Hi, and welcome back to The Gastronauts Podcast. My name is Peter and I’ll be your host. Here at Gastronauts we are committed to exploring communication throughout the body, with a particular focus on the crosstalk between gut and brain. We invite experts in this field to share both their research and their incredible journeys. So come join me as we explore the steps that go into shaping a scientist on the Gastronauts podcast.
We have two more young scientists who have been incredibly successful in studying how microbes or bacteria in our gut can affect our brain. First up, we have Dr. Carlotta Ronda, who is a postdoctoral researcher in the department of systems biology at Columbia University in Dr. Harris Wang’s lab. She received her PhD from the Technical University of Denmark in Dr. Alex Toftgaard Nielson’s lab, where she designed new genetic engineering tools to accelerate the development of biosustainable cell factories. She is currently a Simon’s Society Junior fellow and her research focuses on engineering tools to modulate or modify the gut microbiome.
So thanks so much for being on Dr. Ronda. So the first thing I want to ask about is to [have] you elaborate a little bit more on the two things that I introduced and tell us a little bit about some of the projects that you’re working on.
So as you know, the gut microbiome is inhabited with a variety of different bacteria and a lot of them are not very readily amenable to manipulations or genetic manipulation. So it’s very difficult to try to understand the physiology of the gut without considering our microbiomes. It can be skin, it can be gut. And so if we want to really understand this, given these microbial communities, we need to be able to cultivate them or manipulate them and try to assemble their functions. And so what I’m doing is trying to devise methods that allow us to unravel or deconvolute this complexity. The ability to create tools that allow us to shine some light on their functions and their physiology and how they interact with the host, which is us. It’s really important to really understand the physiology. And so like, my work is trying to devise new methods to understand how these communities behave, and how these communities interact with the host, and allow us to better understand their functions and their role in the human physiology.
So I really want to take a […] 30,000 foot view step back. So we’ve talked a lot about the microbes within the gut. Are there bacteria living on other organ systems within our body? What made you choose to focus specifically on the gut microbes?
Dr. Ronda [3:35]
So yes, there are other microbiomes: we have skin microbiomes, we have eye microbiomes […] we discover new microbiome everywhere every every day […] they even discussed about a potential brain microbiome which is kind of very controversial. The reason to delve into the gut is because it’s one example of a microbiome that has been already extensively studied. And so people are very interested in understanding it, because its role in physiology in disease has become extremely evident in the past like five to 10 years. So that’s why I’ve decided to work on the gut. But I will expand my work and my tool are expandable [to other] microbiomes.
The gut microbiome is the most densely enriched population of microbes throughout our entire body. We may have these bacteria living on different organs, but the gut is the most well studied and the most number of bacteria live on the gut. Could you speak a little bit to the stability and the transient nature of our gut microbiome and how you will potentially target those populations?
Dr. Ronda [4:52]
The gut microbiome is extremely dynamic and it constantly changes: with the circadian rhythm, it changes based on the food we eat, the place we live, so it’s a very dynamic system. And so, it is very difficult to really engineer them and have them stably maintain the same community as at the beginning, unless you have a specific fitness advantage that you can compare to specific spaces. So you can give, for example, if you want to select for specific members of the community, you can provide them specific stress substrates that they grow on and give them a fitness advantage to persist within the community and to bloom within a community and change their abundance within the community. So if you want to modulate the community, not at a specific genus or species level, but at the genetic level, then it’s a completely different matter. Because at that point, the reprogrammed function that you want to give to the community is genetically encoded and when it is genetically encoded, it can be hosted by different species. And it’s not necessarily linked, you can make it to be broad and hosted by different species and not directly linked to a one single populations. And so, in that scenario, you want to give genetic stability to reprogram functions that you engineer within the community. So engineering the community, it’s actually a very broad term, but it involves multiple levels, you can work at that populations, the genus and species level and their fluctuations within the community. You can work at the genetic content.
And is a lot of your work on the engineering focused on modifying it at the genetic level- not so much on the species level or population level. You’re more interested, your work is currently more focused on genetic reprogramming or targeting wide variety of species just based off of their genomes. Is that correct?
Dr. Ronda [7:10]
Yeah. So right now I’m working on genetic reprogramming, because you have more stability on genetic programming. And it’s not a trivial problem to give an increase of fitness or like you provide a fitness advantage to specific spaces because the gut microbiome has incredible metabolic capacity and plasticity. So it’s very difficult to find molecular metabolites that are unique, and you can use [these] as a driving force […] to give the populations [we] are interested in a fitness advantage […]
To allow us more tight control essentially.
Dr. Ronda [7:52]
To get more tight control and also allow the reprogramming function [to be] more pervasive. Because you can target multiple spaces, so the reprogram function will be propagated within the populations and not restricted to only one species. So if you have a beneficial function and you want to enhance your microbiome capacity, and you want to have […] a substantial difference from your baseline in terms of like production, and maybe one species is not enough to drive that enhancement. So if you actually reprogram the functions within multiple species, then you can increase [and] propagate it and you can increase the performance. So you can increase the enhancement if you want to reprogram in the function.
So by genetically reprogramming, you’re introducing kind of a new type of DNA into this bacteria to give it a fitness advantage or to allow it to produce a particular metabolite- is that correct?
Dr. Ronda [9:02]
So the best scenario would be to to link the fitness advantage with a specific function you’re interested in. Let’s assume that you want to increase the serotonin level and instead of taking antidepressant you want to increase the serotonin level [through the gut]. So the gut isactually the major producer of serotonin. And so a [depressed] person doesn’t produce it that much and you want to increase the productions and use it as an alternative to antidepressant-
Are you focusing on any particular bacterial populations? Or do you just see it as just increasing the total amount of serotonin for this example?
Dr. Ronda [9:48]
So microbiome engineering is a very broad term and it is actually composite of multiple nuances. And it depends on the question you’re asking or what you’re looking for. And so, if you are looking for just an increased production from one single species, then my suggestion is, which I have other projects that I’m working on where you engineer a single probiotic, which is specialized to produce that specific molecule. And then you give […] a single entity that is optimized for the production of the molecules and you will have a lot of release. But the problem with these specific probiotics is that they cannot stay, they cannot stick in the microbiome, they cannot colonize. They just will be washed out pretty fast […] It’s a major factor when we’re discussing about probiotics. So if you reprogram your own microbiome to a certain function, then you don’t have this colonization problem. And then you can have a constant release. So […] you can modulate the time of release of your of your drug, and the and you can maintain the release of your drug. Okay, let’s assume that you eradicated completely species, which can happen extinction of a species in your microbiome, those have died because of abuse of antibiotics, then how can you perform their functions? How can you try to reintroduce those species? You’re not sure they will engraft because you already have your own community, and they might not engraft. So if you want that function to be performed, you can just record it in and deliver it and reprogram already existing spaces to actually do that […]
So this genetic engineering is more like a personalized approach as opposed to using one probiotic to give to everyone you change your individual microbiome.
Dr. Ronda [12:12]
Exactly. The idea is to try to go towards a personalized approach where you don’t take a generic probiotic, you don’t take other people’s microbiome. Getting microbial community from other individuals has been shown to be an extremely effective system for C diff infections. And so it is a very powerful and effective treatment, but there are still open questions if it’s the best approach because there’s so many things unknown about the process [that can be] more controlled with genetic engineering. Yeah, and also what is the best microbiome to give you we don’t know. Like, there are super donors where the microbiome of those super donor seems to be more effective and to be able to colonize better, but what are the rules that make a super donor a super donor? We don’t know them yet. There are efforts in trying to understand what is the holy grail of microbiome to cherry-pick specific bacteria and create like a perfect for microbiome, but you never know […] Sorry, I have to correct myself. We don’t know, at this point, what can happen in the host because there is also host genetic changes as well, [and] host physiology and genetic can have an influence […] the colonization process and the shaping of the community but also into specific species. So these are still open questions that we haven’t we haven’t addressed yet.
It’s an exciting place [to be conducting research]
So we’ve definitely talked a lot about the uncertainties with regards to the whole microbiome sphere currently, which makes it such an appealing avenue for people to do genetic engineering, for people to study what exactly in these microbial populations is beneficial. And I was wondering, as you start to transition to running your own laboratory, what are some of the big questions that you want to answer with are using microbial and genetic [engineering]?
Dr. Ronda [14:32]
So the fundamental questions that we’re still trying to address in the field is the mechanism of how deep microbial communities can affect human physiology. At the mechanistic level, we are still lacking a lot of knowledge. If we wanted to really understand and unravel the complexity of the community that inhabits us, we want to try to modify them and understand how they interact with the host. If you conceptualize the microbiome as a complex network of different nodes and different points where each node is a species or micro-consortia, then you try to simplify a problem, which is if you want to understand that network, what you’re going to do, you’re going to try to twitch and manipulate and take away or introduce new nodes. So you can see how the network reacts to the specific changes and by looking at how the [system] reshapes after you change these nodes, and understand the role of those nodes. So the method the genome engineering, it’s the tool of genome engineering of this allows us to manipulate specific bacteria that will allow us to take out or put in a new node in this network. This allows us to really deconvolute the complexity of this network, because-
The microbial community and even host physiology communities are so complex, that we have to break it down, we have to take it kind of one piece at a time and then look at everything that changes from this one manipulation because if we try and change many things at the same time, you don’t know what is causing the whole change in the network. So will [there] come a time where we have all the tools to understand each of the nodes within the network? Do you think that is kind of within the near future far away with regards to understanding kind of these subpopulations of bacteria and how each one of these subpopulations affects the entire network?
Dr. Ronda [16:53]
I think there are multiple efforts to actually do that to try to understand what is the contribution of each species within the community, at the community level? And also how do individual species affect the physiology of the host? I think they all try to really understand and map out these interactions and these roles. I can give a definite answer. Maybe at one point they will know everything because it’s like asking if we’ll know everything about biology at one point. It is so difficult to say […] and so much to unravel, that I don’t see it as I complete work within a timeframe that I can picture […] It’s a very exciting, flourishing field. And people are tackling the problem from different angles. That’s what I find […] very fascinating.
That’s really great. Well, thank you so much for sharing your excitement with us, Dr. Ronda, and thank you for being on our podcast.
Dr. Ronda [18:08]
Thanks a lot for having me here. It’s been great.
We also have Dr. Martina Sgritta here with us today. She is a postdoctoral researcher at Baylor College of Medicine in Dr. Mauro Costa-Mattioli’s laboratory. She completed her PhD at the University of Pavia on spike-timing dependent plasticity in the laboratory of Dr. D’Angelo. Her current research is quite different and focuses on understanding mechanisms that underlie social behavioral deficits in autism spectrum disorder. A recent publication in the journal Neuron showed how transplantation of a specific bacterial strain in the gut is able to enhance social behavior within mice. Can you tell us a little bit more about this project and additional projects that you’re working on?
Dr. Sgritta [19:10]
Of course. Hi, everybody. So my project was kind of a follow up from previous work published in our lab. So a former colleague, Shelly Buffington found how a specific bacterial strain was reduced the gut microbiota [in an] environmental model of Mouse Mouse model for ASD, autism spectrum disorder, and this was a maternal high fat diet model. So she found that mice that were born from mother fed with a high fat diet were socially impaired and these specific microbial strains were reduced in the gut, and essentially found that reconstituting these […] lactobacillus strain in their gut could correct these social deficits. So a lot of questions were open, remain open. And that’s how my work started. My projects are [aimed at] understanding whether this same treatment could also correct this social behavior using another mouse model, not just the one coming from the environmental factors, but also [a] mouse model related to genetic factors or a combination of genetic and environmental factors. And so we started considering another model and treating the mice with the same bacteria. And we found that the same single bacterial strain was able to correct social deficits in the other mouse model. And this was very nice because the regardless the cause of the ASD regarding this the first insult, these bacteria were still able to correct social deficits.
Do you think that these bacterial strains could be more generalized and not even just mice that had social deficits, perhaps even extending beyond the autism spectrum disorders [and] taking this to just in general enhancing sociability or does it change sociability?
Dr. Sgritta [21:07]
Well, we hope that. We also are trying to understand whether it is the bacteria strain is also correcting other behavior. And because as you know, autism spectrum disorder is heterogeneous and is a spectrum. So, there are a lot of other co-morbidities and phenotype like repetitive behavior language impairment. So it would be nice if it’s just one single treatment that could cure all the co-morbidities, but it is not very realistic. I guess I think the most amazing thing would be to understand, [what] is the function of different bacteria and maybe to combine different bacterial strains to have a collection of different phenotypes.
This is really interesting. You’re getting into the bacterial sphere, but your previous work in your PhD was more electrophysiology […] Did you need any convincing to kind of study bacteria or did Mauro say that you’re going to work on bacteria now or how did this come about?
Dr. Sgritta [22:00]
Not at all. Well, I started working basic science very basic like on cerebellar circuitry and synaptic plasticity in the cerebellum […] I have always been attracted by something that was more preclinical and I tried to be involved in projects that were more clinical during my PhD, but it was very difficult because I was in a very electrophysiology-based lab. So we were really just studying basic neural circuitry. And so, I decided I wanted to move and I wanted to try to do research in the US because there is a lot of money here, and so I think, that you have to do right when you do research to try to travel and to have an experience other countries. So I looked for a lab that I could have been interested in. I actually I heard about Mauro during a talk at FENS in Europe. And I got attracted by the research he was doing in his lab. So I asked him for an interview. And when I got in the lab, they just started this Gut-Brain Axis Project. And actually I didn’t need to be convinced because I’ve been always fascinated about this aspect of science.
Really cool. Yeah. I wanted to unpack a little bit more about your [comments] about needing to travel places. You were previously doing your PhD in Italy, and you decided to come to the US because you wanted to expand your opportunities. And here, I’m from the US doing my PhD here. I don’t really think about going to other countries, and I haven’t thought about it until right now. I was wondering, what made you decide to focus on this in the United States, or was it a lab specific thing? Just walk us through a little bit of your thoughts?
Dr. Sgritta [23:52]
Yeah, well, it was United States because, you know, Italy is an amazing country, but we don’t have a lot of funding for search. For scientific research and we always look at the US as you know the dream place where you can do all the research you want because there is so much funding there. You know everything is accessible, you get to learn a specific technique and your boss can send you in another you know lab and for like one week to learn a technique or you need specific antibodies just order it. In Italy, we were really desperate we were exchanging: I give you an antibody and you give me a solution. Yeah, it was crazy. And so you know, and I always want you to think that
Do you think that made you more careful with your reagents?
Dr. Sgritta [24:39]
Absolutely. When I started in the US, I was putting so much attention to the prices. Eventually, [my PI said] Martina, don’t worry about it. I mean, we can buy this antibody.
Yeah. But it’s still crazy, right? Because the amount of money that we spend in the US on research, people feel is too much. But other researchers, we show you We need more research-
Dr. Sgritta [25:01]
Exactly. And like such as anything in our life, we should just be more careful to not spend too much. And yeah, so I wanted to go to the US, for this reason, because of the more accessible life of scientists. Everything was more accessible. And in particular Mauro’s lab just because I was attracted by the the work that has been done in his lab.
Are there any challenges for applying to the United States as a foreigner and joining their lab? I know, I’ve talked to some other people who are graduate students, and they tell me that the process to getting into a graduate program in the United States is much more challenging. Is a similar process that you face going for a postdoc?
Dr. Sgritta [25:39]
Yeah, well, initially, the PhD process, I think it’s easier from one point of view and less from the other side. So let me explain this. So basically, we have usually a strict three year PhD program, so it’s shorter [than the US]. And this could be a good thing from one side. From the other side, doing a PhD in the US is much longer as you probably know, but at least you can have the opportunity to go out from the lab with much more experience. Stronger maybe to start, your postdoc can have more publications, especially because it’s not that easy to publish a paper in three years. If something goes wrong, you’re like, you know. And so this is one part. And the other part of it is that you basically have these admission problems [of getting into the US] that [take] much longer. So it’s probably get, you know, is expanding even more the time you have to spend trying to get into program while in Italy.
Yeah. And I want to jump back to your research a little bit more. We talked about looking at how this particular strain of bacteria (L. Reuteri) is able to modify social behavior in the autism spectrum disorder in the mouse and I was wondering, where do you see your next projects going? Are they even related, are you going on a different front?
Dr. Sgritta [27:01]
They are related just because I got so passionate about this that I don’t want to leave it. So this the thing. There are so many other things to understand about these and I feel like I’m not done with this. I want to understand how […] the mechanism underlying how these bacteria can correct social behaviors depend on the vagus nerve and [how] they [act] on the oxytocin and dopamine system. But we don’t know how exactly. We don’t know how the vagus nerve is activated by the bacteria. [We don’t know] what is activating the vehicles or something released by the bacteria or something released by the particular cells in the gut that are activated by the bacteria. And so, there is so much work to do.
So, looking [specifically], are you moving on to studying particular components of the bacteria? Are you looking at specific subsets of these oxytocin cells?
Dr. Sgritta [27:55]
Well, we need to dig deeper in any of these steps. So we want to understand what is released by the bacteria? So, what is the molecule responsible. Also what is the gene in the bacteria there is responsible to give this capability of L. Reuteri to correct social behavior and genetically modify other bacteria. So exactly there’s so many things that can be done. And then also at the [systems] level, the vagus nerve is activated. So is the activity changing upon the perfusion of the bacteria and how the stasis increased. So is the activation of these paraventricular nuclei of the hypothalamus, which is the oxytocin is produced that is, through the activation of the vagus nerve that is increasing oxytocin production. So there are you know, many things to understand in any of the steps bring into the change in behavior from the bacteria to the behaviors.
Certainly. And if you’re thinking this oxytocin production is involved in having more social behavior than in an ASD model, why not just give oxytocin? Why go through this pathway?
Dr. Sgritta [28:57]
Well, this is a good question because oxytocin has been shown to increase social skill to improve social behavior. And yet we’re still seeing the problem with oxytocin is that it’s temporary. So there are two hours of the effect. And there’s also the reason why we administrate intranasal access into the mice, 30 minutes before behavior. And the problem is that it’s so temporary the fact that the children with that use oxytocin to improve the quality of life, they have to spray oxytocin, you know, every day every couple of hours. It’s you know, it’s a pretty invasive treatment and not very long lasting. So L. Reuteri can increase endogenously oxytocin it will be a less invasive treatment that children can, you know, be treated all over life.
So ideally, you’re looking for a mechanism kind of to treat the brain without having to have such an invasive procedure and whether or not L. Reuteri is the answer to that we still have to do the research to figure out [the] specific pathways.
Dr. Sgritta [30:00]
Exactly, exactly. I think we have an amazing opportunity now that we have understand that specific microbes can modulate brain function, we have this amazing opportunity to [develop] a non-invasive treatment that can be combined, or by itself, to improve some of the behavior. Of course, we cannot, you know, we cannot say that we can improve all the symptoms, but at least some of them.
Yeah. So, as you start to kind of get to the end of your postdoc, I know, most people start thinking about how they’re going to start up their own lab afterwards. And how do you see yourself moving into this microbiome, social behavior field while differentiating yourself from the work that you’ve done previously?
Dr. Sgritta [30:45]
So well, actually, I’m very, very much in attracted by the translation of research to the clinic, so I don’t […] see myself in the academia system forever, but I still want to be in science, because I’m passionate about science. So I think I want to keep on being a scientist and work on these fields, but maybe not in the not in academia.
Yeah, that’s really nice to hear. Because I know as we go through the graduate school track, most people most of the advice that we get is to pursue the academia field. And there are other ways to be a scientist outside of academia. And I think it’s important to get that realization. I also noticed when I went to your LinkedIn and saw that you had gone to the Rice Jones Business School for learning about entrepreneurship. What do you think what is the value of kind of studying entrepreneurship is for a scientist?
Dr. Sgritta [31:40]
I think it’s amazing. And I suggest these courses to anybody who’s interested in expanding their knowledge. It is very important also, for a scientist who wants to stay in academia because we have to deal with industry and companies all the time also in academia for collaboration. Very important collaborations sometimes are born between these two different words. So yeah, it was super interesting and I think anybody working in academia should also expand their knowledge on the startup company system.
Are there any other fields that we think are helpful for scientists? Should we go into like studying law school?
Dr. Sgritta [32:22]
Well, if you’re interested in patents, you know, it could also be helpful because you have to, you know, carry out some patents sometimes where we are in academia. But I think the most important thing is to also be able to share scientific knowledge in the right way. So to be able to communicate with people that are not scientists. It is a very important thing because you know, anytime you publish a paper and then there is this mini coverage that keeps bringing your information to the public, […] many different voices from people […]
Yeah, certainly, I think communication is important in science. And we talk about, you know, we always have teams of varying degrees of expertise. We have some neurobiologists, and they work with microbiologists, and they are both studying the microbiome together. So I think it’s important to differentiate your expertise, have a group that has a bunch of different skill sets and bring them together. And I was wondering what advice you have for someone who’s more younger, in the research field, someone who’s kind of just getting into the field of a PhD? What advice would you have for them to kind of figure out what projects they want to pursue?
Dr. Sgritta [33:31]
Explore a lot. Be surrounded by people who are older than you, more experienced than you and ask a lot of questions. Just be driven by curiosity. And don’t be afraid to ask any of the more simple questions because you know, this is what actually then drives you. Especially if you a scientist, you have to keep your passion alive otherwise, it was a difficult war.
Yeah, but if you have a little bit of that social anxiety and you’re not sure, could I take L. Reuteri? Maybe to help with that or no? So I was wondering, in addition to where you see your lab moving forward […] what kind of aspects are important for the career development of younger postdocs or people who are moving into postdoctoral positions. You mentioned you were looking mainly at Mauro’s research in this opportunity to really go into a new field that was different than your own and PhD, but what else do you think is important for the career development of a young postdoc?
Dr. Sgritta [34:34]
I think one of the most important thing is to learn also how to deal with people and collaborate with people in the most productive way. Not just in the lab, but also outside the lab. And this allows you not only to learn new techniques, and to increase you know, to dig deeper in expand your knowledge and other field but you know, networking is very important. It is part of our job. And most of the times scientists are very much concentrated on themselves like so you know, these idea of the scientist closing the lab without a social life. But he’s you know, a very important aspect that will come back and help ourselves in many other ways in the future when you are a post-doc when you are a PI, so you know, networking is also very important.
And then I was wondering what questions do you think the field needs to answer with regards to kind of social behavior or even, our understanding of autism spectrum disorder is so kind of superficial, it’s on a very surface level, what questions do you think are the next big ones that we really need to hit on regarding social behavior or microbiome modification, since those are the two kind of fields that you’re working in right now?
Dr. Sgritta [35:53]
Okay, well, I think understanding the mechanism by which the bacteria modulate brain function will be very important so that we can understand whether there are other alternative therapies because we don’t know whether we can use these therapeutical approach for the future. So understanding mechanisms so if we know that the bacteria is acting on the vagus, there may be this nerve stimulation could be important for ASD. So understanding mechanisms that will bring us a lot of other inputs and would expand our knowledge to be able to understand whether other therapies can be used. And yeah, I think this is one of the most important thing to understand
You want to understand these specific mechanisms. And you think that with these mechanisms understood, we’ll be able to develop therapeutics that are specific enough?
Dr. Sgritta [36:44]
Maybe not for all of the symptoms, but for some of these symptoms, yes. And of course, we have to remember that this is basic science done in animals. So before being able to say that this can be translated to human we have to reproduce this data in and other, more translational animal models and do clinical trials. So you know, there is a long, long road.
Yeah. Cool. Well, I can’t wait to see what you’re gonna come up with next. Well, thank you so much for being on the podcast.
Dr. Sgritta [37:17]
Thank you so much for having me.
Dr. Ronda and Dr. Sgritta has shared with us two different ways of studying the microbiome and gave us a look into what they have done to position themselves to be successful. To study a system as complex as the microbiome, it is important to really break it down and not be afraid to ask what you feel are the fundamental questions.
I want to thank you all so much for listening, and we’ll see you next time. For more of our content, you can follow us on Twitter @gutbrains or visit our website at thinkgastronauts.com. The Gastronauts Podcast would be impossible without the incredible team that we have here. Meredith Schmehl is our producer and theme music composer. And special thanks to the founders of Gastronauts, Dr. Diego Bohórquez, and the Bohórquez laboratory.