Loose stools or diarrhoea means increased stool frequency, urgency, or liquid consistency, Rome IV and clinical practice distinguish acute (often infection or medication) from chronic patterns (IBS-D, IBD, malabsorption). A stool microbiome report showing dysbiosis or low diversity does not tell you whether the mechanism is inflammatory, osmotic, secretory, or rapid transit, see Osmotic load and diarrhoea and Luminal environment.
This page routes by pattern and alarms first; Foundations carry mechanism depth.
Before anything else, red flags
Seek medical assessment promptly if you have:
- Blood in stool, nocturnal diarrhoea (waking to pass stool), or weight loss
- Fever, severe pain, or dehydration
- New diarrhoea after age 50 without workup
- Recent antibiotics with profuse or bloody diarrhoea (consider C. difficile)
See Red flags.
Decision tree, start with pattern, not taxa
Step 1, Acute vs chronic?
| Pattern | Think about | Read next |
|---|---|---|
| Acute (<2 weeks), fever, travel, sick contacts | Infection, food poisoning | Clinical stool testing, not consumer sequencing first |
| Started with antibiotics | AAD, C. diff risk | Post-antibiotic recovery |
| After resolved gastroenteritis, symptoms persist ≥3 months | Post-infectious IBS | Post-infectious IBS |
| Chronic, pain related to defecation, no alarms | IBS-D pattern | IBS subtypes, FODMAPs |
Step 2, Inflammatory vs functional clues
| Toward inflammatory workup | Toward functional / dietary |
|---|---|
| Blood, nocturnal symptoms, weight loss | Long-standing pattern, stress correlation |
| Elevated fecal calprotectin | Normal calprotectin + IBS criteria |
| Family history of IBD | Worse after wheat/onion/milk (FODMAP load) |
IBD vs functional gut · Gut inflammation markers · Calprotectin
Step 3, Mechanism branches (routing only)
| Pattern | Hypothesis direction | Foundation |
|---|---|---|
| Worse after fatty meals, greasy stools | Bile acid diarrhoea (clinical diagnosis) | Gastroenterology workup, not taxa lists |
| Worse after milk | Lactose malabsorption | FODMAPs |
| Worse after wheat/onion/beans | Fermentable load / IBS-D | FODMAPs, Low-FODMAP trial |
| Urgent morning rush, post-meal | Rapid transit | Gut motility |
| Upper bloating + diarrhoea | Small-intestinal fermentation overlap | SIBO & breath testing |
Evidence-tier table, what to try first (framing, not prescription)
| Approach | Evidence tier | Notes |
|---|---|---|
| Clinical workup for alarms / calprotectin | Strong when inflammatory features | Before microbiome-led diets |
| Dietitian-supervised low-FODMAP trial (IBS-D) | Strong in IBS RCT meta-analyses | Not permanent restriction |
| Treat confirmed infection / IBD | Strong | Panel does not replace this |
| Review medications (metformin, SSRIs, PPIs, antibiotics) | Moderate (clinical logic) | Medications and microbiome |
| Specific probiotics for AAD prevention | Strong for diarrhoea prevention in meta-analyses | Not restoration guarantee, Probiotics |
| Stool microbiome to find cause | Low as sole workup | Reading your report |
What a stool microbiome report cannot answer
| Question | Can sequencing answer it? |
|---|---|
| Do I have IBD? | No, calprotectin, clinical assessment |
| Is this C. diff or salmonella? | No, pathogen PCR/culture |
| Is this bile acid diarrhoea? | No |
| Should I restrict FODMAPs? | No, symptom and diet trial |
| Did my probiotic fix diarrhoea? | No, clinical endpoints first |
Reports may show post-antibiotic dysbiosis or opportunistic reads, context-dependent, not diagnostic alone. Opportunistic bacteria · Multi-marker synthesis