Microbial interactions of the necrobiome

Over the last several years there has been an increasing recognition of the importance of establishing a strong basic science foundation in forensics. With the development, reliability and increasingly widespread use of high-throughput metagenomic sequencing techniques, the forensic sciences are poised to harness ‘-omics’ technology to bridge basic science with medicolegal applications and applied microbiology. Previous studies have demonstrated the ability to detect and identify unique host-associated microbial communities of living humans, and more recently the potential use for these human associated microbial communities in forensics e.g., tracing a keyboard to its user via hand microbial communities. These communities have been described as the post-mortem microbial communities, the post-mortem microbiome and the carrion microbiome, along with several other terms and descriptions. However, for this article, we use the human post-mortem microbiome (HPMM) to describe this community and argue that the characterization and assessment of intra-individual variation of the HPMM remains understudied.

An increased understanding of the HPMM and microbiomes of other organisms associated with cadavers (e.g., insects) could lead to identification of novel biological markers useful in forensics. Trace evidence is typically physical in nature, such as fibres, hair or pollen, that link a perpetrator to a victim or crime. However, as technology continues to advance and the computation power increases to efficiently analyze large data sets (e.g., high-throughput metagenomics), scientists and practitioners within applied microbiology will be positioned to explore alternative and underexplored research avenues linking widely distributed microorganisms (e.g., bacteria, fungi, protists, and algae) to human cadavers or other objects at a death scene investigation. To do so, a more comprehensive understanding of the ecological factors that affect these linkages is necessary.

To better appreciate the biotic interactions of microbial taxa during vertebrate carrion decomposition, it is necessary to place this community within the larger network of cadaver associated organisms (e.g., invertebrates and vertebrate scavengers) – the network of species that has been defined as the necrobiome. The necrobiome is composed of the community of organisms associated with decomposing animals that includes members of all three domains of life (Bacteria, Archaea, and Eukarya).). The primary eukaryotes of the necrobiome are often considered the insects, particularly blow flies (Diptera: Calliphoridae); these flies thrive in decomposing vertebrate remains, organic materials (e.g., garbage), and vertebrate wastes (e.g., manure). Blow fly adults are primary colonizers of decomposing vertebrate remains, and are commonly the first forensically important insect taxa to arrive at human remains in response to odours given off by the metabolism of microbial communities associated with the carcass. The microbial members of the necrobiome are considered the epinecrotic microbial communities. These microorganisms are associated with carrion, including human cadavers, throughout the decomposition process, and research into these communities has seen an increase in studies and publications over the past several years.

An increase in the basic knowledge of interactions amongst microbial communities during decomposition is proving to be important for developing hypothesis-driven questions that could be applied in future forensic work and microbiology. One of the more provocative and applicable questions related to epinecrotic communities is: How do these complex assemblages of microorganisms interact with primary consumers, such as the necrophagous insects commonly used in forensic investigations, of a carcass or human corpse?

The interactions between microbes and necrophagous insects can begin within hours after death when the first insects are attracted to, evaluate and consider colonizing a cadaver; this period of decomposition time with extensive interactions occurring is also where both insect and microbial evidence can be easily collected. During this time, epinecrotic communities are hypothesized to be altering the quality of the resource and thus mediating insect community colonization. Support for this hypothesis has been demonstrated in studies where the production of metabolically-derived volatile organic compound signatures from microbes were shown to influence necrophagous fly behavior. A better understanding of mechanisms controlling community assembly patterns that influence carrion/corpse necrobiome diversity and interactions is key since decomposition is a consumer driven process, and changes in the organisms utilizing the remains ultimately dictates decomposition process and rates. These mechanisms can influence how potential microbial and entomological evidence could be used in legal investigations. One common way that biological evidence is used in forensics is for estimating the minimum range of time between death and the discovery of human or animal remains, or the minimum postmortem interval (PMImin).

Estimating a PMImin range with strong statistical inference continues to be a challenge for forensic scientists. In 2009, the US National Research Council (NRC) called for a need to provide quantitative error rates in inferences derived from most forensic evidence. Many studies concerning community assembly for either the insect or microbial taxa do not employ validations to define error rates. Consequently, regardless of their admittance into a court of law, these techniques fail to meet the Daubert guidelines which govern the admissibility of evidence into the courtroom in the USA or the defined parameters outlined by the NRC. There is a timely need for increased hypothesis driven forensic microbiological studies that can facilitate defining and refining error rates related to PMImin estimates and other ways that microbes can be potentially used in forensics. However, as it has been shown in other emerging disciplines, a strong foundation in the basic biology and ecology of a system is necessary for identifying applications for improving the human condition. The necrobiome and interactions of microbes and insects on decomposing humans is no exception within the broader field of microbiology.

M. Eric Benbow
Department of Entomology and Department of Osteopathic Medical Specialties

Jennifer L. Pechal
Department of Entomology



Categories: Feature Articles, Uncategorized

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