Gut dysbiosis and SIBO

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The gut contains trillions of micro-organisms including a large variety of bacteria. These bacteria, also called our ‘gut flora’, have a symbiotic relationship with us. They assist in the breakdown and absorption of foods, they produce certain vitamins and they help prevent dangerous pathogens from entering the gut or bloodstream. In return, they depend on us for food and shelter.

While most of these bacteria are beneficial and important to our health, some are pathogenic and can contribute to physical as well as mental health issues.

The right balance of beneficial bacteria in the gut is therefore essential for proper physical and mental health. Healthy gut flora supports:

  • Optimal digestion of food
  • Hormone balance
  • Immune function
  • Reduction of inflammation
  • Balanced neurotransmitter levels
  • Optimal levels of vitamins and minerals

Gut dysbiosis

Gut dysbiosis can be defined as an overgrowth of pathogenic or harmful bacteria, yeasts and/or parasites, and too few beneficial bacteria.

Once large colonies of harmful pathogens have taken residence in our gut, our ability to digest and absorb food may be affected, which can eventually lead to digestive distress and nutrient deficiencies.

Harmful pathogens also have the ability to affect the integrity of the gut lining and can be a driving factor in the development of ‘leaky gut’, a condition which can lead to low grade inflammation, food intolerances and allergies, autoimmune disease and depression.

  • Viral, parasitical, yeast and bacterial infections
  • An overgrowth of toxins which can accelerate irritation and leakiness of the gut
  • Low grade, systemic inflammation and auto-immune issues
  • Inflammatory bowel disease
  • Food intolerances and allergies
  • Poor digestion and absorption of nutrients which can lead to vitamin, mineral, fat and amino acid deficiencies
  • Irritable Bowel Syndrome (IBS)
  • Inflammatory Bowel Disease (IDB)
  • Small Intestinal Bacterial Overgrowth (SIBO)

Kwiatkowska, I., Hermanowicz, J.M., Mysliwiec, Z. and Pawlak, D., 2024. Insights into gut dysbiosis: inflammatory diseases, obesity, and restoration approaches. International Journal of Molecular Sciences, 25(17), p.9715.

  • Antibiotic use (past and present)
    • Regular use of antibiotics has become common practice in our society
    • Although antibiotics can serve an important function by eradicating harmful microbes, they are unable to distinguish between the good and the bad, and during a course of antibiotics many of our beneficial gut bacteria are eradicated too
    • Without these good bacteria the gut’s defence system becomes weakened, leaving it open to colonisation by pathogenic bacteria, yeast and parasites
  • A diet high in processed foods and sugars
  • Undiagnosed food intolerances and allergies
  • Stress
  • Pharmaceuticals such as NSAIDs, birth control pill, steroids, chemo- and radiotherapy
  • High dose iron supplementation
  • Lowered immunity
  • Irregular/slow bowel movements
  • Infection
  • Diabetes
  • Gastrointestinal surgery
  • Ageing

Gut dysbiosis and mental health

Harmful pathogens such as viruses, yeasts and bacteria are capable of excreting biotoxins and waste products which can enter our bloodstream and impact our brain chemistry. They can contribute to mental health issues such as mood swings, depression, anxiety, insomnia, etc.Luqman, A., He, M., Hassan, A., Ullah, M., Zhang, L., Rashid Khan, M., Din, A.U., Ullah, K., Wang, W. and Wang, G., 2024. Mood and microbes: a comprehensive review of intestinal microbiota’s impact on depression. Frontiers in Psychiatry, 15, p.1295766.

The first 1000 days from conception are critical in how nurture (environmental factors) affects nature (genetic expression).

Through the gut-brain axis, gut microbes play an important part in early brain development, and studies show the ability of gut microbes to influence pre- and postnatal maturation of the brain:Naspolini, N.F., Schüroff, P.A., Figueiredo, M.J., Sbardellotto, G.E., Ferreira, F.R., Fatori, D., Polanczyk, G.V., Campos, A.C. and Taddei, C.R., 2024. The gut microbiome in the first one thousand days of neurodevelopment: a systematic review from the microbiome perspective. Microorganisms, 12(3), p.424.

  • The prenatal period
    • The exact mechanism by which maternal microbes influence the prenatal brain have yet to be determined but research has shown the placenta as being a likely conduitSajdel-Sulkowska, E.M., 2023. The impact of maternal gut microbiota during pregnancy on fetal gut–brain axis development and life-long health outcomes. Microorganisms, 11(9), p.2199.
    • It is thought that maternal microbe breakdown products can cross the placenta influencing the development of the fetal brain
    • The role of the placenta in increasing serotonin production and the HPA-axis has been demonstrated in experimentsSajdel-Sulkowska, E.M., 2023. The impact of maternal gut microbiota during pregnancy on fetal gut–brain axis development and life-long health outcomes. Microorganisms, 11(9), p.2199.
  • The postnatal period
    • The microbiota of breastfed infants is more diverse, and infants who are breastfed have better neurodevelopmental outcomesBiagioli, V., Sortino, V., Falsaperla, R. and Striano, P., 2024. Role of human milk microbiota in infant neurodevelopment: mechanisms and clinical implications. Children, 11(12), p.1476.
    • The ‘microflora’ hypothesis states that insufficient exposure to microbiota in early life may affect the composition of adult microbiota, which can increase susceptibility to neurodevelopmental disorders such as autismZuffa, S., Schimmel, P., Gonzalez-Santana, A., Belzer, C., Knol, J., Bölte, S., Falck-Ytter, T., Forssberg, H., Swann, J. and Diaz Heijtz, R., 2023. Early-life differences in the gut microbiota composition and functionality of infants at elevated likelihood of developing autism spectrum disorder. Translational Psychiatry, 13, p.257.
    • Imbalanced gut microbiota in early life have long-lasting immune and physiological effects making individuals more susceptible to developing PTSD (post-traumatic stress disorder) in later lifeKe, S., Hartmann, J., Ressler, K.J., Liu, Y.Y. and Koenen, K.C., 2023. The emerging role of the gut microbiome in posttraumatic stress disorder. Brain, Behavior, and Immunity, 114, pp.360–370.
  • Cognitive development in children is critically dependent on gut microbes and their activityMcMath, A.L., Aguilar-Lopez, M., Cannavale, C.N., Khan, N.A. and Donovan, S.M., 2023. A systematic review on the impact of gastrointestinal microbiota composition and function on cognition in healthy infants and children. Frontiers in Neuroscience, 17, p.1171970.
  • Evidence shows that cognitive activity is highly dependent on the microbiota and its metabolic activityAlavian, F. and Safaeian, M., 2025. How the gut microbiome shapes learning and memory: a comprehensive review. IBRO Neuroscience Reports, 19, pp.491–506.
  • Studies have demonstrated a difference in the diversity of gut micro-organisms between those suffering with Alzheimer’s and healthy controls
    • The diversity of gut microbes is the lowest in the frail elderly and those with Alzheimer’s diseaseJimenez-García, N. et al., 2024. A systematic review and meta-analysis of basal microbiota and cognitive function in Alzheimer’s disease: a potential target for treatment or a contributor to disease progression? Alzheimer’s & Dementia: Diagnosis, Assessment & Disease Monitoring, 16, e70057.
  • Gut microbes are important for the development of hippocampus-dependent memory
    • Experiments involving mice with and without gut colonization with microbes demonstrates an absence of working memory and therefore cognitive deficit, in the non-colonized miceAlavian, F. and Safaeian, M., 2025. How the gut microbiome shapes learning and memory: a comprehensive review. IBRO Neuroscience Reports, 19, pp.491–506.
  • Certain gut bacteria can secrete amyloids and lipopolysaccharides (LPS) which can cause the growth of pro-inflammatory cytokines associated with Alzheimer’sYang, J., Liang, J., Hu, N., He, N., Liu, B., Liu, G. and Qin, Y., 2024. The gut microbiota modulates neuroinflammation in Alzheimer’s disease: elucidating crucial factors and mechanistic underpinnings. CNS Neuroscience & Therapeutics.
  • Gut dysbiosis can lead to increased permeability of the gut (leaky gut) and blood-brain barrier, which may play a role in Alzheimer’s disease and other neurodegenerative disorders associated with ageing

Administering probiotics has been shown to have a positive effect on mental health:

  • Evidence shows that adding Lactobacillus and Bifidobacterium to the diet is associated with an improvement in mood and a decrease in anxiety and psychological stress
    • This particularly applies to individuals with low cortisol levelsJain, M., Anand, A., Sharma, N., Shamim, M.A. and Enioutina, E.Y., 2024. Effect of probiotics supplementation on cortisol levels: a systematic review and meta-analysis. Nutrients, 16(20), p.3564.
  • Evidence shows that probiotic treatments may be a useful alternative to treat stress-related disorders like anxiety and depressionYang, Y., Yang, L., Wan, M., Pan, D., Sun, G. and Yang, C., 2024. Assessment of optimal combinations of therapeutic probiotics for depression, anxiety, and stress. Psychological Medicine, 54(10), pp.2547–2561.
  • Harmful pathogens can also be the foundation for the development of gut-based illnesses such as Irritable Bowel Syndrome (IBS), Inflammatory Bowel Disease (IDB) and Small Intestinal Bacterial Overgrowth (SIBO), all conditions which are strongly linked to anxiety and depressionBogielski, B., Michalczyk, K., Głodek, P., Tempka, B., Gębski, W. and Stygar, D., 2024. Association between small intestine bacterial overgrowth and psychiatric disorders. Frontiers in Endocrinology, 15, p.1438066.
  • Neurotransmitters are required in specific areas of the brain for effective brain function
  • The primary raw material for neurotransmitter synthesis in the brain are nutrients such as amino acids, vitamins, minerals and other biochemicals which are absorbed and processed by gut bacteria
  • Intestinal bacteria can also produce neurotransmitters in the gut
    • Serotonin
    • Melatonin
    • Histamine
    • Acetylcholine
  • These neurotransmitters are of bacterial origin and communicate with the brain and affect brain functionAhmadi, S., Taghizadieh, M., Mehdizadehfar, E., Hasani, A., Khalili Fard, J., Feizi, H., Hamishehkar, H., Ansarin, M., Yekani, M. and Memar, M.Y., 2024. Gut microbiota in neurological diseases: melatonin plays an important regulatory role. Biomedicine & Pharmacotherapy, 174, p.116487.
  • The altered balance of bacteria in the gut can cause an inappropriate immune response, where the presence of normal gut bacteria are perceived as a threat by the body
  • The resulting immune reaction can damage the gut wall affecting ‘leakiness’Macura, B., Kiecka, A. and Szczepanik, M., 2024. Intestinal permeability disturbances: causes, diseases and therapy. Clinical and Experimental Medicine, 24(1), p.232.
  • Pathogens such as candida, allowed to flourish due to gut dysbiosis, can cause leaky gut

Small Intestinal Bacterial Overgrowth (SIBO)

Small Intestinal Bacterial Overgrowth (SIBO) is a form of gut dysbiosis where abnormally large numbers of bacteria reside in the small intestine. Even though these bacteria in themselves may not be harmful, in excessive numbers they can cause a host of physical and mental symptoms.

  • Bloating
  • Gas
  • Abdominal pain
  • Bowel movement irregularities (constipation/diarrhoea)
  • Acid reflux
  • Nausea
  • Pain
  • Fatigue and lethargy
  • Anxiety
  • Poor concentration and attention
  • Poor memory
  • Depression
  • Sleep issues

Bogielski, B., Michalczyk, K., Głodek, P., Tempka, B., Gębski, W. and Stygar, D., 2024. Association between small intestine bacterial overgrowth and psychiatric disorders. Frontiers in Endocrinology, 15, p.1438066.

  • Irritable Bowel Syndrome (IBS) and Inflammatory Bowel Disease (IBD)
  • Coeliac
  • Autism
  • Fibromyalgia
  • Interstitial Cystitis
  • Restless leg syndrome
  • Acne rosacea
  • Depression
  • Insomnia
  • Decreased motility after surgery
  • Chronic stress
  • Pharmaceuticals such as
    • Antibiotics
    • Oral contraceptives
    • Antacids
  • Neurological conditions and inflammation affecting the vagus nerve
  • Hypothyroidism
  • Irritable bowel disease
  • Pancreatitis
  • sIgA (secretory immunoglobuline A) deficiency
  • High carbohydrate diet
  • Use/over-use of proton-pump inhibitors
  • Deficiency in B12 and/or folate, both of which can cause microvilli malformation

SIBO can be diagnosed by your medical practitioner using a breath test, although accuracy of this test is only about 54%.

Once diagnosed, SIBO symptoms can be kept under control:

  • By following a low FODMAP diet
  • Antibiotics may be recommended
  • A more gentle yet effective solution would be to take herbal antimicrobials as these tend to have less of a negative impact on overall gut flora, and yet are proven to be as effective or more effective than antibioticsChedid, V., Dhalla, S., Clarke, J., Roland, B., Dunbar, K., Koh, J., Justino, E., Tomakin, E. and Mullin, G. (2014). Herbal Therapy Is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth. [online] Global Advances in Health and Medicine, 3 (3), pp. 16-24. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4030608/ [accessed 27 Dec. 2017].