Timing Decomposition with Microbes

By: Helen Beilinson

The last decade has seen many new discoveries that have revolutionized science. Arguably, one of the most influential of these advances has been the appreciation of the impact of microorganisms on human health. In particular, the important roles played by the bacteria, viruses, and other bugs (collectively called the microbiota) that live in or on us, continue to be enumerated. Numerous elegant studies have characterized changes that happen in a person’s microbiota throughout the course of a regular year, during the progression of an infection, or even how a space environment can affect the composition of bacteria in our gut. Recently, a group from the University of California, San Diego explored the changes in bacterial composition during a different phase of life—corpse decomposition.

It might sound a bit gruesome, but the decay of once living things is critical for the cycling of nutrients on earth. The completion of this task requires an extensive arsenal of microbial and biochemical activity. Previous studies had shown that decomposition occurs in a somewhat predictable, stepwise fashion. It was also known that bacteria and other microorganisms are critical for this natural process to occur properly. However, the details of this process were not well understood. The authors of this specific study wanted to know if the environment an organism inhabits dictates the microbial decomposers, whether these microbes come from the host or the environment, and how a decomposed organism changes the environment around it.

To answer these questions, the authors determined the composition of the communities of microorganisms in decaying mice and humans in various environments. Using human cadavers might sound a bit grisly, but it’s important. Mice are good models of various human diseases and are great tools to study many aspects of biology and organismal biochemistry. However, human and mice are still two different organisms, and human subjects were required in this study to verify that their findings in mice matched what occurs in humans. The use of human cadavers is important for the implications and potential applications of this study, as it may be the newest tool in forensic science... but I’m getting ahead of myself.

To identify the families that make up the microbial communities in their samples, the authors utilized a precise technique, 16S rRNA sequencing. This technique takes advantage of the fact that there are some genes that are pretty similar in bacteria that are closely related, and grow more different the less related they are. By sequencing all the microbes, the authors are able to group them into their families and compare how similar or different the microbial populations are between different experimental groups.

An exciting preliminary piece of evidence these authors observed is that the previously described stages of decomposition followed hand in hand with a very precise and dynamic microbial community. The microbes present on day 1 are different from those that emerge on day 4 which again are different from those on day 10. At every stage, between day 1 and day 71, the microbial communities were unique. Perhaps surprisingly, when the authors changed the location of where their mouse specimen was decomposing, there was no effect on the microbial decomposers! A microbial community from a mouse decomposing in a desert environment on day 7 was almost identical to that from a mouse decomposing in a forest on day 7. Seasons also did not significantly impact microbial populations. These same data were obtained using human cadavers.

Based on the latter piece of information, one might expect that if microbial decomposers are more or less the same in different environments, which these decomposers would come from within the host itself. However, the authors found that the soil is the primary source of the microbes, even if the soil type and environment is different. It’s important to note that 16S rRNA sequencing is not the best technique for identifying specific microbes. It is mostly used to identify families of microbes that are closely related. Families of microbes tend to have similar functions, meaning they can carry out similar reactions. These data together imply that because specific microbes carry out specific reactions and that there is a predictable change in microbes over the course of decomposition, one could predict that the biochemical changes carried out by microbes can be tracked in sequential steps during the course of decomposition.

To further explore this question, the authors examined biochemical reactions taking place in the abdomen of the decaying specimen. They found that indeed, throughout the process of decomposition, there are specific reactions that can be detected at each step. The biochemical reactions that take place correlate almost perfectly with the presence of particular microbes that can carry out this process. Interestingly, the authors were also able to show that the soil around decomposing organisms also has such post-death dating properties, in that the products of the biochemical reactions occurring in the organism seep into the soil surround it, changing its chemical properties. The products produced, such as nitrate and ammonium, are used by plants to grow. Although it is a tad ghastly to think about, mammalian decomposition is important for the cycle of life on Earth. The products of decomposition allow for plants to grow which feed the living mammals.

Although now a fairly simple technology, sequencing of the microbiota of an organism has been an incredibly powerful tool in the biomedical sciences. This study has shown that another, perhaps surprising, field that may benefit from this technology is forensic science. Although there are technologies in place to help forensic scientists identify when a person has died, these are often not very precise. This paper’s methods were able to distinguish time of death with a one to two day accuracy based on the microbes found in that body and the biochemical reactions occurring. The microbes around us clearly have a constant influence on our lives: from our birth to our death, microorganisms make us who we are.