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Bacterial Overgrowth and Leaky Gut

Bacterial Overgrowth and Leaky Gut

Bacterial Overgrowth and Leaky Gut

Causes, Symptoms and Treatment for Bacterial overgrowth and leaky gut

Bacterial overgrowth and leaky gut are two common conditions that go hand in hand and cause a wide range of symptoms to affected patients.

Overgrowth of dysbiotic bacteria, gut infections and parasites cause intestinal dysbiosis.

Intestinal dysbiosis refers to microbial imbalance within the digestive tract, when potentially harmful microorganisms such as bacteria, yeasts, parasites or protozoa outweigh the beneficial flora.

Indigenous microflora are found all over the body (indeed, 90% of the human body is not human!), but are found in greatest numbers in the colorectal tract. There are thought to be over 500+ species of bacteria in the digestive tract, as well as yeasts, parasites and protozoa, making up 1-2 kg in weight.

While some bacteria are potentially harmful or pathogenic, the majority are beneficial. These beneficial species exert control over potentially pathogenic species, preventing their uncontrolled growth and replication.

Under certain conditions, such as antibiotic use, poor immunity, high sugar diets etc, the harmful species can begin to grow and outnumber the beneficial flora, leading to a state of dysbiosis.

Intestinal dysbiosis, bacterial and fungal overgrowth including candida overgrowth can cause a variety of digestive symptoms, these include;

  • Bloating
  • Gas
  • diarrhea and/or constipation
  • Irritable bowel

Leaky Gut Symptoms

In addition to the above symptoms, the presence of unwanted bacteria, infections or parasites in the gut cause damage to the intestinal lining allowing the passage of endotoxins and undigested proteins into the bloodstream. 

This condition is known as intestinal permeability or more commonly as “Leaky Gut”, which can cause a variety of symptoms elsewhere in the body

Many seemingly unrelated symptoms commonly occur as a result of leaky gut, we regularly see the following systemic symptoms in clinic;

  • skin disorders and rashes
  • fatigue
  • headaches
  • cramps after eating
  • increase in food allergies
  • brain fog
  • itchy vagina or anus
  • Increase in PMS and menstrual irregularities

Harmful microorganisms can also excrete waste products which can overburden the body’s waste removal mechanisms causing systemic inflammation.

The role of our gut microbiome is likely the single most important thing that affects all systems of our body and keeping a well-balanced and healthy microbiome is essential to optimal health.

Role of intestinal flora

  • Suppression of pathogenic flora such as candida by competing for nutrients and attachment sites
  • Immune function: gut flora are an essential component in the development and maintenance of gut and systemic immunity. They are thought to play a role in 70-80% of immune responses, an overgrowth of candida or other fungus or bacteria can seriously compromise the immune system
  • Stimulation of gut-associated lymphoid tissue (GALT)
  • Expression of toll-like receptors (TLRs) which help repair tissue damage due to injury
  • Increased oral tolerance to antigens, thus reducing over-reactive immune responses (e.g. allergy, autoimmune disease etc)
  • Stimulation of T-cells, macrophages and cytokines – An overgrowth of candida or other bacteria will seriously reduce your immune cell function
  • Carbohydrate fermentation and absorption & production of SCFAs: gut bacteria can digest and ferment certain starches, dietary fibres, oligosaccharides and sugars into short-chain fatty acids (SCFAs).

The role of SCFAs

  • Source of energy and nutrients
  • Facilitates absorption of minerals such as calcium, magnesium and iron
  • Lowers pH of colon, helping to prevent the development of malignancies and inhibiting the growth of certain unfavourable bacteria such as Escherichia coli and Salmonella spp.
  • Promote growth and repair of intestinal epithelial cells
  • Promote immune function
  • Reduction of serum cholesterol levels (proprionic acid)
  • Production of vitamin K
  • Gut microflora are an important source of vitamin K which is absorbed into the bloodstream from the large intestine
  • Production of vitamin B12
  • Metabolism of dietary carcinogens: e.g. heterocyclic amines (HCAs) produced by cooking proteins at high temperatures (e.g. char-grilled steak)
  • Preventing gastrointestinal disease: studies suggest that the production of SCFAs help prevent inflammation in the bowel, thus reducing the risk of inflammatory bowel disease, irritable bowel syndrome, gastritis, peptic ulceration, etc.

It is easy to see from the above that a leaky gut, bacterial or fungal overgrowth such as Candida overgrowth or bacterial dysbiosis can have far reaching effects, much further reaching than just the typical gut symptoms most would associate with this condition. 

Nutrient deficiencies, hormonal system imbalances, compromised adrenal and brain function, chronic fatigue etc. are all often related back to a gut imbalance.

Causes of Bacterial Overgrowth & Leaky Gut

Microorganisms in the gut that may cause dysbiosis and leaky gut include:

  • Bacteria: E.coli, Salmonella, Helicobacter pylori (H.pylori), Clostridia spp. Enterococcus, Faecalis, Morganella species, Pseudomonas species, Staphyloccus species, Stepococcus species
  • Potential Autoimmune Triggers – Citrobacter species, Citrobacter fruendii, Klebsiella species, Prevotella, Proteus mirabilis
  • Yeasts: Candida albicans, Candida species, Geotrichum species, Microsporidium species, Rhodotorula species
  • Helminths: tapeworms, flukes, hookworm and various roundworms
  • Parasites:   Cryptosporidium, Entamoeba histolytica, Giardia lamblia, Blastocystis hominis. Dientamoeba fragilis, Entamoeba coli, Endolimax nana, Pentatrichomonas hominisamoeba, Giardia, microsporiodes

Risk factors of Bacterial Overgrowth & Leaky Gut

  • Early, repeated and/or long-term antibiotic use: believed to be the most important factor in dysbiosis and chronic candidiasis. Broad-spectrum antibiotics, in particular, kill bacteria indiscriminately; however, they do not kill yeasts such as Candida, which can then become overgrown
  • High sugar and refined carbohydrate diet
  • Low fibre diet: fibre, especially soluble fibre, is a prebiotic  and needed for growth of beneficial flora
  • Overconsumption of alcohol
  • Stress
  • Oral contraceptive use
  • Caesarian birth and/or lack of breastfeeding
  • Overseas travel
  • Compromised immune system (e.g. serious illness, diabetes, HIV infection, long term corticosteroid use, poor nutrition, stress, lack of sleep etc)

Signs & Symptoms of Bacterial Overgrowth & Leaky Gut

  • Digestive symptoms such as bloating, flatulence, cramps, altered bowel movements, cravings for sugars and carbohydrates
  • Genito-urinary: recurrent thrush or UTIs
  • Itchy anus and nose
  • Skin: persistent rashes found most commonly in the groin, between fingers and toes, under the breast and in the axillae; itchy skin (especially around the anus and nose); painful fissures at corners of mouth
  • Mouth: white patches on the oral mucosa (oral thrush)
  • Nervous system: depression, irritability, poor concentration and memory, mood swings, confusion, anxiety, headaches
  • Systemic symptoms: fatigue, lethargy, intolerance to chemicals, allergies, obesity, autoimmune disease and cardiovascular disease have all been linked to dysbiosis
  • Severe acute infections may also be apparent with vomiting, diarrhoea, fever etc.

Investigative Test options

  • Advanced Stool analysis
  • SIBO breathe test
  • Intestinal Permeability
  • Organic Acids Test
  • Food intolerance testing


  • Identify and address species and genus of fungal, bacterial, or parasite and eradicate accordingly
  • Repair gut mucosa
  • Promote and rebuild healthy bowel flora balance
  • Support digestive function and elimination
  • Manage diet to assist with removal process

Diet plan guidelines for bacterial overgrowth and leaky gut

  • Fresh wholefood diet, high fruit and vegetables, wholegrains, legumes, nuts and seeds, fish and healthy fats
  • Eliminate sugars, sweeteners, refined carbohydrates, fruit juices, processed foods, junk foods
  • Eliminate any known or suspected food sensitivities: gluten and casein may be particularly indicated
  • Limit intake of high-sugar fruits (melon, bananas, grapes, dried fruits), red meat, starchy vegetables, wheat and dairy products

Supplements for bacterial overgrowth and leaky gut

  • A wide range of antimicrobial herbs to kill specific gut pathogens, we test our patients and use specific herbal treatments to eradicate the bacterial strains present.  Guidance with an experienced practitioner is recommended.
  • Probiotics: We only prescribe probiotics in most cases once we have identified the bacterial mix of the microbiome.  Probiotics in many instances can make symptoms worse by feeding and disturbing the pathogenic bacteria.
  • Prebiotics: including FOS, GOS, inulin and lactulose. Start with low doses and slowly increase.  Again, this can make symptoms worse if the pathogenic bacteria are not cleared before supplementing.
  • Biotin: inhibits pseudohyphae form of Candida which is most irritating to mucous membranes
  • Glutamine: prevents pathogens attaching to gut wall; repairs gut mucosa
  • Biofilm disrupters: NAC, etc – assists in breaking down cell wall protective barriers of pathogens

Herbal medicine treatment for bacterial overgrowth and leaky gut

  • Broad-spectrum antimicrobial: aniseed, barberry, goldenseal, echinacea, andrographis, chamomile, garlic, thyme, citrus seed extract, oregano, pau d’arco
  • Antiparasitic: wormwood, qing hao, black walnut, thyme, tansy, goldenseal, barberry, Oregon grape
  • Antifungal: pau d’arco, cat’s claw, grapefruit seed extract
  • Immune support: echinacea, andrographis, reishi/shitake mushroom


The above considerations are general and when used correctly along with other measures can resolve bacterial, fungal or parasitic overgrowth and eradication of these species.  Overgrowths such as Candida and other fungal, bacterial and parasitic overgrowths are tricky to remove and require a tailored plan based on investigative testing prior to treatment.

At our Perth clinic of Advanced Functional Medicine we have extensive experience in gut health and the removal of Candida and other bacterial, fungal and parasitic infections. 

Focussing on the removal of bacterial infections, parasites and fungal overgrowths and restoring gut microbiomes to a healthy balance, eradicating symptoms can improve overall health.

Many patients that come to us have had multiple attempts previously to remove parasites or bacterial infections without success.

We retest all patients after treatment to ensure we have successfully removed the parasite or fungal and bacterial overgrowth.

If you or a family member are suffering from a fungal, bacterial or parasite infection we would love to hear from you, how were you diagnosed?  What treatments have been successful? Where did you get your parasite?  Please write a comment below.

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The above information is intended to be general, educational advice only, on topics which are of interest to us. It is not intended to represent specific or individual health or medical advice and is not specific to your situation. The below information is educative and is not intended to advertise any service.

Before making any decisions in relation to your health, you should always discuss your individual situation with your own health practitioners to ensure that any advice you have read is right for you.

Jarrod Cooper – ND

Jarrod Cooper – ND

Jarrod Cooper - ND is the founder of Advanced Functional Medicine Australia. He is a Naturopathic Doctor with extensive functional medicine training from leading practitioners in the USA and worldwide.

He is leading the way with advancements of functional medicine, clinically implementing worldwide best practices in Functional Medicine throughout Australia.

Jarrod consults in person from Perth, Western Australia and also online via Telehealth throughout Australia and worldwide.

If you are looking for personalised treatment, we highly recommend contacting Jarrod Cooper’s Advanced Functional Medicine clinic in Australia.

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