Small Intestinal Fungal Overgrowth (SIFO)
Candidiasis caused by Candida overgrowth has been long associated with gastrointestinal (GI) symptoms, particularly in individuals with compromised immune systems or those on antibiotics and steroids. What we’ve recently discovered is it can colonise the small intestine effectively and cause Small Intestinal Fungal Overgrowth (SIFO).
Recent research reveals that even individuals with healthy immune function may experience symptoms due to fungal overgrowth in their small intestine, now widely recognised as Small Intestinal Fungal Overgrowth (SIFO).
There is emerging scientific evidence that an overgrowth of Candida in the small intestine of people with normally functioning immune responses may cause unexplained gut symptoms. Studies indicate that Candida albicans is the primary fungal species responsible, with SIFO present in up to 25% of individuals with unexplained GI symptoms, often overlapping with conditions like IBS (Erdogan et al., 2015).
More recent research has revealed that fungal species in our gut such as Candida albicans influence our immune responses of by dampening or stimulating inflammatory responses in the gut (Pérez 2021).
What Is SIFO?
Small Intestinal Fungal Overgrowth (SIFO) occurs when fungal organisms, primarily Candida species, grow excessively in a person’s small intestine, disrupting the gut’s natural balance.
While fungi like Candida albicans are a normal part of the gut microbiota and typically reside harmlessly in the large intestine, their overgrowth in the small intestine can trigger symptoms like bloating, gas, nausea, diarrhoea, and abdominal discomfort.
Unlike bacterial overgrowths such as SIBO, SIFO is fungal in origin and is commonly linked to Candida albicans, which was identified in over 97% of cases in a study (Erdogan et al., 2013).
Although SIFO is more frequently seen in individuals with compromised immune systems or those taking certain medications (e.g., proton pump inhibitors), studies show that SIFO can also affect people with no clear underlying conditions such as immune dysfunction. For instance, about 25% of people with unexplained gastrointestinal symptoms tested positive for SIFO (Erdogan et al., 2015).
Key Differences: SIBO vs. SIFO
While both SIBO and SIFO involve overgrowth in the small intestine, their causes and management differ significantly:
The Mystery Patients
Intestinal dysbiosis, a disruption in the balance of gut bacteria and microorganisms, is linked to many gastrointestinal and systemic diseases. This imbalance drives chronic inflammation, destabilises the body’s natural equilibrium, and can lead to significant health challenges (Hrncir 2022).
Naturopaths have long understood the concept of dysbiosis, recognising it as a functional condition with symptoms like abdominal pain, bloating, gas, diarrhoea, and constipation—issues that can significantly diminish quality of life. I’ve found in many chronic cases, patients with functional gut dysbiosis may remain undiagnosed for years, visiting one doctor after another.
The dysbiosis patients are often the “mystery patients” we often see, those whose medical doctor has found no known cause for their symptoms. In many cases, these individuals are dealing with SIBO, SIFO, Candida overgrowth, or mix of these conditions simultaneously.
While SIBO is the most extensively studied, with research from Cedars-Sinai revealing its presence in 78% of IBS patients (Pimental et al., 2000), SIFO remains less understood but equally concerning, particularly for those with weakened immune systems or unresolved gut symptoms.
Despite growing scientific interest in the gut microbiome, much remains unknown about its intricate role in health and disease. In my clinical experience, a natural whole-foods diet along with avoiding poor food and beverage choices is fundamental to maintaining gut balance.
When symptoms persist, natural treatments like antimicrobial natural medicines can be highly effective and gentler on the body than pharmaceutical antifungals, especially when taken with probiotics. A deeper understanding of dysbiosis, and more importantly—and how to prevent it—is key to creating effective, long-term solutions for optimal gut health.
Medical And Natural Medical Viewpoints Differ
Our understanding of the microbiome’s role in health has exploded the past decade to include fungi such as Candida, and the important role they play in balancing our gut function. The shift towards understanding our human microbiome (bacteria) and mycobiome (fungi) has sparked more investigation and awareness in medicine regarding Candida overgrowth and its connection to symptoms and the development of health conditions.
Despite its potential role in various conditions, studying Candida in the human gut faces considerable challenges, including limitations in current diagnostic methods and the variability between Candida strains (Kreulen et al., 2023). While research increasingly confirms associations between Candida and gut diseases, much still remains unanswered.
Widespread Skepticism Held In The Past
Evidence-based medicine has held wide-spread skepticism regarding the notion of yeast syndrome, especially when it comes to linking intestinal gut yeast overgrowth to various symptoms. And they have for good reason, some individuals have made (and continue to make) false claims regarding “balancing Candida levels” or “killing all that yeast” in the body (Quigley 2022).
More recently, evidence-based medicine has however started to uncover the impact of yeast overgrowth in the human digestive system, especially due to Candida (Kreulen et al., 2023). The global threat of Candida auris recently has put Candida species into the spotlight. Besides causing life-threatening systemic candidiasis, we know today that Candida species can cause a chronic form of intestinal Candida overgrowth. (Otašević et al.,. 2018).
Funding For Candida A Low Priority
The emphasis on bacteria may have disregarded the importance of yeast, including Candida, in health and disease. Fungal infections can cause severe disease and death and impose a substantial economic burden on healthcare systems. The medical community has overlooked the concept of yeast syndrome until only recently, yet funding for fungal diseases remains critically low. Fungal disease is not typically considered a priority when considering funding, research, and health policy, only 3% of infectious disease research budgets support medical mycology. (Gow et al., 2022)
Candida And Other Fungal Species Linked To Gut Diseases
Candida species are the most common causes of fungal infection. Approximately 90% of infections are caused by five species: Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei (Turner et al., 2014). Known for its opportunistic and intelligent behaviour, Candida is linked to several gastrointestinal diseases such as invasive intestinal candidiasis, IBS, IBD, and even colorectal cancer and primary sclerosing cholangitis (PSC).
In our gut microbiome, many micro-organisms exist as biofilms. Studies have found Candida albicans usually exists in our gut as a biofilm along with other micro-organisms One researcher found that infections caused by Candida albicans are “poly-microbial” diseases in 30–60% of cases, meaning they are infections caused by several microorganisms at once, including Candida albicans and Staphylococcus aureus. (Sheehan et al., 2020).
Symptoms of SIFO
Small Intestinal Fungal Overgrowth (SIFO) symptoms are often non-specific and can mimic other gastrointestinal conditions like SIBO or IBS, making diagnosis challenging (Erdogan et al., 2015).
Common symptoms include belching, bloating, indigestion, nausea, diarrhoea, constipation, and upper abdominal discomfort. Systemic signs such as fatigue, oral thrush, or skin rashes may also occur, especially when fungal overgrowth becomes widespread (Dukowicz et al., 2007).
The similarity in symptoms between SIFO and SIBO complicates diagnosis, as both conditions involve bloating, gas, and digestive upset. However, SIFO differs in its fungal origin, and treatment with antifungal medications often brings significant relief. Beyond digestive symptoms, I’ve found that many patients report improvements in non-gut symptoms such as joint pain, headaches, and chronic fatigue when SIFO is effectively treated.
Key Symptoms of SIFO
Pages of Interest
SIFO and Inflammation
Research increasingly links Candida colonization in the gut to gastrointestinal (GI) inflammation and chronic inflammatory conditions.
The pro-inflammatory cytokine IL-17 has been found to play a significant role in both Candida overgrowth and the development of inflammatory bowel diseases (IBD) like ulcerative colitis and Crohn’s disease (Kumamoto, 2011).
High levels of Candida fungal colonisation may exacerbate these conditions by promoting inflammation and disrupting the intestinal barrier (Huang et al., 2024).
In addition to IBD, Candida overgrowth in the small intestine is suspected to contribute to irritable bowel syndrome (IBS). While evidence is still emerging, the inflammatory potential of Candida and its ability to alter gut microbiota dynamics suggest its role in IBS symptoms (Gu et al., 2019).
A compelling case study demonstrates the importance of addressing fungal dysbiosis in systemic inflammatory conditions. A 48-year-old woman with Sjogren’s syndrome and malnutrition linked to small intestinal bacterial and fungal overgrowth improved dramatically through targeted dietary and lifestyle interventions.
Nutrient repletion and gradual fungal eradication restored her intestinal absorptive function, enabling weight gain and improved functional status (Singh, 2017).
Key Points on SIFO and Inflammation:
Causes and Risk Factors of SIFO
Emerging evidence points to SIFO as a significant contributor to unexplained gastrointestinal symptoms, even in healthy people. Studies found that approximately 25% of patients with unexplained GI symptoms tested positive for SIFO, highlighting the need to consider fungal overgrowth in differential diagnoses (Erdogan et al., 2015).
SIFO can develop due to various factors that disrupt gut balance or weaken immune defences. One key factor is low stomach acid, which normally helps prevent microbial overgrowth by killing fungi and bacteria before they reach the small intestine (Shah et al., 2022).
Conditions such as anaemia, autoimmune disorders, aging, or chronic use of antacids and painkillers can reduce stomach acid production, increasing the risk of SIFO. Other risk factors include excessive use of antibiotics, proton pump inhibitors (PPIs), immunosuppressants, and underlying conditions like diabetes, motility disorders, and Ehlers-Danlos syndrome (Lin et al., 2021).
Multiple Risk Factors
Proton Pump Inhibitors and SIFO
Long-term use of PPIs is a major contributor to fungal and bacterial overgrowth in the gut. PPIs reduce stomach acid production, impairing the gut’s natural defence against microbial colonisation. This increases the risk of SIFO and other dysbiosis-related conditions, as fungi like Candida can thrive in the small intestine under these circumstances (Bruno et al., 2019).
Antibiotics and Fungal Dysbiosis
The widespread use of antibiotics, especially broad-spectrum types, has transformed modern medicine by saving lives from bacterial infections. However, this success comes at a cost: antibiotics deplete beneficial gut bacteria, leading to fungal overgrowth (Aminov 2010).
Research spanning decades has demonstrated a link between broad-spectrum antibiotic use and fungal infections, including disseminated candidiasis
(Seelig b-1966) (Seelig a-1966) (Mason et al., 2012) (Dollive et al., 2013)
This imbalance, known as fungal dysbiosis, highlights the unintended consequences of antibiotic overuse. Proper diagnosis and a cautious approach to medication use, alongside dietary and lifestyle changes, are essential to managing SIFO and restoring gut health.
Page of Interest: Candida Causes
SIFO Risk Factors
While Candida overgrowth is more commonly associated with vulnerable groups such as older adults, young children, and those with compromised immune systems, SIFO can also develop in individuals with robust immune systems. The exact mechanisms remain unclear, but several risk factors have been identified.
Key Risk Factors for SIFO:
Caution with PPI Drugs
Proton pump inhibitors may be invaluable for short-term management of conditions like GERD or stomach ulcers, but in my clinical experience many patients often rely on these drugs for symptomatic treatments, sometimes for many years.
However, overuse or prolonged use can lead to unintended and even serious consequences, including bacterial and fungal overgrowth (Shi et al., 2023).
Using these medications carefully and seeking alternative treatments when possible can reduce this risk.
Proper diagnosis and a balanced approach to medication use, alongside targeted antifungal or antibacterial treatment, are crucial for managing SIFO and maintaining a healthy and balanced gut microbiome.
Testing For SIFO
Small intestinal fungal overgrowth occurs when fungal organisms, primarily Candida species, grow excessively in the small intestine, disrupting the gut’s natural balance of bacteria, fungi, viruses, and other micro-organisms.
While fungi are a normal part of the gut microbiota and typically reside harmlessly in the large intestine, their overgrowth in the small intestine can trigger symptoms like bloating, gas, nausea, diarrhoea, and abdominal discomfort.
Unlike bacterial overgrowths such as SIBO, SIFO is fungal in origin and is commonly linked to Candida albicans, which was identified in over 97% of cases in a study (Erdogan et al., 2013).
Although SIFO is more frequently seen in individuals with compromised immune systems or those taking certain medications (e.g., proton pump inhibitors), studies show that SIFO can also affect people with no clear underlying conditions such as immune dysfunction. For instance, about 25% of people with unexplained gastrointestinal symptoms tested positive for SIFO (Erdogan et al., 2015).
Stool Testing For Yeast
Diagnosing SIFO can be challenging due to the lack of a standardised, non-invasive test. While stool tests and breath tests are valuable tools for identifying bacterial pathogens or SIBO, they were not designed specifically to detect fungal overgrowth, but in chronic cases they often do.
I’ve seen many comprehensive stool tests return a positive for Candida albicans (and other species) culture. Live yeast and dead yeast can also be found in stool tests, as can other species of fungi, at least, this has been my experience for many years until I retired in 2019.
Currently, the definitive diagnostic method for SIFO is a small bowel aspirate, a procedure requiring the collection of fluid directly from the small intestine using an endoscope. This sample is analysed in a lab to identify fungal species and their antifungal sensitivity.
Small Bowel Aspirate:
Challenges in SIFO Diagnosis
Emerging Approaches:
While advancements in diagnostics are underway, empiric treatment often remains the most practical approach for suspected SIFO cases. This involves treating based on symptoms and ruling out other causes such as SIBO, IBS, IBD, or other infections.
Page of Interest: Candida Testing
SIFO Treatment
The Medical Treatment Of SIFO
Addressing SIFO effectively requires a combination of dietary changes, lifestyle modifications, and targeted treatments.
Diagnosis remains challenging due to overlapping symptoms with other gastrointestinal conditions, such as SIBO. I’ve consistently found in clinical practice, testing the effectiveness of antifungal therapy based on symptoms often serves as the best diagnostic tool, as invasive testing like small intestine fluid sampling is impractical. This form of treatment is called empiric treatment based on empirical observation.
Empirical observation is the process of gathering knowledge through experimentation and direct sensory experience, rather than relying on theory or speculation. It’s a key part of the scientific method, and is used to test hypotheses and develop new theories. I’ve always found this method to work well with “mystery patients” we’ll soon discuss.
Prescription antifungals such as fluconazole are commonly used and are considered safe, though they may only provide modest improvements (Rao 2018).
Alternative options like itraconazole or posaconazole are also available, but have more powerful side-effects, while drugs like nystatin may be less effective due to its poor stability in stomach acid.
It is important to note that these medications antifungal drugs can have interactions ranging from mild to severe, particularly if the patient is also taking drugs for heart conditions or blood sugar regulation, emphasising the need for medical supervision during treatment, particularly if the case is chronic.
Advancing Our Understanding of SIFO
Medical science is increasingly recognising SIFO as a significant contributor to unexplained gastrointestinal symptoms and systemic health issues. Despite this progress, substantial gaps remain in understanding its pathophysiology (diseases development), diagnosis, and optimal treatment.
Research underscores the importance of a comprehensive approach, addressing underlying factors such as low stomach acid, poor gut motility (constipation), and immune dysfunction, which can predispose people to fungal overgrowth (Bhagatwala et al., 2019).
An overlooked factor often in the medical treatment of SIFO is diet and lifestyle, something we’ll soon discuss, and it’s no fault of medical professionals due to increasing demands placed on their time in addition to SIFO only very recently becoming a recognised gut disease..
As scientific interest in the gut microbiome grows, integrating natural therapies with medical treatments offers a promising avenue for restoring gut health and preventing recurrence (Durack et al., 2019)
According to another researcher, adding proper nutrients and slowly eradicating the dysbiotic fungi in the small intestine can help in resolution of GI symptoms and return to functional status (Sing et al., 2017).
Take-Away
Natural Treatment and Dietary Strategies for SIFO
The Natural Treatment Of SIFO
SIFO is a condition marked by an overgrowth of fungi, typically Candida albicans, in the small intestine. This fungal imbalance can cause a wide range of symptoms. While research into SIFO remains limited, evidence suggests that dietary modifications and natural antifungal interventions can play a significant role in managing the condition.
Natural remedies can play a critical role in managing SIFO, often with fewer side effects than pharmaceutical options. Several probiotic strains have shown antifungal activity and can help rebalance the gut microbiome, especially when SIFO coexists with SIBO.
Herbal antimicrobials like caprylic acid, oregano, berberine, and grapefruit seed extract exhibit antifungal properties and may serve as effective alternatives or adjuncts to conventional treatments.
Diet is also crucial; reducing refined sugars, alcohol, and starchy carbohydrates while incorporating gut-healing foods like garlic, coconut oil, and bone broth can support recovery. Clinically I’ve always found it best to tailor dietary interventions to individual needs, as overly restrictive diets can sometimes harm gut health. I’ll discuss the best food choices for SIFO shortly, but you’ll find them the same as the Candida diet recommendations I make on this website.
Avoiding High-Carbohydrate
A diet low in refined sugars and high-glycemic carbohydrates is also crucial, as fungi thrive on these nutrients.
Research supports those consuming diets rich in amino acids, proteins, and healthy fats are less likely to develop fungal overgrowth compared to those with high-carbohydrate diets (Hoffman, 2013).
Moreover, incorporating natural antifungals such as garlic, oregano oil, and berberine as antifungals into our SIFO management plan can further suppress fungal growth while supporting overall gut health.
Research into diet and fungal overgrowth highlights the importance of avoiding high-carbohydrate and sugar-rich foods. A study found that individuals consuming less refined wheat flour and more alternatives like aged cheese and (sour) quark had significantly lower rates of Candida colonisation (Jeziorek et al,. 2019).
Studies indicate that coconut oil is one of the most effective natural antifungal agents, disrupting fungal cell membranes and reducing Candida colonisation in the gut (Gunsalus et al., 2016).
These findings suggest that dietary shifts can have a measurable impact on fungal balance in the gut.
Key Diet and Nutrition Pages
SIFO Diet: Foods to Eat and Avoid
The foundation of a SIFO-friendly diet is reducing foods that stimulate fungal dysbiosis and emphasising fresh and whole foods that support gut health. Consider the Candida Cleanse Program if you have SIFO, it’s a good way of cleaning and re-balancing a disturbed gut microbiome.
Below is a comprehensive list, click on any links to take you to the desired page of interest:
The YES Foods (Support Gut Health and Fight Fungal Overgrowth):
The NO Foods (Stimulate Fungal and Bacterial Dysbiosis):
Take-Aways
With proper dietary adjustments and natural interventions, SIFO can be managed effectively, restoring balance to the gut microbiome and improving overall health.
Eric Bakker N.D.
Greetings! I am a naturopathic physician from New Zealand. Although I’ve retired from clinical practice since 2019, I remain passionate about helping people improve their lives. You’ll find I’m active online with a focus on natural health and wellbeing education through my Facebook page and YouTube channel, including this website.
