Probiotics and gut flora: how to restore and protect your microbiome

What is gut flora?

Gut microbiota: an ecosystem at the heart of your health

Gut flora, or gut microbiota, refers to all the microorganisms — bacteria, yeasts, viruses and fungi — that colonise our digestive system. This ecosystem, unique to each individual, weighs between 1 and 2 kg in the human body and includes over 800 different bacterial species. A large proportion of these microorganisms reside in the colon and small intestine. To maintain this balance, probiotics — living microorganisms with documented benefits — are one of the most studied approaches in research.

The 4 major bacterial families of the gut

The health of the microbiome depends less on quantity than on the diversity of species present. Four major groups (phyla) dominate:

Gut flora, microbiota, microbiome: what are the differences?

The microbiota refers to the microorganisms themselves. The microbiome encompasses their genetic material (150 times more genes than the human genome). The term "gut flora", although historically imprecise (bacteria are not plants), remains the most commonly used expression.

Why your gut flora is essential

The role of the microbiome extends far beyond simple digestion. Your gut flora is involved in three major vital functions.

Digestion and nutrient absorption

The microbiome plays a central role in digestive health. Gut bacteria break down dietary fibres that our own enzymes cannot process. They produce SCFAs (butyrate, propionate, acetate) that nourish the cells of the colon, regulate bowel movements and contribute to daily digestive comfort. They also synthesise essential vitamins: B12, K2, B9, B6.

70% of your immunity resides in the gut

The gut-brain axis: when flora influences mood

The gut communicates with the brain via the vagus nerve and the enteric nervous system. An imbalanced flora can accompany periods of stress, anxiety or emotional fatigue, with a direct impact on mental health. This is why it is referred to as the "second brain".

Imbalanced gut flora: how to recognise it

The symptoms of dysbiosis

Dysbiosis refers to the disruption of the balance between beneficial and pathogenic bacteria in the gut. The most common signs:

Note: prolonged dysbiosis is also associated with more serious intestinal disorders such as irritable bowel syndrome or Crohn's disease, and can disrupt the vaginal flora in women. If you experience persistent digestive problems, it is essential to consult a healthcare professional to rule out other causes.

The causes that destroy gut flora

Several factors weaken the microbiome: certain medications such as antibiotics (which eliminate both pathogenic and beneficial bacteria indiscriminately), chronic stress (via cortisol secretion), a diet low in fibre and high in refined sugars, excessive alcohol consumption, lack of sleep, and natural ageing (bacterial diversity declines from age 65).

Should you get a microbiome test in Switzerland?

Microbiome analyses using DNA sequencing are available in Switzerland, notably through specialised laboratories such as Medisyn or home kits. They provide an overview of bacterial diversity and potential imbalances. However, interpretation remains complex and "norms" vary from person to person. These tests do not replace a consultation with a gastroenterologist or nutritional physician. In Switzerland, the gastroenterology departments at University Hospital Zurich (USZ), Inselspital Bern or University Hospital Basel can support cases of severe dysbiosis or chronic digestive disorders.

What role do probiotics play in gut flora?

How probiotics work in the gut

Probiotics are living microorganisms that, when ingested in sufficient quantities, confer a health benefit. Available as food supplements (in capsule, powder or liquid form) or naturally present in certain foods, the most studied strains belong to the genera Lactobacillus, Bifidobacterium and the yeast Saccharomyces. To learn how to choose the right probiotic and understand their mechanism of action, read our guide to probiotics: strains, benefits and selection criteria.

In summary, probiotics colonise the intestinal mucosa, compete with pathogenic germs, produce lactic acid and antimicrobial substances, and help strengthen the intestinal barrier and the local immune response.

What the research says: a real but nuanced effect

Probiotics can thus help relieve gastrointestinal symptoms and prevent certain complications. However, a meta-analysis published in BMC Medicine (Éliás et al., 2023, 15 RCTs) shows that probiotics do not significantly improve microbial diversity during antibiotic treatment. The restoration of this diversity appears to occur naturally within 3 to 8 weeks, with or without probiotics.

Probiotics and prebiotics: an essential duo

Prebiotics are non-digestible fibres (inulin, FOS, GOS) that selectively nourish beneficial bacteria. The combination of probiotics + prebiotics (synbiotics) promotes the establishment and growth of good bacteria. The best dietary sources of prebiotics: garlic, onion, leek, banana, oats, legumes and chicory.

Restoring gut flora with probiotics: protocols by situation

After antibiotic treatment

Broad-spectrum antibiotics can reduce microbiome diversity by 30 to 50%. Certain species do not return for 6 months (Schwartz et al., Genome Medicine, 2020). When should you take probiotics in this case? The ideal time to start a multi-strain probiotic (L. rhamnosus GG, S. boulardii) is from the beginning of treatment, taken at least 2 hours apart from the medication, and continuing for 2 to 4 weeks after the course ends. Combine with a balanced diet rich in prebiotic fibres to accelerate recolonisation.

Irritable bowel syndrome (IBS)

A meta-analysis of 82 trials including over 10'000 patients (Goodoory et al., Gastroenterology, 2023) suggests that certain strains may relieve IBS symptoms: Escherichia strains with moderate evidence on global symptoms, and Lactobacillus plantarum 299v with low-level evidence. Bifidobacterium strains show a possible effect on abdominal pain. Recommended course duration: 4 to 12 weeks. The authors note, however, that the certainty of evidence remains overall low to very low. For any prolonged use, seek advice from your doctor.

Gut flora during pregnancy and in infants

The microbiome is established from birth, influenced by the mode of delivery and breastfeeding. Breast milk contains natural prebiotics (oligosaccharides) that nourish the infant's first bacteria. In pregnant women, probiotics support bowel regularity, help maintain the balance of the vaginal flora and promote an optimal microbiome passed on to the baby. In infants, L. reuteri is the most studied strain for colic. Any mother wishing to supplement her child should seek medical advice first.

Chronic stress and gut flora

The cortisol secreted during stress weakens the intestinal barrier and promotes pathogenic bacteria. Certain strains, known as "psychobiotics", are being studied for their positive effect on the gut-brain axis: L. helveticus R0052 and B. longum R0175 showed a reduction in psychological distress and urinary cortisol in a randomised clinical trial involving healthy volunteers (Messaoudi et al., British Journal of Nutrition, 2011). However, probiotics do not replace work on the root causes of stress, nor psychological support if needed.

Good to know: traveller's diarrhoea

When travelling to high-risk areas, traveller's diarrhoea is often caused by germs such as Escherichia coli. S. boulardii, started a few days before departure, may modestly reduce the risk. Consulting a healthcare professional before travelling is recommended.

🇨🇭 Developed and manufactured in Switzerland

FloraPro 7 — Multi-strain probiotic by Swilab

Our formula contains the strains mentioned in these protocols: L. rhamnosus, B. lactis, L. plantarum and 4 other documented strains. 25 billion CFU per gastro-resistant vegetable capsule.

• L. rhamnosus — post-antibiotic support
• B. lactis · B. longum — Bifidobacterium family
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• Gastro-resistant HPMC capsules

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⚠️ Food supplement. Does not replace a varied and balanced diet or a healthy lifestyle. If in doubt, consult a healthcare professional.

How long does it take to rebuild gut flora?

What the studies show

The duration of restoration depends on the cause of the imbalance, age and lifestyle. Here are the approximate timeframes from the scientific literature:

Lifestyle habits that protect your microbiome every day

Beyond probiotic courses, several habits help support the microbiome sustainably: a balanced and diverse diet rich in fibre (30 g/day recommended), regular consumption of natural probiotic foods and fermented drinks (kefir, kombucha), regular physical activity, quality sleep and stress management. In Switzerland, access to local fermented products (mountain yoghurts, raw milk cheeses) is an asset worth leveraging to maintain healthy gut flora.

FAQ — Probiotics and gut flora