Reading your microbiome report
A stool microbiome report describes who was detected (and sometimes inferred functions) in one sample at one time. It is not a complete picture of gut health, barrier integrity, motility, inflammation, or small-intestinal overgrowth.
Use this page as a routing hub. For mechanism depth, follow the linked Foundations articles.
Step 1, Know your test method
| Method | What you get | Main limits |
|---|---|---|
| 16S rRNA | Genus-level (sometimes species) bacterial profiles | Misses many microbes; resolution and bias depend on variable region and database |
| Shotgun metagenomics | More species/strains; gene and pathway counts | Depth, DNA extraction, and annotation quality still limit calls |
| Add-on scores | Diversity, dysbiosis, health indexes | Often proprietary; validation varies |
See also: Interpretation Guide (test types and reliability tiers).
Step 2, Match report lines to site pages
Scores and labels
| Report element | Read this | Do not conclude |
|---|---|---|
| Dysbiosis / imbalance score | Dysbiosis | You are diseased or need a cleanse |
| Low diversity | Alpha diversity | Permanent poor gut health |
| Enterotype label | Enterotypes | Fixed diet type for life |
| Firmicutes/Bacteroidetes ratio | F:B ratio | Obesity or health destiny |
| Phylum / genus balance score | Balance scores | Clinical diagnosis from proprietary index |
| Pathway / butyrate production score | Metagenomic pathway scores | Measured SCFA output, see SCFAs |
| Inflammation score (from sequencing) | Sequencing inflammation score | Same as calprotectin, see Gut inflammation markers |
| Stool pH / chemistry panel | Stool pH and chemistry, Luminal environment | Direct SCFA concentration or osmolarity |
| β-Glucuronidase activity | β-Glucuronidase | Hormone or cancer risk diagnosis |
Taxa commonly highlighted
| Taxon / group | Species / concept page | Dedicated test line (if shown) |
|---|---|---|
| Faecalibacterium prausnitzii | /species/faecalibacterium-prausnitzii | - |
| Bifidobacterium | /species/bifidobacterium | - |
| Akkermansia muciniphila | /species/akkermansia | Akkermansia abundance |
| Roseburia / butyrate producers | /species/roseburia | Pathway scores → Metagenomic pathway scores |
| Coprococcus | /species/coprococcus | - |
| Ruminococcus bromii (RS) | /species/ruminococcus-bromii | - |
| Bacteroides / Prevotella | /species/bacteroides-prevotella | Enterotype context → Enterotypes |
| Methanobrevibacter | /species/methanobrevibacter-smithii | Not breath IMO, Methane and gas |
| Lactobacillus | /species/lactobacillus | Probiotic strain ≠ genus readout |
| Klebsiella / Proteobacteria blooms | /species/klebsiella-proteobacteria | Opportunistic lists |
| ”Opportunistic” lists | /tests/opportunistic-bacteria | Infection without clinical correlation |
Biomarkers sometimes bundled
| Marker | Test page | Foundation context |
|---|---|---|
| Zonulin | /tests/zonulin | Intestinal barrier |
| Calprotectin | /tests/calprotectin | Gut inflammation markers |
| Secretory IgA | /tests/secretory-iga | Intestinal barrier (distinct from calprotectin) |
Step 3, Match symptoms to synthesis pages
| If your main concern is… | Start here |
|---|---|
| Bloating / distension | Chronic bloating |
| Constipation | Constipation |
| Diarrhoea | Loose stools / diarrhoea |
| Abdominal pain | Abdominal pain |
| Fatigue + gut symptoms | Fatigue |
| Brain fog + gut symptoms | Brain fog |
Red flags (weight loss, blood, nocturnal symptoms, fever): When to seek clinical care, not a microbiome-test problem first.
Gut–organ axes (when marketing merges systems)
| If the narrative links gut to… | Hub page |
|---|---|
| Mood, stress, brain fog, sleep | Gut–brain axis |
| Immunity, sIgA, inflammation scores | Gut–immune axis |
| Skin, acne, eczema from stool lines | Gut–skin axis |
Step 4, Diet and mechanism context
| Report narrative | Foundations |
|---|---|
| ”Increase fiber / prebiotics” | Dietary fiber paradox, SCFAs, Fiber supplements |
| ”Avoid FODMAPs” | FODMAPs |
| ”Leaky gut / barrier support” | Intestinal barrier |
| ”Slow transit / methane” | Gut motility, Methane and gas, SIBO & breath testing |
| After antibiotics | Post-antibiotic recovery |
| Gluten / dairy mentioned | Gluten-related disorders |
| High protein / putrefaction narrative | Protein fermentation & BCFAs |
| IBS subtype language | IBS subtypes |
| Medications listed as factors | Medications and microbiome |
| Food chemical / histamine overlap | Histamine, MCAS & food chemicals |
Step 5, Retesting, conflicts, and interventions
| Question | Start here |
|---|---|
| Conflicting lines on one report | Multi-marker report synthesis |
| Same lab comparison over time | Retesting over time |
| Stool vs saliva vs blood kit | Sample types |
| When to see a clinician first | Red flags |
| Bringing results to an appointment | Talking to clinicians |
Intervention evidence (by class, not brands):
- Probiotics & prebiotics · Low-FODMAP trial · High-fiber diet · Resistant starch · All interventions index
Weeks to months may be needed to see dietary or probiotic shifts on a repeat sample, single-timepoint “failure” is often over-interpreted.