eLife Episode 5: Human Sperm, Gut Bugs and Decomposition

Forensic scientists have range of techniques to work out how long a person has been dead. These include looking at things like insects that may have moved in to help decomposition along. Unfortunately, these measures are fraught with difficulties and they tend to be quite inaccurate. But now, University of Boulder, Colorado, scientist Jess Metcalf has been looking at another potentially much more accurate way of doing it. She's looking at the communities of microorganisms that grow in and on the body...

Jess - So, we know microbes play an important role in decomposition, that's no secret. Forensic scientists have known this for a long time. However, we haven't had the tools to really study the microbes and because decomposition is driven by biological processes, forensic scientists try to use biological information to estimate the time since death. For example, if you watch CSI or some similar program, you might always see a forensic scientist sampling blue fly larvae. Oh, it's at this stage this means that this body could have only been dead for so long and so our question was, can we use microbes to try to answer the same type of question? Because every approach in forensic science for estimating the time since death, they all have some amount of uncertainty around them, and if you combine these different approaches, you can narrow that window of uncertainty. And our question is, can we use the information about microbial community change during decomposition to help narrow this window?

Chris - Why should that be better than what the other measures can already offer, Jess?

Jess - Every type of approach has its limitations. So, for example, body temperature and really, that's only going to be relevant in the first 48 hours. And then things like the succession of insects might be limited by the seasons. So, sometimes in the winter, insects never show up at a body. So, you can't use that. However, we all have microbes in us and on us when we're alive, and so, we already have the organisms at the time of death.

Chris - It's like our own an in-built biomarker. So, how did you do this?

Jess - We used a mouse model system. And the reason we did that is that because really, what this question is about is if you have lots of replicates. Are you going to see the same microbial community change in each replicate or is it some stochastic response of the microbial community? What we want it to be, to be able to use it as sort of a biomarker to estimate the time since death is, we want it to be consistent across replicates. And that's really hard to do in using, for example, donated human corpses or even, what's often used in forensic sciences, is a swine model. Those experiments are usually limited to one to three individuals. And so, with a model system, like a mouse model system, we were able to use 40 individuals and we sampled 5 at a time over 8 time points. And this was the first time, someone was able to characterize that bacterial community change.

Chris - Could you also look, not just in the body, but in the environment because the body, by virtue of breaking down, is going to release various chemicals and nutrients into the surrounding environment, that which will in turn, surely alter the microbial communities there too?

Jess - That's a great question. And that's one of the things that we looked at in this study - how decomposition of a corpse affects the surround soil. Often times, you know, in a crime scene, you'll find a body on the soil outside and so, if someone moves a body, can we test the soil and say that something was decomposing on it? And so, for the soil, we're kind of interested in two different questions. One, can we also use the change in soil microbes to estimate the time since death? But also, is there a really significant signature left by the decomposition process? And the answer to both of those questions was, yes. Then at every site, we saw really significant change, in both the bacteria and sort of the nematodes and other microbial eukaryotes that were present. Everything changed very significantly.

Chris - How were you measuring the microbes? Was this using a DNA technique?

Jess - Exactly. So, what we did is we borrowed the techniques that are now more commonly used to really understand the human gut microbiome and take a sample at the depths of like millions of sequences, then characterized the community of bacterial species and the community of, say fungi and nematodes that are present.

Chris - But obviously, where the majority of the bugs are in a human is inside us, in our guts. And so, that's going to really strongly dictate what we then get rotted down by, at least initially, isn't it? So, does it make a difference to your assay do you think, or will it, whether you got a person from one culture or another culture, one sex or a different sex, because we all know that our microbial spectrum is as unique as a fingerprint? (We're not all)(12:15) you genetically identical study mice. So, will it still work in a highly genetically diverse and microbiologically diverse human population?

Jess - That's a really good question, and that's what our follow up experiments are getting at. Now, we're going to look across different host species. So, obviously, mice have different gut microbes than pigs or swine than do humans, and so, one of the things we're going to do with all our different studies is then compare across different host organisms or species. Does that influence what your decomposer community looks like? And that sort of gets at the same question of like, different diets and different sort of gut microbiomes.

Where do the cells lining the airway arise, and how does smoking affect them? A study recently carried out indicates that the airways of smokers age twice as quickly as non-smokers, having serious consequences for their health.

Sam - So, my name is Sam Janes, and I'm working as a Wellcome Senior fellow at University College London. For some time, many have felt that the organs of our body rely on stem cells to repopulate all the cells in our organs when we need them. So, these stem cells should be capable of producing daughter cells of lots of different types. Now, most of this has come from data from mice, where it's possible to track individual cells over time, but this has never been possible in humans. So, we were looking to see whether stem cells really existed in the airways, and in the lungs, there are cells that secrete mucus, there are cells that have little cilia on them, and there are basal cells which are chunky little cells which sit right at the bottom on what we call the basement membrane, which is like the pavement of the lining of the airways.

Chris - And those chunky cells, are they the stem cells?

Sam - From mice, it has been felt that basal cells are stem cells of the airways. So, I suppose that was what we were expecting to see with our work.

Chris - And now, tell us how you actually did this?

Sam - It's quite a challenge in humans, because what we actually need to do this, is to be able to see a stem cell and then see how it divides and look at what we would call it's daughter cells to see what type of cells they are. And to do that in a human, is pretty well impossible on any internal organ in particular. But what we found was that there was a scientist, Sir Nicholas Wright at Barts and the London, and he had worked on a way of staining and seeing individual cells for an enzyme that was produced by the mitochondria within our cells. And what he found actually was if this mitochondria had some sort of genetic mutation, which just actually occurs by chance. If those mutations collected, eventually an individual cell would stop expressing that enzyme. Now that means that with this stain, you can see that cell and you can also see daughter cells which have come from that individual mutation.

Chris - Because they also carry the same mutation and therefore, will have the same funny staining pattern.

Sam - Exactly.

Chris - So, you can use this unique labelling of cells in order to track individual lineages of cells.

Sam - That's right. So, when we look down the microscope at these cells, so these are in patients that have undergone some sort of lung surgery and had an area of lung taken out. We put the stain on so we can see these cells that are lacking the enzyme, and when we actually pluck out these cells individually and test their DNA, we can prove that they are indeed all related.

Chris - And returning to the question you started with, which is what do these stem cells turn into? What do you find when you examine all of those clones of cells that have come from one source stem cell?

Sam - Well, what we found was actually pretty interesting. So, the individual clones of cells were all identical and within them, they had lots of different cell types. But there were two really important things. One, was that every cluster had a basal cell, whereas other cells were sometimes missing from these clusters. So, that means that the basal cells are indeed the progenitor cells, but what was really intriguing was that when we showed the results to a mathematician in Cambridge called Ben Simons, he looked at these and said, actually these aren't related and in fact, what these clones are doing is entirely by chance. So, in fact these aren't preprogrammed stem cells that are doing a particular job but in fact, basal cells that are just dividing by chance and so they may divide to reproduce themselves, they may divide to become a different type of cell type, or they may just die.

Chris - So, what are the implications of this?

Sam - There are a number of implications. The first is, as many of us know, there's a great deal of research looking at regeneration of organs and there's been a feeling that you must get the stem cells and understand what the stem cells of an organ are, to be able to regenerate it. Our data from the airways of humans suggests that that isn't the case - you simply need to collect a broad population of these basal cells. The second thing that was quite interesting was that we looked at non-smokers and compared them to smokers, and what we found in smokers was that the whole process is basically speeded up by two. Now this is quite important because, one, it suggests that the airways of smokers are aging twice as quickly as they should, but the second thing is, these clones are expanding twice as quickly. So, if you ended up with a clone with genetic mutation which may contribute to forming a cancer, then that clone is already spreading twice as quickly.

Chris - But going back to your method, is it possible that what you're seeing is an artefact of the fact that the cells have a mutation?

Sam - Yes. So, that's a really important point because you're quite right. If the mutation led to some sort of advantage for these cells, then they may be expanding more quickly than we would expect. But, quite a lot of work has been done with these mitochondrial mutations, and these mutations aren't thought to effect the way the cells proliferate or survive at all.