GLP-1's Don’t Fix the Root Cause — Your Gut Might Be the Missing Piece

A prescription is not a root cause answer.

I say that as a physician who prescribes GLP-1 medications and believes in their role in obesity care. But when a patient comes to me having already tried semaglutide or tirzepatide, has lost weight, felt hopeful, then watched it slowly come back, the question I’m asking isn’t “what’s the next medication?”

It’s “what was driving this in the first place, and did we ever actually address it?”

More often than not, the answer lives somewhere most people haven’t looked yet: the gut.

Your Gut Microbiome and Weight Are More Connected Than You Think.

Inside your digestive tract lives a complex ecosystem of trillions of bacteria, your gut microbiome. These bacteria don’t just help you digest food. They influence your metabolism, your inflammation levels, your hunger hormones, and how many calories your body extracts from what you eat.

One bacterial group keeps coming up in the obesity research: Firmicutes.

People with obesity tend to have a higher ratio of Firmicutes bacteria relative to a group called Bacteroidetes. This matters because Firmicutes are exceptionally efficient at breaking down carbohydrates and extracting energy from food. Meaning a gut dominated by these bacteria can pull more calories from the same meal than a balanced microbiome would.

It goes further than calories. An overgrowth of certain Firmicutes species is associated with increased intestinal permeability, what many call “leaky gut", which triggers low-grade systemic inflammation. That inflammation interferes with insulin signaling, disrupts leptin (your satiety hormone), and makes fat loss harder even when you’re doing everything right.

This is why two people can eat the same diet and have completely different metabolic outcomes. The gut is a major piece of that puzzle.

So Where Do GLP-1s Fit In?

GLP-1 medications work! The clinical data is clear. A 2025 joint advisory from the Obesity Medicine Association confirmed that semaglutide and tirzepatide can produce 5% to nearly 21% body weight reduction, with meaningful improvements in blood pressure, blood sugar, and cardiovascular risk.

But the same advisory was equally clear: GLP-1s alone are not enough. Without addressing the underlying metabolic environment, results plateau, muscle mass is lost, and most people regain the majority of their weight within a year of stopping the medication.

What the advisory doesn’t yet fully address, because the research is still catching up, is the gut microbiome’s role in all of this. And this is where the most underutilized clinical work is happening right now.

The Root Cause Question Nobody Is Asking

Here’s what I wish more of my patients had been told before their first GLP-1 prescription: weight is a symptom.

It is a symptom of metabolic dysfunction that has been building, sometimes for decades. Shaped by your diet, stress, sleep, hormones, and the health of your gut. Prescribing a GLP-1 without understanding that underlying terrain is like treating a fever without looking for the infection.

When I work with patients at KIWI MED®, we ask a different set of questions: What does your microbiome look like? What does your inflammatory profile tell us? Are your hormones contributing to where you are? What is your body actually asking for?

That is a root cause conversation and it changes everything about how we approach treatment, whether that includes a GLP-1 or not.

Where to Start

You don’t have to wait for a comprehensive workup to begin supporting your gut:

Feed your Bacteroidetes. A diet rich in fiber: vegetables, legumes, whole grains, fruits support the bacterial diversity that counterbalances Firmicutes overgrowth. The 2025 advisory specifically highlights minimally processed, nutrient-dense foods as essential alongside GLP-1 therapy.

Cut ultraprocessed foods. These are strongly associated with gut dysbiosis and the Firmicutes-dominant pattern linked to obesity and inflammation.

Address sleep and stress. Chronic stress and poor sleep disrupt the gut-brain axis and alter microbiome composition. This is not separate from your metabolic health, it is central to it.

The Longer-Lasting Path

The patients I see who achieve lasting results not just weight loss, but genuine metabolic health are the ones who used the window that GLP-1 therapy opened to build something real underneath it.

A healthier gut. A stronger body. A metabolic environment that supports them long after any medication changes.

That’s the work I find most meaningful as a physician. And it’s the work I believe you deserve access to. 🌿

Dr. Julaine Braham a double board-certified physician in Internal Medicine and Obesity Medicine and the founder of KIWI MED®, a virtual functional medicine and obesity medicine practice serving patients in Florida and Georgia, with education consultations available nationwide. Learn more at kiwi-med.com.

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References: Mozaffarian D, et al. Nutritional priorities to support GLP-1 therapy for obesity: A joint Advisory from the American College of Lifestyle Medicine, the American Society for Nutrition, the Obesity Medicine Association, and The Obesity Society. Obesity (Silver Spring). 2025;33(8):1475–1503.