Candida vs SIBO: How to Know What’s Really Going On in Your Gut

Do you feel bloated after every meal, constantly crave sugar, or suffer from fatigue, brain fog, or irregular bowel movements? If so, you might be wondering whether Candida overgrowth or SIBO (Small Intestinal Bacterial Overgrowth) is at the root of your symptoms.

Candida overgrowth is a yeast imbalance, while SIBO (Small Intestinal Bacterial Overgrowth) is a bacterial imbalance. Both can cause bloating, fatigue, and gut issues, but Candida is linked to thrush and sugar cravings, while SIBO causes more severe post-meal bloating and bowel changes. Testing (stool vs breath tests) is key to tell them apart.

These two gut imbalances share many overlapping symptoms and often get mistaken for one another. Both are common in people with IBS-like symptoms and may not show up on standard NHS tests, making them incredibly frustrating to deal with especially if you’ve already tried dietary changes, probiotics, or prescriptions with little relief.

In clinic, we regularly see clients dealing with either Candida, SIBO, or both at once. Knowing which is the dominant issue is key to choosing the right treatment the wrong one can make things worse.

In this guide, I’ll explain the difference between Candida and SIBO, the symptoms they share (and those they don’t), how to test for each, and how we approach treatment from a functional medicine perspective.

What Is Candida Overgrowth?

Candida is a type of yeast that naturally lives in the gut, mouth, skin, and vaginal tract. In small amounts, it’s harmless — even beneficial. But when the delicate balance of your gut microbiome is disrupted, Candida can multiply and cause a range of symptoms.

This is known as Candida overgrowth or intestinal candidiasis.

What causes Candida?

• Broad-spectrum antibiotics (which kill good bacteria)
• High-sugar or refined carbohydrate diets
• Oral contraceptives or HRT
• Immune suppression or high stress
• Low stomach acid or digestive enzyme deficiency

Key Symptoms of Candida Overgrowth:

• Strong sugar and carbohydrate cravings
• Recurrent thrush (vaginal, oral), fungal rashes or athlete’s foot
• Bloating, flatulence, loose stools or diarrhoea
• Brain fog and poor concentration
• Fatigue and low energy
• Skin problems (eczema, hives, rashes, acne)
• White coating on tongue (oral candidiasis)
• PMS or mood swings

Candida can also impact the vaginal microbiome, making it a common cause of recurring thrush — particularly after antibiotic use.

Research Insight: A study published in Clinical Microbiology Reviews highlights how Candida albicans can disrupt the gut lining and immune signalling, contributing to leaky gut, inflammation, and even systemic symptoms.

What Is SIBO?

SIBO, or Small Intestinal Bacterial Overgrowth, occurs when bacteria that normally reside in the large intestine migrate up into the small intestine, where they don’t belong. These bacteria begin to ferment undigested carbohydrates, producing gas, inflammation, and a wide range of uncomfortable symptoms.

Unlike Candida (a yeast), SIBO involves bacterial overgrowth, and the symptoms are often more digestion-specific especially immediately after meals.

Common Causes of SIBO:

• A history of food poisoning or traveller’s diarrhoea
• Irritable Bowel Syndrome (IBS) – Research shows SIBO is found in up to 78% of people with IBS (Pimentel et al., 2021).
• Slow motility (e.g. due to hypothyroidism, vagus nerve dysfunction, Ehlers-Danlos Syndrome)
• Long-term use of proton pump inhibitors (like omeprazole or lansoprazole)
• Adhesions or scarring from abdominal surgery
• Low stomach acid or enzyme insufficiency

Types of SIBO:

• Hydrogen SIBO – often linked with loose stools or diarrhoea
• Methane SIBO (now known as IMO) – associated with constipation and bloating
• Hydrogen Sulfide SIBO – often leads to gas with a rotten egg smell, fatigue, and more systemic symptoms

Key Symptoms of SIBO:

• Severe bloating and fullness after meals
• Reflux or belching
• Excessive gas (often sulphuric-smelling)
• Abdominal pain or discomfort
• Diarrhoea, constipation, or alternating between the two
• Nutrient deficiencies (especially B12, iron, and fat-soluble vitamins)
• Brain fog and fatigue

Breath testing is the gold standard for SIBO diagnosis, measuring hydrogen, methane, and hydrogen sulfide gas levels after drinking a sugar solution.

Research Insight: According to a 2021 review in Gastroenterology, SIBO is increasingly recognised as a contributor to IBS symptoms, particularly bloating and diarrhoea.

Candida vs SIBO: Key Differences

Because Candida and SIBO can both disrupt gut function and affect the immune and nervous systems, there’s often significant symptom overlap but also some important differences. Understanding these distinctions can help point you toward the right diagnosis and treatment approach.

Here’s a side-by-side comparison of the most common symptoms:

Is it Candida or SIBO?

If you have both sets of symptoms, you may have both conditions simultaneously

If you have sugar cravings, thrush, skin rashes, and brain fog → think Candida

If you have bloating after meals, constipation or diarrhoea, and gas/reflux → think SIBO

Because both conditions affect the gut, they share many symptoms such as bloating, distension and changes in bowel habits.
However, there are key differences in the wider symptom picture that can give important clues.

Can You Have Both Candida and SIBO?

Yes and in fact, this is more common than you might think.

In clinic, we often see clients struggling with both Candida and SIBO at the same time. This overlap can lead to more persistent, confusing, and treatment-resistant symptoms especially if the root causes aren’t fully addressed.

Why Do Candida and SIBO Coexist?

There are several reasons Candida and SIBO tend to occur together:

• Antibiotic use: Antibiotics used to treat SIBO can wipe out beneficial bacteria and allow Candida to flourish.
• Slow motility: Poor movement through the small intestine allows both bacteria and yeast to overgrow.
• Weakened immune function: A compromised gut immune barrier (low secretory IgA) can create a permissive environment for both.
• Biofilms: Both Candida and bacteria can form biofilms — protective layers that make them harder to eliminate.
• Dietary habits: Diets high in sugar, alcohol, yeast or refined carbohydrates can feed both organisms.

Treating one without addressing the other may lead to temporary improvements followed by relapse — which is why a proper diagnosis and sequenced treatment is essential.

How to Know Which Is Dominant?

When symptoms overlap, it can be difficult to know which condition is driving the problem. While clinical history and symptom patterns offer clues, the most accurate way to differentiate is through testing.

Clues From Symptoms & History:

• Recent antibiotic use → think Candida
• Persistent reflux and bloating after meals → think SIBO
• Recurrent thrush, fungal skin issues → Candida
• IBS diagnosis with alternating stools → SIBO
• Strong sugar cravings and fatigue → Candida
• Rotten egg-smelling gas → possible Hydrogen Sulfide SIBO

Testing Options:

Candida vs SIBO Treatment: What’s the Difference?

Although both Candida and SIBO require antimicrobial support and gut healing strategies, the approach differs significantly depending on which organism is dominant. Using the wrong protocol for example, a candida diet for someone with active SIBO can worsen symptoms or delay progress.

Here’s how the treatment strategies compare:

Treatment: Candida vs SIBO

Although symptoms often overlap, Candida overgrowth and SIBO require different treatment strategies. In functional medicine, treatment is always tailored to test results and your individual history, but here’s an overview of how approaches typically differ.

Candida Overgrowth Treatment

1. Dietary Support

• Reduce yeast‑feeding foods: limit sugar, refined carbs, and alcohol and foods contiaing yeast to deprive yeast of its preferred fuel.
• Emphasise whole foods: vegetables, lean proteins, low‑sugar fruits (like berries), and anti‑inflammatory fats (olive oil, avocado).
  
  

2. Antifungal Support

• Clinically, we often use targeted herbs or nutrients that have been shown to reduce yeast overgrowth, such as:
  • Caprylic acid
  • Garlic
  • Berberine
  • Grapefruit seed
• In some cases, a doctor may prescribe antifungal medications (e.g., nystatin or fluconazole) if needed.
  
  

3. Rebuild and Protect the Gut

• Support gut lining integrity with nutrients like L‑glutamine and zinc carnosine.
• Introduce probiotics and prebiotics gradually once yeast levels are reduced to restore balance.
  
  

SIBO Treatment

1. Dietary Support

• Short‑term low‑FODMAP or SIBO‑specific diets to reduce fermentable carbs that feed bacteria in the small intestine.
• Focus on easily digested proteins and non‑starchy vegetables while avoiding triggers (onions, garlic, high‑lactose dairy) during treatment.
  

2. Antimicrobial Therapy

• Depending on breath test results (hydrogen‑dominant, methane‑dominant, or mixed), treatment may include:
  • Herbal antimicrobials (e.g., oregano, berberine, neem)
  • Or prescription antibiotics like rifaximin ± neomycin (for methane‑dominant SIBO).
    

3. Motility and Prevention

• Because SIBO often returns if underlying motility issues aren’t addressed, prokinetics are key.
  • Ginger, Iberogast, or prescription options can help keep food and bacteria moving in the small intestine.
• Correct nutrient deficiencies (e.g., B12, iron) that often occur in SIBO.
  
  

Summary Key Differences between Candida and SIBO

How to Figure Out Which Condition Is Predominant (and Why It Matters)

When symptoms overlap, it can feel confusing to know where to start.
In functional medicine, we rarely try to treat everything at once. Instead, we look for the predominant driver of symptoms and begin there.
This staged approach reduces side effects, prevents overwhelm, and usually gives faster relief.

Step 1: Look at your symptoms

Certain symptom patterns point more strongly to one condition:

• SIBO tends to dominate when:
  – Bloating is prevalent
  – There’s marked constipation or diarrhoea (or both),
  – There are nutrient deficiencies (e.g. low B12, iron) or significant weight changes.
  
• Candida tends to dominate when:
  – There’s recurrent thrush, jock itch, athlete’s foot or fungal nail infections,
  – Intense sugar cravings are present,
  – There’s a white coating on the tongue or sinus/fungal symptoms beyond the gut.

Step 2: Use functional testing where possible

While symptoms offer clues, testing removes guesswork:

• SIBO: Hydrogen/methane breath test (lactulose or glucose).
• Candida: Stool analysis or Organic Acids Test (looking for yeast metabolites such as arabinose or tartaric acid).

Results show which overgrowth is most significant or active.

Step 3: Focus treatment on the main driver

Once we know which overgrowth is most active:

• Start with the condition causing the most symptoms or showing the strongest test markers.
• Support overall gut health during treatment to make the environment less favourable for both overgrowths.
• Once symptoms settle, reassess and, if needed, target the second condition.
  
  

Why focus on one first

• Treating both aggressively at the same time can cause significant die‑off reactions (worsening bloating, fatigue, headaches).
• By focusing on the main driver, you reduce the overall microbial load in a controlled way, making it easier to handle the next phase.

In clinic:
I often see clients whose breath tests show high methane levels (SIBO dominant) but who also have a mild yeast overgrowth on stool testing. In these cases, we focus first on normalising motility and reducing SIBO, while maintaining a low‑sugar, anti‑yeast diet in the background. Once symptoms improve, we retest and address any residual Candida

Key Takeaways

• Candida overgrowth = fungal imbalance, often with skin and mucosal symptoms.
• SIBO = bacterial overgrowth in the small intestine, often with malabsorption.
• Symptoms overlap, so testing is essential for clarity.
• Both require targeted, staged treatment — diet alone rarely resolves them.

Book a consultation

If you’re struggling with bloating, distension, or digestive issues despite normal scans and tests, functional medicine testing can uncover hidden imbalances like Candida or SIBO.

Feel free to get in touch if you’d like to discuss testing options or book a consultation.

Frequently Asked Questions (FAQs)

Can you have Candida and SIBO at the same time?

Yes, you can. Candida (a yeast overgrowth) and SIBO (a bacterial overgrowth) often coexist, especially in people with chronic gut symptoms or a history of antibiotic use. Treating one may not fully resolve symptoms if the other is also present. A combined protocol may be necessary.

How do I know if I have Candida or SIBO?

Candida and SIBO share many symptomslike bloating, brain fog, and fatigue but there are subtle differences:

• Candida is more often linked to thrush, fungal infections, sugar cravings, and itching.
• SIBO tends to cause more gas, distension, and bowel changes (diarrhea or constipation).

Testing is the best way to confirm. SIBO is diagnosed with a breath test, while Candida is typically found via stool tests, urine organic acids, or symptom patterns.

Which should I treat first: SIBO or Candida?

It depends on the individual. In many cases, it’s best to address SIBO first, especially if symptoms are severe or linked to bloating and constipation. However, if fungal symptoms are dominant (e.g. thrush, athlete’s foot, vaginal infections), a dual treatment approach may be needed.

An experienced practitioner can help sequence the plan based on your test results and history.

Can SIBO cause yeast infections or thrush?

Indirectly, yes. Antibiotics used for SIBO (especially without antifungal support) can suppress beneficial bacteria, giving Candida an opportunity to overgrow. SIBO may also impair immune function and gut integrity, both of which can contribute to vaginal thrush, oral Candida, or fungal skin infections.

What is the best diet for Candida and SIBO?

For Candida: a low-sugar, low yeast diet is key—avoiding refined carbs, alcohol, and yeasty foods.
For SIBO: a low FODMAP or SIBO-specific diet helps reduce fermentable carbs that feed bacteria.

If you have both, a modified plan that reduces sugar and FODMAPs short term—without being overly restrictive can be effective. It’s important to reintroduce foods gradually once overgrowth is under control.

How long does it take to treat Candida or SIBO?

• SIBO: Treatment typically lasts 4–8 weeks, sometimes longer depending on severity and recurrence.
• Candida: Antifungal protocols may take 6–12 weeks, and maintenance may be needed to prevent rebound overgrowth.

Gut healing is gradual—it’s best approached in phases: reduce overgrowth, repair the gut lining, and restore the microbiome.

Trying to deal with SIBO and Candida on your own can be very challenging we always recommend consulting a qualified practioner. Book a consultation at our sister clinic ibs-solutions.co.uk

References

Candida Overgrowth

• Calderone RA, Clancy CJ. Candida and Candidiasis. ASM Press; 2012. (Good authoritative book on pathophysiology)
• Moyes DL, Naglik JR. Mucosal immunity and Candida albicans infection. Clin Dev Immunol. 2011;2011:346307. doi:10.1155/2011/346307
• Kumamoto CA. Inhibition and evasion of host defenses by Candida albicans. Microbiol Mol Biol Rev. 2011;75(2):281-310.

Candida symptoms & systemic impact

• Koh AY. Murine models of Candida gastrointestinal colonization and dissemination. Eukaryot Cell. 2013;12(11):1416-22.
• Neville BA, d’Enfert C, Bougnoux ME. Candida albicans commensalism in the gastrointestinal tract. FEMS Yeast Res. 2015;15(7).

SIBO (general pathophysiology & IBS link)

• Ghoshal UC, Shukla R, Ghoshal U. Small intestinal bacterial overgrowth and irritable bowel syndrome: A bridge between functional organic dichotomy. Gut Liver. 2017;11(2):196-208.
• Rezaie A, Buresi M, Lembo A, et al. Hydrogen and methane-based breath testing in gastrointestinal disorders: The North American Consensus. Am J Gastroenterol. 2017;112(5):775-84.
• Pimentel M, Lembo A, Chey WD, et al. Rifaximin therapy for patients with irritable bowel syndrome without constipation. N Engl J Med. 2011;364:22-32.

Hydrogen Sulfide SIBO

• Rezaie A, Park SC, Morales W, et al. Assessment of hydrogen sulfide (H2S) production in irritable bowel syndrome (IBS) patients. Gastroenterology. 2017;152(5):S932.

Candida–SIBO coexistence / biofilms

• Ouwehand AC, et al. Probiotic and other functional microbes: From markets to mechanisms. Curr Opin Biotechnol. 2015;32:225-33. (biofilm/competition angle)
• Morales DK, Hogan DA. Candida albicans interactions with bacteria in the context of human health and disease. PLoS Pathog. 2010;6(4):e1000886.

• Shah SC, Day LW, Somsouk M, Sewell JL. Meta-analysis: antibiotic therapy for small intestinal bacterial overgrowth. Aliment Pharmacol Ther. 2013;38(8):925-34.
• LaTuga MS, Ellis JC, Cotton CM, et al. Beyond bacteria: a study of the enteric microbial consortium in extremely low birth weight infants. PLoS One. 2011;6(12):e27858. (GI-MAP/OAT relevance)

Author – Victoria Tyler BSc Hons MBANT

Victoria Tyler owns and runs two busy clinics : Nutrition and Vitality and the IBS and Gut Disorder Clinic.

Nutrition and Vitality, along with the IBS and Gut Disorder Clinic, were founded with the goal of helping patients alleviate IBS symptoms by uncovering and addressing the root causes of their digestive issues.

As a Registered Nutritional Therapist, Victoria holds a BSc (Hons) in Nutritional Therapy and has trained with the Institute of Functional Medicine. She is also accredited by BANT and CNHC.

Before transitioning into health, Victoria earned a degree in Economics and an MBA, working with corporations including Canon and Vodafone. However, her own health challenges led her to pursue a career in Nutritional Therapy.

With a passion for learning, Victoria is committed to staying at the forefront of Functional Medicine. She helps patients manage IBS and other digestive disorders, including SIBO, Candida, and IBD, by identifying and addressing their root causes.

Victoria strongly believes that every symptom has an underlying cause, and there is always a solution to every health condition. To learn more, or to see patient reviews, visit Victoria’s profile on Google.

DISCLAIMER: The information provided in this article is intended for general informational purposes only and should not be construed as medical advice, diagnosis, or treatment. The products and methods mentioned are not a substitute for professional medical advice from a trained healthcare specialist. Always seek the guidance of your doctor or other qualified health professional with any questions you may have regardin