What are the signs of an unbalanced intestinal flora?

What to remember :

• The intestinal microbiota is a key player in digestive, immune, metabolic and even mental health.

• An imbalance (dysbiosis) can manifest itself through digestive disorders, persistent fatigue, mood disorders, skin or weight problems.

• The main causes include ultra-processed diets, antibiotics, stress, lack of sleep and a sedentary lifestyle.

• Rebalancing your flora requires a diet rich in fiber and fermented foods, a healthy lifestyle and, if necessary, probiotic supplementation.

• Good news : dysbiosis isn't inevitable! With simple, sustainable actions, it's possible to restore your microbiota and improve your overall health.

Introduction

The intestinal microbiota —also called gut flora—is a key player in our overall health. It influences our digestion , immunity, mood, skin, and even weight. When it's unbalanced, we speak of intestinal dysbiosis , a condition that's increasingly common in our modern lifestyles. How can we recognize it? And, more importantly, how can we prevent or remedy it?

What is intestinal flora?

Intestinal flora refers to all the microorganisms (bacteria, yeasts, viruses, fungi, etc.) that colonize our intestines, mainly the colon. There are approximately 100,000 billion of them, from more than 1,000 different species. This microbial population acts as an organ in its own right, fulfilling numerous functions:

• Digestion of fiber and production of short-chain fatty acids (SCFAs);

• Synthesis of vitamins (K, B12);

• Barrier effect against pathogens;

• Regulation of the immune system and neurotransmitters.

A healthy intestinal microbiota is characterized by a microbial community that is both diverse and balanced, capable of ensuring functions essential to the proper functioning of the body.

What is a microbiota imbalance (dysbiosis)?

Dysbiosis can be the result of a number of factors. It is defined by:

• A loss of microbial diversity or...

• An overgrowth of pathogenic bacteria or...

• A decrease or even absence of good bacteria (such as Bifidobacterium , Faecalibacterium );

• And often inflammation of the intestinal mucosa.

It can be silent… or cause a cascade of disturbances.

What are the signs of an unbalanced intestinal flora?

Chronic digestive disorders

Digestive disorders are the most common manifestations of a microbiota imbalance. Bloating, gas, irregular transit ( constipation or diarrhea ), difficult digestion , abdominal pain, gastroesophageal reflux ... so many signs that can reflect an alteration of the intestinal ecosystem. In cases of dysbiosis, fiber digestion is less efficient, the production of short-chain fatty acids (SCFAs) decreases, and the intestinal barrier can become more permeable. This phenomenon, intestinal hyperpermeability or "leaky gut," allows unwanted molecules to pass into the circulation, maintaining low-grade inflammation that is often silent.

Anxiety, depression, sleep disturbances

The gut microbiota constantly communicates with the brain via what is known as the gut-brain axis—a complex network connecting the enteric nervous system, the immune system, the vagus nerve, and chemical messengers. It plays a key role in the production of neurotransmitters like serotonin, GABA, and dopamine, which regulate mood, stress, and sleep. When imbalanced, this dialogue can be disrupted, contributing to the onset or worsening of conditions such as anxiety,depression , sleep disturbances , and mood swings.

Weight gain or difficulty losing weight

When depleted or dominated by pro-inflammatory bacteria, the gut microbiota can disrupt several key mechanisms involved in weight management, including hunger, satiety, energy metabolism, and insulin sensitivity. In the long term, this imbalance can promote weight gain or make it more difficult to lose fat mass, despite nutritional efforts.

Frequent illnesses or persistent fatigue

The intestinal microbiota actively participates in the body's defense by acting as a natural immune barrier. It stimulates immune cells, prevents the proliferation of pathogens, and contributes to the balance of the inflammatory response. In cases of dysbiosis, these protective functions are weakened, which can lead to increased susceptibility to recurring infections—whether ENT, digestive, or urinary—as well as a feeling of persistent fatigue, often difficult to explain otherwise.

Autoimmune diseases

When imbalanced, the gut microbiota can alter the integrity of the intestinal barrier, promoting what is called intestinal permeability. This abnormal "porosity" allows certain inflammatory molecules or antigens to cross the digestive mucosa, which can trigger inappropriate activation of the immune system. This phenomenon is increasingly recognized in the development or worsening of autoimmune diseases such as rheumatoid arthritis, Hashimoto's thyroiditis, lupus, celiac disease, and type 1 diabetes.

Skin problems (acne, eczema, rosacea)

This gut-skin link, known as the gut-skin axis, relies on complex interactions between the gut microbiota, the immune system, and systemic inflammation. In cases of dysbiosis, certain pro-inflammatory bacteria release toxins and metabolites that can disrupt the immune balance, promoting the onset or worsening of skin disorders such as acne, eczema, psoriasis, and rosacea.

Antibiotic treatments

Antibiotics do not distinguish between pathogenic and beneficial bacteria: by eliminating them all, they can significantly impoverish the diversity of the microbiota. This imbalance weakens the intestinal ecosystem, increases the risk of digestive disorders such as diarrhea, and promotes the emergence of opportunistic pathogens such as Clostridium difficile, which can sometimes cause severe infections.

What are the main causes of dysbiosis?

The following table lists the main factors identified as contributors to intestinal dysbiosis.

How to rebalance your intestinal flora?

Focus on prebiotic fibers

Dietary fiber (vegetables, fruits, legumes, nuts, whole grains) - part of prebiotics - feeds the bacteria that produce SCFAs (butyrate, propionate, acetate), essential for intestinal and immune health. They are found in the plant kingdom: fruits, vegetables, legumes, oilseeds, and whole grains.

The idea is to move towards 25 to 30g of fiber per day, incorporating it gradually if its presence in the diet is initially low.

Introduce fermented foods rich in natural probiotics

Raw sauerkraut, kefir , kombucha , unpasteurized pickles, lactofermented tofu , etc. are all fermented foods rich in natural probiotics . It is best to choose unpasteurized foods in the fresh produce section to guarantee the presence of these microorganisms. This ensures that these foods provide live strains that enrich the intestinal flora such as Lactobacillus and Bifidobacterium bacteria, proven beneficial in IBD, acne and digestive disorders.

Limit ultra-processed foods

Rich in added sugars, refined fats and additives, these products have the characteristic of being pro-inflammatory and promote systemic inflammation , intestinal permeability and dysbiosis.
It's not a matter of banning them completely, but of consuming them in moderation. Occasionally, they won't have a major impact, unlike daily consumption: it's the repetition that unbalances the microbiota.

Move, sleep well, breathe: promote an overall healthy lifestyle

• Moderate physical activity (walking, cycling, etc.) : it improves intestinal motility as well as microbial diversity;

• Regular sleep (7-9 hours) : quality sleep promotes microbial diversity and limits systemic inflammation;

• Stress management (cardiac coherence, yoga, meditation, etc.) : this helps modulate the gut-brain axis while reducing the level of cortisol, the stress hormone.

Consider taking probiotics if necessary

Probiotics contribute to the balance of intestinal flora, which can help restore order in cases of dysbiosis.

Conclusion

Our intestinal flora is a valuable ally... but also a fragile one. When it's unbalanced, it can manifest as digestive problems, persistent fatigue, weight fluctuations, low morale, autoimmune diseases, and even skin problems. These signs should be considered warning signals.

The good news is that a damaged microbiota can be rebalanced. By adopting a diet rich in fiber and probiotic-rich fermented foods , promoting a healthy lifestyle, and if necessary, incorporating targeted probiotics, it is possible to restore a lasting balance... and at the same time, improve your overall health.

Sources :

[1] Inserm. 2021. Intestinal microbiota (intestinal flora) - A serious avenue for understanding the origin of many diseases, consulted from: https://www.inserm.fr/dossier/microbiote-intestinal-flore-intestinale/

[2] Shen, Y., Fan, N., Ma, SX, Cheng, X., Yang, X., & Wang, G. (2025). Gut Microbiota Dysbiosis: Pathogenesis, Diseases, Prevention, and Therapy. MedComm, 6(5), e70168. https://doi.org/10.1002/mco2.70168

[3] Nikel, K., Stojko, M., Smolarczyk, J., & Piegza, M. (2025). The Impact of Gut Microbiota on the Development of Anxiety Symptoms—A Narrative Review. Nutrients, 17(6), 933. https://doi.org/10.3390/nu17060933

[4] Van Hul, M., Cani, PD, Petitfils, C., De Vos, WM, Tilg, H., & El-Omar, EM (2024). What defines a healthy gut microbiome? Gut, 73(11), 1893–1908. https://doi.org/10.1136/gutjnl-2024-333378