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Universal Microbial Network Breaks Down Human Flesh

A forensic scientist observes a crime scene.
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The breakdown of biological material by microbes is an integral process to life on
Earth. While some genetic studies have probed the microbial communities that
plant matter, surprisingly, we know very little about the decomposition of vertebrates such as humans.

That was until a recent study by scientists from Colorado State University (CSU) identified a network of microbes that appear to “universally” drive the decomposition of animal flesh, regardless of environmental variables.

The research team, led by Dr. Jessica Metcalf, associate professor in the Department of Animal Sciences, tracked the decomposition of 36 human cadavers across 3 willed-body donation sites: the University of Tennessee, Sam Houston State University and Colorado Mesa University.

Over the multi-year study, cadavers were placed in cages and exposed to the elements
across all four seasons. After 21 days of exposure, Metcalf and colleagues
collected skin and soil samples from each cadaver, which were then subject to
various molecular and genomics studies including genetic sequencing and metabolite

Strikingly, the same 20 microbes were identified across all 36 bodies, regardless of the
climate or type of soil to which they had been exposed.

The network, including characters such as Oblitimonas alkaliphila, Ignatzschineria, Wohlfahrtiimonas, Bacteroides and Vagococcus lutrae, represented a “unique phylogenetic diversity” that was rare or undetected in host–association or soil microbial communities in the American Gut Project or the Earth Microbiome Project data sets, two large studies characterizing microbial communities in humans. The microbes are found on insects, however, suggesting that insects act as “vectors”, delivering microbes
to the cadavers for decomposition.

“We see similar microbes arrive at similar times during decomposition,
regardless of any number of outdoor variables you can think of,” Metcalf said.

Uncovering the makeup and timing of the microbes that decompose human flesh carries important implications for the field of forensic science. Metcalf and collaborators applied machine learning approaches to the data and built a tool that is capable of predicting – with high accuracy – the time that has passed since a body’s
death. This period, also known as the postmortem interval, can be difficult to
decipher when remains have been exposed to harsh environmental conditions.

Technology Networks spoke with the CSU research team to understand how the study – which builds on over 10 years of work – was conducted, and the how the data could
help in modulating decomposition processes in human death industries.

Q: Can you explain why little was known about the ecology of vertebrate decomposition, prior to this study?

A: Microbes have been known to be one of the major players when it comes to decomposing vertebrate remains, including humans. However, some of the intricacies of how the decomposer microbial community members respond and interact with each other isn’t well known, particularly comparisons of these activities across climates.
The reason for this lack of knowledge is that most prior research in the
decomposition field has focused on the decomposition of plant material due to
its vastly larger global biomass.

Q: Why did you choose a 21-day observation period?

A: The 21-day period was chosen because this is when vertebrate decomposition is most dynamic. We see the largest changes to the body, surrounding environment and
the microbial communities. So, by choosing this timeframe we capture how the
microbes are responding to these dynamic changes.

Q: The study generated a significant amount of molecular and genomic information from the samples. Can you summarize the different methods that you used to analyze this data, and why?

A: We sequenced an essential gene for all prokaryotes called the 16S rRNA gene. Sequencing this gene allows us to identify the microbial members in the system and get a relative measurement of their prevalence at each time point. We also sequenced
a eukaryotic gene, 18S rRNA, that has the same role in eukaryotes to look at
the microscopic eukaryotes in the system.

Further, we performed metagenomic sequencing to study the functional genes of bacteria, such as the ability to create or use specific nutrients. We were also able to assemble genomes of some key bacteria with the metagenomic data, which provides the first microbial decomposer database to our field. Lastly, we generated metabolomics data which is a profile of some of the nutrients and resource types within the environment.

Q: Can you tell us a bit more about the universal decomposers? What are some of the key microorganisms in that community? Were there any that surprised you?

A: These universal decomposers are organisms we found to be associated with active and advanced stages of decomposition at all our climate locations. Some of these
organisms include bacteria known to be associated with blow flies that feed on
remains, such as Ignatzschineria. None of them were particularly surprising, but there are some which we don’t know a lot about, such as Oblitimonas.

Q: You found the universal decomposers on insects, which implies that insects “bring them in” to cadavers. Can you talk more about these insects – are they found all over the world, and do they face any environmental pressures?

A: Yes, insects serve as vectors both to and from the cadavers. They bring their
microbes in and deposit them via feeding and defecating. In the case of flies,
they also lay eggs that hatch to maggots and deposit/pick up their own
microbes. Then, once the flies/maggots leave, they take some of these microbes
with them to the next location. These insects include a broad subset including flies,
beetles and ants.

There are studies in which decomposition has controlled settings to exclude insects, and some of the same microbes we detect do occur, but the insect specific microbes are missing. The decomposition process still occurs, but the lack of insects can lead to slower progression and even tissue remaining on the cadaver longer.

“I feel like we’re opening a whole lot of avenues in basic ecology and nutrient cycling,” Metcalf said.

Q: The setup of the experiment – human bodies exposed to the elements in cages across research sites – might be interpreted as quite grim by some. I appreciate that this is the only way to gather data such that it reflects real life scenarios of human decomposition, but can you explain how you, as a research team, felt during the experience of the study?

A: The ultimate goal for studying human decomposition specifically is to better
improve society. This can be through discovering greener ways to handle the
deceased, improving our understanding of essential ecological processes so we
can mediate them, and for forensic investigations to ensure justice is upheld.

As a researcher, it is important to keep these benefits in mind when performing these studies. It is also extremely important that these donors, and the samples from them, are treated with the utmost respect as they willingly donated themselves to better our society.

Q: Can you talk about the cadaver donation process for your study?

A: The three facilities we worked with in this study are what we consider “willed-body
donation” facilities. Because of this, the donors in this study willingly signed up to donate their body to their specific facility during life. This request was approved by the facility and the donor’s next of kin, attorney or physician ensured that the donor’s wishes were known and granted.

Q: The discussion of the paper states that the data might help in modulating decomposition processes in human death industries – can you explain what you mean by this?

A: The human death industry has issues with things such as space availability in
cemeteries for burials and the generation of volatiles and greenhouse gases
from cremation. Because of this, other more green methods of handling the
deceased have been researched. For example, human composting works to convert
the human remains into nutrient-rich soil in a completely natural way that can
be used to support growth of plants or recover damaged habitats.

Through the study of the microorganisms associated with decomposition, we can work towards increasing our understanding of these processes in a way that we can hopefully increase their efficiency.

Dr. Jessica Metcalf and Dr. Zachary Burcham were speaking to Molly Campbell, Senior Science Writer for Technology Networks.