Abdominal pain with gut symptoms may reflect visceral hypersensitivity (common in IBS), inflammation (IBD, infection), motility or obstruction, gynecologic disease, or functional overlap, often more than one. A microbiome report listing dysbiosis or low Faecalibacterium does not tell you whether pain is upper vs lower, inflammatory vs functional, or related to bowel movements in the Rome IV sense.
This page is a routing guide only.
Before anything else, red flags
Seek urgent or prompt medical assessment for:
- Severe or worsening pain with fever, vomiting, or rigid abdomen
- Rectal bleeding, black stools, or unintentional weight loss
- Pain waking you from sleep persistently (context-dependent, not always IBD, but needs evaluation)
- New pain after age 50 without prior workup
See Red flags.
Decision tree, localization and pattern first
Step 1, Where is the pain?
| Location / timing | Think about | Read next |
|---|---|---|
| Upper abdomen, within 1–2 h of meals | Gastric emptying, dyspepsia, small-intestinal fermentation | SIBO & breath testing |
| Lower abdomen, cramping with bowel movements | IBS, constipation, IBS-C/D overlap | IBS subtypes, Constipation |
| Diffuse bloating + pain | FODMAP load, distension, hypersensitivity | Chronic bloating, FODMAPs |
| Cyclical pain, pelvic focus (women) | Endometriosis, gynecologic causes | Women’s health & cycle, clinical gynecology first |
| Right upper quadrant | Biliary, hepatic, not microbiome-first | Clinical assessment |
Step 2, Inflammatory vs functional
| Inflammatory clues | Functional (IBS-type) clues |
|---|---|
| Blood in stool, nocturnal diarrhoea | Pain related to defecation (Rome IV) |
| Elevated calprotectin | Long history since young adulthood, normal calprotectin |
| Weight loss, anemia | Stress correlation, normal labs |
IBD vs functional gut · Calprotectin · Gut inflammation markers
Step 3, Rome IV pain criterion (IBS context)
IBS is defined in part by recurrent abdominal pain related to defecation and associated with stool form/frequency changes. Meeting IBS criteria does not rule out coexisting organic disease if alarms are present, it is a symptom framework, not a microbiome diagnosis.
Evidence-tier table, framing only
| Approach | Evidence tier | Notes |
|---|---|---|
| Exclude alarms / inflammatory disease | Strong | Calprotectin, clinical pathway |
| Low-FODMAP trial (IBS with pain) | Strong in IBS meta-analyses | Low-FODMAP intervention |
| Gut–brain therapies (CBT, hypnotherapy) | Moderate for IBS pain clusters | Stress, sleep & exercise |
| Generic probiotics from report | Weak / strain-specific | Probiotics |
| Microbiome test to explain pain | Low | Association literature only |
What microbiome reports cannot show
| Question | Can a stool panel answer it? |
|---|---|
| Is pain from endometriosis? | No |
| Is this IBD vs IBS? | No, calprotectin, endoscopy when indicated |
| Upper vs lower mechanism? | No |
| Which probiotic strain might help? | No |
Use Multi-marker synthesis if the report drives conflicting actions.