Why Your Gut Still Isn't Better (Even Though You've Tried Everything)

By Jessica Haskin, MS, RD, CDN, Integrative GI Registered Dietitianas featured on the Fed by Science podcast, hosted by Claire Goldwitz, founder of Square Fare

Overview

If you have chronic digestive issues, chances are you've already tried a lot. Elimination diets, rounds of antibiotics or herbal protocols, supplements, things you read online. And you're still bloated, still uncomfortable, still spending more mental energy on your gut than on anything else in your life. In this post I want to explain why so many people stay stuck despite doing all the right things, how to actually rebuild your gut microbiome (which is more nuanced than most people realize), why the gut-brain connection is influencing your symptoms in ways you might not expect, and what a slower, less restrictive, more sustainable approach actually looks like in practice.

How I got here and what my own gut taught me

I've wanted to be a nutritionist since I was young. I grew up watching food work in both directions: my dad reversed prediabetes through diet at a time when that went against almost everything conventional medicine was recommending, and my aunt with lymphoma lost her appetite during chemotherapy in a way that made everything harder. I became fascinated by this thing that we have so much control over that can play such a big role in our life, because when we're healthy, that impacts our life, and when we're not, that impacts our life.

What I didn't expect was that my own gut would become part of the education.

When I was working on a GI surgery floor early in my career, I noticed something that bothered me: patients would have surgery or complete a course of treatment and still not feel better. Something else was going on beyond the physical intervention, in their gut, in their nervous system, in how everything was working together. At the same time I was dealing with my own symptoms that I hadn't fully recognized as symptoms. What I now know to be constipation I just thought was normal: some days a lot of pain, a stomach ache, a cycle that continued. It didn't really affect my day-to-day life so I never really did much about it.

Then when I was a freshman in college, my dad found what we now call a functional medicine doctor, not nearly as common 15 years ago, who walked me through a targeted elimination diet. I found that when I removed gluten, I wasn't as constipated. When I put it back in, I'd feel those effects again. I don't have celiac disease, but once I removed gluten more regularly, I really did feel so much better. I kind of used myself as an experiment, learning about gut motility, the gut microbiome, how the variety of what I eat, not eating the same thing day in and day out, can add more variety to my gut microbiome, which in turn helps GI symptoms.

I saw how much can change not just with what I was eating, but how I was eating, how I thought about my food, how I was moving, when I was moving. And I really just wanted to be able to help other people with that, because so much of the story around gut health is just about the food, and it's not about all these other things surrounding what we're eating.

Who I work with

Many of my clients come to me with longstanding chronic GI issues or chronic illnesses that impact their GI system. A lot with gut motility issues, including history of SIBO (small intestinal bacterial overgrowth), chronic constipation, diarrhea, bloating, an overall feeling of discomfort and pain that may carry a diagnosis of IBS.

And often these things are overlapping with other health conditions that make it even more complex. A lot of times I'll see clients with MCAS (Mast Cell Activation Syndrome), or POTS (Posterior Orthostatic Tachycardia Syndrome), or Ehlers-Danlos and other connective tissue disorders that can affect the GI tract and the way it works. These conditions can also affect the nervous system and our vagus nerve, the largest nerve that runs from our brain through our gut and has a lot to do with our rest and digest mode, which is how we digest our food. So many of my clients have a few of these overlapping symptoms, diseases, and disorders.

What I really look at is the big picture: not just each individual symptom or diagnosis or disorder, but how they're working together in the body. Like putting together the pieces of a puzzle, not just with their diagnoses, but how they're feeling day to day, what their lifestyle has, what their routine is, and combining it all to figure out where we can make the most impact.

Why trying everything isn't working

Most of the clients I see have already tried a lot of different things: conventional therapies, medications, surgeries, supplements, protocols that weren't necessarily individualized to them, or sometimes things they found on the internet or social media. And we can get a lot of great information online. I love that people can take ownership of their health. But it's so important for everything to be very personalized to you, not just your diagnoses, but your symptoms and your lifestyle.

Someone who has a nine-to-five job is going to need something different than someone who works the overnight shift. Someone with a sedentary desk job is going to look different than someone who works construction. And so many of my clients have done all of the things, but if they're not sustainable, if they don't fit into their routine and their life, we end up right back where we started.

My approach is to take a big step back and look at their history, not just health history but history of life, starting in childhood. Their diagnoses, their symptoms, what they're eating in a day, what their current routines are, what they have the capacity for. And then I start very, very, very small. One or two or maybe three really small action steps that feel doable, that we can build on and build on until we have a routine and a foundation that really works. These are often called the basics, but they're not very basic to do, which is why I don't love calling them that. The effects accumulate in the body. The needle moves 5%, then 10%, then 20%, then 30%. We start small, but it all adds up.

How to actually rebuild the gut microbiome

This is one of the questions I get most, and it's more nuanced than most people realize.

The overarching theme is that the more variety we get in our diet, the more different types of fiber and different nutrients we're getting for our gut microbiome, which means more food sources for different types of gut microbes. Certain gut microbes will only feed on certain fiber sources or certain nutrient sources. So if we only have one or two of those coming in, it can lead to an overgrowth of that type of microbe, which alters the balance of bacteria in our gut. And then when we eat other types of foods, there aren't enough bacteria that are able to break down those other fibers. When they're not broken down, those fibers can irritate the gut and the gut lining and cause symptoms.

So sometimes our symptoms can be from too much fermentation, and sometimes they can also be from there not being enough gut microbes to actually eat and ferment those foods. That can happen when you're reintroducing something: there's not the right microbe to break that down yet. If you go slowly, we can slowly build that up.

But the microbiome isn't the only piece. There are other factors that influence microbiome diversity, specifically the inflammation in our gut and the status of our gut lining. You may have heard the term leaky gut. Our gut is only supposed to let really small, broken-down molecules through. When we have inflammation in our gut, it can open up those villi and allow bigger particles through that aren't supposed to be in our system, which leads to more inflammation and perpetuates the cycle.

So when we're thinking about rebuilding the gut microbiome: yes, always food first, and adding more variety rather than taking things out as much as we're able to. But also focusing on anti-inflammatory components and rebuilding the gut lining, which can happen through food. Not getting enough protein, and especially not enough collagen, can play a role. Sometimes through supplements. And sometimes through mucilaginous herbs like aloe vera, which can help coat that gut lining and decrease inflammation, which in turn helps the gut microbiome flourish. They're all in sync with each other. If the gut microbiome is off, that can affect the gut lining. And if the gut lining is inflamed and leaky, that can affect what microbes do grow.

My five tips for lasting gut health

1. Start with how you eat, before you change what you eat.

Before going on a restrictive diet, adding supplements, or doing any testing, really evaluate what your environment is like when you're eating. Are you in a rush? Are you stressed? Are you sitting all day and never moving? Those things are going to impact your digestive system just as much, if not more, than what you're eating.

Sitting down to your meals and chewing your food really, really, really well: that action might sound simple, but for a lot of us it's not in our day-to-day. It helps your brain communicate with your body that you're eating something, that it's time to digest your food. It increases gut motility. It helps your body put out enzymes and acid to break down what you're consuming. Even taking a few deep breaths before a meal, so at least your body is in a little bit of a calmer state, can make a real difference.

2. Move more, and it doesn't have to be what you think.

One of the ways our digestive system moves is literally when we move. Our bodies were made to be moving all the time. Getting up and moving more doesn't have to mean going out for a 30-minute walk, though that's lovely. It could just mean standing up and taking a lap around your office or apartment. Using the farther bathroom instead of the closest one. Standing up from your desk and doing a few squats if you can't leave the room. If you do one minute of extra movement 10 times a day, that's 10 minutes of extra movement your body is getting that it wasn't getting before. These things seem silly, but it all adds up.

3. Make changes slowly, not all at once.

This is the one people consistently rush, and it's the one where slowing down pays the biggest dividends. Whatever you're changing, whether it's adding foods back in, trying a new protocol, or increasing fiber and variety in your diet, go slowly, very very very slowly. I usually tell my clients: if you feel silly eating that small amount of a new food, or making that small a change, then that's probably a good place to start.

If you haven't eaten a variety of foods for a while, and then you suddenly eat a lot of them, it might not be that your body doesn't tolerate those foods. It might just be that your body isn't used to breaking them down, or your gut microbes aren't used to fermenting them yet. It's going to take a little while for the body to adjust. Going slowly helps you adjust with the minimal amount of symptoms or reaction that we possibly can. The same is true for any protocol change: build gradually, let the body catch up, and you'll get further faster than if you try to overhaul everything at once.

4. Have two to three go-to meals and snacks that require no thinking.

When you don't know what you're in the mood for, can't think of what to cook, or are just drained by always trying to make food choices that will make you feel better, you need a go-to list so you can take the decision out of it. One of the most important things when it comes to gut health is actually eating enough. We have to be eating enough to stimulate digestion, stimulate gut motility, and help repair the gut and feed the gut microbiome. If the decision of what to eat makes us not eat at all because it's just too much, that's going to make our GI symptoms worse long-term.

Have two to three meals and two to three snacks that use ingredients you always have around or can get very quickly, that are easy to make, and don't require a lot of effort or thinking. On the days when you've just had enough of thinking about it, you have really solid options. It's one of the reasons I like Square Fare so much: my clients can have these meals and they're just in there, ready to go. They don't have to think so much about what they're going to eat.

5. Have something in your life that gets you out of your head about your symptoms.

This one isn't nutrition-related, but it might be the most important. It can feel so isolating and so lonely when you're in the thick of it. Your world gets smaller as your diet gets more restricted and your symptoms grow. When we only focus on our symptoms, when we only focus on healing, it can feel like so much, and it can also turn into hypervigilance where we're just constantly thinking about how we're feeling and whether we're going to feel okay.

Having a community, a person, or an activity that gets you out of that doesn't have to be something big. It can be getting outside with your dog, going to a tennis court and meeting people, something that has nothing to do with your health. Just something that brings you happiness or joy. And of course, having someone you can actually talk to about these symptoms, whether that's a practitioner, friends, family, or an online community, is unmatched.

The gut-brain connection, and why both directions matter

I am obsessed with the gut-brain connection. The gut and the brain are constantly communicating through the nervous system, hormones, and immune signals, and it's not a one-way street. They're influencing each other all day, every day.

You can feel this in real life. The expression "butterflies in my stomach" when you're nervous or excited, that's the gut-brain connection at play. And when it comes to our gut microbiome, our gut has a symbiotic relationship with those microbes. The gut microbiome can produce byproducts that affect our hormones, especially serotonin, our happy hormone, and influence how we feel from day to day. So our gut microbiome helps influence the hormones that influence how we feel. And in turn, when our mood is influenced, that affects our nervous system. If we're happy and relaxed and in rest and digest mode, we digest well, which helps our gut microbiome flourish, which in turn creates an environment to make more of these byproducts that help us feel happier.

And when our gut is struggling, it can increase our stress levels, make us feel sad and angry and upset beyond just being in pain. It can really impact what types of hormones are being signaled, which in turn affects how we're digesting our food. It's why, when I'm working on GI symptoms, we have to work on it from both angles. If we only focus on the gut microbiome physically, we can still have the brain communicating with the gut in ways that disrupt the system. And if we only focus on the nervous system or mood aspect, we're only affecting what the brain says to the gut. What I find most helpful is when we address the combination of the two.

When I recommend Square Fare to my clients

As a dietitian who works a lot on building people's systems and routines that can really fit into their lifestyle, along with the fact that many of my clients have overlapping conditions and symptoms that lead them to needing certain types of foods in certain amounts, that is so overwhelming. And I've talked about the mental load a lot, but it's real.

I recommend Square Fare when clients have a lot of restrictions that make it really hard to cook their own meals or find healthy options. And I want to point out: a lot of my clients are not restricting unhealthy foods. Some of their restrictions are fruits, or vegetables, or different types of healthy foods. It can be really hard to find a program where you don't sacrifice health for flavor or flavor for health. Square Fare does that.

I also find it really helpful for clients who need more specific, targeted portions: more protein if weight loss or body composition is a goal alongside gut healing. And critically, a lot of my clients' needs change as we work together. At the beginning, maybe we need less fiber, spread out way more throughout the day. Over time, many of my clients can eventually eat more variety and tolerate more fiber. Through Square Fare, we can very easily add that in. I don't have to find a different meal delivery service every time we go through a change in their diet. It's very easy to adjust: a little more fiber, a little less fiber, a little more protein. For my clients who are often having changes to what they can tolerate throughout our time together, it's so helpful to have it all in one place.

I had a client, one who stands out to me so much, one of the early clients I referred to Square Fare, where most of our sessions before that were just about planning. What can you eat? How do you make it? What do you need to get at the grocery store? When are you going to cook it? What things can you have for leftovers? So much of our session was just about the planning and prep. And that's important, but it didn't allow us time or room to build routines, to build the system, to focus on the gut-brain connection. It was only about what she was eating, and really more about how she was making what she was eating.

And then when she started Square Fare, she wasn't getting every meal from there, but she didn't have to think so much. She didn't have to think about her grocery list, her meal plan, what she was going to cook, when she had time, how it was going to taste. That decrease in mental load and overwhelm allowed us to go so much deeper and really build the other foundations we needed to build, which ultimately allowed her to not have as many restrictions and not need to think so much about what she was eating day to day. The impact of taking something off someone's plate that's so big, especially for clients like mine who are so overwhelmed by food choices, but still having something fresh and nutritious that tastes amazing and can be customized, is so impactful when it comes to helping to heal and build those routines. We can't do everything at once. Taking something away, outsourcing something, delegating something, is just so helpful.

A client case that stayed with me

One of my recent clients has a history of Hashimoto's thyroiditis and SIBO, and had done multiple rounds of antibiotics and herbal antibiotics, kill protocols. But she still had ongoing symptoms: bloating, altered bowel habits, more constipation, incomplete evacuation. She came to me after a recent antibiotic round and was on a low-FODMAP diet, but she really wasn't feeling any better, and felt so restricted. Like she couldn't eat out anywhere. Couldn't go enjoy with her friends. And my philosophy is really about the less restriction the better, and usually the slower the approach the better.

So we stopped most of the supplements she was on, especially any acting as antimicrobials, and very slowly, in a structured way, added back in the FODMAP foods. When it comes to FODMAPs, a lot of times it's a bucket concept: most people can have trouble tolerating a lot of them in large amounts, but little amounts and small portions are fine. We learned her limits for the time being and were able to expand her diet a little more.

Then we really focused on how she was eating. She was someone who was very busy, little kids, full-time job, always on. When we are go-go-go all the time, our nervous system is turned on all the time. Our fight or flight response is activated. And when fight or flight is activated, we are not in rest and digest mode, which is the only place we can digest food in. So it's really hard to have good gut motility, help your gut microbiome, or have regular bowel movements if our digestive system isn't digesting food properly. We focused on her sitting down to meals as often as she could, not every meal has to be perfect, taking a few deep breaths pre-meal. And really upping her movement throughout the day. She got a walking pad. Added short five-to-ten minute breaks. Whatever was feasible for her work schedule.

Then I did a GI map, the stool test that shows different types of bacteria in your gut and markers of gut inflammation and how well you're digesting. We made a targeted plan using the GI map results, her bloodwork, and how she was feeling. A low and slow approach: starting with improving motility and digestive capacity, then using targeted food and fiber recommendations to heal the gut lining and decrease inflammation, which is especially important in Hashimoto's as an autoimmune and inflammatory condition. And I use a build-up approach almost always. I try not to kill off bacteria as much as we don't need to, as opposed to crowding out what we don't want by promoting the growth of more beneficial bacteria.

I want to be clear: this took time. Almost a year of really building on the foundations and moving through the process and integrating them into her life. Now she doesn't need most of the supplements or specific diet recommendations anymore. She's having regular bowel movements most days. She has minimal bloating, especially when she puts the foundations into practice.

But the most impactful thing she told me is that she doesn't really think about her GI tract and her symptoms anymore. Whenever I ask a client about their bowel movements and they say "I haven't thought about it," that to me is the best answer. It's inconsequential enough that it's not on their radar. And what most clients tell me after is that taking away that space in their brain, how much they were thinking about their symptoms, about what they were going to eat, if it was going to make them feel good, whether they wanted to go out to eat with friends, frees up so much. Most people tell me they're more productive. They're getting more done. They're having more fun in their free time and they didn't even realize they weren't having fun. The foundational things are more permanent, and we built them in slowly enough into her life that they can be permanent without feeling like she's bogged down in them.

Jessica Haskin, MS, RD, CDN is an integrative GI registered dietitian based in New York City specializing in IBS, SIBO, leaky gut, histamine intolerance, IBD, gastroparesis, GERD, and autoimmune conditions including Hashimoto's. jessicahaskinnutrition.com

This post is based on a conversation from the Fed by Science podcast, hosted by Claire Goldwitz, founder of Square Fare, a New York City meal delivery service that prepares fresh, personalized meals built around each client's exact macros, dietary restrictions, and health goals. Every meal is made from scratch, portioned individually, and ready in two minutes. getsquarefare.com — use code CHERRY for 20% off your first order.