The microbiology, pH, and oxidation reduction potential of larval masses in decomposing carcasses on Oahu, Hawaii

From flesh to bones: Multi-omics approaches in forensic science

Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.

Bridging the gap between decomposition theory and forensic research on postmortem interval

Knowledge of the decomposition of vertebrate animals has advanced considerably in recent years and revealed complex interactions among biological and environmental factors that affect rates of decay. Yet this complexity remains to be fully incorporated into research or models of the postmortem interval (PMI). We suggest there is both opportunity and a need to use recent advances in decomposition theory to guide forensic research and its applications to understanding the PMI. Here we synthesise knowledge of the biological and environmental factors driving variation in decomposition and the acknowledged limitations among current models of the PMI. To guide improvement in this area, we introduce a conceptual framework that highlights the multiple interdependencies affecting decay rates throughout the decomposition process. Our framework reinforces the need for a multidisciplinary approach to PMI research, and calls for an adaptive research cycle that aims to reduce uncertainty in PMI estimates via experimentation, modelling, and validation.

Application of omics techniques in forensic entomology research

With the advent of the post-genome era, omics technologies have developed rapidly and are widely used, including in genomics, transcriptomics, proteomics, metabolomics, and microbiome research. These omics techniques are often based on comprehensive and systematic analysis of biological samples using high-throughput analysis methods and bioinformatics, to provide new insights into biological phenomena. Currently, omics techniques are gradually being applied to forensic entomology research and are useful in species identification, phylogenetics, screening for developmentally relevant differentially expressed genes, and the interpretation of behavioral characteristics of forensic-related species at the genetic level. These all provide valuable information for estimating the postmortem interval (PMI). This review mainly discusses the available omics techniques, summarizes the application of omics techniques in forensic entomology, and their future in the field.

A synthesis of carcass decomposition studies conducted at a tropical (Aw) taphonomy facility: 2013-2022

Decomposition studies have been conducted in several regions of the world, but relatively few have investigated taphonomy in tropical environments. Even fewer have explored carcass decomposition during multiple tropical seasons, leaving the relationships between season and decomposition in tropical environments poorly understood. Ten decomposition studies using 30 carcasses were conducted in Honolulu, Hawaii, USA to start addressing this knowledge gap. These studies show that some postmortem processes were observed regardless of season. Carcass temperature and chemistry were spatiotemporally variable. Fly larval masses were consistently observed within 3 days (∼75 ADD) postmortem and carcasses lost 60%-90% of mass by 10 days (∼250 ADD) postmortem (Total Body Score ∼26). Season had a significant effect on decomposition, yet the warmest and most humid seasons did not always result in the most rapid and extensive decomposition. Seasonal variation appears to be less pronounced than at other tropical decomposition sites.

Aggregation in an heterospecific population of blowfly larvae: social behaviour is impacted by species-specific thermal requirements and settlement order

Larvae of several blowfly species grow on carcasses and actively aggregate together. They face harsh developmental conditions resulting in a strong pressure to reduce development time: this is achieved either through thermoregulation or aggregation. We investigate how these two developmental strategies are modulated within heterospecific groups. In a first experiment, larvae of two species with different thermal requirements were deposited simultaneously on a thermal gradient. This resulted in the formation of two monospecific groups, each located at the species-specific thermal preferendum. However, when Calliphora vomitoria (Linnaeus) larvae were placed first, the later arriving Lucilia sericata (Meigen) larvae attracted the whole group to its own thermal preferendum. In the reverse experiment, half of the replicates resulted in single dense heterospecific groups observed at temperatures ranging from C. vomitoria to L. sericata preferendum. The other half of the replicates resulted in loose groups spread out on the thermal gradient. These results highlight the emergence of collective decisions ranging from thermal optimization to heterospecific aggregation at suboptimal temperatures. They demonstrate that species settlement order strongly affects self-organization processes and mixed-species group formation. We conclude that thermal optimization and heterospecific niche construction are two developmental strategies of carrion fly larvae. This article is part of the theme issue 'Mixed-species groups and aggregations: shaping ecological and behavioural patterns and processes'.

Corpse decomposition of freshwater economic fish leads to similar resistomes and the enrichment of high-risk antibiotic resistance genes in different water types

Animal carcass decay produces many poisonous metabolites and chemical pollutants, which pose potential ecological risks to the aquatic environment and human health. However, the effects of animal cadaver decomposition on high-risk antibiotic resistance genes (ARGs) and potential pathogens in different water types are still unknown. In this study, fifteen freshwater economic fish (Carassius auratus) corpses were put into three types of water (i.e., pond water, tap water, and domestic sewage) for a 100-day decomposition. Next generation sequencing and HT-qPCR were used to illustrate how corpse decomposition affected microbial communities and ARG profiles. Our results revealed that fish corpse degradation caused similar resistomes and microbiome in different water types. MLSB (Macrolide-Lincosamide-Streptogramin B), β-lactamase, sulfonamide, tetracycline resistance genes and transposase genes in the experimental groups were increased. Among them, tetracycline resistance genes were enriched by 224 to 136,218-fold during the process of corpse degradation. Furthermore, high-risk ARGs (ermB, floR and dfrA1), which resist to MLSB, multidrug and sulfonamide respectively, were significantly enriched in the cadaver groups and had co-occurrence patterns with opportunistic pathogens, such as Bacteroidetes, which was more than 37 times in carcass groups than that in control groups. The study is able to draw a general conclusion that cadaver decomposition of freshwater economic fish deteriorates the aquatic environment by affecting high-risk ARGs and pathogenic microorganisms regardless of water types, which poses potential threats to human health. Therefore, timely management and treatment of animal carcasses is of great significance to the protection of water environment.

Corpse decomposition increases the diversity and abundance of antibiotic resistance genes in different soil types in a fish model

As a common natural phenomenon, corpse decomposition may lead to serious environmental pollution such as nitrogen pollution. However, less is known about antibiotic resistance genes (ARGs), an emerging contaminant, during corpse degradation. Here, ARGs and microbiome in three soil types (black, red and yellow soil) have been investigated between experimental and control groups based on next-generation sequencing and high-throughput quantitative PCR techniques. We found that the absolute abundance of total ARGs and mobile genetic elements (MGEs) in the experimental groups were respectively enriched 536.96 and 240.60 times in different soil types, and the number of ARGs in experimental groups was 7-25 more than that in control groups. For experimental groups, the distribution of ARGs was distinct in different soil types, but sulfonamide resistance genes were always enriched. Corpse decomposition was a primary determinant for ARGs profiles. Microbiome, NH₄⁺ concentrates and pH also significantly affected ARGs profiles. Nevertheless, soil types had few effects on ARGs. For soil microbiome, some genera were elevated in experimental groups such as the Ignatzschineria and Myroides. The alpha diversity is decreased in experimental groups and microbial community structures are different between treatments. Additionally, the Escherichia and Neisseria were potential pathogens elevated in experimental groups. Network analysis indicated that most of ARGs like sulfonamide and multidrug resistance genes presented strong positively correlations with NH₄⁺ concentrates and pH, and some genera like Ignatzschineria and Dysgonomonas were positively correlated with several ARGs such as aminoglycoside and sulfonamide resistance genes. Our study reveals a law of ARGs' enrichment markedly during corpse decomposing in different soil types, and these ARGs contaminant maintaining in environment may pose a potential threat to environmental safety and human health.

Water volume influences antibiotic resistomes and microbiomes during fish corpse decomposition

Corpse decomposition may cause serious pollution (e.g., releasing antibiotic resistance genes) to the water environment, thereby threatening public health. However, whether antibiotic resistance genes (ARGs) and microbiomes are affected by different water volumes during carcass decomposition remains unknown. Here, we investigated the effects of large/small water volumes on microbial communities and ARGs during fish cadaver decomposition by 16S rRNA high-throughput sequencing and high-throughput quantitative PCR. The results showed that the large water volume almost eliminated the effects of corpse decomposition on pH, total organic carbon (TOC), and total nitrogen (TN). When the water volume enlarged by 62.5 fold, the relative abundances of some ARGs resisting tetracycline and sulfonamide during carcass decomposition decreased by 217 fold on average, while there was also a mean 5267 fold increase of vancomycin resistance genes. Compared with the control group, the enriched types of ARGs varied between the large and small volume. Water volume, mobile genetic elements, and carcass decomposition were the most important factors affecting ARG profiles. Many opportunistic pathogens (like Bacteroides and Comamonas) were enriched in the corpse group. Bacteroides and Comamonas may be potential hosts of ARGs, indicating the potential for the spread of ARGs to humans by water pathogenic bacteria. This research highlights that the "dilution effect" can contribute to eliminating this adverse effect during corpse decomposition to a certain extent. It may provide references for environmental governance and public health.

Convergence of Social Strategies in Carrion Breeding Insects

Carrion is a highly ephemeral and nutrient rich resource, characterized by extreme biotic and abiotic stressors. We hypothesized that specific constraints of the carrion ecosystem, and especially its nutrient richness, ephemerality, and competition with microbes, have promoted the evolution of social behaviors in necrophagous insects. We show that group living is prevalent among early succession carrion breeding insects, suggesting that this trait has emerged as an adaptation to facilitate survival in the highly competitive environment of fresh carrion. We then highlight how developmental niche construction allows larvae to compete with microbes, efficiently feed on fresh cadavers, and rapidly reach maturity. We observed that larval societies and parental care are two different strategies responding to similar competitive and environmental constraints. We conclude that intra and interspecific competition on carrion are mitigated by social behavior.

Temporal succession of water microbiomes and resistomes during carcass decomposition in a fish model

Carcass decomposition in water may cause serious environmental pollution, which poses a great threat to water quality and public health. However, water microbial community succession and antibiotic resistance genes (ARGs) during carcass decomposition process are less explored. Using high-throughput sequencing and high-throughput quantitative PCR techniques, the temporal succession of water bacterial communities and ARGs profiles in experimental groups (fish carcasses) and control groups (no carcasses) containing two different types of water (the Yellow River water and tap water) in different successional stages were studied. Our results showed that NH₃-N concentration in the corpse groups has greatly risen and exceeded more than 28 times on average over the safety thresholds of water quality. Some potential pathogenic genera Comamonas, Bacteroides and Pseudomonas significantly increased during carcass decomposition process. The bacterial communities of the Yellow River water and tap water in the experimental groups exhibited similar succession patterns, and community dissimilarities between the two groups decreased and smaller over time, indicating that bacterial community convergence. NH₃-N, NO₃-N and time were three most important factors in determining bacteria community structures. The influence of water type on corpse bacterial community structures was significant but weak. The gene copy number of seven detected ARGs (cmlA1-01, floR, sul1, sul2, tetG-01, tetM-01 and tetQ) in the experimental groups was more abundant than that in the control groups. The ARGs concentrations in the corpse groups were even enriched 19-fold (minimum) to 148-fold (maximum) compared to the gene tetQ of the Yellow River water in the control groups on the initial stage. Redundancy analysis (RDA) indicated that Bacteroidetes and Firmicutes were significantly correlated with all detected ARGs. This study emphasizes that cadaver degradation leads to the deterioration of nitrogen pollution, the abundance increase of potential pathogens, and the transfer of ARGs from dead animals to water environment, thereby uncovering the harmful effects of related water pollution for human health.

New contributions to the relationship between sequential changes of ATP-related metabolites and post-mortem interval in rats

In recent years, it has become a new research direction to post-mortem interval (PMI) estimation from the changes in metabolite content generated during the process of cadaver corruption, and lead to more and more attention has been paid to the biochemical changes of muscles after death. The ATP degradation process has long been accepted as a precise manner to estimate freshness of meat products in food science. ATP-related metabolites may also serve as an indicator for PMI estimation of corpses. The purpose of this study was to test this possibility. Firstly, this study optimized the detection method of ATP-related metabolites in skeletal muscles of rat. Moreover, in animal experiment, ATP-related metabolites (ATP, ADP, AMP, IMP, Ino, Hx) in lower hind limb skeletal muscles of sixty rats were measured by RP-HPLC at different PMI for 168 h at 20 °C ± 1 °C, the change of freshness indicators (K value, K1 value, K0 value, H value, P value, G value, IMP ratio) were carefully analyzed, and investigate the relationship between them and PMI. The overall results showed that IMP, AMP, Hx, Total metabolites, K value, K1 value, K0 value, H value, P value, G value, and IMP ratio in skeletal muscles changed significantly with PMI (R2 = 0.864-0.971, all P < 0.01) while ATP, ADP, Ino, IMP precursors and IMP degradants had minor changes during the same period (R2 = 0.171-0.706). Specifically, significant linear positive correlations between H value of skeletal muscles and PMI were found, and the coefficients of their regression functions were R2 = 0.971. The correlation between AMP and PMI was slightly lower (R2 = 0.864), but the scope of PMI estimation was the widest (168 h). It can be concluded that the determination of ATP-related metabolites in skeletal muscle may be a potential tool in the PMI estimation. However, more researches on its influencing factors are needed to facilitate its final use in practice.

Corpse decomposition increases nitrogen pollution and alters the succession of nirK-type denitrifying communities in different water types

Cadaver decomposition as high-quality nutrient inputs may exert strong perturbation on the aquatic environments, such as high nitrogen or nitrate pollution. Denitrifying bacteria may reduce nitrate to nitrogen gas, thereby decreasing the nitrogen pollution and improving self-purification ability of aquatic ecosystem. However, how nirK denitrifying communities in water respond to cadaver decomposition remains unknown. Thus, we employed high-throughput sequencing and chemical analysis to investigate the succession of nirK-type denitrifying communities in tap water and Yellow river water (experimental groups) as well as their corresponding control groups during two important stages of fish corpse decomposition called advanced floating decay and sunken remains. Our data showed that the concentration of NH₄⁺-N in the experimental groups increased approximately 3-4 times compared with the control groups. Proteobacteria was the predominant phylum for nirK denitrifying communities. Several potential pathogenic genera, such as Brucella and Achromobacter, were enriched in the corpse groups. Notably, nirK-type community structures were significantly impacted by cadaver decomposition. Community structures in the corpse groups become more similar with succession, indicating community convergence at the final stage. Water pH, oxidation-reduction potential (ORP) and treatment were three important factors affecting the community structures. However, water type was not a main driving factor determining carcass-associated nirK-type bacterial communities. Four phylogenetic clusters were detected in the denitrifying communities, but showed significantly different distribution between the corpse and control groups. These results provide an in-depth understanding for nirK denitrifying functional bacteria and potential pathogenic bacteria during carrion decomposition process, which offer valuable reference to environmental evaluation and management.

Effects of Extended Postmortem Interval on Microbial Communities in Organs of the Human Cadaver

Human thanatomicrobiota studies have shown that microorganisms inhabit and proliferate externally and internally throughout the body and are the primary mediators of putrefaction after death. Yet little is known about the source and diversity of the thanatomicrobiome or the underlying factors leading to delayed decomposition exhibited by reproductive organs. The use of the V4 hypervariable region of bacterial 16S rRNA gene sequences for taxonomic classification ("barcoding") and phylogenetic analyses of human postmortem microbiota has recently emerged as a possible tool in forensic microbiology. The goal of this study was to apply a 16S rRNA barcoding approach to investigate variation among different organs, as well as the extent to which microbial associations among different body organs in human cadavers can be used to predict forensically important determinations, such as cause and time of death. We assessed microbiota of organ tissues including brain, heart, liver, spleen, prostate, and uterus collected at autopsy from criminal casework of 40 Italian cadavers with times of death ranging from 24 to 432 h. Both the uterus and prostate had a significantly higher alpha diversity compared to other anatomical sites, and exhibited a significantly different microbial community composition from non-reproductive organs, which we found to be dominated by the bacterial orders MLE1-12, Saprospirales, and Burkholderiales. In contrast, reproductive organs were dominated by Clostridiales, Lactobacillales, and showed a marked decrease in relative abundance of MLE1-12. These results provide insight into the observation that the uterus and prostate are the last internal organs to decay during human decomposition. We conclude that distinct community profiles of reproductive versus non-reproductive organs may help guide the application of forensic microbiology tools to investigations of human cadavers.