What's eating you?

Georgia Jones shares a little of her expertise into what happens in your body after death - and the organisms that take up residence when you're gone. Take a look at the post-mortem microbiome and decomposition process.

A pathologist’s view 

The harsh florescent lights made everyone in the mortuary look ghostly pale. There’s a pathologist in his mid-fifties, in head-to-toe tweed. He is soft-spoken and has a gentle, country-doctor manner as he narrates his actions whilst working on the corpse in front of us. The body is badly burned, he explains, which makes his work much harder (and more dangerous) as he uses a viciously sharp scalpel to make the first incision. The tougher the skin and muscle, the harder you have to work to get the scalpel through it; the more chance there is of a slip-up and the scalpel piercing the living flesh of the doctor, or the nurses that are assisting him. The pathologist works systematically, opening the body from the back (as the front is too badly charred). He expertly cuts the flesh holding the peritoneum (abdominal sack) away from its fleshy anchor, until he has the entire contents of the abdomen in a stainless-steel bowl. One-by-one he removes each organ and cuts it into slices, checking for abnormalities – an aneurysm perhaps, or a blockage in the gut. I point to some purplish discoloration in the intestines and ask the pathologist : ‘”what’s this?” he glances at me, and replies, ‘the onset of putrefaction.’ I nod, feeling slightly silly. 

So - what actually happens after death? Rather than a discrete sequence of events, death is an overlapping process that follows a characteristic pattern.   

Rigor and liver Mortis 

The ‘stiffness of death’ can onset as quickly as four hours after death. The absence of oxygen in the body after death halts glycolysis (the processing of sugar to make energy) and leads to a glycogen deficient in the body. Rigor is caused by the inability for the muscle’s fibres (actin and myosin) to relax because of this deficit. Muscles in the face (most notably the eyelids) are affected first, with  rigor moving gradually down the body. 

Livor Mortis (livor – "bluish colour", mortis – "of death") or ‘lividity’ starts 20-30 minutes after death and is visible around 3 hours after death. This is the purplish discoloration of the skin caused by the settling of heavy red blood cells through the action of gravity to the lowest parts of the body. This has considerable forensic applicability, as the blood will settle in a characteristic way depending on the position the person was in when they died. If the pattern of lividity is inconsistent with them sitting in a chair, for example, this can indicate that the body was moved soon after death.


Post-mortem decomposition (putrefaction) is a gradual breakdown of soft tissue in the body, after death. It is brought on by the action of bacteria, fungi and enzymes in a process called ‘autolysis’. Autolysis is the release of the cells’ lysosomes into the cytoplasm to breakdown proteins by means of digestive enzymes (proteases).

This process actually begins directly after death itself but may not present itself in a detectable form for 2 or 3 days (depending on the climate). A number of the characteristic changes that happen in humans occur after death. Perhaps unsurprisingly, putrefaction occurs first in the abdomen (the intestines have such a large population of bacteria that this is often where autolysis begins) and a greenish discolouration of the skin begins on the right flank and spreads across the entire abdomen. This discolouration is due to the breakdown of haemoglobin in red blood cells by the action of intestinal bacteria.  

Bloating and decay 

During the early stages of death, the bacteria that runs rampant in the intestinal system is largely made up of the body’s natural microbiome. But soon after, with the immune system ceased, fungi (particularly yeasts such as Candida and Malassezia) and the bacteria normally kept in check begin to run the show.

As the bacteria processes the decaying tissue, they release methane, carbon dioxide, nitrogen and hydrogen sulphide. This causes the body to bloat and pressure begins to build. The body can double in size during this process and this causes the expulsion of fluids through the body’s natural orifices such as the mouth and nose. 

Heterotrophic bacteria such as Bacillius are responsible for the breakdown of the complex proteins in animal flesh and are the key players in the conversion of nitrogen, carbon and sulphur into a form that can be utilised by plant life and vegetation.

Next comes active decay; the stage of decomposition where the majority of the mass of the body is lost into the surrounding environment. At this stage, maggots make their presence known, feeding on the bodies’ decaying tissues and blowflies lay eggs in exposed orifices such as the eyes, mouth and nose. Advanced decay follows, where a reduction in insect life is often seen. 
As human flesh buried in the earth continues to break down, it releases a high concentration of phosphate and nitrogen, which will initially poison vegetation and plant life in the vicinity, causing it to die. This is especially true of clandestine burials (such as those of forensic interest, like murders) where the body is buried without a coffin. Within several years however, the burial site will undergo a change – the plants and vegetation in the vicinity will grow especially lush, thick and green.

During these stages of decomposition, the human body becomes a bustling ecosystem, alive with bacteria, insect life and fungi. 

The Thanatomicrobiome 

In a living human, colonies of bacteria and fungi live symbiotically inside and on the surface of their host, hiding on the skin and mucosal surfaces such as the mouth, nose and stomach. The ‘microbiome’, as this is called, has been the subject of much scientific interest in recent years. The Human Microbiome Project (HMP) was launched in 2007 by the US National Institutes of Health to better understand the human microbial flora. Findings from this ongoing project revealed that the abundance and type of bacteria present varies from person to person. Bacteria from the skin and vagina were found to be less diverse than the colonies living in the mouth and gut. An estimated 1000 species of bacteria can live in the human gut belonging to only a few phyla – the most commonly found are Firmicutes and Bacteroidetes with Proteobacteria, Actinobacteria, Verrumicrobia, Cyanobacteria and Fusobacteria also found in lesser abundance. 

Other kinds of bacteria such as Actinomyces viscosus and A. naeslundii, are known to live in the mouth, with certain bacteria often colonising a particular part of the mouth. These bacteria produce acid as a by-product that can contribute to tooth erosion.

In a dead human, the story is rather different. The ‘thanatomicrobiome’ (thanatos—Greek for death) is a phrase first coined in 2014 and is used to describe the colony of characteristic bacteria that exists in the heart, brain, spleen, liver and blood after death. The thanatomicrobiome is made up of bacterial and fungal microorganisms. These microorganisms use the lymphatic and vascular system as a highway to the rest of the body, disseminating colonies throughout the body and speeding up the rate of decay.  

Research on the thanatomicrobiome mostly comes from donated cadavers, body farms or from autopsies preformed. Research concluded that the best places to sample from were the liver, the lymph nodes and the fluids surrounding the heart – this is because they remain microbe-free for up to five days after death, presenting a true to life (or death) snapshot of the microbiome, post-mortem. 21 types of bacteria were found in different samples - the most commonly found bacterium were Staphylococcus spp., Streptococcus spp., Clostridium spp., Enterococcus spp., and Escherichia spp. 

Interestingly, one study found a significant difference between the types of bacteria present in male and female cadavers. Aerobic, Gram-negative bacteria was present most abundantly in female cadavers, and only males contained Gram-positive Rothia. While female cadavers had a large population of  Pseudomonas and Clostridiales, males had an abundance of Clostridium, Clostridiales, and Streptococcus

In another study using just two corpses, buccal scrapes were taken from both at pre- and post-bloat stages. In the mouth of one corpse, (pre-bloat) aerobic bacterium Pseudomonas alone, was found. After 1 week, the Pseudomonas had changed to anaerobic bacteria Peptoniphilus and Clostridium. Although the sample size is small, this is consistent with other research that suggests that the microbiome changes from aerobic to anaerobic microbiome during decay.

So, there you have it. Most of us do not particularly like contemplating what happens to our bodies after we shuffle off this mortal coil; but far from being dead, a human cadaver is teeming with life.


Georgia Jones