Necrobiome

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The necrobiome has been defined as the community of species associated with decaying remains after the death of an organism. [1] The process of decomposition is complex. Microbes decompose cadavers, but other organisms including fungi, nematodes, insects, and larger scavenger animals also contribute. [2] Once the immune system is no longer active, microbes colonizing the intestines and lungs decompose their respective tissues and then travel throughout the body via the circulatory and lymphatic systems to break down other tissue and bone. [3] During this process, gases are released as a by-product and accumulate, causing bloating. [4] Eventually, the gases seep through the body's wounds and natural openings, providing a way for some microbes to exit from the inside of the cadaver and inhabit the outside. [3] The microbial communities colonizing the internal organs of a cadaver are referred to as the thanatomicrobiome. [5] The region outside of the cadaver that is exposed to the external environment is referred to as the epinecrotic microbial communities of the necrobiome, [6] [7] [5] and is especially important when determining the time and location of death for an individual. [6] Different microbes play specific roles during each stage of the decomposition process. The microbes that colonize the cadaver and the rate of their activity are determined by the cadaver itself and the cadaver's surrounding environmental conditions. [7]

Contents

History

There is textual evidence that human cadavers were first studied around the third century BC to gain an understanding of human anatomy. [8] Many of the first human cadaver studies took place in Italy, where the earliest record of determining the cause of death from a human corpse dates back to 1286. [8] However, understanding of the human body progressed slowly, in part because the spread of Christianity and other religious beliefs resulted in human dissection becoming illegal. [8]

Non-human animals only were dissected for anatomical understanding until the 13th century when officials realized human cadavers were necessary for a better understanding of the human body. [8] It was not until 1676 that Antonie van Leeuwenhoek designed a lens that made it possible to visualize microbes, [9] and not until the late 18th century when microbes were considered useful in understanding the body after death. [10]

Necrobiome on pig cadaver Necrobiome on a pig cadaver.png
Necrobiome on pig cadaver

In modern times, human cadavers are used for research, but other animal models can provide larger sample sizes and produce more controlled studies. [11] [12] Microbial colonization between humans and some non-human animals is so similar that those models can be used to understand the decomposition process for humans. [13] Swine have been used repeatedly to understand the human decomposition process in terrestrial environments. [14] [15] Pigs are suitable for studying human decomposition because of their size, sparse hairs, and similar bacteria found in their GI tracts. [16] Pig carcasses also minimizing the issue of variation that exists when using human cadavers as study subjects. [17]

Sophisticed molecular techniques have made it possible to identify the microbial communities that inhabit and decompose cadavers; however, this research is fairly new. [5] Studying the necrobiome has become increasingly useful in determining the time and cause of death, [7] [5] which is useful in crime scene investigations. [18]

Applications in forensics

Microbial forensics

As the necrobiome deals with the various communities of bacteria and other organisms that catalyze the decomposition of plants and animals, this particular biome is an increasingly vital part of forensic science. The microbes occupying the space underneath and around a decomposing body are unique to it—similar to how fingerprints are exclusively unique to only one person. [19] Using this differentiation, forensic investigators at a crime scene are able to distinguish between burial sites, as well as gain concrete factual information about how long the body has been there and the predicted area in which the death possibly occurred. [20]

Forensic microbiologists investigate ways to determine time and place of death by analyzing the microbes present on the corpse. [21] The microbial timeline of how a body decays is known as the microbial clock. It estimates how long a body has been in a certain place based on microbes present or missing. [22] The succession of bacterial species populating the body after a period of four days is an indicator of minimum time since death. [23] Recent studies have taken place to determine if bacteria alone can inform the post-mortem interval. [11] Bacteria responsible for decomposing cadavers can be difficult to study because the bacteria found on a cadaver vary and change quickly. [24] [11] Bacteria can be brought to a cadaver by scavengers, air, or water. [25] Other environmental factors like temperature and soil can impact the microbes found on a cadaver. [25]

The time of death can be estimated not only by the type and amount of bacteria on a cadaver, but also by the chemical compounds produced by those bacteria. Forensic anthropologist Arpad Vass determined, from research he undertook in the 1990s, that three types of fatty acids, produced when bacteria break down fat tissues, muscles, and food remnants in the stomach are useful in predicting the time since death during forensic investigations. [26]

Forensic entomology

Forensic entomology, the study of insects (arthropods) found in decomposing humans, is useful in determining the post-mortem interval after 3-4 days have passed since the death. [27] Various types of flies are usually drawn to a cadaver and typically lay their eggs there. [26] Therefore, both the developmental stages of one species of fly and the succession of different species can give an estimate of how long the person has been deceased. Since the presence and life cycle of insects varies by temperature and environmental conditions, this type of analysis cannot give the actual time of death, but results only in a minimum time since death. The deceased could not have been dead longer than the oldest maggot found. [27]

Insect activity can also indicate the cause of death. Blowflies typically lay their eggs in natural body cavities that are easily assessible, yet also sheltered. If the pattern of maggot activity appears elsewhere, that could indicate an injury, such as a stab wound, even if the surrounding tissue has decomposed. In the event of a death caused by poison, traces of the toxin may have been consumed by the maggots, without harming them. [27]

Since insect species tend to have certain geographic ranges and known habitat preferences, forensic entomologists can determine if a body has been moved after death. Analysis of the insects in the necrobiome can indicate if the death occurred in a different ecological or geographical environment than where the cadaver was found. [27]

Research

Human cadavers

The decomposition of human bodies is studied at research facilities known as body farms. Seven educational institution house such facilities in the United States: University of Tennessee in Knoxville, Western Carolina University, Texas State University, Sam Houston State University, Southern Illinois University, Colorado Mesa University, and University of South Florida. These facilities study the decomposition of cadavers in all possible manners of decay, including in open or frozen environments, buried underground, or within cars. [28] Through the study of the cadavers, experts examine the microbial timeline and document what is typical in each stage in the various locations that each body is placed. [28]

In 2013, at the Southeast Texas Applied Forensics Science facility at Sam Houston State University, researchers documented the bacteria growing in two decomposing cadavers placed in a natural outdoor environment. Their focus was on the bloat stage, when hydrogen sulfide and methane produced by bacteria build up and inflate the cadaver. They found that "by the end of the bloat period...anaerobic bacteria such as Clostridia had become dominant" and swaps of the oral cavity "showed a shift toward Firmicutes, a group of bacteria that includes Clostridia." [26]

By 2019, Jennifer Pechal, a forensic science researcher at Michigan State University, had worked with microbes on almost 2,000 human remains in a spectrum of conditions. She proposed a pattern in the necrobiome that concurs with data from scientists in Italy, Austria, and France. They found that a "large, consistent shift in the microbial community" occurs about 48 hours after death, making it "fairly easy to tell if a body has been dead for more or less than 2 days." Pechal also hopes that microbial tests can be used in the future to help pathologists determine undiagnosed medical conditions that were the cause of death. [26]

Non-human remains

A 2019 study at the University of Huddersfield in West Yorkshire, United Kingdom sought to investigate the influence fur has on the necrobiome of rabbits. The experiment involved six dead rabbits purchased from the pet food company, Kiezebrink. The fur was removed from the torsos of three of the test subjects. All six samples were placed on "sterile sand in clean plastic containers." [29] Lids covering the containers prevented birds and other scavengers from accessing the carcasses, while small holes drilled into the sides of the containers allowed air flow and insect activity while the containers were exposed on the roof of a university building. Samples were collected from inside of the mouth, the upper skin of the torso exposed to the air environment, and the bottom skin of the torso in contact with the sand. Proteobacteria were the most abundant present, followed by Firmicutes, Bacteroidetes, and Actinobacteria during the active stage of decomposition. During the advanced stage of decomposition, Proteobacteria decreased from 99.4% to 81.6% in the oral cavity but were most abundant in the non-fur samples. Firmicutes were the most abundant for the skin samples in both fur and non-fur samples. Finally, Proteobacteria was most abundant in the soil interface during the beginning of decomposition in both fur and non-fur samples. The researchers also noted that Actinobacteria was the least abundant in the active stage and decreased even more during the dry stage. The conclusion of the experiment was that while bacterial communities changed over the course of decomposition, the most significant variation is attributed to different anatomical regions "but independently of the presence of the fur." [29]

Technology and techniques

Techniques for analyzing the necrobiome involve phospholipid fatty acid (PLFA) analysis, [17] total soil fatty acid methyl esters, [17] and DNA profiling. [17] This technology is used to simplify the sample collection into sequences that scientists can read. The simplified sequence of the necrobiome is run through a data bank to match the name of it. Due to the lack of universal algorithm technology, there is a knowledge gap in various platforms across different regions of the world. In order to close that gap, there needs to be an expansion of the technology. However, there are a few obstacles, including identifying needs, research, prototype development, acceptance, and adoption. [30]

Researchers are working on an algorithm to predict time since death with an accuracy of within two days, which would be an improvement over time frames given by forensic entomology. [31] Jennifer Pechal states that those computer models must "be tested on bodies with a known time of death to ensure they are accurate." As of 2020, that technology is still 5 to 10 years away from becoming available. [26]

See also

Related Research Articles

<span class="mw-page-title-main">Forensic entomology</span> Application of insect and other arthropod biology to forensics

Forensic entomology is a branch of forensic science that uses insects found on corpses to help solve criminal cases. This includes studying the types of insects commonly found on cadavers, their life cycles, their presence in different environments, and how insect assemblages change with decomposition.

<span class="mw-page-title-main">Decomposition</span> Process in which organic substances are broken down into simpler organic matter

Decomposition or rot is the process by which dead organic substances are broken down into simpler organic or inorganic matter such as carbon dioxide, water, simple sugars and mineral salts. The process is a part of the nutrient cycle and is essential for recycling the finite matter that occupies physical space in the biosphere. Bodies of living organisms begin to decompose shortly after death. Animals, such as earthworms, also help decompose the organic materials. Organisms that do this are known as decomposers or detritivores. Although no two organisms decompose in the same way, they all undergo the same sequential stages of decomposition. The science which studies decomposition is generally referred to as taphonomy from the Greek word taphos, meaning tomb. Decomposition can also be a gradual process for organisms that have extended periods of dormancy.

<span class="mw-page-title-main">Human microbiome</span> Microorganisms in or on human skin and biofluids

The human microbiome is the aggregate of all microbiota that reside on or within human tissues and biofluids along with the corresponding anatomical sites in which they reside, including the gastrointestinal tract, skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, and the biliary tract. Types of human microbiota include bacteria, archaea, fungi, protists, and viruses. Though micro-animals can also live on the human body, they are typically excluded from this definition. In the context of genomics, the term human microbiome is sometimes used to refer to the collective genomes of resident microorganisms; however, the term human metagenome has the same meaning.

Putrefaction is the fifth stage of death, following pallor mortis, livor mortis, algor mortis, and rigor mortis. This process references the breaking down of a body of an animal post-mortem. In broad terms, it can be viewed as the decomposition of proteins, and the eventual breakdown of the cohesiveness between tissues, and the liquefaction of most organs. This is caused by the decomposition of organic matter by bacterial or fungal digestion, which causes the release of gases that infiltrate the body's tissues, and leads to the deterioration of the tissues and organs. The approximate time it takes putrefaction to occur is dependent on various factors. Internal factors that affect the rate of putrefaction include the age at which death has occurred, the overall structure and condition of the body, the cause of death, and external injuries arising before or after death. External factors include environmental temperature, moisture and air exposure, clothing, burial factors, and light exposure. Body farms are facilities that study the way various factors affect the putrefaction process.

<span class="mw-page-title-main">Maggot</span> Larva of a fly

A maggot is the larva of a fly ; it is applied in particular to the larvae of Brachycera flies, such as houseflies, cheese flies, and blowflies, rather than larvae of the Nematocera, such as mosquitoes and crane flies.

A body farm is a research facility where decomposition of humans and animals can be studied in a variety of settings. The initial facility was conceived by anthropologist William M. Bass in 1981 at the University of Tennessee in Knoxville, Tennessee, where Bass was interested in studying the decomposition of a human corpse from the time of death to the time of decay. The aim was to gain a better understanding of the decomposition process, permitting the development of techniques for extracting information such as the timing and circumstances of death from human remains. Body farm research is of particular interest in forensic anthropology and related disciplines, and has applications in the fields of law enforcement and forensic science. By placing the bodies outside to face the elements, researchers are able to get a better understanding of the decomposition process.

<span class="mw-page-title-main">Post-mortem interval</span> Time that has elapsed since a person has died

The post-mortem interval (PMI) is the time that has elapsed since an individual's death. When the time of death is not known, the interval may be estimated, and so an approximate time of death established. Postmortem interval estimations can range from hours, to days or even years depending on the type of evidence present. There are standard medical and scientific techniques supporting such an estimation.

<span class="mw-page-title-main">Microbial ecology</span> Study of the relationship of microorganisms with their environment

Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.

<span class="mw-page-title-main">Forensic biology</span> Forensic application of the study of biology

Forensic biology is the application of biological principles and techniques in the investigation of criminal and civil cases. Forensic biology is primarily concerned with analyzing biological and serological evidence in order to obtain a DNA profile, which aids law enforcement in the identification of potential suspects or unidentified remains. This field encompasses various sub-branches, including forensic anthropology, forensic entomology, forensic odontology, forensic pathology, and forensic toxicology.

Forensic entomological decomposition is how insects decompose and what that means for timing and information in criminal investigations. Medicolegal entomology is a branch of forensic entomology that applies the study of insects to criminal investigations, and is commonly used in death investigations for estimating the post-mortem interval (PMI). One method of obtaining this estimate uses the time and pattern of arthropod colonization. This method will provide an estimation of the period of insect activity, which may or may not correlate exactly with the time of death. While insect successional data may not provide as accurate an estimate during the early stages of decomposition as developmental data, it is applicable for later decompositional stages and can be accurate for periods up to a few years.

Arpad Alexander Vass is a forensic anthropologist. He has researched the processes involved in human decomposition. Vass claims to have developed several devices and methods to locate human remains; however, those claims have not been validated by other experts.

Oral ecology is the microbial ecology of the microorganisms found in mouths. Oral ecology, like all forms of ecology, involves the study of the living things found in oral cavities as well as their interactions with each other and with their environment. Oral ecology is frequently investigated from the perspective of oral disease prevention, often focusing on conditions such as dental caries, candidiasis ("thrush"), gingivitis, periodontal disease, and others. However, many of the interactions between the microbiota and oral environment protect from disease and support a healthy oral cavity. Interactions between microbes and their environment can result in the stabilization or destabilization of the oral microbiome, with destabilization believed to result in disease states. Destabilization of the microbiome can be influenced by several factors, including diet changes, drugs or immune system disorders.

<span class="mw-page-title-main">Microbiology of decomposition</span>

Microbiology of decomposition is the study of all microorganisms involved in decomposition, the chemical and physical processes during which organic matter is broken down and reduced to its original elements.

<span class="mw-page-title-main">Carrion insects</span> Insects associated with decomposing remains

Carrion insects are insects associated with decomposing remains. The processes of decomposition begin within a few minutes of death. Decomposing remains offer a temporary, changing site of concentrated resources which are exploited by a wide range of organisms, of which arthropods are often the first to arrive and the predominant exploitive group. However, not all arthropods found on or near decomposing remains will have an active role in the decay process.

Decomposition in animals is a process that begins immediately after death and involves the destruction of soft tissue, leaving behind skeletonized remains. The chemical process of decomposition is complex and involves the breakdown of soft tissue, as the body passes through the sequential stages of decomposition. Autolysis and putrefaction also play major roles in the disintegration of cells and tissues.

<span class="mw-page-title-main">Microbiome</span> Microbial community assemblage and activity

A microbiome is the community of microorganisms that can usually be found living together in any given habitat. It was defined more precisely in 1988 by Whipps et al. as "a characteristic microbial community occupying a reasonably well-defined habitat which has distinct physio-chemical properties. The term thus not only refers to the microorganisms involved but also encompasses their theatre of activity". In 2020, an international panel of experts published the outcome of their discussions on the definition of the microbiome. They proposed a definition of the microbiome based on a revival of the "compact, clear, and comprehensive description of the term" as originally provided by Whipps et al., but supplemented with two explanatory paragraphs, the first pronouncing the dynamic character of the microbiome, and the second clearly separating the term microbiota from the term microbiome.

<span class="mw-page-title-main">Thanatotranscriptome</span> Part of the genome still active in the time immediately following death

The thanatotranscriptome denotes all RNA transcripts produced from the portions of the genome still active or awakened in the internal organs of a body following its death. It is relevant to the study of the biochemistry, microbiology, and biophysics of thanatology, in particular within forensic science. Some genes may continue to be expressed in cells for up to 48 hours after death, producing new mRNA. Certain genes that are generally inhibited since the end of fetal development may be expressed again at this time.

<span class="mw-page-title-main">Corpse decomposition</span> Process in which bodies break down

Decomposition is the process in which the organs and complex molecules of animal and human bodies break down into simple organic matter over time. In vertebrates, five stages of decomposition are typically recognized: fresh, bloat, active decay, advanced decay, and dry/skeletonized. Knowing the different stages of decomposition can help investigators in determining the post-mortem interval (PMI). The rate of decomposition of human remains can vary due to environmental factors and other factors. Environmental factors include temperature, burning, humidity, and the availability of oxygen. Other factors include body size, clothing, and the cause of death.

Vertical transmission of symbionts is the transfer of a microbial symbiont from the parent directly to the offspring. Many metazoan species carry symbiotic bacteria which play a mutualistic, commensal, or parasitic role. A symbiont is acquired by a host via horizontal, vertical, or mixed transmission.

The stages of death of a human being have medical, biochemical and legal aspects. The term taphonomy from palaeontology applies to the fate of all kinds of remains of organisms. Forensic taphonomy is concerned with remains of the human body.

References

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