Necrobiome

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The necrobiome has been defined as the community of species associated with decaying corpse remains. [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 [2] Once the immune system is no longer active, microbes colonizing the intestines and lungs decompose their respective tissues and then travel throughout the body via the blood and lymphatic systems to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 portion 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 will 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] Thus, non-human animals were solely 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] Modern sophisticated molecular techniques have made it possible to identify the microbial communities that inhabit and decompose cadavers, but more advanced research is fairly new, and therefore poorly understood. [5] Studying the necrobiome has become increasingly useful in determining the time and cause of death. [7] [5] so more recent research can have crime-solving applications. [11]

Necrobiome applications

Forensic entomology

Forensic entomology, the study of insects (arthropods) found in decomposing humans is the most popular field of study used in determining the post-mortem interval (PMI). This technique, however, is still new and consistently being improved, and—as such—it can work well with other techniques such as forensic anthropology, though forensic entomology is not as dependable on its own yet. Forensic entomologists often work within the field of crime scene investigations and are a part of the crime scene expert team that analyzes and collects evidence regarding a suspicious death. Typically, the minimum education required for this particular position is a Doctorate in Forensic Science. Forensic entomologists are experts in their field, and thus require a professional certification with the American Board of Forensic Entomology. As another relatively new field, forensic microbiologists, studying the presence of microbes, began investigating ways to determine time and place of death by analyzing the microbes present on the corpse. [12] This would become an integral part of crime solving in later years upon the invention of the microbial clock process. The microbial timeline in which the body decays has been given the term “microbial clock,” this estimates how long a body has been in a certain place based on microbes present or missing. [13] The succession of bacterial species populating the body after a period of four days is an indicator of minimum time since death (MTD). [14] The presence or absence of maggots, as well as their age, can also be used to determine time of death; If the maggot is only a few days old, then the cadaver could not have been dead for longer than this time. [15]

Microbial forensics

As the necrobiome deals with the various communities of bacteria and organisms that catalyze the decomposition of plants and animals (See Figure 1), 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. [16] Using this differentiation, forensic investigators at a crime scene are able to distinguish between burial sites. This would provide concrete factual information about how long the body has been there and the predicted area in which the death possibly occurred. [1] As the progression of research regarding microbial forensics and the necrobiome continues to be refined and improved, the need for new forensic scientists and microbiologists becomes increasingly necessary. When a crime such as murder has transpired, a team of crime scene specialists or forensic science experts are called to the scene to collect evidence and examine the body. [17] These experts range from forensic odontologists to forensic microbiologists (See Figure 2). Together, they can obtain the necessary elements needed in order to properly reconstruct the victim's demise.[ citation needed ]

Cadavers and carcasses

One way many people study how bodies decompose is through the use of body farms. There are seven research facilities in the US that are home to body farms: 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. [18] Through the study of the cadavers, experts examine the microbial timeline and document what's normal in each stage in the various locations that each body is placed. [18] An experiment was conducted to study the change in the necrobiome within a carcass and they performed it. [19] The experiment was conducted to study the relative abundance of organisms in the necrobiome and the changes that occur during three different stages. For the experiment, they used six dead rabbits purchased from a pet food company. The rabbits were purchased from Kiezebank and exposed on top of a roof at the University of Huddersfield in West Yorkshire, United Kingdom. The rabbits were dead prior to purchase. Three of the rabbits’ fur were removed from the torso to identify any difference in necrobiome abundance. 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 that's touched by the soil. Active, advanced, and decay stages were examined, and proteobacteria were the most abundant present, followed by Firmicutes, Bacteroidetes, and Actinobacteria during the active stage of decomposition (Figure 3). 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. It was distinguished that 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. Also, they noted that Actinobacteria was the least abundant in the active stage and decreased even more during the dry stage. [19]

Decomposition

The manner in which bacteria colonize a cadaver is predictable when examining the time since death. [20] Only recent studies have taken place to determine if bacteria alone can inform the postmortem interval. [21] Bacteria responsible for decomposing cadavers can be difficult to study because the bacteria found on a cadaver varies and changes quickly. [22] [21] Bacteria can be brought to a cadaver by scavengers, air, or water. [23] Other environmental factors like temperature and soil can impact the microbes found on a cadaver. [23] Fortunately, microbial colonization between humans and animals is so similar, that animal models can be used to understand the decomposition process for humans. [24] Human cadavers are used for research, but animal models provide larger sample sizes and produce more controlled studies. [21] [20] Swine models have been used repeatedly to understand the human decomposition process in terrestrial environments. [25] [26] Swine are suitable for studying human decomposition because of their size, sparse hairs, and similar bacteria found in their GI tracts. [27]

Technology and techniques

An algorithm has been developed to accurately predict time since death with an accuracy of within two days. [28]

Techniques for analyzing the necrobiome have now been coupled with forensic entomology, such as phospholipid fatty acid (PLFA) analysis, [29] total soil fatty acid methyl esters, [29] and DNA profiling. [29] Pig carcasses have also become a tool to understand human microbiology, minimizing the issue of variation that exists when using human cadavers as study subjects. [29] 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] Overcoming these obstacles would assist many organizations that are involved with forensic science. Also, it would increase the understanding of the necrobiome and growth of developing a successful accurate multi-step experiment. The samples are loaded into a machine to generate and analyze DNA sequences of the microbiome. Algorithms are done in a lab on a computer program to read and match the sequences within the data bank. The results return very quickly within a few minutes to the latest days.

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 the scientific study of the colonization of a dead body by arthropods. This includes the study of insect types commonly associated with cadavers, their respective life cycles, their ecological presences in a given environment, as well as the changes in insect assemblage with the progression of decomposition. Insect succession patterns are identified based on the time a given species of insect spends in a given developmental stage, and how many generations have been produced since the insects introduction to a given food source. Insect development alongside environmental data such as temperature and vapor density, can be used to estimate the time since death, due to the fact that flying insects are attracted to a body immediately after death. The identification of postmortem interval to aid in death investigations is the primary scope of this scientific field. However, forensic entomology is not limited to homicides, it has also been used in cases of neglect and abuse, in toxicology contexts to detect the presence of drugs, and in dry shelf food contamination incidents. Equally, insect assemblages present on a body, can be used to approximate a given location, as certain insects may be unique to certain areas. Therefore, forensic entomology can be divided into three subfields: urban, stored-product and medico-legal/medico-criminal entomology.

<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 worms, 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 skin, mammary glands, seminal fluid, uterus, ovarian follicles, lung, saliva, oral mucosa, conjunctiva, biliary tract, and gastrointestinal 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 other 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">Metagenomics</span> Study of genes found in the environment

Metagenomics is the study of genetic material recovered directly from environmental or clinical samples by a method called sequencing. The broad field may also be referred to as environmental genomics, ecogenomics, community genomics or microbiomics.

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

Forensic biology is the use of biological principles and techniques in the context of law enforcement investigations.

<span class="mw-page-title-main">Cadaver</span> Dead body used for study or instruction

A cadaver or corpse is a dead human body. Cadavers are used by medical students, physicians and other scientists to study anatomy, identify disease sites, determine causes of death, and provide tissue to repair a defect in a living human being. Students in medical school study and dissect cadavers as a part of their education. Others who study cadavers include archaeologists and arts students. In addition, a cadaver may be used in the development and evaluation of surgical instruments.

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 research scientist and forensic anthropologist. He is also a teaching associate with the Law Enforcement Innovation Center, which is part of the University of Tennessee's Institute for Public Service.

<span class="mw-page-title-main">Microbiota</span> Community of microorganisms

Microbiota are the range of microorganisms that may be commensal, mutualistic, or pathogenic found in and on all multicellular organisms, including plants. Microbiota include bacteria, archaea, protists, fungi, and viruses, and have been found to be crucial for immunologic, hormonal, and metabolic homeostasis of their host.

<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.

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 explanatory paragraph pronounces the dynamic character of the microbiome, and the second explanatory paragraph clearly separates 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 animal 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.

<span class="mw-page-title-main">Marine microbiome</span>

All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of marine microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment.

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.

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