...how your immune system knows good microbes from bad? (with Joël Babdor)

Ever Wonder? / March 30, 2022
USCF_Joël Babdor
Image attribution
Courtesy of Joël Babdor
Joel Babdor in lab
Image attribution
Courtesy of Joël Babdor

Our immune systems are always hard at work protecting us from viruses, bacteria, and other critters that can infect our bodies and make us sick.  

But on an earlier episode, we learned that the human body is teeming with microscopic creatures. These microbes—collectively known as the human microbiome—are always with us, coexisting with us and even benefiting our health. 

Ever wonder how your immune system knows good microbes from bad? 

To find out, we talked to Dr. Joël Babdor (@JoelBabdor), an immunologist at UCSF who studies how the immune system and microbiome interact with each other. Joël walks us through how our immune system works, and how studying the microbiome in health can help us understand and treat a wide variety of diseases. Joël is also the co-founder of Black In Immuno, an organization that aims to amplify, celebrate, and support Black people in immunology. 

Have a question you've been wondering about? Send an email or voice recording to the podcast team to tell us what you'd like to hear in future episodes. 

Subscribe to our show on Apple Podcasts, Spotify, or Google Podcasts. To see a full list of episodes, visit our show’s webpage


Perry Roth-Johnson (00:00):

Dr. Joël Babdor, you are an immuno. Uh, sorry. Let me try that again. Immunologist is a tongue twister!

Perry Roth-Johnson (00:05):

Hello! This is Ever Wonder? from the California Science Center. I'm Perry Roth-Johnson.

Perry Roth-Johnson (00:18):

Our immune systems are always hard at work protecting us from viruses, bacteria, and other critters that can infect our bodies and make us sick. But on an earlier episode, we also learned that the human body is teeming with microscopic creatures. These microbes—collectively known as the human microbiome—are always with us, coexisting with us and even benefitting our health. Ever wonder how your immune system knows good microbes from bad? To find out, we talked to Dr. Joël Babdor, an immunologist at UCSF who studies how the immune system and microbiome interact with each other. Joël walks us through how our immune system works, and how studying the microbiome in health can help us understand and treat a wide variety of diseases. Joël is also the co-founder of Black in Immuno, an organization that aims to amplify celebrate and support Black people in immunology. This was a fun interview! Take a listen. Dr. Joël Babdor, you are an immunologist at UCSF—Joël, welcome to the show!

Joël Babdor (01:28):

Thank you. I'm so glad to be here.

Perry Roth-Johnson (01:30):

Yeah. And Jenny Aguirre, producer and co-host of the show is also here with us. Hi Jenny!

Jennifer Aguirre (01:34):

Hey Perry. And hey Joël!

Perry Roth-Johnson (01:35):

So Joel, I know you study how our immune system interacts with our microbiome. And I gotta tell you, I'm so curious and grateful to talk to a scientist, an expert like you, because I feel like for the past couple of years, we've all been forced to get a crash course in how our immune system works. And I know I still find it a little mystifying and confusing. So why don't we start there? What exactly is our immune system?

Joël Babdor (01:59):

So our immune system is what protects our body. It's a set of barriers and also, uh, a lot of cells that actively patrol a body. And, um, they find and destroy pathogens, any kind of microbes that could be harmful, uh, and make us sick. So these cells are in our, our blood, in our organs everywhere in the body. And, and they're looking out for us, basically.

Jennifer Aguirre (02:29):

The other thing you study is the microbiome. We know it's made up of a bunch of microbes, but what exactly are microbes and our microbiome?

Joël Babdor (02:37):

Oh, that's a great question. So microbes are very small organisms. And so they are life forms and, you know, they're doing the same thing that, that we do, right? They, they eat, they reproduce, uh, and they die at some point. And, um, the microbiome is a set of bacterial communities that live inside our body. They're very different depending on the host. So in the human microbiome is, is a very specific set of bacterial communities. Um, but you have, you know, other, um, forms of bacterial communities, some in the soil, some in the air, some in our fridge, um, yeah, there, uh, there are different bacterial communities and, uh, human microbiome is the community of microbes that live in the body.

Jennifer Aguirre (03:27):

What does our microbiome do for us? Any examples?

Joël Babdor (03:31):

Yeah, it does a lot actually. Um, historically we used to think of as bacteria in the body being something bad but, um, at some point we've started to think of, uh, the bacteria in our body as something that, uh, is helping us and that we live together, uh, and that there is a reason for, uh, for why we are we're living together and because we're actually helping each other. A good example is when we toot, we're not able to digest and utilize some of the energy that is containing the food, because we're just not capable of digesting some of the nutrients that compose the food that we eat. So some of the bacteria in our gut can help with that. Let's say, you're eating an apple, for example, some of the sugar in the apple is not immediately digestible by your intestine. Uh, and some of these sugars are called pectin, those are sugars, but they're, uh, actually we call them dietary fibers and some bacteria in your gut can break these fibers down into sugars that you can digest and utilize. Um, and it's not only pectin, there are like thousands of example where our microbiome, um, the bacteria in our gut work with us to process the food that we eat so we can utilize the energy that is containing the food.

Perry Roth-Johnson (04:56):

Okay. Okay. But, but our immune system is supposed to keep the badies out, you know, the germs out. Right. So how, how does our immune system know the difference between good quote unquote and bad quote unquote microbes?

Joël Babdor (05:09):

Yeah, that's a great question. Uh, I think so far we don't have the full answer to that, but

Perry Roth-Johnson (05:15):


Joël Babdor (05:16):

we have a sense of what's going on. Um, so when, uh, you know, like, uh, microbe enters the body, uh, you have some immune cells that are gonna, uh, pick up this microbe, the cells that are responsible for this first encounter are called dendritic cells. And so dendritic cells are going to catch the microbe, ingest it, and then chop it up in small pieces and look at those small pieces and try to see if those small pieces are good or bad. So basically trying to find within, you know, the, um, the parts of the microbe, if there is anything that looks dangerous basically, if it's not the case, while the dendritic cells are gonna just signal to the, to the rest of the body that everything's okay, that's, you know, a false alarm, uh, this is a, this is an okay bacteria, right? Um, but in a case of a dangerous pathogen, uh, something that would be harmful, um, the dendritic cells are gonna be able to detect some molecules at the surface of this, um, pathogen that are bad news. Right. Um, and we call those, um, molecules, dangerous signals basically. Right. And so, yeah, if there is a dangerous signal, you know, then the dendritic cell is like, okay, well, this is dangerous. Something is going on. And the dendritic cell is gonna ring the alarm basically and alert the entire immune system, that there is an attack and that we need to find the pathogen and destroy them. And so that's how we start having immune responses against the, let's say, bad microbes.

Perry Roth-Johnson (07:06):

Okay. So at the risk of maybe putting too much human characteristics on the cells, inside our body, but just to anthropomorphize it for a second. So it sounds like these cells are kind of like the bouncers at a club and, but they're, it, it almost sounds more gruesome. It's like, somebody's trying to get into the club and like, I'm gonna chop you up into tiny pieces instead of just checking your ID. <laugh>

Joël Babdor (07:32):

Well, to some extent, yeah. I guess it's a good metaphor. I would say that. Yeah. Checking the ideas, like chopping into pieces version of, you know, dendritic cells bouncing, you know, bad microbes out of the club. Yes. Uh, it's a good metaphor. I like it.

Perry Roth-Johnson (07:48):

Okay. And then if they don't like the ID, then they call security and, you know, get you out of the line, but if it's okay, then they let you into the body and you can hang out with all the other cells.

Joël Babdor (07:57):

Yeah, yeah. To some extent that's, that's correct. I think it's, it's a good metaphor.

Perry Roth-Johnson (08:02):

Okay. Yeah. It might, it might be a little rough around the edges, which is something for our listeners to kind of hang their hat on.

Joël Babdor (08:07):

Yeah. Yeah. I don't like bouncers. Uh <laugh>.

Perry Roth-Johnson (08:11):

Oh, what, what would you prefer? <laugh>

Joël Babdor (08:13):

I guess, I guess, no. I mean, I guess, I guess as a teenager, I guess, you know, I was, I was, you know, trying to get into the club and, and oh, okay. I was maybe stressed out. So I feel like maybe I'm, you know, feeling what the bacteria, the bad, you know, uh, bacteria would feel, you know, like trying to get in the club and being stressed out because there are those dendritic cells at the door and God. Yeah, yeah. Get stressed for the bacteria for sure.

Jennifer Aguirre (08:42):

<laugh>, I'm, I'm a visual person. So I just played that all out in my head.

Joël Babdor (08:47):

Me too. <laugh>

Jennifer Aguirre (08:49):

Uh, how, how do good microbes affect our immune system?

Joël Babdor (08:53):

Well, the good microbes, um, they're with us, they've been with us for a long time. They've been with us for ages actually, uh, because we've co-evolved with, with these microbes that are part of our microbiome. And so they're not only helping us digesting food, but they're also helping us with other biological functions and, you know, sometimes doing multiple things at a time. Um, we can take the example of, um, apple pectin again, you know, when we're, uh, digesting, um, the well, part of the nutrients of the apple, um, the bacteria are helping it with digesting the pectin from the apple. Um, so it gives us extra sugar, but at the same time, the digestion of these dietary fibers, um, is, is also going into the process of producing some metabolites from the bacteria. And one example of the metabolites that are beneficial for the, uh, organism, uh, are butyrate. Butyrate is a short chain fatty acid that is produced by, uh, the fermentation of dietary fibers like pectin. And so butyrate is a molecule that, uh, help to regulate the immune system. And it's been shown that the production of butyrate by the microbiome or by some microbiome communities, um, prevents us prevent the immune system to overreact. And so it's protected against what we call autoimmunity or sometimes inflammatory diseases. Um, so basically thanks to this, um, microbiome communities, uh, we have metabolites that are helping to regulate our immune system.

Perry Roth-Johnson (10:55):

How much do we know or not know, you know, today about the connection between our microbes and our immune system?

Joël Babdor (11:02):

Yeah, that's a, that's a hard question. <laugh> uh, but it's, it's, it's an important question. And, and I would say that we probably, we're probably only scratching the surface for now. There is a lot of research out there, but I feel like we still don't fully comprehend. Um, the ways that the microbiome and the immune system are communicating and in particular, it goes in both directions. Right. And I think that that's maybe an area that is not, uh, extremely developed in terms of, uh, research. Right. Um, we don't fully understand how, you know, there is this mutual dialogue, right. We know that the immune system is doing a series of things on the microbiome. We know that the microbiome is doing a series of thing on the, uh, immune system, but, you know, it's more like a dialogue and then back and forth, right and we, we have a poor idea of, uh, this dialogue and how it's taking place and how it's like mutually, um, shaping both biological systems. So I think that's an area where there is a lot of work to, to be done, to understand more the dialogue, more than, you know, like knowing that, you know, we know that they can say some things. Um, now we need to understand the full conversation basically, right?

Perry Roth-Johnson (12:30):

Mm-hmm, it's like we need a Rosetta stone to translate what's happening.

Joël Babdor (12:33):


Perry Roth-Johnson (12:34):

You know, something is being said, but you don't know what.

Joël Babdor (12:38):

Yeah. We have a glimpse <laugh> we have some glimpse of what, what is being said, but yeah, we don't, we don't capture the, the full conversation, I think. And it's the reason is that it's extremely complex, right? They're like all these, uh, you know, we have hundreds of bacterial species. And actually, if you look closer within each species, you have different strains because one species has actually like different forms and carry different, um, version of the genome of these species. So it's like extremely complex to understand what they do. And then on the immune system side, the immune system is such an incredibly complex machine as well. So it's like trying to understand fully each of these biological compartments is already an important task. Um and once we'll be able to do that, I guess we'll, we'll have a good sense of the dialogue, but also investigating directly the interactions I think is, is a good way to, um, to get more insight of these four conversation that is happening.

Perry Roth-Johnson (13:49):

Wow, it's a whole another world.

Jennifer Aguirre (13:52):

It really is.

Joël Babdor (13:52):

Actually two other worlds that are colliding to some extent.

Perry Roth-Johnson (13:56):

Oh right, right, yeah, yeah two worlds. <laugh>.

Jennifer Aguirre (13:58):

Lets talk about your immuno microbiome study, where you're looking at how the microbiome affects our immune system.

Joël Babdor (14:05):

So immuno microbiome study is basically looking at the immune system, the microbiome and the metabolome in healthy humans.

Perry Roth-Johnson (14:16):

And just for our listeners, uh, you mentioned another fancy word metabolome what exactly is that how's that different from the microbiome?

Joël Babdor (14:24):

Yes, the metabolome is, I would say the collection of metabolites that are circulating in the body, uh, and metabolites are this small molecules that are produced, um, by the host, by the cells in our body, but also by the micro, the microbiome, um, the bac, the bacterial communities in the microbiome.

Jennifer Aguirre (14:47):

What questions are you trying to answer with your research?

Joël Babdor (14:50):

For immuno microbiome study in particular? I think what we are trying to assess is this dialogue between the microbiome and immune system, right. Um, I think it's a fascinating question and, you know, it can, it can take a lot of different forms. Um, I think, you know, what people, people have been doing a lot is trying to understand this dialogue in pathological contexts. When, you know, there are patients that are suffering from particular disease. Uh, people have been looking into their microbiome, people have been looking into their immune system. So there are a lot of studies that are starting to put together in clinical context that well, that's interesting, you know, in some cases, um, a subgroup of patient have a different microbiome than another group of patient, and they're doing better or they're responding better to treatment or something like that. It's the case for cancer immunotherapy.

Joël Babdor (15:49):

Um, so this new line of treatment that actually try to activate the immune system to fight cancer. And so what scientists have realized in the last maybe 15 years is that people can respond or not to immunotherapy. And we don't fully understand why, but the people that respond to this treatment and, you know, end up having a better outcome, they have a different microbiome than the people that do not respond to the treatment. So, you know, this sort of insight are like, yeah, the microbiome is like doing something very important for patient to, um, to survive or to respond to a treatment. Now, my question is like, well, that's great. Um, but we don't understand what's going on. So there is more research to be done, but in the first place we don't fully capture the interactions of the microbiome and the immune system in health. You know, when there is no pathological context. And so, uh, the reason I, I created immuno microbiome study is exactly that I, I was working on a pathological or a clinical projects, uh, one with cancer immunotherapy and another one, you know, to autoimmunity and another one in, uh, kidney transplantation. And so in all these studies and like asking the question, how does the microbiome influence the way that people are responding to, uh, treatments that motivate their immune system? Um, but I realize that I need to understand better how the this is taking place in health when there is no pathological context. And so that's basically, um, the reason why, uh, I created immuno microbiome studies. Like we want to try to understand better the dialogue that is taking place in health, so we can understand better how we can utilize this knowledge in the clinical context, where we see that the microbiome can benefit patients.

Perry Roth-Johnson (17:57):

I wanna pivot a little bit to things sort of outside the lab. Um, I know you've, co-founded two organizations, uh, Black in Immuno and Immuno Diverse. So I, I, I've seen a lot of these organizations, you know, black and X popping up the past couple years is Black in Immuno a similar idea. Maybe we just start with that one.

Joël Babdor (18:18):

Yeah, absolutely. Black in Immuno is, is part of this black in X movement or black in STEM movement that, you know, started in 2020. And so, yeah, so the goal of Black in Immuno is to amplify black immunologists that are making extremely important contributions in the field of science and particular immunology.

Perry Roth-Johnson (18:45):

Can you tell us a little bit about, um, how it got started?

Joël Babdor (18:50):

So I was, I was on Twitter, actually. I, when 2020 started, I think early January 2020, I started my Twitter account. I discovered something that was missing a lot in the way that I navigated academy. I was able to see a lot of other black scientists and to hear about the awesome research that they do and seeing a lot of other black scientists thriving and, you know, um, taking space in, in academia. And, uh, and I, I think that this is something that has been missing a lot for me. And I actually probably for a lot of black scientist, we are, um, oftentimes the only one or two, you know, in the department or sometimes in the whole building or, um, so it's hard to have, you know, like role models that look like us and, you know, to think of people being successful. And, um, and so it's, you know, it's, it's something to consider when you're thinking that a lot of the motivation, um, to keep going is to have role models and, and seeing people that look like you in the field. Right. So I was on Twitter and I, I was amazed by seeing all these black scientists and I was really happy about it. And I started what I, uh, called initially just a, a list of black he immunologists and turned out that other people were also trying to, you know, uh, do the same, or were actually excited of seeing a list of black immunologists. Um, and so I remember seeing some messages from other black immunologist that were, you know, really happy that they were doing this list and encouraging other people to, um, add new people in the list and to basically amplifying the list, because I think that, you know, other people like me were trying to find this, you know, sense of community and, and, um, having, you know, role models at the same time, there's been the murders of George Floyd and, and all the black people, uh, and the fact that there was a lot going on in the country at the time. I think it, it helped, um, to ask hard questions about the academic fields and the way that black people are navigating this field as well. Uh, and not only black people, but, um, I would say that minorities in general, um, and all the black in STEM movement is part of that. I think the first one were black that started Black Birder's week. And then I don't remember exactly what order, but we've seen Black in Cardio, Black in Neuro and black, in other STEM, uh, weeks starting. And so the people that I interacted with that were, you know, excited about the black knowledge list, um, we're actually starting to, you know, get excited about maybe starting Black in Immuno a week as well. I basically created a slack channel and we defined the time to see each other on zoom. And we just started to interact like that probably be on Saturday morning because, uh, mm-hmm, I guess that's what we're doing now. And actually we've been doing that for well, since we started in September 2020, I guess we are still seeing each other every Saturday and we are working on, you know, amplifying black immunologists. And so, yeah, and together we've created two Black in Immuno weeks, um, in 2020 and in 2021, and it's been fantastic to basically be able to invite black immunologists to present their work or talk about the, the work that they're doing in, in the, in STEM in general. And, you know, some of it can be diversity, equity and inclusion work, and some of it is scientific work. And so basically black in the week is, is this is like a full week of having black  immunologists sharing about their science and their activism, uh, in the space of academia.

Perry Roth-Johnson (23:05):

I love that. I love that you just created your own space, um, you know, for you guys to support each other and, and, and see each other, cause it is a little weird sometimes when like, you know, people are out there doing good work, you just don't, you don't see them. And, and it's one of the aspects of like, I don't know, hacking social media, you know, like you could just use the internet to go find people and then create the space if it doesn't exist physically, like where you already are. So kudos to you for, for spearheading that.

Joël Babdor (23:34):

Thanks. Yeah. And exact what you say is, is exactly right. You know, like conceptually we know that there are black researchers in the field of immunology, but visibility is so important. So we can actually grasp that these people are doing this awesome work and contributing in, in awesome ways. Um, and that, that's what, you know, Black in Immuno is about, is giving visibility to people that are out there and that are the doing great work. And not only for us, I think, you know, that that's one component, right. Um, being able to, to, to know more black immunologists and, you know, building this network of black immunologists across the world. But also I think another important benefit of that is that a lot of allies, um, are now more connected to this network of black immunologist and, and a lot of people are, uh, supportive of black immunologist that they didn't know before. And now they know.

Jennifer Aguirre (24:42):

I, I think that's great, but it's also so impactful for, for the youth community too, you know, myself as a minority, like being able to see someone like myself, do something huge, it's super impactful.

Joël Babdor (24:54):

Yeah. We hope that we can help, um, you know, the next generation of black students and learners to feel that science is something that they can do, that they can be excited about. That stem is something that is accessible. Um, and we want to encourage them and to support them. Um, we, we want them to reach out to us and to ask us questions about how to navigate and, um, yeah, and that's, that's, that's a huge part of our mission too.

Perry Roth-Johnson (25:25):

We've run a little bit long. So, uh, I, I wanna wrap up here. Thank you for encouraging, you know, our listeners to tweet at people, uh, as scientists they admire, you know, I think finding people on social media is, is a, is great advice, you know, to start building that network and on that note, where can people follow you online and find your work?

Joël Babdor (25:42):

Yeah, absolutely. People can find me on Twitter. Um, my handle is @JoelBabdor. So J O E L B A B D O R. And then there is the Black in Immuno website, um, where there is all the programming for Black in Immuno. You can also find the recordings on YouTube of Black in Immuno week 2020 and Black in Immuno week 2021. Everything is there on the website. Um, so there are a lot of really cool talks, scientific talks and di conversations, panel discussions that can be found on the website. So yeah, feel free to, to visit blackinimmuno.org.

Perry Roth-Johnson (26:20):

It's been wonderful talking to you, Joel, thank you for demystifying. Uh, the immune system a little bit for us. Thanks for joining us on the show.

Joël Babdor (26:28):

Thank you. It was so fun to be here. Thank you so much.

Perry Roth-Johnson (26:31):

That's our show, and thanks for listening. Until next time, keep wondering. Ever Wonder? from the California Science Center is produced by me, Perry Roth-Johnson, along with Devin Stewart and Jennifer Aguirre. Liz Roth-Johnson is our editor. Theme music provided by Michael Nickolas and Pond5. We'll drop new episodes every other Wednesday. If you're a fan of the show, be sure to subscribe and leave us a rating or review on Apple Podcasts. It really helps other people discover our show. Have a question you've been wondering about? Send an email or voice recording to [email protected] to tell us what you'd like to hear in future episodes.