Gregory Dutton, a physical scientist at NIJ, and science writer Jim Dawson continue their conversation on the microbiome: what it is, how it applies to forensics, and the evolution of its role in forensic science. Read the transcript.
Listen to the first half of Jim and Greg’s microbiome discussion.
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JIM DAWSON: Hi, everyone. It's Jim Dawson. I'm a science writer for NIJ. This is the second half of my conversation with NIJ scientist Greg Dutton about the microbiome. Be sure to listen to part one, if you haven't already.
So, now I understand that they've, for some years, been able to--if I touch something, I leave my DNA on the surface and that’s stray DNA analysis. But I've noticed in one of our reports that if we don't leave very much DNA, we may leave a lot of bacteria or microbes and that kind of thing that makes it useful. But when you have those microbes as kind of living evidence, how do you--I mean, is there DNA analysis of the microbes? How do you process those? What's involved in that?
GREG DUTTON: Yes, absolutely. I'm actually glad you mentioned. We do transfer our own DNA when we touch things. And, you know, an investigator is going to want to first see if they can collect human DNA, right, because that can be tied to an individual. And so if you can get that, you're going to take it. Problem is, you know, we often don't transfer a lot, right? So it's often a challenge to collect enough human DNA and make sure that you, you know, you can get a complete profile to search a database. That doesn't, you know, that's challenging. You know, the current technology for collecting human DNA from touch samples, it works sometimes; it doesn't always work. Microbiome can be another source of information if the human DNA profile from a touch sample either doesn't return a hit from a database or you don't get a complete profile. So that's one of the reasons that this is really being sort of put--the microbiome, touch microbiome, is being pushed forward is as another tool of additional information.
You asked, what are you really looking at when you're--when you're collecting and analyzing microbial DNA? So, you know, just think about it, you're--you know, we're taking an object or surface and swabbing it, right? Collecting DNA, that's a soup of information, a soup of stuff, right? So first you need to extract the DNA from that, right? Then you need to analyze it. And I mentioned before this bacterial microbiome standard, so it's called 16S ribosomal RNA. This is a gene that all bacteria have, right? There's some portions that are confirmed so that are the same across all species and there's some regions that are variable. So it's a very convenient, specific place that you can look in a bacterial genome to classify ‘what kind of bacteria do I have.’ So the sequences in the 16S rRNA region are characteristic of the type and species of bacteria. So you can use sequencing of that region to say, oh, I've got this bacterium, this one, this one, these types you can cluster them into types of bacteria and you can quantify relative ratios of those to get a profile. So that's what we're really talking about. We're looking at this specific part of the bacterial genome and we're sequencing that to identify groups and species of bacteria.
JIM DAWSON: Okay. It sounds like a challenge to process that much DNA and distinguish between bacteria with it. Yeah.
GREG DUTTON: The point is that, you know, once you sort of specify the process, the researchers in this area, they often call it a data pipeline. Once you sort of specify what it is that you are analyzing, then you can analyze, you know, lots and lots and lots of samples, if you analyze them in the same way then you're going to get useful information in order to compare samples. You just have to sort of specify the standards and the process and you're set.
JIM DAWSON: Okay. And is the goal here--then I want to know what the variety or the mix in the population is as opposed to, I mean, the value of knowing one bacteria type is not as valuable as knowing who all is in the swab, right? I mean, if we've got a bunch of different bacteria, what the mix is, I assume that's where the identifying nature of this comes, right?
GREG DUTTON: Yeah. It's both, so it's actually--this is challenging and so the more recent research in trace microbiome is looking for specific species that may be more--may give us more ability to differentiate between individuals. So a lot of these, you know, skin microbiome profiles are they're common to all of us, right? And we may have, you know, certain groups of bacteria in different proportions, but that, you know, can sort of just tell you, oh, this is likely to be a male. Or this is, you know, likely to be a person, you know, over the age of whatever. That's useful, right? And an investigator is going to want that information if they can get it. But on the forensic end, right, in terms of trying to associate evidence with an individual or assess whether this evidence could be associated with an individual, you're going to need more specific handles to look at. And so, you know, they're looking for more specific species level bacteria, yup.
JIM DAWSON: Okay. And would that tell us what the person eats, what drugs they're on, other things like that, I mean does it get that specific, what kind of portrait does it paint?
GREG DUTTON: It could. Yeah. A lot of that stuff is maybe not yet known, right? Certainly the types of bacteria that live on us, you know, they're adapted to the environment. So a lot of those characteristics would go into determining why it is that we have a certain, you know, microbiome profile that we do. And, you know, many of those things just aren't understood yet.
JIM DAWSON: Okay. And I understand that there's a thing called shedders with microbiomes that some people leave a lot of material behind, some less, is that understood? I mean, is that true, number one, and are some people just naturally kind of leaving clouds of their biome behind them as they go through a room, or something?
GREG DUTTON: Yeah. I believe that that is understood to be true for microbiome. I know that it's pretty well established for human DNA, right? So the--there's documented to be big differences between--they do call them shedders, people who tend to leave a lot of DNA behind them. You know, they may be for whatever reason, slopping off more skin cells than other people. And I would--I would expect that people who are high shedders for human DNA, means they're leaving behind a lot of, you know, skin cells that probably they're also leaving a lot of--a lot more microbial content behind as, you know, the bacteria and viruses that live on our skin, they're kind of just they're on everything that we leave behind.
And, you know, you mentioned the sort of bacterial cloud, so there have been a couple of really interesting studies recently showing that we actually--you can actually collect bacteria that must have been transported through the air, right? So not some touch contact, but through air contact. Even more recently, this isn't microbiome but, you know, actual human DNA, it's been shown that we actually exhale small amounts of our own DNA into the air, into the little droplets that are in the exhaled breath that we breathe out. So there's a--I think there's a lot of potential for sensing these ways that we can deposit DNA and microbiome. But, you know, that's some interesting stuff that I think that we'll see in the future.
JIM DAWSON: Okay. And of the future, one of the problems I know with most fields of forensics is trying to get them--the advances accepted in crime labs, medical examiners, routines, and then ultimately get them into the courts. I--a lot of funding is more on the science than the--how it's accepted by law enforcement, but they're tied together. So how do you--how do you work with law enforcement to get them to understand what it is you're doing and to start using it?
GREG DUTTON: Yeah. That's a good point that, you know, what we've been talking about now is, you know, applied research to show a potential for forensic use for these techniques. Actual, practical use in forensic labs is going to need a few things. One of the big things is adoption of new DNA sequencing technology. Most forensic labs now, they are--they're built to analyze human DNA and specifically the FBI Core CODIS Loci, right? So they're really set up for that. This, doing microbiome routinely in a forensic lab would require next-gen sequencing instruments in their labs. Most labs don’t have that yet. There are other reasons for human--for human DNA analysis that labs should be adopting next-gen sequencing technology sometime soon. It's not clear how long that would take. Once they have that, they could incorporate microbiome analysis. But they need that technology first. Another thing that--that's really necessary is I'll go back to standards, right? The community would have to really arrive at a set of forensic standards for microbiome analysis and comparison and that really hasn't happened yet. NIST is leading—so NIST is the place in the federal government that, you know, really works to help establish standards, you know, for scientific communities. And they just started a new International Microbiome Standards Alliance, so there are first steps towards that, but still quite a ways away from established standards for how to analyze microbiome.
JIM DAWSON: So, you're talking expenses in getting new machines in crime labs, that kind of thing. And then once you've established that, then you have to get it accepted in the courts. And that is the thing that's a whole different standard, right?
GREG DUTTON: [INDISTINCT] Yeah. I'm glad you mentioned that too, the courts. So one of the key things that the courts really require is a peer reviewed literature foundation. And that's what we're building now with this research, right? So everything that we are doing, that our researchers are doing, to work out exactly the parameters of what can be done and what--what's possible, that's going to be the foundation that the courts will rely on to determine whether or not it's reliable. So that's a key part.
JIM DAWSON: All right. And I have one of the researchers that has been on this for a number of years talked about how he looks back at the work he did in this 10 or 12 years ago, and I think he might've used the word laughable, but just by how hard and how crude it was. And then he said the work we're doing right now is very sophisticated, but 20 years from now, we'll look back on it as being stone age, that's kind of how science is, right? I mean, no matter how sophisticated you are, it always, in retrospect, looks crude when you look back after it's done. Yeah.
GREG DUTTON: Absolutely. That's right. There's not an endpoint, right? You're always learning, yup. Standing on the shoulders of giants, they say. Science is incremental, right? And, I mean, even at the point that this is now a forensic microbiome trace, it's amazing that we got to this point. It isn't ready yet, but, you know, we can see it moving in that direction. And, you know, these researches are--these are the steps that we need to take in order to get there.
JIM DAWSON: All right. And I want to talk just one last thing about the push-pull between science and more general, you know, I guess medical practices or is--I know some of the NIJ supported microbiome research was used, the techniques, to detect the COVID virus in college classrooms and to look at waste water from dorms and that kind of thing, just this identifying microbes on a massive scale, some of the work transferred over to doing that. Does it work the other way around where we get the pandemic research push mircobiome science more generally forward and have that feedback on forensics?
GREG DUTTON: So I think you're right. So, you know, specifically I think devices for quick detection of, you know, for COVID, it's specifically viral but, I think, you know, the more generalizable devices for quick detection of microbial agents, absolutely. That I think has moved ahead quite a bit because of the pandemic. But you mentioned the research, I was so happy to hear that, that those researchers were able to use the expertise that they developed in their lab, put it to good use during the pandemic, to, you know, they--they're experts at collecting microbial evidence, so they typically work with bacteria, but in this case, viruses is no different, right? They're collecting DNA or RNA and they're sequencing it, and so they put their expertise to use to collect trace samples, collect waste water samples, so that was one thing that was found in this: that waste water for detecting viral infections in a certain area, right? Collect the waste water from say specific dorm and you may be able to tell if there's an infection outbreak in that dorm and the pandemic has shown that waste water detection is very, very useful. More so than surface swabbing. So it was just really great to see those researchers put their expertise to good use during the pandemic.
JIM DAWSON: Well, thanks, Greg. This is an interesting discussion about the microbiome and where it's going in forensics. And I hope we can get together and talk again about more of the forensic science that's moving forward with NIJ. Thanks.
GREG DUTTON: Thanks, Jim. I really had a great time talking to you today and really looking forward to another chance to talk about other interesting topics.
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