your gut is a garden

June in Portland means spending lots of time outside in the garden. I usually take some time most days to get my hands in the dirt to pull weeds and make space for the good stuff to thrive.

I bring up the garden because it's an analogy I use in my private practice almost daily. Microbiome support is such a foundational part of my clinical work, and when I'm sitting across from a client trying to explain what's happening in their gut and why, I almost always come back to this image: your gut is a garden. It's the clearest way I've found to describe how the microbiome develops, what disrupts it, and what it actually takes to restore it.

So for this month's blog post, I'm going to take you through that analogy in full. It connects to a topic that is deeply personal to me and one that I see the downstream effects of in my clinical work every single week: childhood antibiotics.

antibiotics aren't the enemy

Now, before I go any further, I want to be very clear about something. Antibiotics are one of the most important medical discoveries in human history, and there are times when they are absolutely necessary and even life-saving. The problem is not with antibiotics themselves, but with the fact that they were overprescribed for decades, and almost always prescribed without any consideration for rebuilding the gut ecosystem.

my story

When I was a little kid, I had chronic ear infections. And the solution at the time was antibiotics. A lot of them. I was on Augmentin, a broad-spectrum antibiotic, daily... for months. As a small child whose microbiome was still in the process of developing. Hi Mom and Dad! If you're reading this... this is not your fault. This was standard of care in the early 90s.

Yes, these antibiotics did eventually stop my ear infections. But they also set the stage for a lot of what I dealt with later. Food sensitivities, rashes, hypothyroidism, on-and-off gut symptoms that didn't follow any easily identifiable pattern... I didn't connect the dots until I was deep into my training in naturopathic medicine. It was a bit of an "aha" moment. All of these things that had felt random and unrelated suddenly had a common thread. And once you get to treating the root cause, which in my case was dysbiosis, all of them are curable.

I share this story because I think a lot of you have a similar one. Maybe it was ear infections like me. Maybe it was strep throat every winter, or recurrent tonsillitis, or chronic sinus infections. Maybe you were a teenager who was handed a prescription for doxycycline to manage your acne and stayed on it for months or even years. Maybe you were the college student dealing with recurring UTIs and cycling through antibiotic after antibiotic.

This was incredibly common, especially for those of us who grew up in the eighties and nineties. Doctors were not trying to cause harm. Antibiotics were the best tool they had, and they used them liberally. But our understanding of the microbiome has changed dramatically in the last 30 years. What we know now about gut health, immune development, and the long-term consequences of early microbial disruption was simply not on anyone's radar when those prescriptions were being written.

Luckily, pediatricians today are much more thoughtful about when antibiotics are truly necessary versus when watchful waiting is the better choice. But for those of us who grew up in the era of "here's another round of amoxicillin," understanding this history is important context for understanding our health today.

your gut is a garden

Picture your microbiome as a garden. In childhood, that garden is being planted and cultivated for the very first time. Your gut is learning what is friend and what is foe. It's training your immune system and establishing the microbial foundation that your adult microbiome will be built on. Those early years represent a critical window of development.

Now imagine someone comes through that garden with a flamethrower. Not once, but repeatedly and relentlessly, during the exact period when everything is trying to take root.

That is what repeated or prolonged courses of broad-spectrum antibiotics do to a developing microbiome. Unfortunately, they don't selectively target the problematic organisms. They end up wiping out everything, the beneficial bacteria right along with the harmful ones.

And for those of you who garden, you'll understand what this means. If you rip everything out of your garden bed and strip it down to bare soil, you know that the first thing to grow back is not the tomatoes and the herbs and the flowers you carefully planted. It's the weeds.

In your gut, this looks like dysbiosis: an overgrowth of the organisms you don't want, a depletion of the beneficial ones you need, and a microbial ecosystem that is fundamentally out of balance.

The effects of dysbiosis are not only confined to your gut. This is one of the most important things I want you to understand. The effects show up systemically. Eczema, acne, brain fog, immune dysregulation, fatigue, joint pain, headaches, food sensitivities... and eventually, maybe a visit to a doctor who looks at you and says, "it sounds like IBS," as though that will give you some relief.

If you've been dealing with any combination of these issues your entire adult life and you've never been able to figure out why, I want you to go back and think about your antibiotic history, as there is a very good chance that may be where the story started.

"just take a probiotic"

You've probably heard this one before. Gut issues? Take a probiotic. Sounds like it should work, right? You're putting the good bacteria back in. Problem solved.

But many people take a probiotic and it either (1) does nothing or (2) makes them the feel worse. More bloating. More gas. More discomfort. And then they give up. They assume probiotics don't work for them, or that their gut is too far gone. Neither of those things is true. The problem is one of timing and sequence. It's not about whether probiotics work, but what needs to happen before they can.

Let's go back to my garden analogy. If your garden is completely overrun with weeds, you can't just scatter seeds on top of the chaos and expect a beautiful harvest. The seeds have nowhere to take root. The weeds are monopolizing all the space, all the nutrients, all the resources, and the good stuff doesn't stand a chance.

The same thing is happening in your gut when dysbiosis is present. When the opportunistic organisms are running the show, adding a probiotic without first addressing what's already overgrown is like pouring seeds into a garden bed that's choked with weeds. You haven't cleared the space. You haven't prepared the soil. And so the beneficial organisms you're introducing have no environment in which to establish themselves.

rebuilding the garden

In my world of functional and naturopathic medicine, we use a framework called the 5R Protocol to heal the gut. It is systematic, evidence-based, and maps beautifully onto the garden analogy.

Remove. Pull the weeds. Identify and remove the things that are causing damage and disruption, whether that's pathogenic organisms, food sensitivities, or environmental triggers that are perpetuating inflammation and imbalance.

Replace. Amend the soil. Replenish the digestive factors that may be missing or depleted, things like digestive enzymes, hydrochloric acid, or bile acids, so that your body can actually break down and absorb the nutrients from the food you eat. You can plant the most beautiful garden in the world, but if the soil has no minerals, nothing will thrive.

Reinoculate. Now we plant the seeds. This is where probiotics and prebiotic-rich foods come in. But notice that this is step three, not step one. We have prepared the environment first. We have cleared theweeds and enriched the soil. Now the beneficial organisms have a fighting chance to establish themselves and flourish.

Repair. Nourish the garden bed itself. Support the healing of theintestinal lining with targeted nutrients that reduce permeability ("leaky gut") and restore integrity. Think of this as reinforcing theborders of your garden, the structures that keep the good stuff in and the harmful stuff out.

Rebalance. Tend the garden for the long term. This means addressing the lifestyle factors that affect your gut health every single day: stress management, sleep quality, movement, and the nervous system patterns that determine whether your body is spending its time in a state of healing or a state of alarm.

This framework reflects one of the foundational principles of naturopathic medicine: the vis medicatrix naturae, or the healing power of nature. Your body has an innate intelligence. It wants to heal. It is wired for balance and restoration. Our job is not to force healing from the outside. Our job is to remove the obstacles that are standing in the way of that vital force, and then to create the conditions under which the body can do what it is designed to do.

That is what the 5R protocol is really about. It's a process of clearing the way so that your body's own healing capacity can flourish.

I talk more about the vis medicatrix naturae here.

what's growing in your garden?

If you've been struggling with digestive issues, skin problems, immune imbalance, or any of the other downstream effects of dysbiosis, and you cannot figure out what you're doing wrong... you're probably not doing anything wrong.

If you have a history of frequent antibiotic use, you are now likely working with a foundation that was compromised before you ever had a say in the matter. That is not your fault. And it does not mean you are broken or that the damage is permanent.

Your microbiome is resilient. It can be rebuilt. Your body is amazingly powerful. You don't need a doctor to "fix you." You need someone to help identify the obstacles standing in the way, and to give you the tools to address them. You do all the healing yourself. Your body already knows how. I'm just here to help you clear the path, and to provide some support and accountability along the way.

If this newsletter hit close to home and you're curious about what's really going on in your gut, I would love to chat. I offer complimentary 15-minute discovery calls where we can talk through your history, your symptoms, and whether working together might be the right fit.

Every garden can be rebuilt. Yours included. And this is a beautiful time of year to start.