This page shows an example of a comprehensive stool analysis — a molecular-genetic gut-microbiome panel. It complements the Lab Panel (blood & urine) and the Gut Biome section of Functional Testing, which explains why gut health matters.
As with the Lab Panel, markers are grouped by what they assess. The first column gives the name as it usually appears on the report; the second column gives a short note on what the marker reflects.
This is an illustrative example, not a prescription. Which markers to test, how to interpret them, and how often to repeat them should be decided together with a physician trained in functional medicine.
Marker Description Color Visual assessment of the stool Consistency Visual assessment of stool texture pH value Acidity of the stool — reflects bacterial fermentation
Marker Description Diversity Species richness of the gut flora — higher is generally healthier Enterotype Microbiome cluster type (Bacteroides-, Prevotella- or Ruminococcus-dominated) Dysbiosis index Composite measure of how far the microbiome deviates from a balanced state Firmicutes / Bacteroidetes ratio Balance of the two dominant phyla Actinobacteria / Proteobacteria ratio Balance of beneficial vs. potentially harmful phyla Prevotella / Bacteroides ratio Dietary-pattern indicator (fiber-rich vs. protein/fat-rich)
Share of the total flora made up by each major phylum.
Marker Description Actinobacteria Phylum including the Bifidobacteria — fiber fermenters Bacteroidetes Major phylum — protein & fat metabolism Firmicutes Major phylum — includes most butyrate producers Fusobacteria Minor phylum — some species pro-inflammatory Proteobacteria Phylum including many potential pathogens Verrucomicrobia Phylum including Akkermansia — supports the mucus layer
Metabolically active bacterial groups — the chemistry the microbiome produces, reported relative to a reference.
Marker Description Secondary bile acids Bacterial transformation of bile acids TMA / TMAO Trimethylamine — a cardiovascular-risk-linked metabolite Indoxyl sulfate Protein-fermentation metabolite — kidney & vascular relevance Phenols Protein-putrefaction products Ammonia Protein-fermentation product Histamine Bacterial histamine production — histamine-intolerance relevance Equol Isoflavone metabolite — only produced by certain microbiomes Beta-glucuronidase Enzyme that can de-conjugate hormones & toxins in the gut
Marker Description Bifidobacterium Fiber-fermenting, immune-supportive genus Bacteroides Versatile commensal genus — defines enterotype 1 Bacteroides fragilis Commensal species — immune modulation (harmful in excess) Prevotella Fiber-associated genus — defines enterotype 2 Christensenellaceae Bacterial family associated with leanness & longevity Dialister spp. Commensal genus Oxalobacter formigenes Degrades dietary oxalate — kidney-stone protection
Butyrate is the main energy source for colon cells and a key anti-inflammatory metabolite.
Marker Description Total butyrate-producer count Combined count of butyrate-forming bacteria Faecalibacterium prausnitzii Major butyrate producer — also supports the mucosal barrier Eubacterium rectale Butyrate producer (syn. Agathobacter rectalis ) Eubacterium hallii Butyrate producer (syn. Anaerobutyricum hallii ) Roseburia spp. Butyrate-producing genus Ruminococcus spp. Fiber-degrading, butyrate-linked genus Coprococcus spp. Butyrate-producing genus Butyrivibrio spp. Butyrate-producing genus Clostridium butyricum Butyrate-producing species
Marker Description Total clostridia count Combined Clostridium count Clostridia cluster I Clostridium cluster I group Clostridium histolyticum Potentially pathogenic species (syn. Hathewaya histolytica ) Clostridium perfringens Potentially pathogenic, toxin-forming species Clostridium sporogenes Protein-putrefying species Clostridioides difficile Pathogen — cause of antibiotic-associated colitis
Marker Description Sulfate-reducing bacteria Produce hydrogen sulfide — excess can irritate the gut lining Desulfovibrio piger Sulfate-reducing species Bilophila wadsworthia Sulfate-reducing, bile-tolerant species
Marker Description Escherichia coli Immune-stimulating commensal — both deficiency and excess matter Enterococcus spp. Immune-stimulating commensal genus Lactobacillus spp. Lactic-acid bacteria — barrier & immune support Akkermansia muciniphila Mucin-layer bacterium — strengthens the gut barrier
Marker Description Haemophilus spp. Potential pathogen (Proteobacteria) Acinetobacter spp. Potential pathogen Proteus spp. Potential pathogen Klebsiella spp. Potential pathogen Enterobacter spp. Potential pathogen Serratia spp. Potential pathogen Hafnia spp. Potential pathogen Morganella spp. Potential pathogen — histamine-forming Citrobacter spp. Potential pathogen Pseudomonas spp. Potential pathogen Providencia spp. Potential pathogen Fusobacterium Potential pathogen — some species pro-inflammatory Fusobacterium nucleatum Species linked to gut inflammation & colorectal cancer
Marker Description Methanobrevibacter spp. Methane-producing archaeon — linked to constipation & bloating
Marker Description Candida albicans Most common gut yeast — relevant in overgrowth Candida dubliniensis Candida species Candida parapsilosis Candida species Candida tropicalis Candida species Candida lusitaniae Candida species Candida krusei Candida species (syn. Pichia kudriavzevii ) Candida glabrata Candida species (syn. Nakaseomyces glabratus )
Marker Description Blastocystis hominis Common protozoan — pathogenic potential debated Dientamoeba fragilis Protozoan — sometimes symptom-associated
Marker Description Giardia lamblia Pathogenic protozoan — causes giardiasis Entamoeba histolytica Pathogenic protozoan — causes amoebic dysentery Cryptosporidium spp. Pathogenic protozoan Cyclospora cayetanensis Pathogenic protozoan
Marker Description Fat Undigested fat in stool — fat-digestion marker Nitrogen Undigested protein — protein-digestion marker Sugar Undigested sugars — carbohydrate-digestion marker Water Stool water content
Marker Description Pancreatic elastase Pancreatic exocrine enzyme output Bile acids in stool Bile-acid loss / fat-digestion marker
Marker Description Calprotectin Intestinal inflammation marker Alpha-1-antitrypsin Gut-permeability / protein-loss marker
Marker Description Secretory IgA (sIgA) Mucosal antibody — first-line gut immune defense Zonulin Intestinal-permeability (“leaky gut”) marker
