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

Forger, Luisa V.; Woolf, M. Shane; Simmons, Tal; Swall, Jenise L.; Singh, Baneshwar

doi:10.1016/j.forsciint.2019.05.054

Cited by 21 publications

(18 citation statements)

References 37 publications

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“…Venn diagrams for presence and absence of bacterial taxa were generated with VennDiagram package version 1.6.20 [40]. Relative abundances were also utilized to predict PMSI via random forest modeling, according to the methods outlined by Forger et al [18].…”

Section: Stacked Bar Graphs Of Taxonomic Level Relative Abundance Formentioning

confidence: 99%

“…The advancement of next-generation sequencing (NGS) and improved bioinformatic pipelines (i.e., QIIME [13] and mothur [14]) have allowed for the comprehensive identification of microbes contributing to community structure and succession. Resulting necromicrobiomefocused studies have successfully identified changes in microbial community structure during terrestrial decomposition using human [15,16], porcine [17,18], and murine remains [19]. Likewise, initial aquatic decomposition studies using salmon and whale carcasses have suggested microbial shifts in both freshwater and marine environments [20][21][22].…”

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confidence: 99%

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Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake

Cartozzo

Singh

Swall

et al. 2021

Journal of Forensic Sciences

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Human remains may be found in, and subsequently recovered from aquatic environments due to natural land erosion (from both modern and archeological cemeteries on flood plains), accidents (drownings as well as boating and/or ferry disasters), criminal activities (intentional drowning or disposal of remains), suicides, or natural disasters (e.g., Hurricane Katrina) [1,2]. The aquatic decomposition cycle, which may include periods of floating, submersion, and fluvial transportation, may make the discovery and recovery of remains

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Section: Stacked Bar Graphs Of Taxonomic Level Relative Abundance Formentioning

confidence: 99%

mentioning

confidence: 99%

Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake

Cartozzo

Singh

Swall

et al. 2021

Journal of Forensic Sciences

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“…Because of challenges in obtaining, and/or restrictions on use of, human cadavers, many forensic taphonomy studies use animal carcasses as proxies. Therefore, much of our knowledge of decomposition timing and processes have relied on various animal carcasses, including pigs (Hopkins et al, 2000;Wilson et al, 2007;Howard et al, 2010;Meyer et al, 2013;Pechal et al, 2013;Forger et al, 2019;Matuszewski et al, 2020), mice (Metcalf et al, 2013;Lauber et al, 2014), rats (Carter et al, 2010), dogs (Reed, 1958), and other vertebrate wildlife (Towne, 2000;Parmenter and MacMahon, 2009;Macdonald et al, 2014;Risch et al, 2020). Domestic pigs (Sus scrofa) are often cited as the most useful analog for humans in decomposition studies, given their physiological and anatomical similarities, including mass, hairiness, and pigmentation (Schoenly et al, 2007;Matuszewski et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

Comparative Decomposition of Humans and Pigs: Soil Biogeochemistry, Microbial Activity and Metabolomic Profiles

et al. 2021

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Vertebrate decomposition processes have important ecological implications and, in the case of human decomposition, forensic applications. Animals, especially domestic pigs (Sus scrofa), are frequently used as human analogs in forensic decomposition studies. However, recent research shows that humans and pigs do not necessarily decompose in the same manner, with differences in decomposition rates, patterns, and scavenging. The objective of our study was to extend these observations and determine if human and pig decomposition in terrestrial settings have different local impacts on soil biogeochemistry and microbial activity. In two seasonal trials (summer and winter), we simultaneously placed replicate human donors and pig carcasses on the soil surface and allowed them to decompose. In both human and pig decomposition-impacted soils, we observed elevated microbial respiration, protease activity, and ammonium, indicative of enhanced microbial ammonification and limited nitrification in soil during soft tissue decomposition. Soil respiration was comparable between summer and winter, indicating similar microbial activity; however, the magnitude of the pulse of decomposition products was greater in the summer. Using untargeted metabolomics and lipidomics approaches, we identified 38 metabolites and 54 lipids that were elevated in both human and pig decomposition-impacted soils. The most frequently detected metabolites were anthranilate, creatine, 5-hydroxyindoleacetic acid, taurine, xanthine, N-acetylglutamine, acetyllysine, and sedoheptulose 1/7-phosphate; the most frequently detected lipids were phosphatidylethanolamine and monogalactosyldiacylglycerol. Decomposition soils were also significantly enriched in metabolites belonging to amino acid metabolic pathways and the TCA cycle. Comparing humans and pigs, we noted several differences in soil biogeochemical responses. Soils under humans decreased in pH as decomposition progressed, while under pigs, soil pH increased. Additionally, under pigs we observed significantly higher ammonium and protease activities compared to humans. We identified several metabolites that were elevated in human decomposition soil compared to pig decomposition soil, including 2-oxo-4-methylthiobutanoate, sn-glycerol 3-phosphate, and tryptophan, suggesting different decomposition chemistries and timing between the two species. Together, our work shows that human and pig decomposition differ in terms of their impacts on soil biogeochemistry and microbial decomposer activities, adding to our understanding of decomposition ecology and informing the use of non-human models in forensic research.

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“…Past research studies on the HPM mainly focused on animal models [ 33 , 34 , 35 ]. They demonstrated successional changes in carrion bacterial communities over decomposition and the potential use of the post-mortem microbial community in PMI estimates [ 36 , 37 , 38 ].…”

Section: Discussionmentioning

confidence: 99%

MALDI-TOF Mass Spectrometry Analysis and Human Post-Mortem Microbial Community: A Pilot Study

Campobasso

Mastroianni

Feola

et al. 2022

IJERPH

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Introduction: The human post-mortem microbiome (HPM) plays a major role in the decomposition process. Successional changes in post-mortem bacterial communities have been recently demonstrated using high throughput metagenomic sequencing techniques, showing great potential as a post-mortem interval (PMI) predictor. The aim of this study is to verify the application of the mass spectrometry technique, better known as MALDI-TOF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry), as a cheap and quick method for microbe taxonomic identification and for studying the PM microbiome. Methods: The study was carried out on 18 human bodies, ranging from 4 months to 82 years old and with a PMI range from 24 h up to 15 days. The storage time interval in the coolers was included in the final PMI estimates. Using the PMI, the sample study was divided into three main groups: seven cases with a PMI < 72 h; six cases with a PMI of 72–168 h and five cases with a PMI > 168 h. For each body, microbiological swabs were sampled from five external anatomical sites (eyes, ears, nose, mouth, and rectum) and four internal organs (brain, spleen, liver, and heart). Results: The HPM became increasingly different from the starting communities over time in the internal organs as well as at skin sites; the HPM microbiome was mostly dominated by Firmicutes and Proteobacteria phyla; and a PM microbial turnover existed during decomposition, evolving with the PMI. Conclusions: MALDI-TOF is a promising method for PMI estimation, given its sample handling, good reproducibility, and high speed and throughput. Although several intrinsic and extrinsic factors can affect the structure of the HPM, MALDI-TOF can detect the overall microbial community turnover of most prevalent phyla during decomposition. Limitations are mainly related to its sensitivity due to the culture-dependent method and bias in the identification of new isolates.

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

Cited by 21 publications

References 37 publications

Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake

Postmortem submersion interval (PMSI) estimation from the microbiome of sus scrofa bone in a freshwater lake

Comparative Decomposition of Humans and Pigs: Soil Biogeochemistry, Microbial Activity and Metabolomic Profiles

MALDI-TOF Mass Spectrometry Analysis and Human Post-Mortem Microbial Community: A Pilot Study

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