SIMD: Small Intestinal Microbial Dysbiosis 

(SIBO: Small Intestinal Bacterial Overgrowth and SIFO: Small Intestinal Fungal Overgrowth)


What is SIBO?

SIBO is a heterogeneous or very diverse syndrome, characterised by an increased number and/or abnormal type of bacteria in the small bowel.

Most authors consider a diagnosis of SIBO to be greater than 105 bacteria [i.e. colony-forming units (CFU)] per mL of proximal jejunal aspiration (the SIBO breath test).

The normal value is less than 104 CFU/mL1

“Gut dysbiosis, including small intestinal bacterial overgrowth (SIBO), causes IBS symptoms. Between 4% and 78% of patients with IBS and 1% and 40% of controls have SIBO”2

UDOF Upper digestive overgrowth of flora3

 Symptoms of SIBO


Diarrea 40% (SIBO-D) or

Constipation 35% (SIBO-C) or both 25% (SIBO-M)


Abdominal pain


Gas especially after meals

Fatty stools



Intestinal permeability and microvilli damage may present as:

Skin rashes

Joint pain

Food allergies and sensitivities to histamines, oxalate’s and chemicals etc.


Causes and Pathophysiology of SIBO

  1. Past gastro infections, gastroenteritis and food poisoning. Past gastro infections increase a reoccurrence 6 fold. So take precautions when overseas e.g. Build up immune prior to trip, SB and Probiotics.

Use of medications such as proton pump inhibitors (PPI’s), opiates and  tricyclic anti-depressants. PPI’s may damage causing low HCL (4),(Hydrochloric acid levels in stomach), deficient pancreatic enzymes and digestive enzymes

  1. Absent or impaired migrating motor complex (MMC) will cause motility issues and therefore sluggish or incomplete bowel movements.
  2. Scar tissue, e.g. endometriosis, hysterectomy, appendix out, gall bladder
  3. Intestinal permeability (Leaky gut)
  4. Inflammatory conditions e.g. IBS, Crohn’s, Celiac, Diabetes causing imbalances of cytokines e.g. high IL6 and low IL10 (needed for epithelial and gut lining integrity).
  5. Histamine and other Mast Cell Activation imbalances
  6. Low Secretory IgA levels that may indicate poor gut immunity
  7. Altered anatomy e.g. faulty ileo-cecal valve, scarring
  8. Fermented bacteria from inappropriate diet e.g. FODMAPS

Is fibre bad for SIBO?

In some cases,  it can feed dysbiotic bacteria and insoluble fibre can be roughage that can damage the intestine lining. But we need do soluble fibre to feed our beneficial bacterial and help produce butyrate that heal our gut lining (A double edge sword) and to be discussed with patient and practitioner as to their specific needs.

Prevalence: “Overall, There is a substantial increase in the prevalence of SIBO in IBD patients compared to controls. Prior surgery and presence of fibrostenosing disease are risk factors for SIBO in IBD”6.


Areas to consider for treatment:

 1. Increase digestive enzymes

 2. MMC Migrating Motor Complex – cyclic reoccurring pattern of motility with enteric hormone motilin, produced by the endocrine cells.

that occurs in the stomach and SI during periods of fasting and is interrupted following food consumption. They repeat every 1.5-2 hours normally.

3. Vagal dysfunction (VD)

The vagus nerve is the main component of the parasympathetic nervous system and the 10th Cranial never extending from the brainstem thought the neck down to the abdomen. Helps manage signalling then muscles in your stomach to contract and push food into the small intestine.

Damage to this nerve can result in decreased production of stomach acid.

In the intestines it regulates the contraction of smooth muscles ad glandular secretion.

It’s a connection between gut and brain sending info to the brain via afferent fibres.

The Vagal tone is correlated with regulation stress responses so can be influenced by breathing techniques, meditation and yoga.

One study on HIV patients with chronic inflammation and SIBO found that participants with VD has delayed gastric emptying and higher prevalence of SIBO.

They also had higher IL 6 markers possibly causing a stimulation inflammatory processes.7

5. Epithelial integrity and mucus membrane restoratives e.g. amino acids are often deficient and needed for regulation of epithelial barrier and intestine immunity.

6. Dietary considerations to reduce SIBO and SIFO

7. Appropriate anti-microbial support for bacteria and fungi (Covered in PART 2, coming soon)



Two recent studies showed that 26% (24/94) and 25.3% (38/150) of a series of patients with unexplained GI symptoms had SIFO

The most common symptoms observed in these patients were belching, bloating, indigestion, nausea, diarrea, and gas.

The underlying mechanism(s) that predisposes to SIFO is unclear but small intestinal dysmotility and use of proton pump inhibitors (PPIs) has been implicated.

Importantly, whether eradication or its treatment leads to resolution of symptoms remains unclear; at present, a 2-3-week course of anti-fungal therapy is recommended and may be effective in improving symptoms, but evidence for eradication is lacking 8.


PART 2: TREATMENTS with Herbal Medicine, Diet and Nutritional Supplements.



  1. Bures J, Cyraney et al. Amall intestinal bacterial overgrowth syndrome.

World J Gastoenterol: WJG. 2010:16 (24):2978.

  1. Ghoshal U, Shakla R, Small intestineal bacterial overgrowth and irritable bowel syndrome: a bridge between functional organic dichotomy. Gut Liver. 2017:11(2):196
  2. Yarnell E. Herbs for upper digestive overgrowth of flora. Alternative and Complementary Therapies. 2018:24 (4): 173-9
  3. Revaiah PC, Kochhar R et al. Risk of small intestineal bacterial overgrowth in patients receiving proton pump inhibitors verses proton pump inhibitors prokinetics. JGH Open
  4. Pimentel M, Soffer EE et al. Lower frequency of MMC is found in IBS subjects with abnormal lactulose breath test, suggesting bacterial overgrowth. Dig Dis Sci.
  5. Shah A, Morrison M et al. Systematic review with meta‐analysis: the prevalence of small intestinal bacterial overgrowth in inflammatory bowel disease. Aliment Pharmacol Ther. 2019;49(6):624-35.
  6. Robinson-Papp J. Nmashie A et al. Vagal dysfunction and small intestinal bacterial overgrowth: novel pathways to chronic inflammation in HIV. AIDS, UK. 2018;32 (9):1147-56
  7. Erdogan A, Rao SS. Small intestinal fungal overgrowth. Curr Gastroenterol Rep. 2015