A 7-Step Approach to Enteropathy Diagnosis

Dr Salt

Here’s how I make the diagnosis or diagnoses of enteropathy. Remember, it’s very common for more than one to be present.

Differential Diagnosis

I always begin with differential diagnosis, which is the process of considering ALL possibilities either causing or contributing to the enteropathy triad of symptoms.

In Article 3, I explained that IBS is the most common initial diagnosis made. This diagnosis usually blocks and blinds both the patient and doctor from considering other differential diagnoses and their interrelationships, as presented in my enteropathy map.

Once the diagnosis of IBS is made, most patients want to move on to treatment considerations. Don’t do it!

STEP 1: Start with a Question

First, make sure to ask your doctor, “What else could this be?”

One important reason we developed the MyGutHealthToday Enteropathy Series is to empower you to think “out of the box” by being familiar with ALL of your differential diagnostic possibilities. Don’t simply accept a diagnosis of IBS until you’ve asked the question and collaborated with your health care professionals. If you don’t ask the question, you and your doctor might miss the diagnosis of Sucrose Intolerance caused by CSID.

STEP 2: Record the Initial Codes

Because of the many possibilities, I begin my diagnosis by entering the diagnosis code (ICD-10-CM) K63.9 into the medical record for enteropathy, “disease of intestine, unspecified,” along with any other important and relevant GI diagnosis (for example, K21.9 — “gastro-esophageal reflux disease without esophagitis”), symptom (R53.83 — “fatigue”), and/or bodily diagnosis (M79.7 — “fibromyalgia”).

STEP 3: Classify Enteropathy Subtype by Bowel Dysfunction

Then I annotate the enteropathy code (E) with the bowel dysfunction subtype, similar to the way IBS is subtyped and described in Article 3 (where the Bristol Stool Form Scale or BSFS helps):

  • E—C (constipation)
  • E—D (diarrhea)
  • E—M (mixed, or both constipation and diarrhea)
  • E—U (unclassified)

However — to simplify, as with IBS — I recommend combining E—D with E—M to recognize two types of enteropathy:

  • E—D/M (Remember, as described in Article 3 under Classification of IBS, bowel dysfunction may not be pure diarrhea, and most individuals have “irregularly” irregular bowel function, form, and frequency, including some constipation.)
  • E—C

STEP 4: Identify Red Flags or Concerning Features. Further Testing May be Needed

You can review these In Article 3. If enteropathy symptoms are present, along with red-flag concerning features, particularly rectal bleeding, I usually recommend a colonoscopy. Other testing may be necessary, including scans.

However, in the absence of red flag/concerning features, a colonoscopy is usually not a necessary procedure for diagnosing enteropathy and IBS, if the physical examination is also normal.

STEP 5: Screen for Colorectal Cancer, If Indicated

Screening implies absence of symptoms. Once you’re 45-years-old, it’s time to start screening for colorectal cancer, which I include in my approach to enteropathy, at least to remind patients about this important self-care step. Here are the top four options:

STEP 6: Explore My Enteropathy Map

Next, I’ll guide you through the newest version of my map (Figure 4.1), so you can appreciate the most common diagnoses and associated conditions, along with their key interrelationships. The black-circled numbers and characters on the map correlate with those in the explanatory keys that follow.

Dr Salts Enteropathy MapFigure 4.1

You’ll also want to refer to Figure 2.1”Gut Health = Your Health” and Figure 2.2 :Unhappy Unhealthy Gut = Unhappy Unhealthy You” as needed.

1. IBS

Remember, while IBS is the most common diagnosis, don’t forget to ask the question in Step 1 and work with your health care professional.

There are two subtypes of IBS:

  • 1-C: IBS-C (constipation)
  • 1-D/M: Combining IBS-D with IBS-M

1-M to C: The dashed arrow from IBS-M to IBS-C indicates that some with IBS-M have either stool loading or obstructed defecation, which should be considered to be types of IBS-C constipation. These constipation disorders can be recognized, respectively, by going multiple days without having bowel movements followed by a troublesome day of diarrhea or by having difficulty getting the stool out of the rectum, including use of a finger or the hand. Diagnosis is facilitated with a special X-ray using Sitzmarks® discussed in Step 7.

2. Dysbiosis of the Gut Microbiome

While very complex, incompletely understood, and the subject of considerable research, you’ll increasingly see discussion of the importance of the gut microbiome to your health. The gut is home to a variety of microbes, including bacteria, archaea, fungi (mostly yeasts), parasites (usually blastocystis in the United States), and viruses/phages.

I’ll focus here on two main types of microbiome dysbiosis with therapeutic implications: SIBO and colonic BLOOM.

2-a: SIBO (Small Intestinal Bacterial Overgrowth)

While an oversimplification, SIBO is a condition in which colonic-type bacteria populate the small intestine, where they aren’t supposed to be, along with an imbalance of unfavorable over favorable microbes. Many problems ensue, impairing gut function and contributing to enteropathy symptoms, including bacterial fermentation of carbohydrates with release of the gases hydrogen (H2) and carbon dioxide (CO2). If hydrogen sulfide (H2S)-producing bacteria are present, the predominant bowel symptom is diarrhea.

The downward arrow emphasizes SIBO is a condition rather than a diagnosis. A careful search for an underlying cause or causes should be conducted. Examples include post-infectious IBS-D/M described in Article 3 and adhesions from surgery, which may not be evident on scans and X-rays.

2-b: Colonic BLOOM (Methanobrevibacter smithii)

The colon can be populated with this archaea microbe, abbreviated as M. smithii, which manufactures methane gas or CH4 made from hydrogen (H2) and carbon dioxide (CO2) released by bacterial fermentation of carbohydrates. Methane contributes to symptoms, particularly constipation. Since M. smithii and methane production are primarily located in the colon, Dr. Mark Pimentel calls this a “colon BLOOM” since it’s not SIBO, which occurs in the small intestine.

3. Dysbiosis of the Gut Mycobiome

This is the presence and imbalance of the fungal population of the gut. It’s considerably less well-understood than is dysbiosis of the gut microbiome.

3-a: SIFO (Small Intestinal Fungal Overgrowth)

This refers to fungal overgrowth in the small bowel, but the colon can also be involved.

4. Gut Microbiome—Gut Mycobiome Interrelationships

It’s becoming increasingly clear that both are normally in a state of balance and that an imbalance can occur. For now, it appears that mycobiome dysbiosis is usually secondary to gut microbiome dysbiosis and/or related to immune impairment.

5. IBS—Dysbiosis of the Gut Microbiome Interrelationships

Note that both are expressed as the enteropathy triad of symptoms; therefore, distinctions cannot be based on symptoms only.


The connection between IBS D/M and SIBO is a bidirectional arrow. Post-infectious IBS-D/M is one of many potential causes of SIBO. Conversely, about 60% of those with IBS-D/M have associated SIBO.


The arrow from Colon BLOOM to IBS-C emphasizes that BLOOM with M. smithii and methane production is present in most individuals with IBS-C.


The dashed arrow from Colon BLOOM to IBS-M emphasizes that some have both hydrogen-sulfide producing bacteria and methane-producing M. smithii. Hydrogen is the fuel source for both, and methane (constipation) usually predominates over hydrogen sulfide (diarrhea).

6. Food, Maldigestion, and Malabsorption

These diagnoses and disorders will be covered in later articles.

7. Mast Cell Activation Syndrome (MCAS)

Mast cells are an important part of the immune system, most of which is located in the gut. Mast cells release histamine, responsible for allergy symptoms. Furthermore, they are located close to nerves, which they can irritate. MCAS is a chronic and recurrent but treatable disorder commonly associated with enteropathies, which can produce symptoms in any organ system. Flushing, hives, and itching are common skin manifestations.

8. Uncommon.

Discussion is beyond the scope of this article.

9. Unexplained “Black Box”

The enteropathy symptom triad is commonly not explained by testing. Nevertheless, effective treatments are available, such as with EnteraGam®.

10. Associated

Treatment of enteropathies co-occurring with these diseases is equally important and may even be beneficial in management of the associated disease or diseases.

11. BODILY and Mind/Body—BrainS/Gut Dysfunction

The BODILY rectangle alludes to the association of enteropathies with non-gut symptoms and diagnoses, such as brain fog, fatigue, anxiety, depression, headaches, and fibromyalgia.

The red star emphasizes that the association is attributable to several underlying processes discussed in Article 3, “Associated Disorders: Mind/Body—Brain/Gut Dysfunction.”

STEP 7: Conduct Appropriate Non-Invasive Testing

I obtain basic blood tests, if not already done.


  • CBC — complete blood count (for anemia, inflammation, and immune deficiency)
  • Fasting blood glucose or hemoglobin A1C (for common insulin resistance and diabetes)
  • TSH/T4 (for the most common autoimmune disease, thyroid disease — usually hypothyroidism)
  • 25-hydroxy Vitamin D (for very common vitamin D deficiency, which impairs gut function)

I also order additional testing, depending upon the differential diagnosis.


  • tTG — tissue TransGlutaminase, DGP IgA and IgG — Deamidated Gliadin Peptide Immunoglobulin A and G, and IgA (for celiac disease and immune deficiency)
  • hsCRP — high-sensitivity C-reactive protein (for chronic inflammation and Crohn’s disease*)
  • IBS-Smart™ — for post-infectious IBS-D/M discussed in Article 3
  • 7aC4 — Bile acid synthesis (for bile acid malabsorption or BAM)


  • Calprotectin (for chronic inflammation and Crohn’s disease*)
  • FIT — fecal immunochemical test for occult blood (for chronic inflammation, Crohn’s disease, and colorectal cancer screening)
  • Fecal fat (for malabsorption)
  • Elastase (for pancreatic insufficiency/malabsorption)

*Research shows that if both hsCRP and stool calprotectin are normal, Crohn’s disease is extremely unlikely.

BREATH TESTING (Hydrogen/Methane)

  • Lactulose (for SIBO and colonic BLOOM)
  • Lactose (for lactose or milk sugar intolerance; however, most have self-diagnosed and dietary restriction is more accurate)
  • Fructose (for fructose or fruit sugar intolerance; however, most will malabsorb fructose if enough is ingested and dietary restriction is more accurate)
  • Sucrose (for sucrose or table sugar intolerance)

(Note: Current hydrogen/methane breath testing does not include detection of hydrogen sulfide (H2S), which is associated with SIBO and diarrhea. However, Dr. Pimentel has developed breath testing that detects all four gases (carbon dioxide, hydrogen, methane, and hydrogen sulfide), which will be available soon. This 4-gas testing will become the SIBO/BLOOM breath testing of choice.)

BREATH TESTING SUCROSE (13C-Sucrose Breath Test)

While hydrogen/methane breath testing can be used, the 13C-Sucrose Breath Test is more sensitive and specific in testing for Sucrose Intolerance caused by CSID.

SUGAR CHALLENGE TEST (Sucrose Intolerance)

This is a simple short test that can be done at home.


(for evaluation of abdominal bloating/distention and/or constipation: free fluid called, ascites, intestinal obstruction, stool loading, and obstructed defecation)

In the next lesson, I’ll discuss food intolerance and sensitivities, along with malabsorption and maldigestion, number 6 on my map).


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