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The Small Intestine - Gut Series pt. 4
small intestine.jfif

The small intestine is anything but small – whether in its size or significance. It is coiled in the centre of the abdominal cavity and usually measures between 6 and 7 metres long. 

It should correctly be called thin and long.

It is THE most extensive part of our digestion. The small intestine receives what the stomach has not completely decomposed and continues the process of separation and absorption. This is the place where we sort out what is important from what is not – on all levels.

There are tiny finger-like formations that line the entire length of the intestine, called villi. These provide a large surface area – about 30m² in total. Villi absorb nutrients from the food and transport them into the bloodstream.

This is the theory and an ideal case scenario, though. From our previous articles we already know that by the time food reaches this part of our gut, we might have encountered issues with lack of stomach acid, congested liver or a lack of pancreatic enzymes (as these depend on the correct level of the stomach acid).

What is more, if we have gluten intolerance and carry on eating it, the inflammation caused by gluten can completely flatten out the villi, thus leading to malabsorption. The small intestine is a natural habitat for a yeast called Candida Albicans. When we lose our villi and suffer from malabsorption, the immune system can no longer keep candida in check – thus we end up suffering with candida overgrowth.

You may remember when I mentioned small intestinal bacterial overgrowth (SIBO) in my stomach article (Healing Begins In the Gut Pt.1 - the Stomach). When the stomach acid is not powerful enough to literary ‘burn through’ microbes entering the gut, bacteria will start proliferating in the small intestine. In a healthy body, the small intestine is fairly sterile, except for a small amount of candida yeast.

It’s important to know that we have good, neutral and bad bacteria and yeasts as part of our normal, healthy microbiome. About 70 to 30 ratio is ideal. When our gut doesn’t work properly, we may see reduction in the beneficial bacteria.

However, our biggest concern should be the neutral bacteria and yeasts, also referred to as opportunistic. Given the right (in this case, compromised) conditions they will start to proliferate out of proportions – into unwanted/harmful bacteria and fungi – e.g. candida overgrowth.

However, no matter if the bacteria growing in the small intestine are essentially considered good or not, they should not be there in the first place. Their habitat should be the large intestine.

Bloating, abdominal pain, IBS and IBD, also diarrhea and constipation are all linked to dysfunction in the small intestine, and are usually a sign of SIBO.

So when we experience SIBO, the bacteria feed on our food – our nutrients. We may become deficient in iron, zinc, magnesium, biotin, B12 and other nutrients. Many of these nutrients are essential for an optimally functioning immune system. Thus, reduced immunity will be another symptom of SIBO. Functional doctors also use a term SIFO – small intestinal fungal overgrowth. It is quite common for both of these situations to be happening at the same time.

How to heal SIBO/SIFO?

One needs to address the inadequate stomach acid (as we discussed in the stomach article here) and reduce the bacterial/fungal population by using and rotating strong natural antibiotics. Yes, they need to be rotated as many microbes are rather smart and can get used to the same active compound (like in the case of antibiotic resistant bacteria where a certain pharmaceutical drug contains one active ingredient to which the bacteria get eventually accustomed). Natural antibiotics are always preferable as they contain many different antibacterial/antifungal active compounds and at the same time they offer nutrients and co-factors to strengthen the immune system. At the end of the day, it is the immune system that keeps all our microbes in check, not the remedies.

What are natural antibiotics?

Spices and herbal remedies like cinnamon, cloves, nutmeg, garlic, oregano, pau d’arco, olive leaf, black seed oil, berberine, grapefruit seed extract, lavender, tea tree. For more information on candida, check my article here: Candida - the Good, the Bad And the Ugly.  

Healing the villi

Once we have addressed the bacterial/fungal overgrowth, we can start healing the villi. If we have lost our villi due to inflammatory response caused by gluten, the only way to heal is to avoid gluten from now on.

The good news is that because the small intestine receives so much blood flow, the villi can start to regenerate/regrow within days. In the case of a very compromised small intestine, the complete healing can take 3-6 months.

Adding probiotics

Just a word of caution - do not think it a good idea to simply add probiotic capsules or powder when you suspect you have a low count of beneficial gut bacteria. First you need to establish the cause: 

1) It is possible that all you need is to add more beneficial fibre (also called prebiotics) to your diet and/or reduce sugar and processed foods. This is the easiest hack ever.

2) Generally speaking, if you just want to maintain your 'good guys' in the long run, then going for probiotic rich foods is the best option. Add fermented foods/drinks like apple cider vinegar, sauerkraut, kimchi, kombucha, kefir (water or milk) and yogurt to your diet several times a week. If you suspect dairy (casein) intolerance, avoid fermented milk or try goat and sheep, rather than cow's milk.

3) If you have no gut issues but need to take antibiotics, it may be a good idea to increase prebiotic fibre and fermented foods in your diet, and possibly take some high strength probiotics for a short time.


4) If there is any kind of unwanted overgrowth in the small intestine, probiotic supplements would make things much worse. In this case, you absolutely need to reduce the unwanted microbes before you can start adding any probiotics, especially highly concentrated supplements. You may also need to reduce your fibre intake for a while. Once you have resolved the SIBO/SIFO problem you can start adding probiotic rich foods, possibly add a high strength probiotic supplement (as a temporary boost to your microbiome).



In the Traditional Chinese Medicine the small intestine belongs to the element of Fire.

As we already mentioned, the small intestine is the place where we sort out what is important and what needs to be discarded – also on the emotional and psychological levels. When we struggle with poor sorting or we lack clarity of emotions and thinking, it may well indicate an imbalance in the chi energy of our small intestine.

A healthy and balanced Fire element means we always have access to our innermost happiness and remain versatile and flexible through many changes, even challenges in life.

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