Keto and Your Microbiome: What You Need to Know

There’s no question the ketogenic diet has gained traction. For many, it brings real benefits—reduced inflammation, improved energy, and sharper focus. It’s a way to step back from the sugar-laden modern diet and calm what we often call the body’s “inflammatory fire.”

But the longer story, the one your microbiome is quietly telling, calls for a deeper look.

At BiotiQuest, we always return to the innate intelligence of the body and the ecosystems that support it. When we understand why certain diets feel good at first—and why they may not be sustainable—we empower ourselves to choose not from trends, but from trust and knowledge.

Why Keto Can Feel Like a Breakthrough

In the short term, reducing carbs and entering ketosis shifts the body’s energy source from glucose to fat. This can lower blood sugar, reduce oxidative stress, and bring clarity, especially for those navigating insulin resistance or inflammatory conditions.

And yes, that initial relief is real.

But what happens when we stay there too long?

Your Microbiome Needs a Broader Diet, But Not Just Plants

During one of our recent Sugar Shift® Challenge calls, gut health expert Dr. Haroldo Magarinos spoke about the unintended long-term consequences of restrictive diets like strict carnivore or extended keto. A participant shared how their health began to unravel after months on a meat-only diet. The missing piece? Microbial diversity, especially bacteria that feed on complex fibers.

Most often, when we hear “fiber,” we think of plants—leafy greens, root vegetables, legumes. And these are crucial. They feed the beneficial bacteria that shape our immune system, regulate mood, and support metabolism.

But here’s where it gets interesting.

One of the most important “fibers” for the microbiome isn’t found in plants at all. It’s hyaluronic acid, a complex molecule found in animal joints, cartilage, and connective tissue. In fact, traditional cultures prized slow-cooked bone broths and organ meats not just for their nutrient density, but for how they nourished the body’s terrain—right down to the microbial level.

So yes, our microbiome needs plants. But it also benefits deeply from nose-to-tail animal nutrition, which modern diets often overlook.

Keto as a Seasonal Tool

If we look through a historical lens, keto—or low-carb, high-fat eating—wasn’t a diet. It was a season. In colder months, when plants were scarce and animals more readily hunted, humans naturally shifted into a ketogenic state. Our **hunting seasons, fall, winter, and early spring, **aligned with nature’s rhythm, not a meal plan.

Spring brought lambs and greens. Summer offered berries, honey, and root vegetables. Autumn meant abundance, animals fattened on summer grasses. Winter called for ketosis.

This concept, seasonal keto, mirrors what the body intuitively knows: change is part of health.

The Real Goal: Metabolic Flexibility

Today, many wellness experts are evolving beyond rigid frameworks. Ben Azadi, once a dedicated keto advocate, now speaks of Metabolic Freedom: the ability to shift between fuel sources (fat and glucose) with ease. In his new book by the same name, Ben shares how true health is rooted in adaptability, not dogma.

We couldn’t agree more.

Metabolic flexibility honors both the scientific and ancestral understanding of food. It means giving your body what it needs now, not what worked six months ago or for someone else online.

Tips for Supporting Your Microbiome on Keto—and Beyond

Whether you’re experimenting with keto or simply curious, here are some ways to support your microbiome along the way:

• Include both plant and animal-based fibers. Think broccoli and bok choy—but also bone broth and collagen-rich cuts.
• Don’t fear seasonal shifts. Allow your diet to change with the rhythms of the earth and your own body.
• Cycle out of keto periodically. This mirrors historical eating and supports diverse microbial populations.
• Incorporate fermented foods like sauerkraut, kefir, or kimchi—especially during low-carb phases.
• Consider a guild-based probiotic like Sugar Shift®, which supports microbial balance during dietary transitions.

In Closing: Embracing the Microbial Wisdom Within

Your microbiome isn’t static—it’s alive, dynamic, and incredibly responsive to your choices. The ketogenic diet can be a beautiful reset, a seasonal pause, a therapeutic tool. But when we stay stuck in any pattern, we lose sight of what the body truly craves: diversity, adaptation, and a connection to nature’s rhythms.

So rather than asking, Is keto good or bad?, we invite you to ask: What season am I in? What does my body need now?

Because that’s where real freedom begins.