SIBO 101: When "eating clean" goes wrong

Written By


Expert Reviewed By

Dr. Lauryn Lax, OTD, MS

Dr. Lauryn, OTD, MS is a doctor of occupational therapy, clinical nutritionists and functional medicine expert with 25 years of clinical and personal experience in healing from complex chronic health issues and helping others do the same.



You do all the “right things” to have good gut health.


Probiotics daily? Check.


A clean diet—rich with nutrient-dense eats; and 80-90% free of gut irritating foods like sugar, grains and dairy? Check.


Chewing your food thoroughly? Check.


Drinking water throughout the day? Check.


Heck, you even take it to the “next level”: incorporating fermented foods into your diet (like Kombucha, fermented veggies, kefir, and/or homemade yogurt), and sipping bone broth on occasion.


But…you still have digestive distress!



Nausea, bloating, gas, heartburn, sluggish digestion, and/or occasional diahrrhea.


You thought gut health should have resolved itself by now with all the time, consistency, and money you’ve invested into promoting a quality ‘healthy gut’ environment.


What gives?!


Despite your efforts to heal your gut lining and promote a healthy gut flora, you still experience the daily woes and wanes you hoped would disappear with newfound knowledge put into practice.


While your digestion is perhaps a bit better (compared to the days you ate pizza on the regular, or doused your system with artificial sweetener overload)…it still sucks.


And then you found out about SIBO…and some things began to make more sense.


SIBO (aka: Small Intestine Bacterial Overgrowth) is a condition of the small intestine where abnormally large amounts of bad bacteria are present.



The small intestine (or small bowel) is the longest part of your digestive system (made up of 3 sections – duodenum, jejunum and ileum)—and it is where 90% of our digestive process and food absorption takes place (the other 10% happens in the stomach and large intestine).


With the majority of your digestive processing going on in there, your small intestine should be nearly sterile (free from bad bacteria and undigested foods) and able to process through your food with ease.


Typically, in a healthy digestive system, the small intestine receives food in a liquid state from the stomach and absorbs nutrients from it, before passing any indigestible food to the large intestine and colon.  The colon then absorbs the water from the undigested food, finally excreting any final remains through your poop.


This process should take a total of about 90-120 minutes for the first part of our meal to pass through the small intestine and reach the large intestine (with the last portion of the meal reaching it up to five hours later).


Unfortunately, when SIBO occurs, your small intestine has large amounts of different types of bacteria that are typically found in the colon. These different types of bacteria slow down the motility of your small intestine and can cause several digestive issues.


 In layman’s terms: The digestive process takes a hit and does NOT go “according to plan.”


Hence, your digestive system becomes compromised…


Common tell-tell signs that you may have a bacterial overgrowth include:


  • Bloating
  • Gas
  • Pain
  • Diarrhea
  • Nausea
  • Constipation


Other, less known symptoms include:


  • Diagnosis of irritable bowel syndrome or inflammatory bowel disease
  • Food intolerances such as gluten, casein, lactose, fructose and more
  • Chronic illnesses such as chronic fatigue syndrome, fibromyalgia, diabetes, neuromuscular disorders and autoimmune diseases
  • B12 deficiency, as well as other vitamins and minerals
  • Fat malabsorption


Pretty broad, huh?


In fact, it is very possible that the onset of symptoms is so gradual or seemingly ‘normal’, that you might not even notice.


SIBO typically goes hand in hand with a leaky gut and can actually perpetuate a leaky gut even after an individual adopts a “healthy” or “real foods” diet (even with a paleo or autoimmunity protocol, and an effort to eat gut-healing foods).


Unlike occasional “flare ups” (instances of bloating, gas, abdominal pain, etc.) that everyone gets at one time or another, with SIBO, these symptoms of indigestion are more constant with your every day eating.


In fact, a good indication that you may have SIBO is if you have continued health issues even after adopting a real-foods or ‘clean eating’ diet (not just GI symptoms, but also things like arthritis, skin conditions such psoriasis, difficulty in losing weight/gaining weight, or continued hormonal, mood and energy level issues).


How do you get all that bacteria in there in the first place anyway?!


A trigger event.


Something as simple as a reaction to antibiotics or a type of food you eat can trigger this change in the small intestine.  When this occurs your small bowel can take on harmful bacteria (the root cause of SIBO).


Unfortunately, SIBO is highly under-diagnosed. Many people brush their symptoms off as being ‘just the way things are’ and don’t seek medical attention for the symptoms, and, even if they do, many doctors aren’t aware of how prevalent SIBO is. [FACT]


While there is testing that can be done, the most commonly used tests (breath tests, measuring levels of hydrogen and methane gas) have high rates of false negatives (i.e. the test results come back as negative, but you actually have the disease).


So, how do you know if the digestive distress you’ve been dealing with is potentially more than just “getting gas after every meal?”


Answer: Being a detective yourself.


In my practice I choose to treat clients I suspect of having SIBO with a gut-healing supplement and dietary protocol, and if they respond to treatment, then we know we have made the diagnosis and treated it at the same time (killing two birds with one stone).


Check out my story, and a few action steps you can do today in your sleuthing process:



I initially discovered this under-discussed condition through personal experience.


I LOVE sweet potatoes! All varieties, shapes and forms—Japanese, Garnet, New Jersey, Purple, Jewel; fries, chips, roasted, baked, crockpot…



If I was a food, I’d probably turn into a sweet potato (random fact: my skin was orange as a baby from all the carrots and sweet potatoes I ate).


However, despite my affection for the nightshade vegetable, and despite how “healthy” sweet potatoes are for you…something was not right.


Stomach pain.


Not every time, but the majority times after consuming the tater, my digestion was…off.


Loss of appetite. Some constipation. Sluggish. Gas or bloating.


What gives? I’d think. I’d eaten sweet potatoes for years—no problem.


I became a sleuth—something I often coach clients to do: Creating awareness about how food makes you feel.


For instance:


  • Some people can eat eggs, others get bellyaches.


  • Some people can bring on the spice, while even a hint of chili powder sets another’s gut into a tizzy.


  • Nutbutter is delicious, but for some, it leaves them hurled over in pain.


  • And for me, I quickly realized, most times I ate a starch (like sweet potatoes) or even fruit, I’d get stomach pains (weird!).


SIBO goes beyond gluten, dairy, processed foods and sugar—frequently touted and cited culprits for indigestion and dysbiosis (dysfunctional digestion).


SIBO (as in my case) is closely related to the consumption of sugars—of course processed and refined carbohydrates, sweets and treats fall in there— but also starchy vegetables (like potatoes, carrots, beets) and fruits.


Certain strains of bacteria feed off of carbohydrates and break them down into short-chain fatty acids, creating gas and causing bloating.


If you have or suspect that you may have SIBO, one of the nutritional recommendations for treating this condition (besides eating real food or “going paleo”) is avoidance of all complex sugars for a time period (including my beloved sweet potatoes, along with other starches if you consume them regularly, like rice, oats, beans, and other starchy vegetables).


The idea behind this protocol is that by eating more complex sugars, you are feeding the bad bacteria.  Monosaccharides (or “single sugars”), such as fructose, glucose and galactose, are the most easily absorbed sugars we can eat, so they are typically already absorbed by the time that meal gets to the lower small intestine where the “bad” bacteria are growing.


 Limiting yourself to monosaccharides helps to starve the bacteria in your small intestine.


Foods that contain glucose include (but are not limited to):

Summer Squash, Oranges, Celery, Raspberries, Pineapple, Grapefruit, Nectarines, Lettuce, Pork, Asparagus, Blackberries, Carrots, Broccoli, Crab, Limes, Green Beans, Butternut Squash, Brussels Sprouts, Avocados, Turnips, Onions, Peppers, Parsley, Paprika, Spinach, Sauerkraut, Eggs, Mustard, Mushrooms, Oregano, Apple Cider Vinegar, Artichokes, Cinnamon, Cloves, Ginger, Curry Powder, Basil, Turnips, Green Peas, Swiss Cheese, Sunflower Seeds, Dried Coconut, Fish, Turmeric, Pistachios, Almonds, Sesame Seeds, Cashews, Hazlenuts, Pine Nuts, Cashews, Macadamia Nuts, Walnuts, Pecans, Eggplant, Cabbage, Cauliflower, Radishes, Onions


Foods that contain fructose include (but are not limited to):

Apples, Peaches, Bananas, Citrus Fruits, Pears, Melons, Berries, Red Cabbage, Green Beans, Fennel, Carrots, Kohlrabi, Pumpkins, Leeks, Peppers, Tomatoes, Turnips, Cabbage, Onions, Brussels Sprouts, Radishes, Cucumbers, Asparagus, Lettuce, Summer Squash, Celery, Green Beans, Broccoli, Butternut Squash, Mushrooms, Beets, Peas, Spinach, Artichokes, Pistachios, Almonds, Cashews, Hazelnuts, Sesame Seeds Pine Nuts, Macadamia Nuts, Walnuts, Pecans, Dried Coconut, Crab, Chicken, Pork, Eggs, Balsamic Vinegar, Apple Cider Vinegar, Paprika, Chili Powder, Ground Ginger, Cinnamon, Oregano, Cloves, Basil, Mustard, Curry Powder


Foods that contain galactose include (but are not limited to):

Celery, Beets, Spinach, Cherries, Plums, Kiwi, Melons, Peaches, Blackberries, Avocados, Figs, Navy Beans, Eggs, Raw Honey, Basil, Paprika, Curry Powder, Ground Ginger, Oregano, Cloves, Mustard, Yogurt


Knowledge is power, and taking this protocol into consideration, I decided to give it a try: cutting back on my sweet potato consumption, while increasing my healthy fats, leafy greens and protein intake to ensure I kept my energy up. In addition, I doubled up on my probiotics, ensured I was drinking plenty of water and taking my digestive enzymes with each meal.


The result?


For me, fortunately, it was a relatively quick turnaround.


Within even a few weeks of following this protocol, I could already tell my digestion was more like a motor (and less like a garbage disposal—getting clogged with food in there).


Now, back to feeling better than I have in awhile (digestively), I have re-incorporated sweet potatoes back into my diet, but not in the copious amounts as before (moderation). In addition, I continue to take my probiotics in the morning and evening, and use digestive enzymes as needed with meals.


All in all…running like a well oiled machine.


Suspect you have some digestive distress?


Let’s connect!


Nutrition Therapy can help you (and your digestive system) get back to thriving—as Mother Nature intended.


Schedule a free consult here to get started.



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