Nutrient deficiencies are an epidemic in the SIBO world. The connection is recognized, but many times unaddressed. Instead, the focus is on clearing and starving the SIBO and less on ensuring optimal nutrient status.

And yes, you do need to clear the SIBO to be able to digest and absorb nutrients properly. But, addressing nutrient status is still critical for healing.

There are three main reasons those with SIBO can start to become deficient in many nutrients. First, the SIBO can disrupt digestion and absorption of nutrients. Second, gut symptoms can lead you to undereat and not consume enough nutrients. Third, restrictive diets attempting to starve the SIBO and/or control symptoms can leave you with limited options to meet nutrient needs.

One of the many drawbacks of long term restricting is the increased risk of nutrient deficiencies. That is why I don’t recommend unnecessary dietary restrictions with my clients. Yes, it is important to remove inflammatory foods and reduce your trigger foods, but you can easily go overboard if your dietary strategy is to starve the SIBO (which I haven’t seen be a successful long term approach).

However, some cases do require more restriction to manage the gut symptoms. In these cases, it is crucial to work with a practitioner that can help you meet any dietary gaps that need to be filled with your diet. If your practitioner is just telling you to avoid certain food groups and not deep diving into the context of your diet, I would look for another practitioner that can help you maximize nutrition and supplement accordingly while you are on the restrictive diet.

In this post, I want to discuss the common nutrient deficiencies that I see with my clients in hopes to equip you with some nutrients to monitor throughout your SIBO journey.


Macronutrients are calories, carbs, protein and fats. Before even addressing micronutrients, you need to make sure you are meeting your macronutrient needs. These are going to differ for each person.

In the SIBO population I have worked with, I tend to see most people failing to meet carb and calorie needs. I have discussed these issues at depth in this post, but I will summarize the big problems that happen when you are undereating calories and carbs.


Chronic undereating of calories is a huge problem in the SIBO world. 80% of my SIBO clients are undereating (and it is usually unintentional). Chronic undereating will lead to chronic stress in the body. Your body needs to have resources to rebuild and heal. It also makes it way more difficult to meet your micronutrient needs if you are failing to meet your calorie needs. Here is a graphic that also demonstrates the effects that chronic undereating can have on the gut function:


Meeting carbohydrate needs is going to vary based on your individual case. Low carb like low calorie diets can stress the body out and lead to hormone imbalances especially in woman.

When you are not consuming enough carbs to maintain blood sugar levels, your body has to make glucose by breaking down protein. This process requires cortisol. So low carb diets have the potential for activating the HPA axis and dysregulating cortisol levels. In short, long term keto style diets can lead to excessive fight or flight activation.

Thyroid hormones are also activated by insulin release. Insulin levels fall when you are on a very low carb diet. Low carb then can prevent the activation of T4 (the inactive thyroid hormone) into T3 (the active thyroid hormone).

Thyroid hormones are critical for regulating our metabolic function, but also play a key role in motility. Hypothyroidism causes delayed motility, which can increase the risk of SIBO developing. Eating enough carbs can prevent downregulation of activate thyroid hormones that can slow motility.

Sex hormones also can go haywire on a lower carb diet. Reproduction is a metabolically expensive process, so the body will shut off reproduction if you dip too low in long and short term fuel reserves. Leptin signaling from body fat is the main way the body gauges long term fuel reserves and insulin signaling is how the body gauges short term fuel reserves.

If you dip too low in weight, your sex hormones will dip from lack of leptin. If you dip to low in carbs and insulin decreases, then you can expect a down regulation of sex hormones.

Hormone balance is a critical piece to healing from SIBO. Finding the optimal amount of carbs for your body to support hormones and gut function can be tricky, but key to finding long term relief. Many SIBO diets can naturally leave you deficient in carbs.

In my aimless pursuit to starve the SIBO in my journey, I was low carb (getting about 75g daily) and felt horrendous for about 4 months. My energy levels were in the toilet. My motility suffered. My hormone labs and gut tests looked worse after this diet. When I added carbs back in at 150-200 grams daily, I felt so much better.

When I say low carb, what do I mean? The term low carb can be confusing depending on what your reference point is. For instance, 100 grams of carbs daily or 20% of your daily calories is considered higher carb in the keto space and many gut health circles. But, when you consider that Americans are advised by nutrition guidelines to eat 45-65% (over 200 grams) of their calorie intake from carbs, 100 grams would be considered low carb in comparison.

Usually there is a happy medium for gut clients with carbs. I typically shoot for around 30-40% of calories coming from carbs for my clients. Some may do better with a little less than that and some may do better with a little more.

Before anyone jumps down my throat about having success with low carb, some people do well on a short term low carb diet. But, much fewer seem to do well on long term low carb diets. If you are implementing a low carb/keto style diet, working with a practitioner is even more important to ensure you are meeting nutrient needs.


Protein is crucial for gut healing. Most people with SIBO are eating enough protein, but some still are missing the mark. Vegetarians and vegans can have a harder time meeting their protein needs than meat eaters.

Don’t panic if you are vegetarian or vegan. You can definitely meet your protein needs sans animal food but it just requires a little bit more creativity and effort. I would work with a practitioner to ensure that you are meeting your protein needs.

Usually a good rule of thumb is to make sure you are getting 0.5g of protein per pounds of body weight. So if you are 150 lbs, you would need at least 75 grams of protein daily.

I also see many going a bit overboard on the protein. A high protein intake creates problems if you are struggling to get enough calories in. Protein makes you feel fuller and more satiated, which is great when you are trying to lose weight but can be problematic if you need to maintain or gain weight.

Reducing protein intake slightly and increasing fat and carb intake can help stabilize weight if you are struggling with weight loss.


Fat can be a great tool to ensure that you are getting enough calories. Usually the SIBO community is pro fat, which is great because who doesn’t love butter and olive oil! Fat usually packs a lot of calories in a small volume making it helpful for filling in calorie gaps.

For instance, a TBSP of olive oil has around 130 calories. While a TBSP of rice has 25 calories or a TSBP broccoli is going to have like 5 calories. You have to eat a large volume of real foods to meet your calorie needs with carbohydrates. Eating a large volume is much easier if you don’t have gut problems that can be aggravated by a large volume of food.

You should certainly still eat veggies and starches, but adding fats to meals for a low volume fuel source can make a big difference. If you are struggling with weight loss, try adding more fat to your meals.


Micronutrients are the vitamins and minerals that our body needs to function effectively! SIBO can leave you susceptible to nutrient deficiencies due to breakdowns in digestion and dietary shifts. I want to touch on the micronutrients that are often deficient in SIBO sufferers.


Iron is a critical nutrient and is well known for its role on oxygen transport in the body. Iron also plays a role in DNA synthesis, the electron transport chain (energy production) and also thyroid hormone production. Not only is iron essential for humans, but bacteria also use iron.

Gut bacteria will often steal iron from their host. Many gut bugs have adapted to have iron acquisition proteins that make them especially efficient at stealing iron.

If your gut is imbalanced and inflamed, iron absorption is poor and can lead to increased theft of iron by pathogenic bacteria. Not only are you not getting iron, but your gut can become more imbalanced. Iron supplements can actually aggravate gut inflammation and imbalance by increasing the replication and virulence (disease promoting factors) of pathogens.

Most iron supplements are extremely high doses and poorly absorbed leave tons of iron for your gut bugs to munch on. Typically, I like working with someone on gut balance before I consider iron supplementation. When I do use iron supplements, I like to use Proferrin ES since it is a reasonable dose and a much more absorbable form of iron compared to other supplements.

So, how do you know if you may be deficient in iron? The signs and symptoms include: weakness, extreme fatigue, exercise intolerance, shortness of breath, chest pain, light headedness, dizziness, poor circulation (cold hands/feet) and unusual cravings for non-food items (I know this is weird but it happens). If you have these symptoms, I would ask your doc to run a full iron panel to see if iron deficiency may be a problem for you.

If you are vegetarian, vegan or just not a big red meat eater, you could also be at risk for a iron deficiency.

Vitamin B12

Vitamin B12 is needed for brain and nervous system function. It is also needed for red blood cell and DNA synthesis. Like Iron, B12 deficiency is common with SIBO sufferers.

B12 can become deficient due to poor absorption, but like iron, it can also become deficient because certain bacteria have been shown to out compete the host for absorption. The bacteria thieves are at it again! Can’t they give us a break!

Antibiotic therapy has actually been shown to resolve B12 deficiency in humans. Treating the SIBO can be key here.

So how do you know if B12 is a problem? There are a lot of similarities with iron because they can both cause anemia (lightheadedness, fatigue, SOB, pale, weak). The major difference is that B12 issues can lead to nerve tingling, mental problems like depression, behavior change or memory problems and you can also have changes in vision.

You can run a blood test for serum B12 levels. The range is broad. I would shoot for levels that are over 500. If you avoid animal products, you have a higher risk of being deficient in this nutrient.

Fat soluble nutrients (Vitamins A, K, D, E)

Fat soluble nutrients require fat to be absorbed into the body. These vitamins play important roles in immune function, blood clotting, controlling inflammation and calcium metabolism.

SIBO can disrupt the absorption of fat leading to steatorrhea (fat in your poop). You can actually see this by looking at your poop. It is important to clue in on what your poop is telling you! If you see a greasy, shiny film in the toilet or around your stool this is a result of an inability to digest and absorb the fats that you are eating.

Bacteria in the small intestine can deactivate bile salts, which are crucial for optimal fat digestion. Lack of activated bile salts will lead to steatorrhea. Restoring microbial balance and optimizing bile flow is key to optimize absorption of fat soluble nutrients.

For SIBO clients, it is so important to get adequate vitamin A because it is needed to make secretory IgA in the gut. Secretory IgA is the main regulator of immune function in the gut. Without adequate IgA levels, immune function in the gut is suppressed. I see low IgA levels in many clients and making sure you are getting enough vitamin A and other IgA supporting nutrients is important for healing the gut (zinc, vitamin C, selenium, glutathione and protein).

If you are suspicious of being deficient in these nutrients, ask your practitioner to run labs to check nutrient status of these nutrients. You also may want to do a stool test to test how well you are absorbing fats and what to determine what your IgA levels are.

Thiamine (Vitamin B1)

Thiamine plays a key role in energy metabolism, nerve signaling and neurotransmitter production. Thiamine is also involved in insulin synthesis and secretion. Insulin is needed to allow glucose to enter our cells.

Low thiamine intake and absorption results in low insulin levels. Blood sugar instability and carb intolerance can occur in a thiamine deficient state.

Thiamine issues are common in SIBO for 2 main reasons. First, SIBO diets often remove many foods high in thiamine like oats, fortified grains, legumes, nuts, eggs and peas. Many high thiamine foods are also high in fiber, which can be problematic for some with SIBO. Second, gut bacteria can steal your thiamine. The pesky gut thieves strike again.

This reduction in thiamine rich foods and thiamine theft from our gut bugs leads to deficiency over time. Then when you add carbs back into your diet, you may not tolerate carbs well (headaches, brain fog, hunger after higher carb meals) due to low insulin levels. Supplementing with thiamine may help increase your tolerance to carbs.

Other nutrient deficiencies and closing thoughts

You are at risk to develop nutrient deficiencies beyond this list if you have SIBO and gut dysfunction. Most nutrients are absorbed in the small intestines. Imbalances and inflammation in the small intestines will inhibit optimal absorption of many different nutrients. Check out this picture of all the nutrients that get absorbed in the small intestines.

While your gut has to be able to digest and absorb nutrients, you also have to be covering your nutrient bases through diet and supplemental sources. Most SIBO clients I work with are taking measures to enhance digestion and absorption, but they fail to meet their nutrient needs through diet (usually because they are overly restrictive).

A great first step to help you figure out if you are meeting your macronutrient and micronutrient needs is to track using the cronometer app. I am not a huge fan of long term tracking, but tracking for 3-7 days to give you a baseline look at your intake can be very valuable.

I like cronometer a lot because it tracks micronutrient status, which is often overlooked by other intake tracking apps. By looking at your micronutrients, you can spot micronutrients gaps that might be hard to discover on your own.

I will check in from time to time using cronometer and I usually have a few nutrients that I am failing to meet through my intake. I usually up dietary sources to fill in my nutrient gaps or in rarer cases I supplement to better meet my needs.

That wraps up nutrient deficiencies for now! Please leave comments below if you have questions or experiences you would like to share.