Universal Microbial Web Destroys Human Flesh

The breakdown of biological material by microbes is an integral process of life
Earth. While some genetic studies have investigated the microbial communities that
decomposed vegetable mattersurprisingly, we know very little about the decomposition of vertebrates such as humans.

That was until recently 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 Metcalfassociate professor in the Department of Animal Sciences, tracked the decomposition of 36 human cadavers at 3 voluntary body donation sites: the University of Tennessee, Sam Houston State University, and Colorado Mesa University.

During the multi-year study, the carcasses were placed in cages and exposed to the elements
in all four seasons. After 21 days of exposure, Metcalf and colleagues
collected skin and soil samples from each corpse, which were then subjected to
various molecular and genomic studies including genetic sequencing and metabolite
the analyses.

Surprisingly, the same 20 microbes were identified in all 36 bodies, regardless of
the climate or type of soil to which they were exposed.

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 associations or soil microbial communities in American Gut Project OR The Earth Microbiome Project datasets, two large studies characterizing microbial communities in humans. The microbes are found in insects, however, suggesting that the insects act as “vectors”, spreading the microbes
to corpses for decomposition.

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

Discovering the composition and timing of the microbes that decompose human flesh carries important implications for the field of forensic science. Metcalf and colleagues 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 the body
death. This period, also known as the postmortem interval, can be difficult
decipher when waste has been exposed to harsh environmental conditions.

Technology Networks spoke with the CSU research team to understand how the study — which is based on more than 10 years of work — was conducted and how the data can
help modulate decomposition processes in human death industries.

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

A: Microbes are known to be one of the main players when it comes to decomposing vertebrate remains, including humans. However, some of the intricacies of how members of the decomposer microbial community react and interact with each other are not well understood, especially comparisons of these activities across climates.
The reason for this lack of knowledge is that most previous research in
the field of decomposition is focused on the breakdown of plant material due to
its much 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 biggest changes in the body, the surrounding environment and
microbial communities. So by choosing this time frame we capture how
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 you used to analyze this data and why?

A: We sequenced a gene essential to all prokaryotes, called the 16S rRNA gene. Sequencing this gene allows us to identify the microbial members in the system and obtain a relative measure of their prevalence at any point in time. We also sorted
a eukaryotic gene, 18S rRNA, that has the same role in eukaryotes to see
microscopic eukaryotes in the system.

Next, we performed metagenomic sequencing to study the bacteria’s functional genes, such as the ability to create or use specific nutrients. We were also able to assemble the genomes of several key bacteria with metagenomic data, which provide the first microbial decomposer database in our field. Finally, we generated metabolic data that is a profile of some of the nutrients and resource types within the environment.

Q: Can you tell us a little more about 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 have found associated with active and advanced stages of decomposition in all our climates. Some of these
organisms include bacteria known to associate with feeding flies
waste, such as Ignatzschineria. None of them were particularly surprising, but there are a few that we don’t know much about, such as Oblitimonas.

Q: You found universal decomposers in insects, which implies that insects “bring them” to corpses. 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 to and from corpses. They bring their own
microbes in and deposited through feeding and defecation. In the case of flies,
they also lay eggs that hatch into larvae and deposit/retrieve their own eggs
microbes. Then, once the flies/larvae leave, they pick up some of these microbes
with them at the next location. These insects include a broad subgroup including flies,
beetles and ants.

There are studies in which the decomposition parameters are controlled to exclude insects, and some of the same microbes we detect occur, but the specific insect microbes are absent. The decomposition process still continues, but the absence of insects can lead to slower progress and even tissue remaining in the carcass longer.

“I feel like we’re breaking ground on basic ecology and nutrient cycling,” Metcalf said.

Q: The set-up of the experiment – ​​human bodies exposed to the elements in cages across research sites – could be interpreted as rather grim by some. I appreciate that this is the only way to collect such data to reflect real-life scenarios of human decomposition, but could you explain how you, as a research team, felt during the study experience?

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

As a researcher, it is important to keep these benefits in mind when conducting these studies. It is also extremely important that these donors, and their samples, are treated with the utmost respect, as they willingly gave of themselves to improve our society.

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

A: The three objects we worked with in this study are what we consider “willing bodies
donation objects. Because of this, the donors in this study voluntarily registered to donate their body to their specific facility during their lifetime. This request was approved by the institution and the donor’s relatives, lawyer or doctor ensured that the donor’s wishes were known and carried out.

Q: The paper discussion says that data can help modulate decomposition processes in human death industries – can you explain what you mean by that?

A: The humane death industry has problems with things like space availability in
cemeteries for burials and the generation of volatile substances and greenhouse gases
from burning. Because of this, other greener methods of treatment
the dead are researched. For example, human composting works to reverse
man remains in nutrient-rich soil in as completely natural a way as he can
be used to support plant growth or to restore damaged habitats.

By studying the microorganisms involved in decomposition, we can work towards increasing our understanding of these processes in a way that will hopefully increase their efficiency.

Dr.