As part of our “People in ME/CFS Research” spotlight series, I talked with Dr. Julia Oh, who is an Assistant Professor in Microbiology at The Jackson Laboratory and the Associate Director of the JAX ME/CFS project, leading the microbiome project. Her lab investigates how our microbes contribute to our health by using diverse technologies like genomics, synthetic biology, and genome engineering to target and manipulate the microbiota. Here is her interesting background, and more about the very exciting research directions she focuses on involving the bacteria that we cohabit with in our bodies. Keep reading for the full interview!
Hey, Julia! Thanks for talking with me today. Can you tell me a little bit about your background and how you ended up here at JAX?
Hi Courtney, so I’m a hybrid experimental and computational biologist. As a PhD student, I developed tools for high-throughput interrogation of genome function and simultaneously, drug discovery. So basically, that’s when I got interested in the microbiome. Back in grad school, E. coli was a model organism. Saccharomyces cerevisiae was a model organism. And really, I thought about microbes as just being model organisms. They grew in a tube and on a plate really nicely, and they just lived on my lab bench. And it was maybe midway through graduate school when one of my lab mates gave a presentation on one of the original soil microbiome papers, and it blew my mind! Like I said, I had just thought about microbes as being model organisms or pathogens, so to learn that microbes live in these complex communities, and that you can use technology to de-convolute who was there in that community, was really cool. For most things in life, I don’t think you can pinpoint the specific moment where you change directions, but I can point to that moment and say that was it for me.
I was also really interested in synthetic biology, which is much more in-line with the work of my graduate advisor Ron Davis and his lab, which was a technology development lab. I loved synthetic biology and I was really captivated by the microbiome, so when I started looking for post-doc positions, I wrote to all these labs like, “I want to use synthetic biology to manipulate the microbiome!” And I pretty much got two answers. It was either “we do synthetic biology but have no interest in the microbiome,” or “ we do microbiome, but we have no interest in synthetic biology.” And I was like, “ok, I don’t really know anything about the microbiome, why don’t I go to a lab and learn about the microbiome?” So that’s what I did for my post-doc, and I had a purely computational post-doc. I created these different computational approaches to create these really high-resolution reconstructions of who’s there and what are they doing in a microbial community. I’d focus primarily on the skin microbiome, which is this really interesting ecological system that has been over-simplified too much. I had always thought about the skin as this single organ that holds everything in, but what I came to realize is that it’s a very complex ecological community, and it’s a complex physiological environment. So you have your oily sites like the face and torso. And then you have your moist sites like your creases and your feet, and you have dry sites like your hands and forearms. And you have crevices, and you have parts that are exposed to light and UV irradiation. And I found in my work that the microbial communities vary significantly based on these physiological aspects of the skin. And you might think that’s intuitive, but at the time, I was like, “aha, this is so interesting!” From a human health perspective, that was also really important because skin disease occurs in a site-specific manner. We get acne on our forehead, we get foot fungus, jock itch, eczema. The site-specificity really speaks to the potential unique interactions with cutaneous immunity at those different sites. And I think that’s why what we’re doing with Derya in terms of these immune interactions is so important.
So when I came to JAX, I didn’t know Derya yet. In fact I don’t even think he was here when I interviewed. But I really liked JAX – it was one of the first places I interviewed at. I really liked the people that were here, and the philosophy of translational medicine. I also really liked the technology here, because the microbiome field was enabled by technology. We wouldn’t have microbiology without the sequencing technology that has come to fruition. So, this strong investment in technology would really be able to drive my biological problems and open doors, accelerate the progress and the understanding we could make in the microbiome. And to date that has been true! So when I started my lab, it was my chance to marry my two interests – the microbiome and systems biology. And we’re doing it! We’re doing a lot of different things, like CRISPR-based engineering of microbiota, and we’re engineering skin microbes to be therapeutics or sense pathogens, which is the synthetic biology aspect. The way that Derya and I started our collaboration is that about a week after I started here, I was like, “hey, let’s have lunch. I want to pitch an idea to you.” And I told him, “I have about 40 strains of bacteria in my strain collection that I’ve been carrying around everywhere since graduate school, and they fit in one box. But we’re happy to grow them up for you and give them to you for your immune assay.” So that was the start of a paper. And now here we are!
You said you primarily focused on the skin microbiome at first, so how did you start looking at the gut microbiome?
The good part about technology is that you can easily apply it to a variety of canvases, and that’s totally true with microbiome technology. In terms of identifying who’s there in the microbial community, you use the same sequencing tools, and the algorithms that we would apply to the data would be the same too regardless of the ecosystems. So it was a pretty easy transition – we just needed to collect different kinds of samples. I guess I didn’t think about it a lot when I came here, whether I would stick with skin or not. But then we started some cancer projects and the gut seemed to be more relevant there, and a lot of the diseases we were interested in were diseases more likely to be impacted by gut flora. That was the beginning of our investment in going after gut microbes and understanding and learning how to cultivate them. And actually manipulating them and cultivating them – that was the harder part, because there’s a whole different set of rules than with skin microbes. Luckily, collecting them is just as easy as with the skin microbes – you just collect stool instead of a skin swab. So in that sense, samples weren’t much harder to collect but we did have some of a learning curve in terms of how to get the microbes out of the sample.
You said that you’re big into technology. What are some of the technologies that you use, and how are you using them in the grant project to help us understand ME/CFS?
The most important technology is of course next generation sequencing, which allows us to very deeply probe and de-construct who’s there in a microbial community. And we’re using the more specific of the two common methods. So one method is 16S ribosomal RNA sequencing, which is basically sequencing a single conserved gene out of the genomes of all of the bacteria. But it has a lot of limitations, because you only get one gene. Mark Adams had a great analogy, he said “ it’s hard to tell everything about a car from just a steering wheel.” You get a limited snapshot of the function of the microbes using 16S. And you can’t go from motorcycle to car to delivery van from the 16S sequencing, because you can’t compare cross-kingdom microbes.
So we use the other method, called shotgun metagenomics, which is where you sequence the full DNA complement in the sample, so DNA of bacteria, viruses, and fungi, and you’re sampling across the entire genome of each. So you can identify who is there with a lot higher resolution than the 16S, which is really important, and you can also reconstruct the genomes and look at functional pathways and do cross-kingdom analyses. Because it’s high-resolution, we can also do strain-level analyses. It’s like how there are different flu strains, for example. Some strains are super-virulent and others are more run-of-the-mill. Or the really bad E. coli strains, the ones that people eat from a hamburger and die are very different than the strains of E. coli we have in the lab. So the strain is really important because different strains of bacteria can have very different pathogenicity, antibiotic resistance, and antigenicity. While all humans have a core set of microbes – like for the skin, we all have Staph, we all have Propionibacterium, etc. In the gut we all have a certain set of Bacteroides and Firmicutes. But what is known is that we almost certainly all have relatively different strains. On that level, if you take a step back, maybe we have similar strains. But in many cases, maybe we have different strains. So what Derya and I have seen is that not only does immunogenicity differ by species, it can also differ by strain. And this is very significant for disease, because we think that ME/CFS patients may have different species composition, but they could also have different strains that are immunogenic, and that could be what is underlying their disease in terms of immune interactions. So that’s what the shotgun sequencing has really allowed us to dive into. And one thing that we hope to do after we identify who’s involved, is to test these microbes in immune assays, going back not just to the species level but to the strain level and asking, “well, why are these strains immunogenic?” And we can computationally predict what the genetic elements that could be underlying these differences are, and then we can go in with our functional tools and see if we can knock out those elements. So the computational predictions help a lot, and the shotgun sequencing really lets us do that kind of analysis.
And culturomics would be the other big technology – so culturing of microbes. A lot of it is brute force, and you have to test a lot of different media conditions and pick a lot of different microbes to figure it out. As part of culturomics we use MALDI technology a lot. This is basically where you put a microbe on a chip, and the machine vaporizes it and looks for ribosomal RNA protein fragments, and different bacteria will have different fragments that are released by the vaporization. And so the weights and sizes of these protein fragments exist in a reference catalog of what the different known species look like. So we just compare our data against these reference databases to figure out what kind of microbe we have. And it’s way faster than sequencing, so that’s why we’ve been using it so much. But it’s absolutely critical in culturomics. A lot of clinics actually use them for pathogen detection and identification because it’s so fast. So those are the two main technologies we’ll be using for the ME/CFS grant project.
So for this project, what would you hope to accomplish in the first year?
First, I want to establish the systematic cultivation pipeline of the gut microbes of the ME/CFS patients. While there are some cultivation pipelines for gut microbes known, we suspect that some of the microbes from ME/CFS patients might be unique and require different culturing conditions that we need to uncover. So I hope that from our first set of patients, we can do the shotgun sequencing to figure out who they have, and who we need to go after for the culturomics. And establishing that pipeline, specifically for the ME/CFS patients, would be a really good goal. And if we could get an idea from the initial patient cohorts of what some of the differences are between them and healthy controls, that would be awesome. And then hopefully we can provide Derya with some hundreds of microbes for him to screen in his immune assay and start to build that immune interactome that we want to go after.
How did you get involved in the ME/CFS field to begin with?
That was 100% through Derya. Derya and I had been going after this immune interactome, and then the RFA for the center came up, and he was like, “this is perfect, let’s apply for this center grant.” And that’s exactly how it got started. He had an R01 very briefly before we applied for this, but yeah, it was totally through Derya. Tangentially, it rang a bell because Ron Davis, my thesis advisor during my PhD, his son has very severe ME/CFS and when I was leaving his lab was when he was really starting to get sick. As a post-doc, I actually analyzed some of his gut microbiome samples, so I knew Ron was going after this and I knew his son had it. That was honestly the first time I had even heard of it, and it was the only way I knew that this was a disease. So when Derya brought it up, I recognized the name but didn’t know much beyond that. But I’m very excited to be part of this exciting project!
It’s such a small world. So then what are your impressions of the field overall?
My knowledge is a little scant. On the patient side, I only know them through Derya but they seem very passionate and they’re having a rough time. People don’t really take it seriously, and nobody knows what it is, and there aren’t good diagnostics for it. But it’s very diverse in terms of the ages and genders of the patients that I’ve seen. In terms of the research, it’s fairly sparse, which is a good and a bad thing. There have been a couple papers from reputable groups that have come out, but there’s no smoking gun. That’s why I think that the very detailed and sophisticated ways that we’re trying to go after this are very necessary and needed. Both the immunology and the microbiome aspects do not have a lot of research done yet. So it’s a small field and it’s not that rigorous yet. Although it’s still a tiny number of people getting funding – only three centers! So a lot of work still needs to be done.
Anything else you wanted to mention about your work?
I do think that the microbiome will directly or indirectly be associated with the immune perturbations. I think there’s microbial dysbiosis, which is when you have a dysfunctional microbiome, but there’s also immune perturbations – and I just love the way that we structured the research project to vary one and then to vary the other, so we can approach it from both sides to see which is causing the issues. I think that either directly through being dysfunctional or through perturbing the immune system, the microbiome will play a big role.
Yes, it will be fascinating to see the results from this project. Thanks for talking with me, Julia!