
The microbiome is back! In 2018, we chatted with Dr. Elaine Hsiao - a UCLA microbiome researcher– and learned all about the hot cauldron of your guts. In this 2025 update bonus, we chat again with Dr. Hsiao to get updates on the last 7 years of her research. We also stop by White Plains, New York to hang out with Dr. Miguel Freitas, lead nutritional microbiologist and director of the non-profit Danone Institute North America, and ask a million questions about good vs bad microbiota, how they simulate a human gut in a lab, what exactly is a pre-biotic vs. probiotic, why are they such good friends, how diet can impact not only your gut health but also your heart and your brain — and if friendly yogurt critters are robust enough to make the journey from your mouth to your toilet. Browse Dr. Freitas’s publications on ResearchGate Visit the Hsiao Lab at UCLA and follow Dr. Hsiao on Google Scholar Donations went to GiveDirectly.org/ologies and the Los Angeles Regional Food Bank Mor...
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Alie Ward
Oh, hey, it's the lady on the bus wearing mismatched socks. Alie Ward this is a special bonus episode of Ologies wherein we travel deep, deep into the busy world of your guts. So in 2018, you may remember, we had a legendary conversation with Dr. Elaine Chao, a microbiome researcher at UCLA, and learned all about the hot cauldron of your guts and who lives there and what they're doing for you around the clock. And in this 2025 update bonus, we chat again with Dr. Hsiao to get some updates on the last seven years of her research. It's a lot, a lot of good stuff. I was also curious about cultured foods and I was invited by Danone to see their brand new research facility in France. But it was two days before your podmother Jarrett's 40th birthday and alas, I could not teleport. But I did the next best thing. And while I was on the east coast this month, I got to hang out with a lead nutritional microbiologist and a director of the nonprofit Danone Institute North America and ask a million questions about good versus bad bad microbiota how they simulate a human gut in a lab. What exactly is a prebiotic versus a probiotic? And why are they such good friends? How diet can impact not only your gut health, but also your heart and your brain. And if friendly yogurt critters are robust enough to make the journey from your mouth to your toilet. So thank you, Danone and Activia, for having me and for acting as a sponsor of this episode, which this week let us donate to the LA Regional Food bank as well as to GiveDirectly.org as a part of this month's Pods Fight Poverty initiative. So thank you sponsors, and do check those links out in the show notes. Let's Real Talk right now. Your diet isn't doing so great this time of year, right? Enter Ritual, the obsessively researched multivitamin. There's a lot of multivitamins out there. There's also a lot of flimflam. And Ritual's essential multis have no shady additives or ingredients that can do more harm to your body than good. They're in a clean, absorbable form and they have the nutrients that most of us don't get enough of from food. I love ritual. I take it every day. It's great because you can take it on an empty stomach if you need to. You can also take it before bed if you want. I've had them for years I also love that they look like a tiny lava lamp, they taste like mint, they go down easy, and right now your body's like, please, pigs in a blanket are not doing it. So instead of striving for perfect health, aim for supporting foundational health. My listeners get 25% off your first month@ritual.com ologies that's ritual.com ologies for 25% off your first month. These statements have not been evaluated by the Food and Drug Administration. This product is not intended to diagnose, treat, cure, or prevent any disease. We have to say that having the.
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Alie Ward
Okay, back to it. Hang out. Bring your ears and your mouth and your intestines to chat with not one, but two gut microbiome microbiologists for this bonus episode with a neuro microbiologist and a nutritional microbiologist, Dr. Elaine Xiao and Dr. Miguel Freitas. And I'm going to have you hold this and you just kind of hold it like if you were doing karaoke. It's like this.
Dr. Miguel Freitas
Like, I don't do very often, but I like it.
Alie Ward
Megalphritis in terms of an ology, let's just say. Would you consider yourself a gut micro, a gut microbe microbiologist, or what would you say that your urology might be?
Dr. Miguel Freitas
I would say that I am cell biologist or cell microbiologist.
Alie Ward
And were you always interested in the little things? Did you have a microscope? When did you start going from big to tiny?
Dr. Miguel Freitas
I did have a microscope.
Alie Ward
You did? How old were you?
Dr. Miguel Freitas
I was young, probably seven, eight. Yeah, I did have a microscope. I grew up in a family of medical professionals. My dad was a radiologist. My mom was a nurse. They both met at the hospital. So I pretty much grew up in a hospital setting. That's where I would go after school. I got the passion of little things in microbiology. I can still see the microscope. It was white. It was quite cool, actually. It was one of those that you can change the lenses. Funny that you mentioned that because I did have One. And I know what it is in my dad's house. And it was a big, important first step for me to get into science for sure.
Alie Ward
I think it's so interesting how much mystery and what's working right in front of our eyes that's keeping us alive. And when we talk about microbes a lot, I feel like a lot of people think viruses or bacteria or bad germs. If it's small and you can't see it, it's probably bad. But as you know, we couldn't live without all the critters inside of us.
Dr. Miguel Freitas
True. Yeah.
Alie Ward
And According to a 2016 study, revised estimates for the number of human and bacteria cells in the body, microbial cells in the body, once they were thought to be 10 times more prevalent than our own human cells. It's actually closer to a one to one ratio. And this study states that thoroughly revised estimates show that the typical adult human body consists of about 30 trillion human cells and about 38 trillion bacteria. So it's actually of the same order as the number of human cells. And their total mass in your gut is about 0.2 kg. So about half a pound of you is other tiny little people, but they outnumber you by 8 trillion. However shocking, maybe no one. Much of the initial research focused on some standard person known as quote reference man, who was a male between the ages of 20 and 30. Did you know that people assigned female at birth have a microbiome also? They do, it's true. They're humans. They also have more in their nethers. And in the 2019 study Sex Differences in gut Microbiota. Oddly, this was in the Journal of Men's Health. And it clarifies that some of the more research notes that there are over 1000 different bacterial species in the human colon, and each individual harbors at least 160 different species. And the ratio of the numbers of bacterial cells to human cells was different between males and females, with the vagina people having about double the microbiome. What? So we're never alone.
Dr. Miguel Freitas
We have trillions of bacteria in our gut, so imagine how small they must be in a little cup of yogurt. We can put billions of bacteria. So it's amazing.
Alie Ward
And we couldn't digest food without all of this help, without all of our roommates.
Dr. Miguel Freitas
We're roomies.
Alie Ward
We're roomies. And I feel like we're hearing more and more about it every year where I don't think when I was growing up, we heard about the microbiome very.
Dr. Miguel Freitas
Much, you know, same for me, I wasn't hearing a lot about the microbiome when I was growing up, and even in school and college, it was quite a new thing to learn. We didn't have the sequencing techniques that we have today that show up 10, 15 years ago to understand what types of bacteria we have inside of us, how many bacteria have inside of us. Now we're starting to understand a little bit better all the functions that the microbiome have. You are far from understanding the whole thing.
Alie Ward
What do those microbes do? From your head to the other end of your body, what kinds of things does a healthy or unhealthy microbiome contribute to?
Dr. Miguel Freitas
That's an interesting question, because the conversation on what a healthy microbiome is or not, it's also still not very well defined. There's a lot of associations between individuals that are, for example, obese in comparison to individuals that are lean. They have a completely different microbiome.
Alie Ward
Wow.
Dr. Miguel Freitas
People that have type 2 diabetes, they have a completely different type of microbiome. People that have anxiety, depression, kids with autism also have different microbiomes. But we're struggling to understand what causes what. We do know that the microbiome is involved by association with many functions around our body, from brain to skin to cardiovascular disease.
Alie Ward
Do you want me to read off some studies as quickly as I can? I do. Okay. There's the Journal of NBC Microbiology 2022 paper. Yogurt consumption is associated with changes in the composition of the human gut microbiome and metabolome, which found that yogurt consumption is associated with reduced visceral fat mass and changes in the gut microbiome. And the 2024 study, Prebiotic Fiber mixtures counteract the manifestation of gut microbial dysbiosis induced by the chemotherapeutic 5 fluorosil in a validated vitro model of the colon, which showed that prebiotic fiber helped the good microbes flourish and then the bad ones decrease, which is important. As a 2017 study in the journal Advances in Nutrition, Yogurt and Cardio Metabolic Diseases, a critical review of potential mechanisms found that disruption to gut microbial balance, also known as dysbiosis, can promote inflammation, unhealthy body composition and type 2 diabetes, plus increased fat storage. In case that's not what you want, I also stumbled upon an eyebrow raising kind of a head scratcher of a 2025 study in the very lauded Frontiers in Nutrition Journal. It was titled Dietary and Environmental Modulation for the Gut Environment. Yogurt promotes microbial diversity while chloride Hot springs improve defecation status in healthy adults. What? Apparently someone really wanted to learn if yogurt and hot springs, when used in well monitored conjunction, could show quote, numerical improvement in defecation scores, which it did. There are literally thousands of yogurt and nutrition studies, but this one is just, it's close to my heart, it's close to my intestines. What a banger. If one day you would love to get to better know your microbiome, but you're not really keen on pooping in a tray and handing it over to a lab tech, I understand. You may want to read this 2025 pilot study titled Yogurt Reintroduction and the Circulating Microbiome in Healthy Volunteers Protocol for a prospective longitudinal species controlled crossover clinical trial, which looked at whether scientists can figure out what's up with your microbiome just by looking at your blood samples. For me, I would opt for the needle over the tray personally.
Dr. Miguel Freitas
So there's so many studies showing those associations. Now we need to understand how can we inverse, how can we change, either through food or through medication, how can we change the microbiome to see if we can also change the health status of somebody? Fibers actually increase the diversity of the microbiome. Certain fermented products increase the diversity of microbiome. We also know that individuals that have typically a higher diversity of microbiome tend to be associated with at least less disease status. So the functions are so many.
Alie Ward
And you may remember very well our 2018 microbiology episode with the wonderful and amazing Dr. Elaine Chao, a researcher and an associate professor at UCLA's Department of Integrative Biology and Physiology. And her work examines, I love this, the interactions between the microbiome and the brain and behavior, as well as the immune system, and even the link between the microbiome and epilepsy. I just adore her. I'm fascinated by her work. She's so great. So I caught up with her this past week to just lavish her with praise and ask, what's new? The number of papers that have come out since I talked to you last is staggering. Your lab is doing so much work. Everything from its serotonin in the gut to extra intestinal symptoms and irritable bowel syndrome associated with stress reactivity and the gut marker. I was like, this is everything. And I wanted to ask a little bit about where your lab's research has gone since we talked last and what have been like, some really interesting studies that you've gotten to work on that you feel like have just changed the game.
Dr. Elaine Hsiao
Yeah, things. I can't believe how much time has flown. Things have really, really changed a lot since then. Some of the main things is that now, at that time, people were just establishing microbiome links to brain and behavior. And now it's not a question of whether it happens, it's more question of how. And so all these, I guess, past seven years have been really focused on figuring out mechanisms for signaling between the gut and the brain and the microbes that are there. We've been really focused on what molecules do microbes make and which ones can actually signal directly to vagal neurons that touch the gut and extend directly in the brain stem.
Alie Ward
And how about Miguel's lab work? When it comes to your research, what does that look like for you? What types of things are you looking at or sampling, or what kind of data do you have to get, or what kinds of scientific research do you have to sift through?
Dr. Miguel Freitas
So interesting you asked that, because a few weeks ago, we just opened a new laboratory at our research center outside of Paris called the One Biome, and it's a laboratory that is focused on understanding the population's microbiome. So when we talk about diversity of the microbiome, we're thinking about all the different genus that exist in our microbiome. And there's many genus, and then there's hundreds of species and thousands of subspecies, and then, as I said, trillions of strains.
Alie Ward
Okay.
Dr. Miguel Freitas
And based on analysis of what's in that microbiome and based on other general science, we know that this person, for example, is lacking Bifidobacterium, which apparently is one of the key species genus to have in the gut. So how can we develop a product, for example, that would promote the growth of certain Bifidobacterium?
Alie Ward
And I know Lactobacillus, Lactobacilicus, Lactobacillus. Yes, I see the word lacto, and I think milk. So is there a reason why it got that name or why it's associated with milk? Probiotics.
Dr. Miguel Freitas
It produces lactic acid, typically.
Alie Ward
Oh, there you go.
Dr. Miguel Freitas
So you can have Lactobacillus bulgaricus, you can have Lactobacillus kci. You can have Lactobacillus, Lactococcus. You can have many types of Lactobacillus, but typically they all produce a certain amount of lactic acid. And that's really important to transform, in this case a matrix that contains lactose, which is milk, into lactic acid and then gives the texture, the taste of fermented dairy products that you're familiar with. That doesn't mean that these bacteria actually are probiotics. We didn't talk about probiotics, but there's quite a big difference between a lactic acid bacteria and a probiotic bacteria.
Alie Ward
Oh, what's the difference?
Dr. Miguel Freitas
There's a lot of experts that looked into this. So it's a term that is used only for bacteria that have been studied, typically in clinical trials to provide a health benefit. So not all Lactococcus or Lactobacillus provide a health benefit. Some of these cultures are used to transform to ferment bread, to ferment the milk, to make kombucha, for example. But that doesn't mean that they provide a health benefit. For example, in terms of supporting gut health, it needs to be studied. It needs to go into an rct, a randomized controlled clinical trial with a placebo to show that it's actually doing something in your body. This is actually helping support your gut health by, for example, reducing the frequency of digestive issues, or this is actually helping support your immune system.
Alie Ward
So to call something probiotic, it has to have quantifiable, proven benefits. And yes, you've probably seen strains of Lactobacillus or Bifidobacteria, and those are the.
Dr. Elaine Hsiao
Ones that you read off of over the counter probiotics or yogurts. And so time is told that they're safe in those strains and that they're culturable and easy to be studied. But I think a lot of the field is also really excited about next generation probiotics that are just really identified from our guts and newly characterized bugs. But yeah, Lactobacillus and Bifidobacterium specifically is really prominent in like infant gut microbiome and is thought to have really beneficial effects for infants.
Alie Ward
And again, Dr. Xiao and I had this really wonderful conversation years back about the research just emerging then, which was why it was just such a treat to catch up with her and talk about the world of laboratory stool samples. And while the conversations make me happy with her, it might also be the subject matter itself that is giving my brain just a little boost. I've read that like 90% of our serotonin is produced in the gut, some huge proportion. And do you people who study this think that there is a correlation between kind of modern mental health and what our diet has become? How much of an effect on mental health are we able to discern from that?
Dr. Miguel Freitas
That's one of my passions. If I had to go back and do A postdoc or two postdocs would be on gut brain. The gut brain axis is very new also. And it's part of all those associations that we've been finding that there's a connection between our gut and our brain. And you're right, a lot of the serotonin is produced in our gut. And maybe something that you also don't know is that after our brain, the gut contains the second most complex nervous system in our body.
Alie Ward
So when people say trust your gut, they're like, they're not getting around.
Dr. Miguel Freitas
That's just one example. Trust your gut. But I have another one. Butterflies in your stomach.
Alie Ward
Where does that come from?
Dr. Miguel Freitas
I'm sure you felt like, oh, yes, oh my God, I'm feeling butterflies in my stomach. Right. Which means what butterflies do in your stomach, they would put their wings like this and it tingles and you know, you're feeling some sensation there. And when does that happen? Usually that happens when either you're a little bit anxious or a little bit nervous for the right or the wrong reasons. I don't know, you're in love and you're about to go on a date and oh my God, I'm so stressed I'm feeling these butterflies in my stomach. That's your brain talking to your gut. This is the connection between the brain and the gut. But it also goes the other way when you don't feel good here. If you have ibs, if you have constipation, or if you have distress in your stomach, typically you're going to feel it in your mind. You're going to be upset, you're going to be anxious, and that's your gut talking to your brain. So it goes both ways.
Alie Ward
Absolutely.
Dr. Miguel Freitas
That's why our gut is called the second brain.
Alie Ward
Let's delve into that VAA 2023 study in the Journal of Biomedical Science titled Butterflies in the Gut. The Interplay between Intestinal Microbiota and stress, which notes this evidence that the gut and its inhabiting microbiomes may regulate stress and stress associated behavioral abnormalities. And that the microbiota can regulate a stress response via intestinal glucocorticoids. Don't worry about those. Or the autonomic nervous system. So in terms of the sympathetic nervous system, that's the one that kicks in with when you get a flood of adrenaline or excitement or dread, you can thank a reduction of blood flow to the stomach for that. That makes those butterflies. However, this study continues that gut microbiota can actively modify your stress response via changing steroid synthesis and metabolism. So that can affect your stress signaling and your brain circuits and it can ultimately impact complex behavior. So if you're an anxious mess or maybe you're jittery with hope, hopefully you can blame those trillions of living things colonizing your innards. Putting the butt in butterflies. Also. Who coined that? Who said that? Was it a peptic lepidopterologist? No, it was a lady named Florence. Florence Converse, a poet, a scholar, a writer to the Atlantic Monthly, a college professor and historic for her time in the early 1900s, a well known lesbian with a long term partner. And Florence Converse wrote this 1908 children's book she wrote. Timothy felt very dull. The three o' clock train going down the valley and the five o' clock train going up gave him a sad feeling as if he had a butterfly in his stomach. So thank Florence Converse of Massachusetts for that. Also, who has the last name Converse? As it turns out, a guy named Marquise Mills Converse, also of Massachusetts and the founder of a rubber shoe company. Converse. Her last name was Converse. I would like you to know I was sucked into like a research vortex that was stronger than my free will. I spent a Friday night going down genealogy trees up and down the limbs to find out that yes, Marquis Mills Converse is the half second cousin twice removed to Florence. And they are buried a scant 30 miles from each other outside Boston. Florence is buried side by side to her long term spouse who was also a literature professor, Vita Julia Dutton Scudder. Anyway, this is a long aside, but I got excited in history. It's enough to give you the butterflies good and bad. And again, back to Elaine. Her research focuses on that gut brain connection from nerve signals to neurochemicals. Also we have a whole episode molecular neurobiology with Dr. Crystal Dilworth, aka Dr. Brain on CBS's Mission Unstoppable about what your neurochemicals are up to in your skull and yes, other locations.
Dr. Elaine Hsiao
A lot of serotonin is like about 90% of the body's serotonin is made in the gut. And then in these past seven years, we've also found that what happens after the gut microbiome stimulates that serotonin is that that serotonin can then signal local neurons that are really important for things like visceral pain and anxiety. And yeah, that's a really nice kind of gut to brain connection through peripheral neurons.
Alie Ward
I always feel like anxiety and IBS and the gut microbiome that, that I hear those discussed kind of in tandem. Do doctors know if that's just kind of the fight or flight response. Or do those kinds of stresses keep giving, like kind of a gut punch to us?
Dr. Elaine Hsiao
Yeah, absolutely. I think there's a really high comorbidity between IBS and anxiety and stress and anxiety. And IBS is also now categorized as a disorder of gut brain interaction.
Alie Ward
Really?
Dr. Elaine Hsiao
And so it's really. Yeah, so it's really clear that there's a gut brain link in IBS and other GI disorders too. Yeah. And I think it goes both directions, where you can have stressors and the anxiety itself that goes, you know, from brain to gut to change the microbiome, but it can also go from the gut brain direction. And so that makes it really complicated but also interesting to tease apart.
Alie Ward
For more on this, you can see, for example, a recent 2025 paper out of her lab titled extra intestinal symptoms and irritable bowel syndrome are associated with stress reactivity in the gut microbiome in a sex depend manner, which found that with ibs, half of the people with it have extra intestinal symptoms. So pain or inflammation elsewhere in the body. And that many IBS patients also have somatic conditions. But that fibromyalgia and chronic fatigue syndrome, chronic pelvic pain and joint disorder, they are more common in females. Fibromyalgia pain may have a gut solution, though. And the journal Neuron noted that transferring fecal microbiota from fibromyalgia patients to rodent models confers pain, hypersensitivity and depression like behavior, which is then reversed by a fecal microbiota transplant to rodents from healthy donors. And that fibromyalgia patients experience significant symptom relief after fecal microbiota transplantation. So what about though, for everyday gut issues that no one wants to talk about? So I talked about it with a guy I had met 20 minutes prior. And I know that everyone's like, looking to have an easier time in the bathroom and also feel healthier. And I've always wondered, when it comes to probiotics, which ones can survive our digestive systems? Like, how do we make sure it goes from our mouth to our gut? How is it determined which ones survive and thrive and which ones are doa?
Dr. Miguel Freitas
So first important thing to know is not all probiotics are the same.
Alie Ward
Okay?
Dr. Miguel Freitas
There's thousands of potential probiotic strains out there. Even Danone has a collection with thousands of bacteria. Some of them that have been studied, some have not been studied. They can all have a potential to have a benefit in your body, but you're Right. In order for them to have a potential benefit in your body, and especially if the benefit is in the gut, they need to survive. Right. So there are several tests and experiments that these tiny little bacteria can go through before they even consider the probiotic for a clinical study. And survivability is very important. We can test it in a model, for example, that mimics our digestive tract with the acidity of the stomach, with the esophagus, with the mouth, with the chewing, all of it. We can mimic all of that in a model and see if that particular strain survives the gut. And then that's when you start considering if it's a potential probiotic or not. And then you do other experiments, you put it in a clinical trial, and then it gets into a product ultimately. But it's a long process. But survivability is important. And I think people don't know that our stomach has a very low ph, it's around 1 to 3 ph. So to give you just an idea, if you could put your finger inside your stomach, you would burn your finger.
Alie Ward
Yikes.
Dr. Miguel Freitas
I always tell this. So this is why it's so important, the survivability aspect. And that's why certain probiotics don't make it. They don't make it either because their cell wall is not prepared for that acidity, because they were just meant to ferment milk and that's it. And then we have a delicious product or because they're not in the right matrix. And dairy is a perfect matrix because the moment you consume a glass of milk or a yogurt gets into your stomach and the PH rises immediately.
Alie Ward
Ah.
Dr. Miguel Freitas
And that makes the probiotics that are in the matrix like dairy survive better that 30 minutes hour passage through the stomach.
Alie Ward
And is fermented dairy like yogurt, is that easier to digest in terms of lactose too, is there less lactose than just whole milk because it's been fermented? I've always wondered about that.
Dr. Miguel Freitas
Correct. Yeah. So that's why the lactic acid bacteria, they transform the lactose into lactic acid. And people that are sensitive to lactose, they typically can consume yogurts, but not necessarily milk.
Alie Ward
So, yes, as we mentioned in the Formology episode with cheese expert Kyra James, some cultured dairy has low lactose because the milk sugar has been gobbled up by what we consider the good bacteria. If you're sensitive and you get bubble tummy from milk products, the harder cheeses and the full fat or strained yogurt may be just fine for you. Although there are other proteins in dairy that can be a problem for folks. So if that's you or if you're entirely plant based, there are non dairy options as well with probiotic strains. I don't really care what you eat. Whatever fermented and cultured foods you like or don't like, you go for it. I'm just here to learn about gut stuff, which we will continue to do in a moment. But first a quick sponsor break which is making it possible to donate to a cause of this time my choosing. And this week we're donating again to the LA Regional Food bank because one in four people in Los Angeles county experiences food insecurity. The LA Food bank feeds hundreds of thousands of individuals every month and hunger affects people from all walks of life, especially now with the rising cost of food and everyday essentials. Just 25 bucks provides the equivalent of 100 meals for kids, seniors and folks who need something to eat. But again, because of the sponsoring this episode, we were also able to donate to a second cause via GiveDirectly.org Ologies, which is a special portal as part of December's Pods Fight Poverty initiative. And your favorite podcasters including Ologies, are stoked to team up to lift over 700 Rwandan families out of poverty. Right now they have a matching fund so your donation will be two times matched, meaning every $100 you can turn into $200 for families in need. Truly any amount helps and it's matched. So go for it. Or maybe request a donation to that charity or your favorite one if you're not feeling consumerism this year. 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And having someone who understands performance anxiety but still encourages me to keep going and tackle things has been really helpful. So if you're waiting for the right moment to level up, this is it. Go to Strawberry Me ologies and get 50% off your first coaching session. So that's Strawberry Me Ologies. Have you ever gotten someone a gift and then you're like, I want that for me. I get it. This happens when you get quints, and that's because Quince has pretty much your whole list covered. They have Mongolian cashmere sweaters for $50 when you. And you'd normally pay like 200 bucks for them. Italian wool coats. The look is designer. They feel amazing. They're made with premium materials. Also, just like everything at Quint, you go, what a good deal. What great quality. Wow, we're really doing it. I Love Quint's I have at least five Mongolian cashmere sweaters from them. Several of my pants are quint. I've got quint dresses. And also my sister in law who's in fashion loves quint too. And every time I see her and I hug her and she's wearing a cashmere sweater, I go, quint. And she goes, you know it. Love Quint. If you have to get gifts for people, it's so affordable, it's so beautiful. So find gifts so good you'll want to keep them with quint. Go to quint.comologies for free shipping on your order and 365 day returns. Now available in Canada too. So that's qu-I n c e.comologies to get free shipping and 365 day returns. Quince.comologies okay, how much should you be feeding your inner critters? Is there something too about doing it habitually, like not just having fermented foods or a probiotic, like once every couple weeks? Is it better to have a habit where like this is my morning yogurt and like grab it on the go and I'm kind of constantly refreshing? Is there something about that routine that helps the gut?
Dr. Miguel Freitas
Yes, I think it's same for any other food. And I'm a proponent of a flexitarian eating diet, which is a diet that majority is made out of plants but includes some animal products. But it's predominantly a plant based diet. I don't know if you know, but most, most of the population is lacking fiber.
Alie Ward
Yes, I've heard this like, so fiber.
Dr. Miguel Freitas
Is, it's really important and you have to consume it on a regular basis. And it's the same with probiotics because these are typically bacteria that don't stay in your digestive tract. So they pass, survive, transition, do their work in the gut and then they go away. So it's better to consume on a regular basis.
Alie Ward
And now you have worked on the Activia brand and the science behind that and I know, I think it was like the first brand that I ever knew. Like, oh, yogurt's got stuff in it that is good for you. That's good to know. And I feel like it's been kind of like this legacy of, oh yeah, get some good critters in your stomach. And I'm curious too, how has the science changed since the launch of that? Do you learn more and more every year, especially since you just opened up this huge lab outside of Paris?
Dr. Miguel Freitas
Yes, it's True. So I think consumer needs change, right? And also science evolves. I came here in 2004 to help prepare a little bit the public perception around bacteria because it was not at all what it is today. As you said before, everyone wanted to get rid of bacteria. It was, you know, that those, you know, alcohol wipes, bacteria is bad. You know, bacteria is bad. Even within the medical professionals that I talk to very often as part of my job, it was complicated to get folks to except to consume bacteria. You know, they were fine in consuming maybe life inactive cultures or cultures. But probiotic bacteria is another stories. And more recently a couple of months actually we've incorporating prebiotics. That's a term we haven't talked about. So it's not a probiotic, it's a prebiotic. So they kind of work kind of together in your gut to continue to support your digestive system and gut health. And the science on prebiotics came a little bit after the science on probiotics.
Alie Ward
What is a prebiotic usually? Is it a type of fiber? Is it kind of a substrate that the probiotics like to live in? Is it like giving them a nice bedding? Kind of.
Dr. Miguel Freitas
It's a type of substrate and typically a fiber. One of the most popular is inulin. And you can get it from whole food. You can get it from onions, artichokes, asparagus, some of the foods that contain prebiotics. But you can also have it from a concentrated form of chicory ruth as inulin. And then you can add it to the products. It is a source of fiber. But that fiber specifically grows what we consider the good bacteria in your gut. So the good bacteria in your gut, like bifidobacterium, they like that fiber and they grow on that fiber. And that's one of the types of bacteria that helps balance out this diversity that I talked before.
Alie Ward
And how does that work? Let's get back to Dr. Hsiao.
Dr. Elaine Hsiao
Well, when microbes digest fiber, they liberate these other molecules called short chain fatty acids. And some of that can be used by the body as energy sources. Again, we thought that maybe the brain is detecting whether the microbe is extracting more energy out of these foods that our body can't digest, but can kind of sense and making choices based on that. So I think it was a nice kind of proof of concept that the brain can tell what the microbiome is doing.
Alie Ward
And another fiber question. Soluble, insoluble fiber. Do our guts like a little bit of both or a lot of bit.
Dr. Elaine Hsiao
Of Both, I think that both have their different functions and would be affect the microbiome in different ways.
Alie Ward
Okay. So fiber, part of the plant we can't break down because we're not cows. And according to the Mayo Clinic, we've got soluble fiber which turns into this jelly substance in water and that can slow blood sugar rises, it can lower your cholesterol. Where do you get this magic then? You can get it in carrots, beans, oats, peas, and psyllium husks, which you have to drink with plenty of water. Okay. You take a metamuce, you chug some water with it. Insoluble fiber, however, doesn't gel up, it just adds bulk and it also just keeps things moving. And it's in beans and veggies and whole grains. If you're eating a western diet, chances are you are not getting enough fiber of either kind. I'm not passing any judgment, I'm just citing studies. And the 2019 Lancet study titled Carbohydrate quality and Human Health, A series of systematic reviews and meta analyses crunched the numbers of nearly 200 different studies involving 135 million person years of data to find that having at least 25 to 29 grams of fiber a day reduced cardiovascular related death, coronary heart disease, strokes, type 2 diabetes and colorectal cancer. And if the inconvenience of cancer and strokes and dying isn't enough, that's not enough of an incentive. High fiber diets also, over time can make it easier to fit into your pants that no longer button. But yes, start upping it slowly. Drink a lot of water with both types of fiber.
Dr. Elaine Hsiao
So yeah, I think diversifying is the key because different microbes digest different types of fibers. And I think for the most part, just having a healthy community of microbes is what we all would be aiming for.
Alie Ward
Yeah. And Americans, we don't do great on fiber from what I understand, right, We're a little deficient in that area. Yeah.
Dr. Elaine Hsiao
I mean there's what the western diet is, a high fat, high sugar diet. And so, yeah, getting closer to Mediterranean diet, I think is, is something that would be a good thing.
Alie Ward
I love that we're also talking like in between Thanksgiving and winter holidays here, feed all your little babies some new friends, get some fibery snacks and some water. Perhaps one of those snackies will be some kind of fermented goody as a treat for you and an emissary to your guts to say, hey, don't worry, this battle's gonna be swift. It's funny that we have to kind of train our bodies like we would a pet. You know what I mean? Like, we have to get ourselves used to it, which is why I think that it's not always easy for me to remember to take a probiotic every day, but it's very easy for me to remember to eat something yummy, that's breakfast, you know what I mean? So I think it helps you make a habit more. But is there anything that you have been researching that really surprised you? You've been working as a cell microbiologist for decades. Is there anything that was a finding that kind of shocked you?
Dr. Miguel Freitas
Well, I did my PhD on trying to understand the interactions between microbes and our own cells. This was back in 2001, and it was a very exciting moment. At that time, there were not even techniques to be able to mix bacteria with our own cells. In most of cell biology laboratories, there weren't. It was something that you always wanted to keep apart. The cell biology lab is on that aisle of the corridor. The microbiology lab is on that aisle. Because bacteria are going to contaminate the cells. And that was my passion, is to put the two together because that's what's happening in our gut. We're putting the two together now. It's much easier. So I did explore a lot of that. The crosstalk between bacteria and the gut. I think this gut brain interaction, I think it's super important, especially in these days, the way we're living, the stress, the going and running everywhere. People are in a constant state of disturbances. Right. And I have a passion for the gut brain axis, so that would be my area.
Alie Ward
It seems like you're the right person for the job for sure. I can see why you've worked here for like over 20 years. Like, Miguel's our guy. What about something that you're really excited about coming up, especially with this, you know, with this new lab. And is there anything that you're just excited to get started on or to learn more about?
Dr. Miguel Freitas
Yeah, of course. I mean, personalized nutrition, food is medicine. I mean, there's so many things that could pass through the microbiome and trying to design better foods for people. Improving people's health, that's always been my passion. And I think food is a good way to do that. I am very passionate about trying to develop foods that address people's needs. And I didn't mention this, but Danone's mission is to bring health through food to as many people as possible. Populations are different. We're a global company. Nutrition Needs in India might not be the same as in the US So we have to think about those differences when we're developing a product. You know, is fiber an issue everywhere? Is iron an issue everywhere? What's the role of a company like Danone in some of these public health issues? Type 2 diabetes, it's a very important thing. We actually obtained from the FDA the first qualified health claim for yogurt ever, associating consumption of yogurts with a reduction of the risk of type 2 diabetes.
Alie Ward
Oh, wow.
Dr. Miguel Freitas
Yeah. After many years of research, many years of petitions and systematic reviews, the FDA granted this claim in 2024. And it was very exciting.
Alie Ward
And if you are seeking any new hobbies, how about looking up FDA documents such as March 2024's 51 page petition for a qualified health claim for yogurt and reduce risk of type 2 diabetes. Docket number FDA2019P1594. I'm going to add, per our diabetology episod 1 and 2 with self described diabetic diabetologist Dr. Mike Natter, that watching added sugars is an important part of regulating blood sugar and blood sugar health. So as always, read those labels folks. There's a lot of science on them.
Dr. Miguel Freitas
We're also thinking about other types of options and products that could support gut health. And two of the products that we launched recently, one is a plant based alternative. So it's not dairy, it's under the brand silk. And it's a plant based dairy alternative that we formulated with pediatricians to get the right nutrition bundle to get into kids that are growing. And part of that bundle is fiber, is inulin. And because it's also important for kids digestive health. Another one that has pre and probiotics, which is also very important, is our Happy family infant formula. So a lot of moms cannot breastfeed. So there's of course alternatives out there, but we made sure that at least for babies who are growing, these first 1,000 days are critical. And we know that one particular genus of bacteria is a keystone in the child gut and if they don't have it, the consequences are not necessarily very good. And this is a bifidobacterium. We add bifidobacterium and prebiotics to kind of mimic what you find in breast milk. So we prepare the kids development of their immune system through the gut.
Alie Ward
I think it's so cool to be on the forefront of this and to be having material benefits for people that are living at the same time as you is pretty cool.
Dr. Miguel Freitas
Yeah. And get healthy. I think it's here to stay. I mean, the trend is, is everyone is talking about gut health and I don't, I TikTok I have it for work. But you know, there's the gut talk. There's. There's so many people talking about gut health of all ages. It's not only for an older person, which typically tends to have more digestive issues just because they don't eat as much fiber, they don't drink as much water, but even the younger people are concerned about their gut health. And this is not only about yogurt. Right. But we think about other options and where we can bring solutions that can improve everybody's life. And a lot of that goes through the gut.
Alie Ward
It's so great that you are able to take a passion that you've had since you were a kid. I feel like you were pretty much born for this. Like you're in the right job. It's gotta be nice to go to work and be like, yeah, I'm definitely in the right job. Yeah, you gotta dust off that microscope just for fun.
Dr. Miguel Freitas
I know, I know. I know exactly what it is.
Alie Ward
It's launched a thousand, thousand million yogurts. Well, thank you so much for doing this. It's so fun to be in my place.
Dr. Miguel Freitas
So much.
Alie Ward
Yeah, I have to visit you guys out in France.
Dr. Miguel Freitas
Yes, yes.
Alie Ward
I'll be at yogurt with you out in France. So ask professional people probiotic questions and if you make good enough friends, maybe you can score a behind the scenes tour at a microbiome lab. She said hoping to see a microbiome lab perhaps in France. Thank you to the folks at Danone and Activia for suggesting the episode and for sponsoring this one. Which means we can give generously to two causes this week. LA Regional Food bank and to GiveDirectly.org ologies. You can see the links in the show notes for more info, we are at Ologies on bluesky and on Instagram. If you're looking for shorter kid friendly episodes we have them in their own feed. Just search smologies S m o l o G I E s and subscribe there. Thank you to Erin Talbert for admin in the Ologies podcast Facebook group Avileen Malik does our professional transcripts. Kelly Ardwyer does the website. Noelle Dilworth is our prebiotics scheduling producer. Susan Hale is multiple strains of managing director. And as a lacto to each other's bacillus are editors Jake Chaffee and Mercedes Maitland, lead editor of Maitland Audio. Also adding to the biome of this episode is the ever beneficial Jarrett sleeper of Mindjam Media. Nick Thorburn tuned the theme music and if you stick around until the end of the episode, I tell you a secret. This week it's that right after college I very reluctantly joined my then boyfriend and his parents on a cruise. It's uncommon for me, it was the right thing to do diplomatically, although I hate sand and sun. But I got a sunburn so bad I had to ask the boat kitchen staff if they could spare some plain yogurt to apply like frosting to my neck and my shoulders and my face. I'm still grateful to those people and all the billions of microbes that soothed me. Thanks yogurt and thanks for listening. Okay, bye Bye. Pachydermatology Cryptozoology Littelpack Geology Nanotechnology Meteorology Mapology Serology Cell phone.
Dr. Miguel Freitas
It's alive. Gas gifts Tolls. This holiday trip is draining my wallet.
Alie Ward
Yeah, but we'll get to see all our family.
Dr. Miguel Freitas
You're festive.
Dr. Elaine Hsiao
What's your deal?
Alie Ward
What's my deal? Holiday savings At Metro. I got one line of 5G for just $25 per month and I kept the phone I love and no activation fees. And a five year price guarantee on my talk text and data detour to Metro. It is get that more for your money feeling only at Metro by T Mobile It's $30 your first month or without. Autopay Price guarantee Exclusion supply. See cipher details.
Dr. Miguel Freitas
The McDonald's Snack Wrap is back. You brought it back. Ranch snack wrap. Spicy snack wrap. You broke the Internet for a snack? Snack wrap is back.
Guests: Dr. Miguel Freitas (Nutritional Microbiologist, Danone Institute North America)
Dr. Elaine Hsiao (Neurobiologist, UCLA)
Date: December 15, 2025
This lively bonus episode revisits the fascinating microscopic world living inside our guts. Alie Ward sits down with Dr. Miguel Freitas and revisits past guest Dr. Elaine Hsiao to deliver a state-of-the-gut update, covering new research, the nuts and bolts (or microbes and fibers) of gut health, the evolving definition of “probiotic,” connections to brain health, and what matters most when it comes to what we eat.
Main Theme:
Gut microbiome science has evolved rapidly, especially regarding how diet, prebiotics, probiotics, and fermented foods influence our physical and mental health. This episode updates listeners on major findings, everyday takeaways, and how our inner microbiota connects our diet, digestion, immunity, and even our moods.
(03:55 - 05:35)
“We couldn’t live without all the critters inside of us.” – Alie Ward (05:10)
(08:06 - 11:13)
“We’re struggling to understand what causes what. But we do know that the microbiome is involved by association with many functions around our body, from brain to skin to cardiovascular disease.” – Dr. Miguel Freitas (08:38)
(09:05 - 11:47)
“Fibers actually increase the diversity of the microbiome… and individuals with a higher diversity tend to be associated with less disease.” – Dr. Miguel Freitas (11:13)
(12:57 - 24:43)
“Now it’s not a question of whether [the gut-brain axis] happens, it’s more a question of how.” (12:57)
“After our brain, the gut contains the second most complex nervous system in our body.” – Dr. Miguel Freitas (18:22) “IBS is now categorized as a disorder of gut-brain interaction.” – Dr. Elaine Hsiao (24:16)
(15:06 - 17:38)
Not all bacteria in yogurt or cultured foods are “probiotics.”
True “probiotics” are defined as bacteria studied in clinical trials that have demonstrated health benefits.
“Not all Lactococcus or Lactobacillus provide a health benefit. It needs to be studied, needs a clinical trial, a placebo... to show that it’s actually doing something in your body.” – Dr. Miguel Freitas (15:51)
Next-gen probiotics:
“A lot of the field is also really excited about next-generation probiotics that are just identified from our guts and newly characterized bugs.” – Dr. Elaine Hsiao (16:59)
(26:13 - 28:20)
“Our stomach has a very low pH… if you could put your finger inside your stomach, you would burn your finger.” – Dr. Miguel Freitas (27:45)
(36:58 - 40:24)
“Prebiotics work together with probiotics… to support your digestive system and gut health.” – Dr. Miguel Freitas (39:27) “When microbes digest fiber, they liberate these other molecules called short-chain fatty acids. The brain can tell what the microbiome is doing.” – Dr. Elaine Hsiao (40:27)
(41:01 - 43:26)
“Diversifying (fiber) is the key because different microbes digest different types of fibers.” – Dr. Elaine Hsiao (42:47)
(45:59 - 49:24)
On changing attitudes towards bacteria:
“Even within the medical professionals… it was complicated to get folks to accept consuming bacteria.” – Dr. Miguel Freitas (38:13)
On why fiber matters:
“A lot of fiber over time can make it easier to fit into your pants that no longer button.” – Alie Ward (42:20)
On the origins of “butterflies in your stomach”:
“So thank Florence Converse of Massachusetts for that. Also, who has the last name Converse? As it turns out, a guy named Marquis Mills Converse, founder of a rubber shoe company. Converse.” – Alie Ward (20:40)
On the gut as our “second brain”:
“Our gut is called the second brain.” – Dr. Miguel Freitas (20:02)
On the journey of probiotics:
“It’s a long process, but survivability is important… That’s why certain probiotics don’t make it. They don’t make it either because their cell wall is not prepared for that acidity, or because they’re not in the right matrix.” – Dr. Miguel Freitas (27:46)
On food as medicine:
“Personalized nutrition, food is medicine… trying to design better foods for people.” – Dr. Miguel Freitas (45:59)
Summary prepared for new listeners—no prior listening required!
Tone and banter preserved as much as possible for the Ologies vibe.