia. During bloat and active decay (87–209 ADD/3–7 Days; exhibiting TBS of 11–20), Diptera was the most abundant eukaryotic taxa. During advanced decay stage (267–448 ADD/9–15 Days; exhibiting TBS of 21–25), Rhabditida was the most dominant eukaryote. Dry/skeletal remains (734–1703 ADD/26–61 Days; TBS≥26) were dominated by fungal families Dipodascaceae, Debaryomycetaceae, Trichosporonaceae, and Sporidiobolaceae. Using the family-level eukaryote taxonomic data for the entire study, random forest modelling explained 89.58% of the variation in ADD/Days, with a root mean square error (RMSE) of 177.55 ADD (≈6 days). Overall, these results highlight the importance of the microbial eukaryote community during the process of decomposition and in estimation of PMI.