When Your Gut Improves, Then Falls Apart Again What’s Actually Missing in Modern Gut Repair

You've tried probiotics. They helped — for a little while. Then the bloating came back. The reactivity returned. Whatever shift you felt didn't hold.

So you tried something else. Different probiotic, different protocol, different elimination approach. Same pattern. Brief improvement, then backslide.

It's not that nothing helps. It's that nothing holds.

In this episode I'm going to tell you why. And it's probably not what you think.

The problem isn't the wrong probiotic or a diet that isn't strict enough. The problem is that your gut ecosystem has lost its keystone species — the specific organisms that hold the entire system together. And until those are restored, nothing you add is going to stick.

I walk through who the keystone species are and what they actually do — Faecalibacterium prausnitzii, Akkermansia, Bifidobacterium, Lactobacillus reuteri, Roseburia — and what the whole system loses when they go missing. Why butyrate production drops and what that costs your gut lining, immune function, motility, and mood. Why fermentation shifts from fiber to protein and produces inflammatory compounds that drive reactivity and brain fog. And why opportunistic species expand — not because they invaded, but because the space opened up.

I also cover what disrupts keystone species in the first place — antibiotics, low fiber diversity, chronic stress, mold exposure, common medications — and what restoration actually requires, in the right sequence, at the pace your system can absorb.

If you've been doing gut work and keep hitting the same ceiling, this episode will reframe what's been missing.

read the full blog post here

Transcript

SPEAKER_00 0:12

Well, hello, hello, and welcome back to the Rewilded Wellness Podcast. I'm your host, Lydia Joy. Today I'm just going to get right into it because this episode is actually the next installment in my terrain map series, and it's a good one. Now, if you'd rather read this as a blog post, the full version is linked in the show notes below. But for those of you who prefer to listen, who want to take this with you on a walk or a drive or while you're doing something with your hands, I've got you. That's exactly why I bring these posts to the podcast. A quick note before we dive in: this show is listener supported, which means no ads, no sponsors, just content I uh create for you. And if you've been finding value here, the best thing you can do is to either leave a review, share an episode with someone who needs it, or um if you'd like to financially support the show, there's a link for that in the show notes too. I appreciate you guys. Alrighty, well, let's talk about your gut and specifically about why so many gut restoration attempts just don't hold. Now, maybe you are someone who has tried probiotics at this point. Pretty much everyone has. And maybe they worked for you for a little bit. Um, maybe I don't know, a week or two, or a month or something, maybe longer. Um, your digestion maybe seemed to settle down, or maybe like some bloating you had calmed down, or maybe you noticed better moods or more energy, and then it stopped. And the bloating came back, and the reactivity returned. Whatever shift you felt just didn't hold. So maybe then you tried a different probiotic, or maybe thought you needed some kind of protocol, or tried a bunch of different strains, or added prebiotics, or maybe even eliminated foods. You did the things, basically. And the same pattern repeated. Brief improvement, then a plateau, and then what you might call a backslide, right? And what I want to say is that it's not that nothing helps. A lot of people get to the point where like, nothing helps. I get it. It's very frustrating. It's really the key is that nothing is actually holding, right? And at some point, you got to start wondering like, what is going on in my gut? Like, is this something I'm gonna have to manage forever? Am I missing something? Maybe something fundamental? And the answer to that last question is yes, but it's probably not what you think. The problem isn't that many people haven't found the right probiotic yet. It's also definitely not that anyone needs a more restrictive diet or like a more aggressive protocol. The problem is that the gut ecosystem has lost something that it can't rebuild on its own. And until you understand what's missing, not just a single species or strain, but the specific keystone species that hold the entire system together, nothing you add is going to stick. So here's what most people don't really know. We we have we want to have a lot of diversity in our gut in terms of bacteria, good, good bacteria. Now, the amount of that isn't the main thing because you could have like a really high species count and still be missing the organisms that regulate immune function and produce the compounds that your gut lining runs on and basically keep the whole entire ecosystem from collapsing under stress, right? You could take every probiotic on the market. And if the keystone species that create the conditions for those probiotics to colonize aren't there, you're essentially like planting seeds in a parking lot, for example. So this is like uh something that a lot of people don't really hear about. And it's really at the root of that um gut repair that is necessary. And it's why so many people's attempts at like gut restoration don't actually hold. Um, it's not like you've failed or something, it's just ecological architecture, loss. It's a loss. And once you understand, you know, which species actually matter, maybe why they disappeared in the first place, or what makes them disappear, the path forward becomes a lot clearer. So let's start with what diversity, when I say diversity, I'm talking about diverse microbes in your gut is actually going to be doing for you because it's worth understanding before we talk about what happens when it erodes. So a diverse microbial ecosystem does something really important. It provides what researchers call functional redundancy. That's a term worth understanding. So let me just break it down real quick. If you think about a forest, right? Multiple species in a forest might actually perform the very same basic job, like decomposing leaf matter, fixing nitrogen, keeping, you know, certain plants from just taking over. Now, if one species disappears, another can step in and the function can continue and the system can stay stable. And your gut works the same way. When you have a diverse microbial community, you've you've got backup, right? Now, if one organism is disrupted by stress or illness or what have you, um others that are there can cover it, uh, or cover for it while the ecosystem hopefully recovers, right? Like that we're built to be able to be resilient like that. However, when the diversity erodes and you lose that redundancy, every disruption to your health costs you way more, right? Like a round of antibiotics uh hits you harder. Like in if you're taking a round of antibiotics in a gut with low keystone species, your bounce back isn't coming. It's like, you know, or like a really hard season of stress. Uh, I have people tell me, like, oh man, I I injured my back, and like next thing you know, I had all these gut problems, right? Um I went through a major breakup and my gut like decided to revolt on me. Um, or you get sick for a while when you already have the low diverse species and it takes you way longer to recover, right? These things hit way, way harder because there's way fewer species that can step in to maintain critical functions while the system tries to recover. There's also something else that happens in a healthy, diverse gut. The organisms are deeply interdependent, right? They feed each other, they regulate each other, they produce compounds that other species need to thrive. It's really a living network. It's it's not just like a collection of isolated bacteria, and you can take one and but, you know, right? It's more of this network, right? And it when it's intact, you know, your whole system is going to be far more stable. Um, and so are those bacteria, right? Like versus any one species trying to do something for you on its own. So that's what I'm really talking about when I talk about diversity. It's not just a number of species in the gut, it's really a whole bunch of friends working together. Basically a living interconnected ecosystem. Now, of all the ways diversity can erode, the loss of the keystones is the most consequential. And I want to spend some time for a second because this makes a big, this makes a it changes a lot for people. So the term keystone species comes from ecology. It was coined in 1966 by an ecologist named Robert Payne. He was studying Pacific tide pools, and he identified a specific species of sea star as a critical predator, and it basically regulated the entire biodiversity of the pool. When he removed the sea stars, the ecosystem didn't just get a little worse, it collapsed. Other things took over, muscles took over, dozens of other species actually disappeared. Now, the sea star wasn't the most abundant organism in the pool. It was just the one whose presence made everything else possible. And your gut has keystone species too, species that regulate your immune function, they support your gut barrier, they produce compounds that feed other beneficial microbes, and they basically hold the entire ecosystem together. And when they go missing, your gut microbiome doesn't just get a little worse, it reorganizes around their absence, often in ways that drive chronic inflammation, which can show up in a myriad of symptoms and ways in each person's body that can look different from person to person. Um, and then also, you know, create that impaired gut barrier function, um, and all the bajillion symptoms that bring people to my work. So I want to talk about them super quick, a couple of them, just so you start to like understand these friends you have in your gut, what they actually do, why the heck does this matter? Um, now a biggie is called Fecalobacterium prosnitsi. It's a heavy hitter. It's one of the most abundant bacteria in a healthy human gut, and one of the most important because it's the primary producer of something called butyrate in your colon. Talk about that more in a minute. It has basically has uh potent anti-inflammatory effects. Um, when, which by the way, I look at biome effects tests all the time, and almost everyone does not have this in their gut, just FYI. So there's a lot of things that when you don't have it detected, uh can go on in your system, right? Like irritable bowel, uh, depression, metabolic syndrome, you know, and then of course the poor gut barrier integrity, which is leaky gut, intestinal permeability. So when this guy is missing, you feel it. Like you say something to me like everything in my body seems to be, you know, firing against me, right? Another one is Acromantia mucinophila. And this species lives in and helps maintain your mucus layer, which is that protective coating that lines your gut wall, right? Now, at healthy levels, it actually strengthens your mucosal barrier and helps you regulate your immune tolerance to things, okay? Now, there's two things about acromancia. One, it can be overly dominant. Okay, I've seen this a lot, without the other species that balance it, which means it can actually degrade the mucus layer faster than it's being replaced. When it's low, it's also a problem. So we don't just always want more of something, by the way. We want balance and proportions. So this is a big one. What we look at if it's too high or too low, you have a version of leaky gut, basically. Um, and that's going to be causing or a piece of what you're feeling. You're going to be feeling so many things in your system that you can't connect the dots to. Um, then we have the bifidobacterium. There's a number of these. These these guys are the earliest colonizers of the infant gut, and they actually remain critical throughout life. Um, you know, not everyone has them optimally as a baby, unfortunately. But they do produce compounds that support and calm the immune function. They actually uh adhere to the gut lining to help protect the barrier. And they feed the butyrate uh producing species through a cross-feeding relationship. Without them, you know, the whole downstream chain of the beneficial fermentation in your gut starts to break down. Um let's see, we also have the lactobacillus species. There's a number of those, and they also help support your immune tolerance, they regulate your gut pH. They can compete with opportunistic species, right? So help keep that in check. And then they also support your mucosal barrier. There's one in particular called Lactobacillus ruteri. This one actually produces a natural antimicrobial compound and supports serotonin production. And a huge amount of serotonin is produced in the gut. Um, and so species like lactobacillus ruteri are part of how that happens. Okay, let's see, we've got roseburia and ubacterium species. These are also major butyrate producers that work hand in hand with the bifidobacterium, um, because bifidobacterium produces acetate, and the roseburia and ubacterium take that acetate and convert it into butyrate. It's like a relay race. You know, if either team drops out, the finish line doesn't get reached. So um, you know, there's a lot going on, right? And you can see just from me sharing those few, like they all are working together. It's never just one thing, right? So those um, those aren't all the keystone species, but they represent, you know, the ecological scaffolding that most other beneficial functions depend on. So when they're present and thriving, your gut has the architecture to self-regulate. You can uh produce protective compounds and maintain the boundaries, namely your gut boundary, right? That helps keep that inflammation from spreading throughout your whole body. When they're missing, that architecture, architecture collapses. And it doesn't do it like all at once. It it's it can be very gradual and it just kind of like shows up over time as a lot of the symptoms that I've been talking about, mapping through this entire series. Um, so you know, people wonder like what the heck is going on with me? What why am I having all these things all at once? Seems like all at once for many people, but really, excuse me, just had to take a sip. It's you know, it's it's a gradual overtime until it's almost like one day you just tipped way over the edge, right? You know what I mean? Um so what actually happens downstream when these species are missing, because this is again, this is where it gets really tangible, right? So the first thing that happens is that short chain fatty acid production drops. These guys are the most important metabolic output of your gut. They're produced when your beneficial bacteria actually can ferment dietary fiber through this whole kind of cross-feeding network I just kind of tried to describe to you. And the main short chain fatty acids are butyrate, you heard me say, acetate, and propionate. And they do an enormous amount of work in your gut. So butyrate in particular is the primary fuel source for the cells that line your colon. If you don't have enough, uh, those cells can't maintain, excuse me, the tight connections between them. They keep the gut barrier intact. So what happens is it begins to just thin, right? And then things that should stay inside the gut start leaking out, right? That's your intestinal permeability. Then your goblet cells, which produce that protective mucus layer, they like lose the signal to keep producing. And so your immune system starts losing the regulatory input that it needs to stay calm. And then the inflammatory tone in there rises and you feel it, right? Your motility slows, your mood's going to be affected, and even your appetite regulation will be affected. All that from one metabolite dropping out, butyrate. Um, right. So the second thing that happens is that the type of fermentation shifts, right? So your um microbes prefer to eat plants, right? They their preferred source of fuel is fiber, carbohydrates. So when you're able to do that well, you can produce um beneficial short chain fatty acids. Um, but if you can't do that well, your gut will then go from fermenting fiber and carbs to fermenting protein instead. And protein fermentation produces a very different set of compounds. We've got like ammonia, hydrogen sulfide, and other metabolites that are bluntly just like inflammatory and at higher concentrations are neurotoxic. They actually drive immune activation, they alter how your nervous system signals, and they basically increase the overall toxic load that your body has to manage. I'll go more into this in another episode, but for now, just know that this fermentation shift is one of the most significant things that happens when keystone species are missing. Right? Excuse me. Now, the third thing that happens is that opportunistic species actually can expand. So when those keystone species decline and their ecological niches open up, organisms that were previously kept in check by competition start to grow. And this is why you can look at a gut test and see a single opportunistic species sitting at like five or 10 times its normal range with no obvious explanation. You know, the explanation isn't that it invaded from somewhere. It's just that the space opened up and the keystones that were keeping in check are gone. Um, the fourth thing, maybe the most important thing for understanding the lived experience of people doing this work is that resilience drops. This is what people are describing when they talk to me. They're like, I feel like my gut has been off. I had a bad infection three years ago, you know, and I just have felt off ever since. Or, you know, I had a prolonged period of extreme stress, or I took an antibiotic last year for a tooth infection, and then I forgot. And then a bunch of months later, I had to take it again for something else, right? Like, and then a year later they're like, I actually feel pretty crappy. I don't know why, you know, and it's because the ecosystem lost keystone species in those disruptions, and it just hasn't been able to rebuild the structural scaffolding that it that would really allow, you know, genuine recovery to happen, right? So every subsequent disruption hits harder and harder, and then what recovery just takes longer, right? And over time, the entire system of you know, you, your whole body, just becomes increasingly fragile. And we're seeing this more and more and more, right? Um so okay, so there's one little nuance. Like, I don't know if anybody even knows about this. So maybe, maybe I'm kind of sharing something that people aren't aware of. But if you get a gut test, right, um, a biome effects is what I use, and you see it like a high species count, maybe you have a good species count, um, you could still be missing these keystone species, right? And like we have to always think about the nuance here. So this is something that it gets so tricky when you're trying to match probiotics to these kinds of things, if you're not looking at the whole, right? Um, because you know, these diversity metrics don't consistently predict like the health of the host, right? If you have a high species, doesn't tell you, you know, whether the right species are present, whether they're in the right proportions, or whether the functional networks between them are intact. So the biggest question that actually matters is which species are present, which are missing, what What are they producing and where are the functional gaps? Right. The difference is like between flying over a forest and counting the trees versus actually walking through it, noticing what species are there, which are gone, how the canopy is structured, whether the soil is healthy, whether the ecosystem has the architecture to survive a storm, right? That's the kind of functional relational view that we use in my work. We're not just trying to count numbers or pathogen hunt or whatever. We're really trying to do a more ecological assessment of what the system is actually doing. Okay, so I'm going to talk about what disrupts these species in the first place. Like, why do they go missing? Um, you know, because it kind of it clarifies what restoration actually requires, right? Obviously, we know antibiotics are the most obvious disruptor, right? They don't just kill pathogens, they're indiscriminate, right? Um it's really hard to recover from this once you've had multiple courses over your lifetime. And most people have, some more than others, right? And the keystone species may not return without deliberate targeted receding. The other biggie is the environment, right? The reduced environmental microbial exposure that we have based on living in a modern built environment, right? Most people aren't really thinking about this because your microbiome is continuously shaped by the microbial world around you, whether it's inside or outside, right? Uh think about what people are doing inside with all these chemicals and anti-uh, what are they called? Um, oh my gosh, we used to like, we spray our counters and we wipe them and we try to get rid of germs, right? All that stuff that many people do, right? Chlorine in the shower, water, like so many things from the indoor life are not friendly to your microbiome. However, in nature, in a more, you know, undisturbed natural setting per se, uh, soil contact, outdoor time, varied environments, um, you know, all the different seasonal foods, right? This whole like exposure to ongoing sources of different things in the outdoor world, the natural world. Um so because most people are indoors, a large portion of their days in their life, that their microbiome has changed because of that. Uh, the other thing, low fiber, right? So we all grew up on processed food, right? I did. I mean, I don't remember eating a whole lot of fiber. We ate apples, we ate packaged oatmeal. I don't know. It's probably got some fiber, you know, not great uh because of all the sugar that's in there. You know, I grew up on processed food. You probably grew up on processed food. The modern diet is very low in fiber and very low in diversity of different types of fibers. And so that's another reason why the keystones can't thrive is because they don't have their preferred source of fuel because that's what they eat. They eat fiber. Um, and they need a wide range, right? And so many of us have not been exposed to enough, and that starves them over time. And then what can happen is whatever is in there, it can ferment, they can ferment protein. Um, you know, because that's actually abundantly available even in a processed food diet. And then that fills in the gap. And you heard me talk about that can lead to serious endotoxins, right? Um, chronic stress suppresses keystone species through the gut brain access, right? Because our stress hormones actually alter our gut motility, our immune function, the mucus production, and the local environment that the keystone species depend on. So ongoing unmanaged stress, chronic stress, your gut is like not able to keep up, right? Like it can't rebuild faster than it's being destabilized. Then we've got things like mycotoxin exposure, right? Meaning mold in the compounds that mold produces. Um, right, another downside of the modern built environment, of course. Um, but because they have specific antimicrobial effects, they actually mycotoxins actually kind of deplete lactobacillus and bifido species. And so then that can damage the gut lining, create an environment that's hostile to the species. And, you know, it's really critical to have them for butyrate production and barrier support. So pretty much everyone who's lived in water damaged housing with mycotoxin exposure is is also getting that antimicrobial effect to their bacteria. Of course, medications, like we we have no known studies on any medication being safe for the microbiome, right? So we've got the NSADS, the proton pump inhibitors, hormonal contraceptives. These all alter our gut environment, um, right, in ways that just like selectively deplete the keystone species over time. I could go on, there's more things, but we can all see ourselves in many of these, right? Um, and obviously none of these are fringe concerns. They're just the lived reality of most people navigating modern life. And if we think about the cumulative effect across years or decades, right, the gut has progressively lost its structural keystones, even in people who eat well, even in people who move their bodies, even in people who are like doing the best they know how to take care of themselves. Every single client I see doing a lot of great things, but their microbiome is a mess, right? So what does restoration actually require? Well, if the problem is like this structural ecological loss, the solution isn't just like uh a single probiotic or, you know, maybe a short-term protocol, if you will, right? Like I'm gonna do this, you know, gut repair thing for 30 days or 90 days or whatever people are doing, right? It's really about stewarding, right? Because we have to rebuild the conditions that allow those species to re-establish and those cross-feeding networks to start to reorganize. And that requires a few things happening in the right order. Okay, so it's a terrain-first approach, right? Because remember what I said? You can't seed a forest in a parking lot, right? Or seed bomb. Just like, let's seed bomb everything and hope stuff grows, right? Um, anyways, I had friends who were like, let's go in a helicopter and throw seed bombs and try to like grow a food forest. I was like, well, that wouldn't be a very effective way to do it. But that's kind of what people are doing. They're like doing that with probiotics, like just trying to throw stuff in there, right? Here's the thing: before you can effectively reintroduce those keystone species, the conditions that allow them to colonize need to be in place, right? There's a number of things. You got to have the right pH in the gut, you got to have adequate mineral substrate, you got to work on reducing your inflammatory load, right? Getting your nervous system to be able to shift into parasympathetic so that it can support the mucosal repair. So without the terrain work, this whole idea of like reseeding often is a large waste of resources, right? If you can do targeted reseeding once the terrain is steadier, um, these keystone species that are absent or depleted can be reinduced reintroduced through that approach, um, versus like a general, like I don't know, a good bacteria supplement that's like universal or something. Um you can actually get the specific organisms matched to what your actual ecology is missing and go from there. So that's a longer game approach, right? Uh another thing that you will need to do is prebiotic support. And, you know, there are some prebiotics that are gentle for most people's guts, you know, but you kind of need to know what prebiotics feed what species, right? Each species like different things. So we have to give the prebiotics so that the species can eat them because that's how they grow, right? Um, so we want diverse plant fibers. We want inulin, resistant starch, pectin, all these things, um, a wide variety of whole plant foods uh to feed the organisms you're trying to establish. Now, a lot of people can't tolerate a lot of prebiotics and fibers when their gut is missing the species, in flame, leaky gut, like so it is tricky to like you gotta do these things in phases. You can't just start throwing a bunch of fibers in and assume you can handle them. Um, right. So this is the long game piece, right? Where you're you're working on what you can tolerate now and you know, trying to rebuild so that you can tolerate more and more and more over time. And of course, another big thing we all need to be doing is like, you know, nature, right? Like nature, rewilding, getting out into the environment, more environmental diversity out of buildings, right? Getting contact with the soil, getting your feet in the ground, getting your hands in healthy soil, being outside deep in the woods in places that are more natural, right? Trying to eat foods in season, eating eating foods outside, excuse me, uh, learning how to make fermented foods, uh, finding which ones you tolerate, even being able to tolerate them, right? Um, you know, the ongoing environmental microbial input is gonna keep the diversity alive and support your immune health, right? Like how your body, um, how those species like educate your immune system. Like, okay, we can do this, we can do that. Uh, the other piece is motility, right? I want to talk about this more in another episode. Um a lot of people think when I say motility, like, oh, moving my bowels, right? Oh, I poop every day. But some many people can move their bowels daily, but still have slow motility, right? You can have a more stagnant gut. Um, and that's actually kind of a hostile environment for restoration. Keystone species need the right flow, the right pH gradient, the right conditions, right? So if you have a slower motility and things are holding longer, um, you're not gonna have the right conditions to like really rebuild those species, breezeed, if you will. Um, and then of course, you want to reduce the disruption, right? Obviously, you know, restoration happens in the space between disruptions. So if stress, antibiotics, poor sleep, mold exposure are ongoing, you know, the ecosystem can't rebuild faster than it's being broken down. So, you know, this is why we have to create the environment, create the spaciousness in our lives, um, and work on our whole system, not just like the gut in isolation. Above all, you know, it takes time. Ecosystems don't rebuild in days or weeks, they rebuild in seasons over years through consistent support of the conditions that allow reorganization to happen. So I know most people don't want to hear this, um, but it's true, right? And I'd rather give people the real timeline than, you know, send you into some quick fix, right? Certainly you could spend a few months, make massive progress, um, and feel a lot better, but it is something worth stewarding over time throughout your life because it's it really matters. So, whatever your current gut ecology looks like, like however compressed, however, you know, last say the word depleted for lack of a better term, you know, most people's guts are remodelable. You know, your biology still has the capacity to reorganize. There's plenty of research consistently showing that measurable shifts in microbiome composition and immune function are possible with targeted ecological support, right? Um, and I've, you know, I've watched people do it. Like I've seen it, you know, in people that are able to rebuild uh over months and years, um, and you know, every year increase their capacity and you know, overcome a lot of challenges. So none of us are starting from zero, right? Like you're we're all starting from wherever our ecology is right now. Um, and you know, there's a possibility of a clear picture of what's missing at, you know, when you have take this terrain first approach, so you can create the conditions for restoration. Um so I find that to be really, really helpful when we can see what is going on in our own gut so we know what we're dealing with and how to kind of stage and phase the repair process. All right, well, in my next episode, I'll go deeper into um endotoxin load and geek out to that because it's really a big deal. Um, a lot of people are dealing with histamine issues and mast cell issues and flare-ups and all these sensitivities. They feel like their nervous system can never stand down, their immune system can never stand down. They got all kinds of weird problems going on. They're like, what is the deal, right? Um, that one's a big player. Okay, well, hopefully you guys found this useful, helpful, interesting, for informative. Um, I mean, I geek out to this all the time. I find it fascinating, uh, super important. This is the work inside my minerals and microbes client program. I'm I'm using the biome effects to look at your gut terrain, right? We're not just looking for any one thing, like, okay, well, what pathogens do I have? Do I need to kill? Right. It's a very functional view of what your gut is actually doing, right? We see who's in there, what they're doing, what your fermentation patterns look like, where the functional gaps are. Um, and from there, we can take the right approach to get going. Plus, uh, we have the mineral analysis to um also target, make sure you have that um mineral substrate to start helping you hold your charge, um, which plays a big role, right? All these pieces work together to start restoring everything. All right, so if that's something you're interested in, you can check out the details in the show notes, see if that's the right thing for you right now. Um, and I hope you guys found this helpful. I'll be back with another episode digging into another layer of the gut, and you can just keep learning um, you know, the what and the why behind why your body could be struggling right now. All right, guys, until the next episode. Stay wild, stay well.