Gregory Dutton, a physical scientist at NIJ, joins science writer Jim Dawson to discuss the microbiome: what it is, how it applies to forensics, and the evolution of its role in forensic science.
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JIM DAWSON: Hello, I’m Jim Dawson, the senior science writer at NIJ. I’m speaking today with Greg Dutton, a forensic science R&D program manager at NIJ, about the microbiome. Greg’s portfolio includes trace evidence, impression and pattern evidence, and the microbiome research being done by NIJ. Over the past decade, the human microbiome – consisting of trillions of bacteria, fungi, and viruses that live in and on every one of us – has become increasingly important to criminal investigators as they’ve realized that we all leave traces of our unique microbial evidence wherever we go. The field of microbial forensics was born out of necessity in response to the 2001 anthrax attacks in New York; Washington, D.C.; and Florida that killed five and infected 17 others. The research in microbial forensics has advanced significantly since then. Greg Dutton has been working with the microbiome researchers funded by NIJ. So, welcome, Greg.
GREG DUTTON: Thanks, Jim. I’m really looking forward to talking about microbiome today. I should note that this is just a small portion of NIJ’s forensic science R&D. But I think it’s a really interesting one.
JIM DAWSON: Let’s start with the basics. Can you describe the microbiome? What is it? Is it unique to me? That kind of thing.
GREG DUTTON: Yeah. So microbiome, if you think about the word biome, biome is a community of living organisms, right? Microbiome is a community of microscopic living organisms. So, we’re talking about things like bacteria, viruses, fungi, right? These are the things that live on us and with us. You know, we carry bacterial communities in and on our bodies. So, our gastrointestinal tract has a microbiome that’s very important to our health. Humans have a microbiome, a community of microorganisms on our skin that actually helps to keep our skin healthy too. So, these communities of bacteria, viruses, they’re adapted to the environments that they live in, right? So, some of those are the environments of our body. So, they’re adapted to the environment of our skin. And, you know, our skin is different between individuals, right? So, you know, some people have drier skin, oilier skin. So, the microbiome that we carry depends, its characteristic of an individual, but it’s not necessarily identifiable to an individual. So, I think that’s the distinction there.
JIM DAWSON: Okay.
GREG DUTTON: We’re talking about communities of bacteria that are characteristic of everything about us, age, sex, diet, health, but not necessarily something that can be tied to a specific individual person.
JIM DAWSON: Okay. Thanks. And I understand, I mean, again, we’re talking huge numbers, right? Each of us has trillions of bacteria on and in us. So, this is a major community that we carry around with us that we just don’t see and are often unaware of, right?
GREG DUTTON: Yes. Yeah. I know, you know, you’ve probably seen it said that, you know, the majority of our body is really not human, right? It’s made up of bacteria. I don’t know to what extent, you know, that’s true, but definitely, there are trillions and trillions of bacteria and viruses that are a part of us. And, you know, they adapt to us, they’re characteristic of us, they tend to be--have some stability over time. So, if you sample a microbiome of an individual over time, it will tend to have some stability, and it will have some differences from others. Another interesting thing is that, you know, it’s been shown that the microbiome of people who live in the same household tends to converge over time to become more similar. Also, people who have pets, they pick up bacterial populations from their pets, that then adapts to live on and with them. So, there are things about the microbiome that are characteristic and telling about us.
JIM DAWSON: I should scare myself thinking about this. But for the most part, this is a good thing, right? They’re there for a reason, they do us good. When things are…
GREG DUTTON: Oh, absolutely.
JIM DAWSON: …functioning normally. Yeah.
GREG DUTTON: Yeah, for the most part, right. We’re living in equilibrium with them, right? And they’re, you know, some that are really critical for our health. So, a lot of the research, you know, that we’re talking about in terms of forensic trace microbiome, the research really was started in health and medicine research, because it has been increasingly understood that our microbiome is critically interrelated with our health and wellness. So that was the spark for this whole research area. And now researchers are just seeing how it can be applied to forensic problems.
JIM DAWSON: Greg, I understand that advances in DNA science and computing over the past decades have increased the likelihood that microbiome can become a useful tool in forensics. What exactly has changed from 10 years ago or so that makes this possible now, that wasn’t possible back then?
GREG DUTTON: Yes. So, there are a few things that have really come together. The first thing was the development of the sequencing technology. So, this really came out of the Human Genome Project in the late ‘90s. So, that set the stage. So, researchers had the tools to sequence the microbiome. And the next thing was really figuring out how to make sense of all the information that they were getting from this, the sequence data. And that really came together under the Human Microbiome Project that followed on in the mid to late 2000s. And the key thing that happened there was the community – the microbiome community really – converged on a standard for analyzing and comparing the microbiome. And so, it’s called the 16S ribosomal RNA profile standard, we can talk about sort of specifically later, you know, what that is, but the key thing was that they all had kind of a standard to use to measure and define how similar or how different, you know, a microbiome was to another. So, those are the key things that came together. Now, you know, with that, then they were able to go on and, you know, apply these analytical techniques to, you know, certain areas and forensic sciences is one of them.
JIM DAWSON: So, when did NIJ become interested in this? I know we support a lot of different research in different areas of forensics, but microbiome, how do we get started on that?
GREG DUTTON: So, our support for microbiome research has grown over the years. I think one of the first forensic areas that microbiome was used to analyze was actually analyzing soil evidence, right? So, that’s a little different, right? Certainly different from, you know, human skin microbiome but, you know, soils have characteristics, microbial profiles, for sure. That was the first area. Then, you know, after the Human Microbiome Project, the researchers under that were looking for places that they could apply their expertise. And so, you know, I think in the early 2010s, we started to see those researchers come to us with ideas for how they could use their microbiome techniques to try to answer forensic questions. And so we started to see proposals looking at--I think the first ones actually were in decomposition. So, using microbiome as a tool to follow the decomposition process to try to determine how long it’s been since, you know, a cadaver has been decomposing. Some of the researchers that started that, they were at the University of Colorado; they moved to UC San Diego. They then got interested in the area that we’re talking about now, which is the skin microbiome and touch transfer of the skin microbiome. And we funded a number of projects under that in recent years but, you know, there are other areas of forensic application that microbiome is active in now. Body fluid ID, for example, if you have a stain that’s collected from a crime scene and you want to figure out, you know, what is that? Is it blood, semen, saliva? Microbiome has a way you can help classify that. So, we’ve seen it touch all kinds of corners of forensic science.
JIM DAWSON: And then, the touch side of this, I understand looking at a couple of research reports that there’s sort of a last person touching. So, if you have four or five people in a room, or I think in one of the studies, they had fake burglars come into a space and touch objects that have been touched by the residents, then they were kind of overlapping, and they couldn’t distinguish earlier touches. So, I guess, how good is this? What does it really tell you at a crime scene when you swab surfaces and find samples? What are you really learning from this?
GREG DUTTON: Yeah. So, that’s an interesting project. So, this is a study from University of Chicago, Jack Gilbert. And that’s interesting because they were building on, you know, some prior studies that sort of established the fundamental questions. So, you know, they first had to, you know, study and determine whether, you know, a person’s skin microbiome is stable over time, right? Does it change?
JIM DAWSON: Uh-hmm.
GREG DUTTON: Can it be differentiated from someone else? So, they had to do those things first, right? Then they went to more sort of classically forensic questions. So, questions there, you know, so this mock crime scene that they did, the questions are, you know, is evidence transferred from a person to a surface at a crime scene? And can you collect that and measure it, right?
JIM DAWSON: Uh-hmm.
GREG DUTTON: So, I agree, you know, it was interesting, they had some success, but they were using a fairly small set of people. So, you know, it wasn’t exactly like a real world scenario. And the most important thing that they found out, that actually is gonna be a challenge for using microbiome as trace evidence in the future, is they found that they had to collect the evidence within an hour of it being deposited. So, you know, one of the things about, you know, our skin microbiome is it lived on us, but it needs our skin, like that’s the best environment for it, right? When it’s transferred to a surface, it’s dying, right? So, if you don’t get to it and collect it and keep it cold pretty quickly, it’s going to change the characteristic profile from the person who deposited it will be decaying, right? So, that’s one challenge is, you know, you need to collect it quickly. You said, you know, they noted that it really attended to retain the information of the last person touching, right? That also is true, although that may not be so bad, from a forensic perspective. If at least you can get the last person touching and you predominantly see that, you may be avoiding getting mixtures, which is a real challenge and problem with human DNA evidence. So, that was an important proof of concept study, but it definitely showed some challenges that forensic microbiome for touch analysis is going to see in the future.
JIM DAWSON: Thanks for listening to part one of my conversation with Greg Dutton. And tune in to part two for the rest of our discussion of the microbiome.
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