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Solving Crimes with the Necrobiome
OVERVIEW
Solving Crimes with the Necrobiome is one of 12 videos in the HHMI series I Contain Multitudes, which explores
the fascinating powers of the microbiome: the world of bacteria, fungi, and other microbes that live on and within
larger lifeforms, including ourselves.
This particular video focuses on the microbes associated with decomposing corpses, or cadavers. Following death,
the microbiome of a body changes dramatically in composition. The community of organisms associated with a
cadaver, which includes these microbes, is known as the necrobiome. In the video, Jessica Metcalf, an associate
professor at Colorado State University, describes how she tracks changes in the necrobiomes in, on, and around
the decaying bodies of dead animals, including humans, over time. She also explains how the predictable
sequence of microbial communities associated with a cadaver can serve as a “microbial clock” for estimating time
since death, providing useful knowledge for crime scene investigators.
Additional information related to pedagogy and implementation can be found on this resource’s webpage
,
including suggested audience, estimated time, and curriculum connections.
KEY CONCEPTS
• Living organisms host a complex community of microbes called a microbiome, which is usually regulated by
the host’s immune system.
• Decomposition is mediated by microbes in predictable stages of ecological succession, which correspond to
measurable and consistent changes in the microbial community.
• Decomposition is fundamental for cycling energy and nutrients in ecosystems.
STUDENT LEARNING TARGETS
• Describe the process of decomposition and the role it plays in an ecosystem.
• Explain how the microbiome associated with a decomposing body can be used to estimate the time since
death.
• Interpret evidence to support or refute a scientific argument.
PRIOR KNOWLEDGE
Students should have a basic understanding of:
• the role of microbes as decomposers
• how matter cycles between the living and nonliving parts of the environment
• what a microbiome is
PAUSE POINTS
The film may be viewed in its entirety or paused at specific points to give students an opportunity to ask
questions, construct explanations, and make predictions. The table below lists suggested pause points, including
the beginning and end times in minutes in the film.
Before starting the film, you may also ask students the following question: “When a person dies, what do you
predict happens to the microbes that live on their skin and inside their body?”
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Begin
Content Description
Discussion Questions
1
0:00
• Death is a major event for microbes because the
environment in, on, and around the body changes.
• After death, microbes that play an important role
in decomposition become abundant.
• During decomposition, patterns of change in
microbial communities are consistent from person
to person.
• You might be surprised to
discover that some scientists
study the microbes in and on
human bodies after death. Why
does Jessica Metcalf think
studying these microbes is
important?
• What are some changes in
microbial communities that
occur after death? Are these
changes similar or different
from person to person? Why do
you think that is?
2
1:26
• A body goes through five basic stages after death:
fresh, bloat, active decay, advanced decay, and
dry remains.
• Microbe communities change rapidly after death,
in part because the immune system has shut
down and is not regulating their spread.
• Microbes in the gut, which were helping the body
digest food, now digest the body.
• Fluids rich in nutrients are released from body
orifices.
• The decomposition process releases gases that
build up and cause the body to bloat and rupture.
• After the body ruptures, microbes from soil, air, or
insects can access the inside of the body.
• The final stage, dry remains, is when all that
remains of the body is a skeleton and dry tissue.
• Why are microbes able to
colonize new areas of the body
after death?
• What causes the body to bloat
and the skin to rupture? What
are the microbes producing?
• Describe what happens during
the “active decay” phase. What
happens to the flesh that
disappears?
3
3:32
•
Predictable changes occur in the microbial
communities associated with a decomposing
body. These changes are precise enough that
scientists can determine when someone has died
(time since death) based on the microbes found in
and around their body.
• When estimating time since death, scientists must
take temperature into account because it greatly
affects the rate of decomposition.
• Scientists conduct research on decomposing
human bodies at anthropological research
facilities (sometimes referred to as body farms).
Scientists sequence the DNA of microbes collected
over time from skin and soil swabs.
•
Explain how microbes collected
from a dead body can act like a
“clock” to determine time since
death.
• Why do scientists care about
temperature when trying to
determine time since death?
• What are anthropological
research facilities?
• Why do scientists sequence
microbial DNA from samples
they collected from a cadaver?
Why do they collect samples
from the skin and the soil?
4
5:37
•
Some microbes are involved in longer processes
that occur during the “dry remains” phase. These
microbes could be present for a long time after
death.
• Research on the necrobiome is important for
crime scene investigations. Microbial data used to
•
Why are crime scene
investigators interested in the
necrobiome?
• Explain the comment “once a
person dies, the recycling
begins.”
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determine time since death can help establish
when a crime occurred.
• Death of one organism is the beginning of new life
for many microbes and other lifeforms.
• Microbes are intricately involved in the processes
of decomposition and nutrient cycling.
BACKGROUND
The necrobiome, the community of organisms associated with a decomposing cadaver, is a microcosm for
studying ecological community interactions and energy transfer. During decomposition, the environment of the
body changes rapidly and interacts with the surrounding environment (for example, the soil, if the body was
buried). Changes in abiotic factors, such as pH and temperature, as well as biotic factors, such as available
nutrients and body composition, will influence the presence of scavengers and microbial species as
decomposition progresses. Because the process of decomposition recycles nutrients essential for life, it is not an
end but a beginning for a variety of organisms.
At the onset of death, the heart stops beating, and the body becomes depleted of internal oxygen. Enzymes in the
body start to destroy cells and tissues in a process called autolysis, or self-digestion. Without immune cells to
keep them in check, bacteria of the microbiome grow rapidly and begin to digest the body. There is a marked shift
from aerobic species, which use oxygen in cellular respiration, to anaerobic ones, which do not. Anaerobic
digestion results in gaseous byproducts, such as methane, hydrogen sulfide, and ammonia. These gases
accumulate within the body, causing the body to bloat and then break open, or rupture. Rupture marks a major
event in the decomposition process because it allows other microbes, insects, and scavengers to access the body
more easily. As decomposition progresses, predictable changes in the microbial communities, as well as in the
scavenger and insect communities, occur.
Because changes in the microbes in and around a dead body are measurable and consistent from person to
person, scientists have been able to build a “microbial clock” that can be used to determine the time since death,
or postmortem interval. Scientists conduct research on human cadavers at anthropological research facilities (also
referred to as “body farms”). They collect samples from cadavers and the soil around them and sequence the
DNA of microbes in these samples to determine which types of microbes are present at various time points after
death. When a body is found, for example, at the scene of a crime, scientists can estimate the time of death by
comparing the microbes found on this body to the microbial clock. Establishing time of death is critical in criminal
investigations. It can be used to establish when a murder occurred, place suspects at the scene, and check alibis.
The microbial clock technique is still in the research phase, and scientists are working with justice practitioners to
bring the new technology into the justice system (e.g., make it admissible as evidence).
DISCUSSION POINTS
• The human body is home to a variety of microbes adapted to live in that environment. When a person dies,
the environment changes, and different species of microbes may become dominant in the new environment.
You may want to review the diversity of microbes and types of microbial metabolic strategies using the
interactive module Winogradsky Column: Microbial Ecology in a Bottle
.
• Many students learn about decomposition when studying ecology and food chains. Set the stage for students
by reminding them of the essential role of decomposers in ecosystem function. After students view the
Solving Crimes with the Necrobiome video, discuss with them how decomposition of a body serves to cycle
nutrients in the ecosystem. This video provides an opportunity for reviewing the concept that matter is never
created or destroyed, just transformed.
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• The changes in the microbial community during decomposition are an example of ecological succession.
Similar to how grasses are the first plants to grow back after a forest fire — followed by ferns, shrubs, and
eventually trees — new species of microbes colonize a dead body in a predictable sequence.
• Students are probably familiar with the fact that crime scene investigators look for DNA evidence left behind
by those involved. Make sure they understand that the DNA that is being sequenced in this context is from
microbes present on or around the body. Identifying these microbes via DNA sequencing allows investigators
to estimate when the crime occurred (time of death).
• Metcalf points out that investigators also consider temperature when determining time of death. Ask
students to clarify why that is important. This is a good opportunity to talk about the role of temperature in
chemical reactions, such as decomposition.
• Ask students how microbial analysis could be used to help solve crimes or test alibis. For example,
investigators may use evidence from microbial DNA to determine when a murder occurred, then ask suspects
to describe their whereabouts during this time period (and verify their statements using other evidence, such
as security camera footage). It’s important to emphasize that investigators should use multiple lines of
evidence to support their claims of how and when a crime occurred, and that establishing a time of death
may involve analyzing other environmental conditions beyond the microbial species present and
temperature.
• Discuss with students how embalming prevents the natural decomposition process and the ecological
implications of embalming. It is important to point out that embalming isn’t universally practiced and that
many religions and cultures have burial practices that do not involve embalming. Students may be interested
in researching alternative burial methods.
STUDENT HANDOUT
The “Stu
dent Handout” is designed as a learning assessment that probes students’ understanding of the key
concepts addressed in the film. It can be used before the film to assess students’ prior knowledge or during the
film to guide students as they watch. You should choose the use that best fits your learning objectives and your
students’ needs. You may modify the handout as needed (e.g., reducing the number of questions, adding
explanations of vocabulary for English learner students, etc.).
ANSWER KEY
1. Death is a major event not only for the person who dies but also for the microbes that inhabit their body.
Which of the following statements best describes why?
a. All the microbes that were living inside the person’s body die when the person dies.
b.
Microbial populations grow and spread to different areas of the body after the person dies.
2. Microbes in the body have fewer resources after the person dies, which increases competition.
Which of the following statements about cadavers (dead bodies) is most likely to be true?
a.
Microbial communities in and around a cadaver change over time.
b. Samples taken from different cadavers always contain the same microbes.
3. The microbial community found in a cadaver is very similar to the one found in a living body.
After death, gases build up inside the body and cause the skin to rupture (break open). Rupture is a significant
event because microbes from outside the body can now access the inside. Which of the following can be a
source of the microbes that enter the body after it ruptures? Select all that apply.
a.
skin
b.
air
c.
soil
d.
insects
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4. Describe how the scientists in the video are using microbes to create a tool to estimate the time since death.
Different specific microbial communities are consistently associated with different stages of body
decomposition. Scientists can sample the body and surrounding soil at multiple time intervals after death and
identify the microbes in the samples. Based on the types and abundances of microbes they find, they can then
determine how long the person has been dead.
5. The law of conservation of energy states that the amount of energy in an isolated system stays constant. In
other words, energy cannot be created or destroyed; it can only change form. Explain how the decomposition
of a cadaver demonstrates this law.
An organism consumes energy in the form of food and may transform that energy into fuel for activity or heat.
It can also store the energy in its body. When the organism dies, the energy stored in its body is not destroyed.
Instead, through the process of decomposition, it is converted into forms that fuel other life processes. For
example, the cadaver becomes food for scavengers and microbes. These organisms also break down the
cadaver into nutrients that are transferred into the surrounding environment, where plants and other
organisms can use them.
6. Examine Figure 1, which shows the five stages of decomposition. In the table below, assign the letters of
these descriptions to the stages in Figure 1.
Stage
1 (First)
2
3
4
5 (Last)
Name
Fresh
Bloat
Active Decay
Advanced Decay
Dry Remains
Description
b
d
e
a
c
A completed version of Figure 1 with additional information is shown on the following page.
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7. Blowflies are often the first scavengers to arrive at a cadaver. They lay their eggs in orifices and open wounds,
and the stage of their development can help determine time since death.
a. How might the presence of blowflies affect the course of decomposition?
The flies and their offspring consume part of the cadaver. They also bring new microbes to the cadaver’s
ecosystem and may attract other scavengers to it.
b. Other scavengers include beetles, wasps, dogs, crows, and crustaceans. Explain how these other
scavengers could also affect decomposition.
The scavengers may consume the cadaver or spread their own microbes to the cadaver, influencing the
microbial community present. Some scavengers, such as insects, may also attract larger scavengers that
prey on both the smaller scavengers and the cadaver.
c. What abiotic factors might affect the kind of scavengers that contribute to a cadaver’s decomposition?
Factors could include temperature or season, as well as the location of the cadaver (above ground or
underground, in water or on land, etc.).
8. The graphs in Figure 2 show some of the data that the scientists in the video collected from decomposing
mice cadavers.
Figure 2. Abundances of different bacterial groups in and around the cadavers over time. In each graph, the x-axis
represents the time since death in days, the y-axis represents the relative abundances of the bacterial groups, and
the thick vertical line represents when the body ruptured. Figure from
Metcalf et al. (2013).
For each of the claims below, use evidence from the graphs to either support or refute it. If you are supporting
the claim, summarize a second experiment that would help to confirm it. If you are refuting the claim, summarize
a second experiment that would help to rule it out.
Answers will vary, as students could make arguments for either side. For each claim, two sample answers (one
that supports the claim and one that refutes it) are shown below, along with a potential experiment that could be
used to either support or refute the claim depending on the results.
Claim A: The rupture of the body during decomposition is associated with changes in bacterial communities in the
abdominal cavity, on the skin of the head, on the skin of the belly, and in the surrounding soil.
Sample Answer 1 (Support): The graphs show that different groups of bacteria change in abundance in these
locations after rupture occurs. For example, the relative abundances of several bacterial groups decrease inside
the abdominal cavity, and the relative abundances of several bacterial groups on the skin and in the soil increase.
Sample Answer 2 (Refute): The graphs show that the soil and belly bacteria do not increase for many hours after
rupture. Some of the abdominal cavity bacteria were also decreasing long before rupture occurred. Since the
timing of these changes do not match the timing of rupture, these changes could be associated with
environmental factors or other decomposition events going on in the body.
Potential Experiment: You could monitor changes in the bacterial groups in and on decomposing bodies in a sterile
vs. outdoor environment. This would allow you to see whether the changes are still associated with rupture under
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different environmental conditions. Students may also propose ways to stop rupture from happening altogether,
to see if the changes in bacterial abundance still occur or not.
Claim B: The changes in bacteria in the abdominal cavity caused the observed changes in bacterial abundance on
the head.
Sample Answer 1 (Support): The graphs show that changes in the abundance of certain bacteria in the abdominal
cavity precede changes in bacterial abundance on the head. This is consistent with what might happen if the claim
were true. (Since the bacteria in the abdominal cavity changed earlier, they could have caused the changes in the
bacteria on the head, once given enough time to replicate and spread.)
Sample Answer 2 (Refute): Although the changes in bacterial populations in the two locations are correlated, we
cannot say if the changes in the abdominal cavity directly caused the changes on the head. Both of the changes
may have been caused by rupture, or there may be other causes that are not measured here.
Potential Experiment: You could remove the head from the body of a decomposing corpse, then measure changes
in bacterial abundance on the head when it is separate from the abdominal rupture.
REFERENCES
Benbow, M. E., A. J. Lewis, J. K. Tomberlin, and J. L. Pechal. “Seasonal necrophagous insect community assembly
during vertebrate carrion decomposition.” Journal of Medical Entomology 50, 2 (2013): 440–450.
https://doi.org/10.1603/me12194
.
Carter, David O., David Yellowlees, and Mark Tibbett. “Cadaver decomposition in terrestrial ecosystems.”
Naturwissenschaften 94, 1 (2006): 12–24. https://doi.org/10.1007/s00114-006-0159-1
.
Metcalf, Jessica L., David O. Carter, and Rob Knight. “Microbiology of death.” Current Biology 26, 13 (2016): R561–
R563. https://doi.org/10.1016/j.cub.2016.03.042
.
Metcalf, Jessica L., Laura Wegener Parfrey, Antonio Gonzalez, Christian L. Lauber, Dan Knights, Gail Ackermann,
Gregory C. Humphrey, et al. "A microbial clock provides an accurate estimate of the postmortem interval in a
mouse model system." eLife 2:e01104 (2013). https://doi.org/10.7554/elife.01104
.
Metcalf, Jessica L., Zhenjiang Z. Xu, Amina Bouslimani, Pieter Dorrestein, David O. Carter, and Rob Knight.
“Microbiome tools for forensic science.” Trends in Biotechnology 35, 9 (2017): 814–823.
https://doi.org/10.1016/j.tibtech.2017.03.006
.
Metcalf, Jessica L., Zhenjiang Zech Xu, Sophie Weiss, Simon Lax, Will Van Treuren, Embriette R. Hyde, Se Jin Song,
et al. “Microbial community assembly and metabolic function during mammalian corpse decomposition.”
Science 351, 6269 (2016): 158–162. https://doi.org/10.1126/science.aad2646
.
Pechal, Jennifer L., Tawni L. Crippen, M. Eric Benbow, Aaron M. Tarone, Scot Dowd, and Jeffery K. Tomberlin. “The
potential use of bacterial community succession in forensics as described by high throughput metagenomic
sequencing.” International Journal of Legal Medicine 128, 1 (2014): 193–205.
https://doi.org/10.1007/s00414-013-0872-1
.
CREDITS
Written by Aileen O’Hearn, HHMI; Amy Fassler, Marshfield High School, Marshfield, MA
Edited by Esther Shyu, HHMI
Scientific review by Jessica Metcalf, Colorado State University
Illustrations by Natalya Zahn