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How ‘experts’ get SIBO wrong

SIBO, Bacterial, IBS, gut, bloating, gas, Hashimoto’s, Thyroid, Doctors, motility, stomach acid, healthy, Lactic Acid bacteria, Butyrate, Saccharomyces boulardii, Streptococcus thermophilus, Enteric Nervous System, (ENS), Brain in the Gut,
How ‘experts’ get SIBO wrong

Small Intestinal Bacterial Overgrowth (SIBO), where an excess of bacteria and yeasts inhabit the small intestine, is far more common than people think and often confused with IBS and gut lining damage when its prime causes are lack of acidity and gut motility.

The Symptoms of SIBO

These include bloating, gas, a sudden change to either diarrhoea or constipation and back again, and sometimes even pain – all rather like IBS (1). In fact, it is easily confused with IBS and other problems in the colon.

SIBO is having bacteria in the wrong place at the wrong time.

You should not really have large numbers of bacteria in your small intestine. To have SIBO, the bacteria don’t have to be bad, they can all be commensal, or good. They just shouldn’t be there.

And it’s not just bacteria (2). You can have archaea – a single cell organism, a prokaryote, older than bacteria! Although officially classed as bacteria, archaea metabolism is more like that of a yeast.

The problem is that these unwanted immigrants rob you of your nourishment. After your stomach has processed your food, the ‘mush’ passes into the small intestine (which is actually 6 feet long) and the nourishment is absorbed into the bloodstream. But with SIBO, the bacteria and/or archaea get in first! They ferment the food producing gas – typically, hydrogen and/or hydrogen sulphide; while the archaea produce methane. Bloating, wind and even pain follow; the same symptoms as IBS. You can then develop diarrhoea from the hydrogen, and constipation from the methane. Your digestion suffers, as does the perfect absorption of minerals and vitamins. Lowered B-12 can be a classic symptom. And fatigue, weakness and irritability.

But it can be even more serious – Hashimoto’s Disease or Hashimoto’s thyroiditis is a good example. This results in damage to the thyroid and Hypothyroidism. One study found that over 50% of Hashimoto’s patients have SIBO. You can read more on Hashimoto Thyroiditis Here. 

Of course, you have to ask, ‘Is it cause or effect?’ but as an ‘autoimmune disease’ our increased knowledge suggests an immune response to issues in the gut, causes damage to the thyroid. Immune responses may be caused locally, but act globally throughout the body.

Although excesses of Bacterioides and low levels of Bifidobacterium and Lactobacillus families have been identified in Hashimoto’s, it is more likely that the immune response is provoked by the higher numbers of bacteria in your small intestine. (However, in Hashimoto’s it is known that pathogens in the body can also be involved – for example, Yersinia enterocolitica, Helicobacter pylori, and Epstein Barr Virus to name just a few.)

There is a very little evidence that Graves’ disease which promotes Hyperthyroidism may be linked to SIBO; however there is more research that it is linked to pathogenic bacteria in the colon (3).

What causes SIBO?

Firstly, let us address the title of this article. Doctors – if they even identify SIBO – often want to use antibiotics to kill off the bacteria. This is a complete waste of time. You do not have a bacterial infection. All the antibiotics will do is wipe out your good bacteria (and bad) everywhere and make you ill. As Hippocrates told us (and the US Human Microbiome Project) you need a healthy microbiome to be well.

So what are the causes of SIBO? And what can you do about them?

i) Low stomach acid

Firstly, it is known that SIBO can be linked to low stomach acid. In a healthy individual, your stomach acidity can go as low as pH 3 (that is very acidic). Your gut will be somewhere between 3 and 7. If it goes north of 7 you will have an alkaline gut, and you certainly don’t want that! Alkalinity in the gut damages the growth and replication of healthy commensal bacteria. When you were a baby, your gut pH was around 5.5, due to all those Lactic Acid bacteria you received from Mum. A high pH, on the other hand, is linked to the presence and development of more pathogens. As a result, the digestion of food and thus movement through the gut can slow down.

So the first thing you should do is put your gut acidity up – a first-thing-in-the-morning drink of room temperature water with lemon juice and apple cider vinegar. Eat more protein and less carbs.

Do NOT consume sodium bicarbonate or use ‘highly alkaline water’ or water filters.

Yes, you should add certain Lactic Acid bacteria into the mix, increasing acidity. A good choice would be Saccharomyces boulardii or Streptococcus thermophilus, neither of which grow in the small intestine.

Avoid stress, smoking, binge drinking, drugs (especially proton pump inhibitors), and antibiotics.

ii) Improve your gut wall

Permeability of the gut well has been linked to SIBO, and to Hashimoto’s (4). Permeability, or leaky gut, can be a big factor in the small intestine and causes compounds to pass into the bloodstream. These cause inflammation and can prompt an immune response.

Take Butyrate to rebuild the gut wall. Butyrate is anyway great for your health. It is a short chain fatty acid; a super molecule produced by about 60 or more helpful bacteria. Other natural gut wall ‘healers’ found in research are presented in our article on Colitis.

iii) A problem with the ileocaecal valve

This is the valve between the small intestine and the colon. It can weaken. If so, it can cause bacteria to rise from the colon into the small intestine. The usual culprits weaken it – smoking, alcohol, stress, poor diet. Start by giving up the bad and improving your diet.

iv) A problem with the Enteric Nervous System (ENS),

Often called the ‘Brain in the Gut’, the ENS links the brain to the gut and vice versa. The ENS is pivotal for gut movement – the passage of food down the gut. It works independently of the other nervous system areas. And in SIBO, it is not working very well.

SIBO is thus also about motility – the movement of food (and bacteria) through the small intestine. This needs to proceed properly, to clear the small intestine.

The ENS controls your gut muscle wall impulses. Called peristalsis, it will work, even when a person is paralised or in a coma when other systems have shut down. The contractions occur about every 90 minutes and push your food down the gut. Of course, these impulses are improved by lubrication – extra virgin olive oil and fish oils being a good place to start – and exercise (yes, and in particular, sit ups!), and they are worsened by factors such as genuine constipation and a parasite.

There are two parts to the ENS – The myenteric plexus control the speed and intensity of contractions in the gut. Something you are not aware of.

Then there’s the submucosal plexus which controls localised events, secretions and absorption.

The ENS is one of the reasons we get ‘Butterflies in the stomach’. It is affected by our mood and particularly anxiety and stress.

Clearing SIBO

To address SIBO – make your gut naturally more acidic, eat foods that promote mobility, lubricate your food with good oils, exercise, and calm your brain – take positive natural steps (not drugs) to calm your brain and your nervous system with therapies such as EFT, Meditation and/or prayer.

Some people try FODMAP – it is not actually a diet but you cut back on food types and reintroduce them one at a time to see if they help or hinder.

Diet is obviously crucial in all this. We are very clear that certain foods produce higher levels of bacteria that make inflammatory molecules, while other foods produce more bacteria that produce anti-inflammatory molecules. The Rainbow Diet is EXCELLENT for producing the latter – we have research from Holland (5) showing exactly that.

How can you test for SIBO?

A breath test is the Gold Standard – after an overnight fast, the patient ingests glucose or lactulose every 20 minutes and levels of methane or hydrogen are measured.

Go to: Hashimoto’s Disease



  1. Small Intestinal Bacterial Overgrowth: Comprehensive Review of Diagnosis, Prevention, and Treatment Methods; Cureus, 2020 June 12(6); Ted George O. Achufusi et al – https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7386065/
  2. Time Magazinehttps://time.com/6155603/sibo-small-intestinal-bacterial-overgrowth/
  3. Intestinal microbiota changes in Graves’ disease: a prospective clinical studyHui-xian Yan et al; Biosci Rep. 2020 Sep 30; 40(9):
  4. Children with Hashimoto’s Thyroiditis Have Increased Intestinal Permeability: Results of a Pilot StudyBanu Küçükemre Aydın et al; J Clin Res Pediatr Endocrinol. 2020 Sep 2;12(3):303-307
  5.  Study links good gut bacteria to Rainbow Diethttps://the-rainbow-diet.com/articles/the-colourful-mediterranean-diet/study-links-rainbow-diet-foods-to-good-health/