RSN Functional Nutrition Institute
Rachel Scheer
Nutrition
The SIBO Root Cause Assessment, Rachel Scheer Nutrition

Most SIBO quizzes tell you whether you might have it. This one tells you what allowed it to happen, which is the part that decides whether it comes back.

Your likelihood

How closely your symptoms match small intestinal bacterial overgrowth.

Your root cause

Which of the four underlying drivers your history points toward.

Your next step

A full report plus the Beyond SIBO masterclass, free.

42 quick questions, about four minutes. Answer honestly rather than optimistically. It makes the report far more useful.

First, the short version

What SIBO actually is

Your large intestine is meant to be full of bacteria. Trillions of them, and you need every one. Your small intestine is meant to stay relatively clean, because that is where you digest food and absorb nutrients from it.

SIBO is what happens when bacteria that belong in the large intestine migrate upward and take up residence in the small one. They are not foreign invaders. They are your own bacteria, living in the wrong place.

And there they start eating your food before you can. When they eat, they ferment, and fermentation produces gas. Inside a closed tube. That is the bloating that arrives an hour after a meal and makes you look six months pregnant by evening.

Normal small intestine, bacteria migrating upward, and fermentation producing gas
Bacteria that belong in the large intestine migrate upward, settle in the small intestine, and ferment your food into gas.

The gas is only the part you feel. Those bacteria also damage the lining of the small intestine, which is how food sensitivities start multiplying. They consume iron and B12 before you absorb them, which is why ferritin stays low no matter what you supplement. They interfere with bile, which impairs fat absorption. And through that damaged lining, bacterial fragments reach your bloodstream, where your immune system reacts to them.

How it shows up

The symptoms, and the ones nobody connects to the gut

Most people recognize the first column immediately. The second column is the one that usually gets treated as a separate problem entirely, by a separate doctor, with separate prescriptions.

In your gut

The symptoms that sent you looking

  • Bloating and abdominal gas, often worse through the day
  • Belching and flatulence
  • Abdominal pain, cramping, or visible distension
  • Constipation, diarrhea, or alternating between them
  • Heartburn and reflux
  • Nausea, or food that sits like a rock
  • Reacting badly to healthy food: salads, beans, garlic, onion, apples

Everywhere else

The symptoms nobody links back

  • Fatigue, particularly after eating
  • Brain fog and trouble concentrating
  • Anxiety, low mood, or wired but tired
  • Joint pain, muscle aches, unexplained body pain
  • Rosacea, acne, eczema, and unexplained rashes
  • Low iron or B12 that will not correct
  • Headaches and fatty, floating stools
SIBO shares nearly every symptom with IBS and a dozen other conditions. Symptoms alone cannot separate them.
SIBO shares nearly every symptom with IBS and a dozen other conditions. Symptoms alone cannot separate them.

Adapted from a 2019 review in the World Journal of Gastroenterology.

Why it happens

Bacteria do not overgrow in a healthy small intestine

This is the part that gets skipped, and it is the part that matters most. Your small intestine has real defenses against overgrowth, and they work well.

Stomach acid, bile, and pancreatic enzymes sterilize what comes in. And every 90 minutes between meals, a cleansing wave called the migrating motor complex sweeps through the small intestine and pushes anything left behind downstream. It only runs when you are not eating, and it is controlled by your nervous system.

Overgrowth happens when one of those defenses breaks. Nearly every case traces back to one of four categories.

The four categories every root cause falls into.
The four categories every root cause falls into.
i

Impaired motility

The cleansing wave slows or stops, so bacteria are never swept out. This is the most common driver and the most commonly missed. A single bout of food poisoning can trigger antibodies that damage the nerves controlling that wave.

Food poisoning, concussion or whiplash, hypothyroidism, chronic stress, diabetes, mold exposure, POTS and EDS, constant snacking

ii

Impaired digestion

Acid, bile, and enzymes are your chemical barrier. When any of them run low, bacteria that should have been killed on arrival survive, and undigested food arrives to feed them.

Low stomach acid, H. pylori, sluggish bile or gallbladder removal, pancreatic insufficiency, chronic stress

iii

Impaired flow through the intestines

Scar tissue forms easily in the abdomen. Adhesions act like a kink in a garden hose, and bacteria multiply in the stagnation behind the kink. This one almost never gets investigated because it shows up on no lab test.

C-section, appendectomy, hysterectomy, gallbladder removal, hernia repair, endometriosis, ileocecal valve dysfunction

iv

Medications

Several common prescriptions suppress motility or digestive secretions as a side effect. This is not a reason to stop anything. It is a reason to know what you are working against.

Acid blockers, opioids, antispasmodics, tricyclic antidepressants, T4-only thyroid medication

The part that matters

Why it keeps coming back

Recurrence after antibiotic therapy, with higher rates in older adults, after appendectomy, and with long-term acid blocker use.
Recurrence after antibiotic therapy, with higher rates in older adults, after appendectomy, and with long-term acid blocker use.

From the SIBO chapter in StatPearls, National Library of Medicine.

Which is why the useful question was never whether you have SIBO. It is which of those four doors your SIBO came through.

Find out which door yours came through

42 quick questions, about four minutes. You will get your likelihood score, your most likely root cause driver, and the full Beyond SIBO masterclass.

Part one of five

How often do you experience the following?

Think about a typical month rather than your best or worst week.

Part two of five

Beyond digestion, do you struggle with any of these?

SIBO rarely stays a gut problem. This tells us how far yours has travelled.

Part three of five

Now your history. This is where the real answers usually are.

Nobody is scored on these. They tell us which door your SIBO came through.

Part four of five

A few more from your history

Surgery, medications, and the things that look like SIBO but are not.

Part five of five

Last few. Where are you in all this?

This helps us meet you where you actually are instead of where we assume you are.

Almost there

Your results are ready

Tell us where to send your SIBO Root Cause Report. You will also get instant access to the Beyond SIBO masterclass replay.

We send gut health education and occasional offers. Unsubscribe any time.

Rachel Scheer Nutrition

2026 Rachel Scheer Nutrition All Rights Reserved ©

This site is not a part of the Facebook website or Facebook Inc.

Additionally, this site is not endorsed by Facebook in any way. Facebook is a trademark of Facebook, Inc.