GUT overview: dysbiosis, SIBO, herbs

[For a list of recent relevant ME/CFS studies and info on dysbiosis testing, see gut studies]

The intestinal microbiota and in particular members of the virome may be a source of the “infectious” trigger of ME/CFS~ 2016 review of ME gut literature

The gut microbiome controls the immune system, and is linked to serotonin and other neurotransmitter levels. Gut bacteria studies show links to depression, anxiety, autism, schizophrenia, rheumatoid arthritis and many others (see Edible or above link for references).

ME/CFS is hypothesised to be autoimmune. One study found individuals with ME/CFS have increased 5-hydroxytryptamine (HT) autoimmune activity associated with activation of inflammatory pathways and increased bacterial translocation, similar to MS. The aetiology is unknown but given the gut microbes, immune cells and immune processes, it may be the source of the autoreactivity. (2015 review)

In mouse models, sterilising the gut reduces autoimmunity symptoms—though a mouse model has not been achieved in ME/CFS. Leaky gut has been shown to have a role though. Chronic intestinal inflammation from bacteria can result in neurological disease, with bacteria-derived LPS generating antibodies cross reactive with host lipoproteins. One ME/CFS study has reported significantly higher titres of serum antibodies to LPS in patients with abdominal discomfort than in controls.  Gastrointestinal symptoms were associated with increased bacterial translocation, which is a potential driver of systemic inflammatory processes.

Up to 92% of ME/CFS patients have co-existent irritable bowel syndrome (IBS). One study reported ‘our patient groups were disproportionately affected with IBS. These results suggest that a common pathogenic mechanism related to bowel dysfunction may underlie CFS, FM, and TMD disorders. In this regard, some investigators have speculated that the serotonin abnormalities observed in patients with FM may be the result of defective absorption of the precursor amino acid tryptophan from the gut’.

42/42- 100% of fibromyalgia patients were shown in study to have Small Intestine Bacterial Overgrowth (SIBO), whereas 77% of CFS patients did, which displays some similar clinical symptoms to ME/CFS.

SIBO can be measured by breath test. After ingesting glucose and/or lactulose, exhaled hydrogen and methane is measured every 15-20 minutes for 2-3 hours. During the time ingested food or sugar is in the small intestine, it should be absorbed not fermented. SIBO fermentation occurs when due to a lack of digestive acid or other issues, there is an overgrowth of endogenous bacteria from the large intestine in the small intestine. This can cause carbohydrate intolerance, and ME/CFS patients often feel better on a high fat/protein, low carb diet as a result.

Breath test results can show elevated hydrogen or methane. About 40% of people are methane dominant producers, with a tendency toward constipation. This is potentially due to the impact of archaea that convert excess hydrogen into methane. bacteria such as methanobrevibacter smithii are also methane producing.


Unlike the small intestine, the large bowel is meant to house bacteria. Optimal bacteria balance is dominated by bacteria that support nutrient absorption and production, maintain gut wall integrity, and suppress yeast and parasite growth. Other bacteria can have toxic metabolites which go into the blood steam, or interfere with immune system signalling. This can lead to a dominance of yeasts and parasites and an absence of good bacteria. This can happen as a result of exposure to antibiotics, which causes an absence of good protective bacteria.

Bacterial imbalance can lead to nutrient deficiency, imbalanced neurotransmitters (esp serotonin), widespread inflammation, including in the brain as depression, impaired gut motility, food allergies and intolerances. A lack of commensual bacteria allows toxins from harmful bacteria and yeast to interfere with gut wall integrity and mucosa—which could be the cause of autoimmunity seen in ME/CFS.

The gut affects the HPA axis directly. EG Stress induced in early life leads to dysbiosis in germ-free mice—which causes abnormal behaviour, and anxiety and aggression can be transferred by fecal transplant. The integrated microbiota-gut-brain-axis, which links the microbiota with the central nervous system (CNS), the autonomic and enteric nervous system and the hypothalamic-pituitary-adrenal (HPA) axis via immune, neural and endocrine pathways, may allow bacteria to affect cognitive function and behaviour. Stress affects this by reducing the MMC (migrating motor complex), which affects the movements, secretions and permeability of the gut. Bacteria can release stress hormones, and germ-free mice show (reversible) exaggerated HPA responses to mild restraint stress, through increased levels of adrenocorticotrophic hormone (ACTH) and corticosterone. Sleep is also controlled by bacteria who release ‘Factor S’.

ME/CFS patients have low levels of Bifidobacteria, who maintain gut wall integrity. A reduction in these beneficial Gram-positive bacteria may allow growth of harmful Gram-negative bacteria. Bifidobacteria are associated with increased plasma tryptophan, serotonin and dopamine. Certain species improve NK cell activity, may lower levels of IL-4, IL-5 and IL-10 cytokines and support the presence of Th1 directed cell-mediated immunity.

Virome: new technology shows viruses are implicated in gut health, and may be more persistent than bacteria. Bacteriophages, which make up 90% of the gut virome composition, drive virome diversity. Chia and colleagues identifying a higher prevalence of enterovirus infection in gastric biopsy samples of ME/CFS patients with significant gastrointestinal symptoms (82%), compared to control subjects (20%) (link above).


Changing the gut biome is not as simple as taking a probiotic. The below protocol is tentative and suggestive. Individuals bacterial and viral biomes differ vastly, and our ability to measure species, understand significance and predict changes is limited. The below is known anecdotally to help in general dysbiosis, and is not specific to ME/CFS. 

Use herbs as food where possible rather than essential oil, which can be poisonous. Best done under the supervision of an experienced practitioner, and with CDSA or other stool, breath & urine testing for known pathogens. Some herbs are specific to certain pathological strains, other are non-discriminative.

Treatment under a naturopath can involve: Weed, Seed and Feed.
For more information see, for example, Kerry & Jason Hewlwreck.


Antiparasitic herbs that kill overgrowth: black walnut, wormwood, garlic, berberine and tannins, golden seal

2 days eating garlic cloves, golden seal, use paragone (tablet).

Antimicrobial: thyme, cinnamon

Garlic, Oregano, Berberine, Grapefruit seed extract, Caprylic acid, Olive leaf extract, Uva ursi

for parasites- oregano, anise, clove and basil.

MYRHH, respiratory herb. new studies in treatment of parasites. clinical advancement, those infecting the liver and the bladder. high in essential oils, use with caution

Tannins as found in black tea and wine may stop overgrowth, but may lead to dehydration, and constipation. Needs to be balanced out with other herbs

Apply herbal fertiliser. althea officinalist root (marshmellow), alow, ulmus rubra (slippery elm)
5 days, slippery elm powder (NOT CAPSULES), marshmellow tea

licorice is also a demulcent and antiviral

Supplements such as bioceuticals clinician only ‘IM’ contains many of these and may be nourishing.

probiotics, once tolerated

Note: SB is immune regulating and can cause side effects such as ulcers & coldsores by affecting viral immunity.



While the widespread blaming of candida as the root of all evil and health scapegoat, it still can be problematic. Candida albicans (fungus) drives allergic responses. Seen as thrush in the mouth or vagina, can be systemic. Can be triggered by hormones, pregnancy, or ongoing infections such as EBV & CMV—or a lack of protective bacteria. Might be present if widespread skin fungal infections, or if organic acids and other tests show metabolite markers of fungal infection, such as elevated oxalates. Diagnosis can be via vaginal or mouth swab, or iridology for systematic infection.

Candida treatment

Pau d’arco can kill yeast overgrowth, if used on a rotating basis. Barberry, echinacea and andrographis (also a bitter) are all immune enhancing.

Sugar cravings: restricted diet, limited yeasts, replacement foods,
low sugar fruit only. Bacteria to combat candida include Lactobacillus acidophilus & reuteri and Bifidobacterium animalis


Low acidity in the gut, contributes to bacterial overgrowth and SIBO. May present as GERD.


Acid reflux coming into the mouth, or heartburn, can go up into the nose can cause problems in the sinuses and at night. May be a problem with digestive enzymes, can be linked to gastroparesis with slow gastric emptying (commonly found in ME/CFS & POTS). GERD is  linked to other digestive problems like IBS and conditions such as EDS. Sjrogens (autoimmune) resulting in decreased salivation may be linked.

Ginger can help gastroparesis, though can be an issue with oxalates (usually linked to joint pain), especially if fungal overgrowth.

Theoretically, problems with the gastric (lower osophogael sphincter) and anal sphincter, which is a muscle, may be linked to ANS regulation, or even muscle tone and muscle exhaustion due to energy production issues in CFS. GERD can be affected by obesity and medications, stress and genetics.

Lying down is a risk factor for reflux in CFS patients who are bedbound. Raising the bedhead 28cm may assist, in the absence of ME/CFS triggered POTS, however in many cases fixing digestion/removing trigger foods will usually alleviate.

Antacids are a bandaid solution. Diet is a big risk factor- gluten, dairy, nightshades, salicylates. Too much fat can also contribute, as these require adequate enzymes in the stomach for digestion. Herbs can be used to reduce inflammation (such as chickweed), support nervous system with herbs like lemon balm. Filipendula ulmaria (meadow sweet) can normalise acid and is astringent.

Functional dyspepsia results in reflux but also has symptoms of diaphragmatic spasm, hyperventilation, shallow breathing, trouble swallowing and palpitations. Treatment is similar, left untreated FD can cause long term damage.


Herbs such as silybum marianum (milk thistle), especially for candida


Zinc (monitor ceruloplasmin and copper)
Strong Bitters: gentian (may cause gallbladder/liver spasms)

Bitter herbs stop reinfestation of parasites, and adjust gastric output by stimulating enzymes.

Gentle herbs may assist with GERD by toning the LOS, increasing acidity and enzyme production, improve gastric emptying time and protect the mucosa. Used with caution if hyperchloric.

wormwood, berberine, synaria, globe artochoke, yarrow

Digestive enzymes act as an anthelmintic (destroys parasites)


  • Dietary Change- see Edible
  • Stress kills good bacteria.
  • Avoiding aspirins and anti-inflammatory drugs like neurophen that can damage the stomach

Other supplements include L-glutamine, magnesium allows blood flow and muscle relaxation, essential fatty acids inhibit bad bacteria and infections such as h.pylori, as does bee pollen/propolis, which is also a great source of vitamins as well

[For a list of recent relevant studies on the gut in ME/CFS and info on dysbiosis testing, see gut studies]