What could be causing a change in the smell of my feces?

Change in Fecal Odor: Diagnostic Approach

A change in stool smell is typically caused by dietary factors, alterations in gut microbiota, or bacterial overgrowth, but requires evaluation for underlying gastrointestinal pathology if accompanied by alarm features such as weight loss, blood in stool, fever, or persistent diarrhea.

Initial Clinical Assessment

The first priority is determining whether this isolated symptom represents benign variation or signals underlying disease. Your immediate focus should be identifying alarm features that mandate further investigation 1.

Red Flag Symptoms Requiring Investigation

• Weight loss (suggests malabsorption, inflammatory bowel disease, or malignancy) 1
• Blood in stools or positive fecal occult blood 1
• Fever (indicates possible infection or inflammation) 1
• Nocturnal symptoms (suggests organic rather than functional disease) 1, 2
• Anemia on examination 1
• Persistent diarrhea lasting >10-14 days 1
• Recent antibiotic use (raises concern for Clostridioides difficile) 1
• Age >50 years without recent colon cancer screening 1

Understanding Fecal Odor Changes

Physiologic Basis

Fecal odor is primarily determined by methyl sulfide compounds (methanethiol, dimethyl disulfide, dimethyl trisulfide) rather than skatole and indole as traditionally believed 3. These volatile organic compounds (VOCs) represent end products of microbial metabolism and can vary significantly with diet, gut microbiota composition, and disease states 4, 5.

Common Benign Causes

• Dietary changes (increased sulfur-containing foods, fiber, FODMAPs) 1, 2
• Normal gut microbiota variation 4, 5
• Medication effects 1

Diagnostic Algorithm

Step 1: Screen for Alarm Features

If no alarm features are present and physical examination is normal:

• Obtain complete blood count to exclude anemia 1, 2
• Perform fecal occult blood test 1, 2
• Ensure age-appropriate colon cancer screening is current 2
• Reassure the patient that isolated odor change without other symptoms is typically benign 2

Step 2: If Alarm Features Present

Proceed with targeted evaluation based on associated symptoms:

For Diarrhea-Predominant Symptoms

Initial laboratory workup 6, 7:

• Complete blood count
• C-reactive protein or ESR
• Anti-tissue transglutaminase IgA with total IgA (celiac screening)
• Basic metabolic panel
• Fecal calprotectin

Stool studies 1:

• Stool culture for bacterial pathogens
• Clostridioides difficile toxin testing (if recent antibiotics or healthcare exposure) 1
• Ova and parasites examination (if travel history or endemic area exposure) 1, 6
• Fecal leukocytes or lactoferrin (if inflammatory features present) 1

For Suspected Malabsorption

If stools are bulky, pale, difficult to flush, or float persistently 2:

• Fecal elastase-1 on semi-solid stool specimen (first-line test for pancreatic insufficiency; <100 μg/g suggests exocrine pancreatic insufficiency) 2
• Consider celiac serology if not already done 6, 7
• Avoid empiric pancreatic enzyme replacement without appropriate testing, as this may mask treatable conditions 2

For Suspected Bacterial Overgrowth

If patient has risk factors (intestinal dysmotility, prior surgery, diabetes) 1:

• Trial of rotating antibiotics (rifaximin preferred if available, alternatively amoxicillin-clavulanate, metronidazole, ciprofloxacin, or doxycycline) 1
• Consider bile salt malabsorption testing if terminal ileum disease or resection present 1

Step 3: Endoscopic Evaluation

Sigmoidoscopy or colonoscopy is indicated for 1:

• Age >50 years at symptom onset
• Family history of colorectal cancer or inflammatory bowel disease
• Persistent symptoms despite initial management
• Any alarm features present
• Biopsy all abnormalities and obtain random biopsies in diarrhea cases to detect microscopic colitis 1

Disease-Specific Considerations

Infectious Causes

Research demonstrates that specific VOC patterns distinguish infectious diarrhea (C. difficile, Campylobacter jejuni) from healthy controls 4. However, this remains investigational and standard microbiological testing remains the clinical standard 1, 8.

Inflammatory Bowel Disease

Patients with ulcerative colitis show distinct fecal VOC patterns compared to healthy individuals 4. Clinical diagnosis requires endoscopy with biopsy, not odor assessment 7.

Irritable Bowel Syndrome

IBS may present with perceived odor changes, but diagnosis requires symptom duration of at least 6 months and exclusion of organic disease 6. Do not diagnose IBS in the acute setting of odor change alone 6.

Common Pitfalls to Avoid

• Do not perform extensive workup for isolated odor change without alarm features, as this increases cost and patient anxiety without improving outcomes 2
• Do not order 72-hour fecal fat collection, as this test is poorly reproducible and non-diagnostic 2
• Do not diagnose functional disorders (like IBS) without meeting duration criteria and excluding organic disease 1, 6
• Do not overlook C. difficile testing in patients with recent antibiotic exposure, even if other symptoms seem mild 1
• Do not attribute symptoms to lactose intolerance without substantial dairy intake (>280 mL/day) 1

Management Based on Findings

If Workup Negative

• Dietary modification trial: reduce fiber, consider low-FODMAP diet temporarily, eliminate gas-producing foods 1, 2
• Reassurance that benign variation in fecal odor is common 2
• Reassessment in 3-6 months if symptoms persist 6

If Specific Pathology Identified

Treat the underlying condition according to disease-specific guidelines (antibiotics for infection, immunosuppression for IBD, gluten-free diet for celiac disease, pancreatic enzyme replacement for exocrine insufficiency) 1, 7.