functional nutrition

Sibo Doctor Approved
Alyssa Simpson RD, CDE, CLT
Alyssa Simpson

(602) 422-9800

Sibo Doctor Approved
certified gastrointestinal nutritionist
Sibo Doctor Approved
certified gastrointestinal nutritionist

How Did I Get SIBO? Answers to Your Puzzling SIBO Root Cause Questions

Share This Post!

Woman looking off into the distance wondering about the root cause of her SIBO.

Table of Contents

Welcome to the final installment of SIBO FAQs! My hope is that these past few weeks have lifted the veil of mystery that often accompanies this digestive issue. But before we get into our last few questions, a quick recap…


➥ SIBO (small intestinal bacterial overgrowth) occurs when your small intestine, which is normally relatively free of bacteria, becomes home to a growing bacterial population.

SIBO symptoms are caused primarily by the gassy bi-products of the uninvited bacteria and include stomach pain and bloating, cramps, diarrhea, constipation, gas, and unexpected weight loss.

➥ Because the bacteria munch on your food before you can absorb all the nutrients, if left untreated, SIBO can cause nutritional deficiencies.

➥ SIBO is treatable, but if you don’t address the root cause it is likely to return.

Diet is a powerful tool in SIBO treatment and management.

SIBO can be challenging to diagnose because the symptoms are so similar to other common digestive issues.

SIBO and IBS often go hand-in-hand.

If you know me at all, you know my passion is figuring out and solving the root cause of my patients’ digestive issues. Calming symptoms is fine in the short-term. I want my clients to experience quick relief after all. But I’m not satisfied until I address the root causes and underlying issues that allow digestive issues like SIBO and IBS to develop in the first place.

So this week, our FAQs are going to focus on the root cause issues that can lead to SIBO. Whether you work with me or another practitioner, I want you to be able to show up to your appointment equipped with the knowledge that will help you get answers faster.

Yes. But you may be thinking of this situation in reverse. Generally, your digestive process runs north to south. That means that whatever happens early on in your digestion can affect everything else down the line. So your acid reflux and SIBO could certainly be connected. But it’s more likely that they’re both affected by the same root cause. In other words, what happens in your stomach affects what happens in your small intestine.

Many people have inadequate stomach acid. You read that right. Not enough stomach acid. Pharmaceutical companies would like us to believe that stomach acid is bad and should be eliminated. And yes, it can cause problems. But the problems caused by low stomach acid affect a wide variety of other digestive issues, including acid reflux. I won’t get into detail about all of the ways low stomach acid affects your digestive system here, but I posted an article on the truth about stomach acid a while back.

But let’s talk about stomach acid and SIBO. The whole purpose of stomach acid is to break your food down enough that your small intestine can effectively absorb all the nutrients. But if your food hits your small intestine before it’s ready, it can hang out there and provide nutrients for that unwanted bacteria. Inadequate stomach acid can also contribute to a condition called leaky gut, which is also a small intestine issue that can be related to SIBO.

Could my autoimmune disease be a root cause of SIBO?

It’s entirely possible. Again, keep in mind that I can’t diagnose anyone of anything in an article. This is all just general information. But there is a possible connection there. Let’s start with what should be happening in your small intestine…

By the time your food leaves your stomach, it should be fully broken down. Then it’s the small intestine’s job to absorb the nutrients so they can fuel your body. Generally, you want your food to hang out in your small intestine just long enough for your body to be able to absorb all the nutrients. But if the muscle contractions that keep food moving along (known as peristalsis) are too slow, food can sit in the small intestine long enough for bacteria to feed and multiply.

Now back to the question. Autoimmune diseases are often related to what’s happening in the small intestine. If the wall of the small intestine is damaged, it can become compromised — that’s the leaky gut I mentioned earlier. And yes, this can be related to inadequate stomach acid and SIBO.

If the wall of your small intestine is compromised, it allows the less-than-digested particles of food to leak out into the bloodstream and trigger the immune system, which can ultimately lead to the development of an autoimmune disease.

There is also evidence that the bacteria growing in the small intestine with SIBO can pass through the compromised intestinal wall and move to nearby organs. And this could be related to autoimmune conditions like fibromyalgia, interstitial cystitis, and chronic fatigue syndrome.

And autoimmune diseases — like celiac disease, ulcerative colitis, or Crohn’s disease — can in turn impact your small intestine by slowing down your food’s journey, allowing it to stay in the small intestine for too long.

Can antibiotics help with SIBO, or can they make it worse?

The answer to this question is yes. I know it wasn’t a yes/no question, but both things are true. Many doctors treat SIBO with antibiotics. It’s bacteria after all. So yes, antibiotics can kill off SIBO. But they also attack the beneficial bacteria that live in your large intestine — where you want it. And if the healthy bacteria in your large intestine is thrown out of balance, then it can migrate up and cause SIBO.

Don’t get me wrong. I don’t hate antibiotics. They are life-saving medications. But, they have pretty significant downsides.

In my practice I use options like herbal antibiotics, which are just as powerful (if not more) than pharmaceutical antibiotics, but with fewer side effects.

Ideally your small intestine should be more like a waterslide than an obstacle course. But sometimes physical abnormalities or scar tissue from surgery can create a rougher road for your food. When that happens you can end up with food that hangs out too long and provides nourishment for that SIBO bacteria. Again… slow transit time can contribute to the development of SIBO.

In the case of abdominal surgery, some people develop adhesions — scar tissue that forms between abdominal tissues and organs. In one study, 82% of patients who tested positive for SIBO had a history of abdominal surgery. It’s likely that the adhesions that result from a surgical procedure may play a role in the onset of SIBO.

I had food poisoning and then developed SIBO. Is this a coincidence?

Probably not. In fact, food poisoning may be the #1 cause of SIBO. Let me explain…

When you get food poisoning, the offending bacteria produce a toxin called cytolethal distending toxin (CDT). And yes, this substance is as bad as it sounds. So your immune system produces antibodies against CDT.

Here’s where it gets interesting. CDT’s shape is very similar to a protein called vinculin. Sometimes, your immune system gets confused and produces antibodies that battle not only the bacterial CDT, but also your own vinculin..

Vinculin regulates the cells responsible for controlling the Migrating Motor Complex (MMC). The MMC does the cleaning in your digestive tract. Its job is to sweep away food debris — and any unwanted bacteria — out of the small intestine and into the colon.

When the body attacks vinculin, it indirectly disrupts the MMC’s clean-up operation. Without a properly functioning MMC, bacteria can hang around in the small intestine instead of moving onto the large intestine where it belongs. And this produces SIBO.

How do I figure out what caused my SIBO?

Your best bet is to work with a practitioner who has expertise in detecting and addressing SIBO root causes. That may be your doctor. But often doctors (even gastroenterologists) have so much on their plates that they don’t necessarily have all the latest information about SIBO and how to treat it.

If you think you might have SIBO, IBS, or just struggle with troublesome digestive symptoms, you don’t have to just live with it — even if your doctor doesn’t have the answers you need. I can work with you to figure out your root cause and develop a personalized plan that works for you. You can schedule a consultation here.

In the meantime, regardless of the root cause of your SIBO, there are ways you can start addressing your symptoms. Click the link below to download your free copy of the IBS Resource Guide. This guide contains some of my favorite resources, the same ones I use every day with my patients.


Free IBS Resource Guide
The Top 5 IBS Resources I Use Every Day
Get your Free Meal Picklist
Join My Free Facebook Group
Meet Alyssa
Alyssa Simpson RD, CDE, CLT
registered dietitian weight loss tips
Is IBS Slowing You Down?

Get Your Free IBS Resource Guide Now and start feeling better fast!