Debunking Gut Health Myths: A Holistic & Functional Medicine Perspective

Gut health has become one of the most talked-about topics in wellness. On the surface, this is encouraging, digestion plays a central role in immune function, inflammation regulation, hormone metabolism, and brain chemistry.

But as interest grows the messaging has become increasingly simplified.

Much of today’s gut health content frames digestion as something broken that must be urgently “fixed,” often through aggressive protocols or rigid rules. In practice, this urgency can create more stress in a system that already struggles to regulate.

At Really Nourished we take a steadier view. Digestion is not a standalone system (nothing in the body is)  it is deeply interconnected with the nervous system, endocrine signaling, immune balance, and metabolic health. Below are some of the most common gut health myths I see in practice, why they make sense, where they fall short, and how we approach them differently.

Myth #1: “If you fix your gut, everything else will fall into place.”

This belief exists for a reason. The gastrointestinal tract houses a large portion of the immune system, produces neurotransmitters like serotonin, and plays a key role in inflammatory signaling.

What’s misleading is the idea that the gut operates independently.

Digestion is regulated by the autonomic nervous system, influenced by cortisol and sex hormones, and highly sensitive to blood sugar stability. Chronic stress alone can reduce stomach acid, slow motility, alter microbial balance, and increase intestinal permeability  even with the perfect healthy diet. 

From a holistic perspective, supporting nervous system regulation, hormonal balance, and metabolic stability is often what allows gut healing to occur.

Myth #2: “More probiotics automatically mean better gut health.”

Probiotics are often marketed as a shortcut to gut health, which makes this belief understandable.

However, introducing bacteria into a system with impaired digestion, sluggish motility, or chronic stress can worsen symptoms like bloating, gas, and discomfort. More bacteria is not always the answer when the digestive environment isn’t ready.

A holistic approach prioritizes digestive capacity first, adequate stomach acid, enzyme activity, bile flow, and coordinated motility and then uses probiotics strategically, based on individual needs and tolerance.

Myth #3: “You must have a bowel movement every day or something is wrong.”

Let’s clarify this one.

From a physiological perspective, daily bowel movements are a healthy and reasonable goal. Regular elimination supports detoxification, hormone clearance (including estrogen), bile recycling, and microbial balance.

Where this belief becomes unhelpful is when frequency alone is treated as the sole marker of gut health.

Holistically, we care just as much about how the body is eliminating. Ease, completeness, consistency, and comfort matter alongside daily frequency. A person having daily bowel movements with straining, urgency, or incomplete evacuation is not experiencing optimal digestion.

Constipation and irregularity are rarely just fiber issues. They are commonly influenced by nervous system regulation, hydration, bile flow, thyroid and sex hormones, mineral status, and chronic stress signaling. Supporting these systems is often what restores daily, comfortable elimination.

Myth #4: “Leaky gut is the root cause of all symptoms.”

Increased intestinal permeability is a real and well-documented phenomenon, which is why this explanation often feels validating.

What’s frequently overlooked is why permeability increases in the first place.

From a holistic lens, barrier dysfunction is often a downstream effect of chronic inflammation, oxidative stress, nutrient depletion, infections, medications, or prolonged stress exposure. Treating permeability as the starting point can miss the upstream drivers that prevent lasting repair.

Myth #5: “If a food bothers you, you should eliminate it long-term.”

Elimination diets often provide fast relief, reinforcing the belief that avoidance is the solution.

But long-term restriction can increase stress hormones, reduce microbial diversity, and decrease oral tolerance over time. The immune system thrives on exposure within a regulated environment.

A holistic approach uses elimination temporarily, to calm inflammation and identify triggers, while rebuilding digestive resilience and gradually expanding dietary variety.

Myth #6: “If labs are normal, your gut is fine.”

Laboratory testing is valuable, but it doesn’t tell the full story.

Many functional imbalances including dysregulated motility, altered stress signaling, or early inflammatory patterns, do not appear on conventional labs. Holistically, symptoms, timing, and patterns offer essential information about how the body is adapting.

Normal labs do not negate lived experience. You know what you feel. 

Myth #7: “Candida or SIBO cleanses are the answer to bloating.”

Targeted protocols can be helpful in the right context.

What’s misleading is the assumption that aggressive eradication should always be the first step. In systems already under strain, intensive cleanses can further disrupt the gut lining, nervous system, and detoxification pathways.

Holistic care focuses on building capacity before targeting, improving digestion, motility, immune balance, and stress resilience so the body can respond appropriately.

Myth #8: “Gut health is mostly about what you eat.”

Nutrition matters but it is not the only variable.

Digestion is influenced by sleep quality, circadian rhythm, medications, physical activity, emotional safety, and chronic stress exposure. The same meal can be digested very differently depending on nervous system state.

Nutrition works best when paired with regulation, rhythm, and support.

Myth #9: “Digestive symptoms mean your gut is broken.”

Persistent symptoms can feel alarming.

Symptoms are not failures they are communication. They reflect how the body is responding to load, stress, and demand. Listening to these signals allows for supportive, targeted intervention rather than force.

Myth #10: “There’s one gut-healing protocol that works for everyone.”

Standardized protocols are appealing because they promise certainty.

But physiology is bio-individual. Sustainable gut healing depends on history, stress exposure, hormone status, nutrient reserves, and current capacity. Healing unfolds at a pace the body can tolerate not one dictated by trends.

A Final Thought

At Really Nourished, we don’t chase fixes, we build capacity. When the nervous system feels safe, digestion is supported, and the body is adequately resourced, regulation often follows naturally. If gut health content has left you feeling overwhelmed or behind, know this: your body isn’t broken. Healing doesn’t require urgency; it requires clarity, context, and support.