Gut & Microbiome

Zonulin is marketed as a direct measure of intestinal tight-junction integrity -- the idea being that higher zonulin loosens the junctions between gut epithelial cells, letting larger molecules leak into the bloodstream ("leaky gut"). It was originally identified as pre-haptoglobin 2, a precursor protein.

Typical range: No consensus clinical reference range exists -- commercial labs report their own assay-specific cutoffs, and there is no FDA-cleared diagnostic threshold for "leaky gut" using zonulin.

Food first: Interventions that plausibly lower zonulin/improve barrier function generally overlap with the broader gut-barrier nutrition section below (fiber, polyphenols, vitamin D, omega-3) -- see those entries. Don't chase a zonulin number in isolation given the assay concerns above.

When to see someone: Be candid with clients: a commercial zonulin test result, especially serum zonulin, should not be presented as a validated diagnosis of "leaky gut." It's reasonable as one data point in a research or pattern-tracking context, not as the sole basis for a treatment plan or an expensive supplement protocol.

A functional (not just structural) test of small intestinal permeability. The patient drinks a solution of two inert sugars -- lactulose (large molecule, normally blocked by healthy tight junctions) and mannitol (small molecule, normally absorbed easily) -- and urine is collected over several hours. A higher-than-expected lactulose:mannitol ratio means more lactulose got through, implying looser tight junctions or mucosal breaches.

Typical range: No single universal cutoff -- ratios vary by lab protocol, collection time window (2hr vs 5hr), and assay method (HPAE-PAD vs LC-MS/MS), which is itself a documented problem (see caveats).

Food first: See L-Glutamine, Zinc-Carnosine, and Polyphenols entries below -- these are the interventions with human trials that specifically used lactulose:mannitol (or lactulose:rhamnose) ratios as their outcome.

When to see someone: This test is considered more physiologically direct than zonulin, but a 2013-2014 methodological review found that variations between labs' collection times, sugar doses, and analytic methods "preclude meaningful comparisons between studies" -- meaning a result from one lab/protocol may not be comparable to another, and there's a large but genuinely conflicting literature on how well it tracks with symptoms or disease in adults outside of research settings. (cite: van Wijck K et al., PLOS ONE, 2013, "Standardising the Lactulose Mannitol Test of Gut Permeability to Minimise Error and Promote Comparability," PMC4047110)

A calcium- and zinc-binding protein released by neutrophils (a type of white blood cell) when they migrate into the gut lining during inflammation. This is genuinely one of the best-validated non-invasive gut tests available -- it is used in mainstream gastroenterology, not just functional medicine.

Typical range: Conventional: <50 mcg/g is typically considered normal, 50-150 mcg/g is a gray zone often prompting a repeat test, and >150-250 mcg/g raises concern for active inflammatory bowel disease (IBD) warranting endoscopic workup. Cutoffs vary somewhat by lab and clinical context (e.g., 152 mcg/g has been used as an optimal cutoff for predicting IBD relapse).

Food first: There is no supplement that reliably "lowers calprotectin" the way, say, fiber lowers LDL -- treating the underlying inflammatory bowel disease (medically) is what lowers it. A polyphenol-rich diet has shown a modest calprotectin reduction in a small RCT of older adults with elevated gut permeability (see Polyphenols entry below), but this is a much smaller effect than treating diagnosed IBD.

When to see someone: An elevated calprotectin always warrants a real GI workup, not a supplement trial -- it doesn't tell you *why* the gut is inflamed (could be IBD, infection, NSAID use, or even recent strenuous exercise, which can transiently raise it). A single mildly elevated result in someone without GI symptoms is not automatically diagnostic of anything.

An iron-binding protein released by neutrophils during intestinal inflammation, similar in concept to calprotectin -- used as an adjunct or alternative inflammation marker, most validated in pediatric IBD.

Typical range: Conventional: typically <7.25 mcg/g considered negative (assay-dependent); values above the lab's cutoff suggest active mucosal inflammation.

Food first: Same as calprotectin -- there's no nutrient lever here beyond treating the underlying inflammatory driver.

When to see someone: Often run alongside calprotectin rather than instead of it; an elevated result still needs the same clinical workup as an elevated calprotectin.

The dominant antibody in mucosal secretions (gut, respiratory tract) -- it coats the intestinal lining and gut bacteria, helping neutralize pathogens and toxins without triggering a full inflammatory response, and plays a role in shaping which bacteria get to live in the gut.

Typical range: No standardized clinical reference range -- functional-medicine labs report a range (often something like 51-204 mcg/mL, but this varies substantially by lab and is not standardized the way tTG-IgA or calprotectin cutoffs are). Both very low sIgA (impaired mucosal immunity) and very high sIgA (active immune reaction to something in the gut) are interpreted as "abnormal" by different practitioners, which itself signals this marker's interpretation isn't settled.

Food first: A generally nutrient-adequate diet (protein, vitamin A, zinc) supports normal mucosal immune function; there's no single supplement proven to reliably normalize an abnormal fecal sIgA result.

When to see someone: Don't over-interpret a single sIgA number -- it's a real and interesting piece of mucosal immunology, but as a standalone stool-panel result it currently sits closer to research-tool status than validated diagnostic status, unlike calprotectin.

A qPCR (DNA-based) stool panel from Diagnostic Solutions Laboratory that screens for a broad list of bacteria, parasites, fungi, viruses, and includes some of the validated markers above (calprotectin, secretory IgA, elastase, zonulin) bundled into one comprehensive report, along with "dysbiosis" pattern markers (e.g., ratios of certain bacterial groups).

Typical range: No single validated composite range -- each analyte within the panel has its own lab-reported reference range, some validated (calprotectin, elastase) and some not (many of the individual bacterial DNA quantities and "dysbiosis patterns").

Food first: Not applicable to the panel as a whole -- any nutrition recommendation should be based on the individually validated components (calprotectin, elastase, confirmed pathogen findings), not the "dysbiosis" narrative sections of the report.

When to see someone: Treat GI-MAP "pathogen detected" flags, especially for organisms at low quantities or ones not matching the clinical picture, with real caution before treating -- confirm with symptoms and, where possible, a second validated method before starting antimicrobial herbs or medications based on this test alone.

A comprehensive stool panel combining PCR (microbial DNA detection), enzyme immunoassay (for calprotectin and similar inflammation markers), microscopy (parasites/yeast), and biochemical assays (short-chain fatty acids, elastase, beta-glucuronidase, fecal fats) grouped into five report categories: maldigestion, inflammation, dysbiosis, metabolite imbalance, and infection.

Typical range: No single composite validated range; Genova has published a proprietary "Dysbiosis Index" and "Inflammation-Associated Dysbiosis" score built from their own patient database (>16,000 samples), but this is an internally derived index, not an externally validated clinical outcome measure the way, say, a HbA1c cutoff is.

Food first: Use the validated individual markers (calprotectin for inflammation, elastase for pancreatic enzyme sufficiency, confirmed pathogens) to guide nutrition and referral decisions; treat the "dysbiosis index" and specific bacterial abundance callouts as a research-grade pattern to watch rather than a confirmed diagnosis to treat aggressively.

When to see someone: Same caution as GI-MAP -- avoid building an expensive, restrictive supplement protocol off the "dysbiosis" or bacterial-abundance sections alone without corroborating symptoms or validated markers.

These are sequencing-based tests (mail-in stool samples, often marketed directly to consumers) that characterize which bacteria are present and in what relative abundance. 16S rRNA sequencing reads one specific bacterial gene fragment and typically identifies bacteria down to genus level; shotgun metagenomic sequencing reads much more of the DNA present and can identify species/strain level, plus fungi and viruses, at a higher cost.

Typical range: No standardized clinical reference range exists for either method -- results are typically reported as relative abundance percentages compared to a proprietary reference database that varies company to company, meaning the same stool sample can look meaningfully different across two different consumer test companies.

Food first: These tests are reasonable for curiosity, self-tracking trends over time (same company, same method, repeated), or research purposes -- they are not currently validated tools for prescribing a specific supplement or elimination diet based on a single snapshot.

When to see someone: Be upfront with clients that a "dysbiosis" result on a $100-200 consumer kit is not the same tier of evidence as a calprotectin or tTG-IgA result -- it's a pattern-recognition tool, not a diagnosis.

A summary statistic describing how many different microbial species are present and how evenly distributed they are in a sample (alpha diversity); higher diversity is generally associated with a "healthier" gut ecosystem in population-level research, though the relationship is not universal across all diseases.

Typical range: No fixed clinical cutoff -- diversity indices are relative/comparative measures, typically reported as a percentile versus a reference population rather than an absolute pass/fail number.

Food first: A varied diet high in different plant fibers (the "eat 30 different plants a week" style recommendation popularized in microbiome research) is the most evidence-aligned lever for raising diversity, more so than any single supplement.

When to see someone: Don't treat a single diversity score as diagnostic of a specific disease state -- its clinical meaning varies by condition and is still an active research area, not a settled clinical test.

Direct measurement of acetate, propionate, and butyrate (and sometimes others) in stool -- the metabolic byproducts of bacterial fermentation of fiber, used as a proxy for how much beneficial fermentation is happening and how much fuel is available for colonocytes (see Butyrate entry below for the mechanism).

Typical range: No standardized clinical reference range -- values are highly dependent on recent diet (especially fiber intake in the days before the sample), transit time, and lab methodology, making single-sample fecal SCFA levels a noisy, hard-to-standardize marker despite butyrate's genuinely well-established biology.

Food first: Increasing fermentable fiber intake (see Fiber/Prebiotics below) is the primary lever for raising fecal SCFA production.

When to see someone: A single stool SCFA measurement reflects very recent diet more than a stable trait -- don't over-interpret one low reading as a permanent "SCFA deficiency" without considering what the person ate that week.

A bacterial enzyme that "de-conjugates" compounds the liver has already packaged for excretion (including estrogen metabolites, some detoxification products, and certain drugs), potentially allowing them to be reabsorbed back into circulation rather than excreted -- this is the biochemical basis of the "estrobolome" concept in estrogen metabolism.

Typical range: No standardized clinical reference range; functional labs report a relative range, but there's no consensus cutoff tied to a specific disease outcome.

Food first: Adequate fiber intake and regular bowel transit are the most evidence-aligned levers; cruciferous vegetables are commonly recommended for estrogen metabolism support, though as noted in the SHBG entry in the Function Health file, the human RCT evidence for cruciferous compounds meaningfully changing hormone outcomes is thinner than the underlying biochemistry suggests.

When to see someone: Avoid presenting a single beta-glucuronidase result as a validated diagnosis of "estrogen dominance" -- it's a real and interesting mechanistic marker, but the leap from enzyme activity to a specific treatment recommendation is not yet supported by outcome trials.

A pancreatic digestive enzyme that passes through the gut largely undegraded, so a low fecal level is a genuinely well-validated proxy for reduced pancreatic enzyme output (exocrine pancreatic insufficiency), which affects fat and nutrient digestion/absorption.

Typical range: Conventional: >200 mcg/g stool is normal, 100-200 mcg/g suggests mild-to-moderate insufficiency, <100 mcg/g suggests severe insufficiency (assay-dependent).

Food first: Confirmed exocrine pancreatic insufficiency is treated with prescription pancreatic enzyme replacement therapy (PERT), not nutrition alone -- diet supports but does not substitute for enzyme replacement in a true deficiency.

When to see someone: A borderline-low result in an asymptomatic person, especially with a watery/unformed stool sample (which can dilute the reading and cause a false-low), should be repeated with a well-formed sample before assuming pancreatic insufficiency.

Three different ways of detecting this bacterium, which colonizes the stomach lining and is a well-established cause of gastritis, peptic ulcers, and a risk factor for gastric cancer.

Typical range: Qualitative positive/negative result for all three methods; no "optimal range" concept applies.

Food first: No dietary intervention reliably eradicates confirmed H. pylori -- that requires prescription antibiotic/PPI combination therapy. Zinc-carnosine has evidence as an adjunct alongside standard antibiotic triple therapy (see Zinc-Carnosine entry below), not as a replacement for it.

When to see someone: Confirm the patient has been off PPIs, bismuth, and antibiotics for the recommended window (commonly 2 weeks for PPIs, 4 weeks for antibiotics/bismuth) before breath or stool antigen testing, or false negatives are likely.

Measures hydrogen and methane gas in the breath after ingesting a lactulose or glucose solution, used as an indirect marker for small intestinal bacterial overgrowth (SIBO) -- the theory being that bacteria fermenting the sugar earlier/more than expected indicates bacterial overgrowth in the small intestine rather than normal colonic fermentation.

Typical range: Per the North American Consensus, a hydrogen rise of ≥20 ppm from baseline by 90 minutes is considered a positive result for bacterial overgrowth, and a methane level ≥10 ppm at any point is considered methane-positive (now often termed "intestinal methanogen overgrowth" rather than classic SIBO). Consensus test doses: lactulose 10g, glucose 75g.

Food first: A confirmed SIBO diagnosis is typically treated with targeted antibiotics (e.g., rifaximin) or, in functional-medicine settings, herbal antimicrobials and a temporary low-fermentation diet (e.g., low-FODMAP) -- these are treatment approaches, not something the breath test itself indicates nutritionally on its own.

When to see someone: Because false positives are a real, documented issue with lactulose breath testing, a positive result should be interpreted alongside symptoms and, ideally, response to treatment -- not treated as gospel on its own, especially before committing a client to a long antimicrobial protocol.

Already covered in full under Inflammation Markers above -- flagged again here specifically because this is one of calprotectin's most clinically useful "functional" applications: helping a clinician decide whether new-onset GI symptoms that look like IBS actually need a colonoscopy to rule out IBD.

Typical range: See Fecal Calprotectin entry above (50 mcg/g cutoff commonly used for this specific IBD-vs-IBS discrimination purpose, with pooled sensitivity/specificity in the low-to-mid 90s%).

Food first: See Fecal Calprotectin entry above.

When to see someone: A normal calprotectin substantially lowers the likelihood of IBD but does not by itself rule out every GI condition -- ongoing red-flag symptoms (rectal bleeding, unintentional weight loss, anemia, family history) still warrant referral regardless of a normal calprotectin.

Commercial panels that test blood for IgG antibodies against dozens to hundreds of foods, marketed as identifying foods a person is "sensitive" to (as distinct from a true IgE-mediated allergy). This is one of the most widely used and most widely criticized tests in the functional-nutrition space, so it's worth being direct about the professional consensus.

Typical range: Not applicable in the traditional sense -- results are typically reported as a "reactivity level" per food, but this reporting format itself is part of the criticism (see below).

Food first: If a client suspects a genuine food reaction, the evidence-based approaches are: a supervised elimination-and-reintroduction diet based on symptoms (not a lab panel), formal allergy testing (skin prick or IgE) if true allergy is suspected, and hydrogen breath testing or genetic testing for specific intolerances like lactose. These are more defensible starting points than a commercial IgG panel.

When to see someone: Be honest with clients about this one specifically -- it's a popular and profitable test, but the major allergy/immunology professional societies across three continents (US, Canada, Europe) have independently advised against using it diagnostically. This is a case where "popular in functional-medicine circles" and "supported by evidence" clearly diverge, and Holistic Hub's credibility depends on saying so plainly rather than softening it.

Tissue transglutaminase IgA antibody (tTG-IgA) is the standard first-line blood test for celiac disease, an autoimmune reaction to gluten that damages the small intestine lining. Total serum IgA is run alongside it to rule out selective IgA deficiency, which would otherwise cause a false-negative tTG-IgA in someone who actually has celiac disease.

Typical range: tTG-IgA sensitivity is commonly cited around 95% and specificity around 99% in patients with normal total IgA, per American College of Gastroenterology (ACG) guidelines, which recommend tTG-IgA as the first-line test for anyone over age 2, with total IgA measured to determine whether IgG-based tests (deamidated gliadin peptide IgG or tTG-IgG) are needed instead.

Food first: Not applicable as a "move the marker" nutrient story -- a positive result requires confirmatory endoscopy/biopsy (in most guideline pathways) and, once confirmed, strict lifelong gluten elimination is the only established treatment; there is no supplement or partial-gluten-reduction strategy validated as sufficient treatment for confirmed celiac disease.

When to see someone: Testing must happen while the person is still eating gluten -- going gluten-free before testing can normalize antibody levels and cause a false negative, delaying accurate diagnosis. Never advise stopping gluten before this test is done.

Typical range: No blood/stool reference range -- typical studied intake ranges are roughly 5-20g/day for inulin/FOS/GOS depending on the study and tolerance, alongside general dietary fiber targets (25-38g/day per standard nutrition guidelines).

Food first: A varied, plant-diverse diet (legumes, oats, garlic/onion, green banana, cooled/reheated potatoes and rice for resistant starch) is the food-first approach; introduce fermentable fibers gradually in anyone with active IBS or SIBO-like symptoms, since a fast increase can worsen bloating/gas before it helps.

When to see someone: With confirmed SIBO or significantly active IBS, high-dose prebiotic fibre can worsen symptoms in the short term. That is a reason to ramp slowly and pick the type carefully, not a reason to avoid fibre.

Typical range: No blood reference range relevant here -- typical studied doses range widely, from ~5g three times daily in IBS trials up to 30g+/day in the doses shown to move permeability testing in a recent meta-analysis.

Food first: Dietary sources include meat, fish, eggs, dairy, and to a lesser extent some plant proteins; supplemental glutamine is generally well tolerated at moderate doses, but note the dose discrepancy above when setting expectations with clients about typical commercial "gut healing" product doses.

When to see someone: High-dose glutamine (the 30g+/day range shown to move permeability testing) is a substantially larger dose than what's in most commercial gut-health supplement blends -- set realistic expectations. Glutamine should be used cautiously or avoided in people with certain seizure disorders and in advanced liver disease (altered ammonia handling) -- check with a physician in those cases.

This marker sits in Transform -- the cofactors enzymes need to turn fuel into usable energy.

Typical range: No blood reference range -- studied doses are typically 37.5mg twice daily (permeability studies) up to 150mg/day (gastric ulcer healing studies).

Food first: This is specifically a supplement-form intervention (the carnosine-chelated form is what's been studied) rather than something reliably obtained from food in equivalent form; zinc itself is available from oysters, red meat, poultry, beans, nuts, and seeds (see Zinc entry in Function-Health-Hyman.md for general zinc nutrition and copper-balance caveats).

When to see someone: Chronic zinc intake from any source above ~40mg/day risks copper deficiency over time (see Zinc entry, Function-Health-Hyman.md) -- factor total zinc intake (diet + zinc-carnosine + any separate zinc supplement) into that ceiling.

This marker sits in Build -- the raw material for making and renewing structure.

Typical range: See Vitamin D entry in `Function-Health-Hyman.md` for standard/functional ranges -- the same 25(OH)D thresholds apply here (deficient <20 ng/mL, sufficient ≥30 ng/mL per Endocrine Society).

Food first: Same as the general Vitamin D entry in Function-Health-Hyman.md -- fatty fish, fortified foods, sensible sun exposure, and supplementation (typically 1,000-4,000 IU/day) to reach sufficiency.

When to see someone: Same toxicity caveats as the general Vitamin D entry -- avoid sustained doses above 10,000 IU/day without monitoring, and use caution in granulomatous disease/hyperparathyroidism.

Typical range: No blood reference range -- studied intervention was a defined food pattern (berries, blood orange, pomegranate juice, green tea, apple, dark chocolate) providing a broad polyphenol mix daily for 8 weeks in the key human trial below.

Food first: Berries, tea (especially green tea), dark chocolate/cocoa, pomegranate, colorful vegetables, olive oil, and coffee are all meaningful polyphenol sources -- this is one of the more genuinely evidence-backed "food as intervention" gut-barrier strategies in this file.

When to see someone: Polyphenol supplements (concentrated extracts) have not been studied nearly as thoroughly as whole-food polyphenol-rich diets for this specific purpose -- prioritize food sources over high-dose isolated extracts, and note some polyphenol-rich foods (dark chocolate, tea) contain caffeine or oxalates worth considering in sensitive individuals.

Typical range: See Omega-3 entries in Function-Health-Hyman.md for the Omega-3 Index framework; no separate gut-specific reference range exists.

Food first: Fatty fish 2-3x/week or an algae-based EPA/DHA supplement for non-fish-eaters -- same food sources as the cardiovascular omega-3 recommendations.

When to see someone: Same bleeding-risk caveats above ~3g/day as covered in Function-Health-Hyman.md.

Typical range: Not applicable -- no blood/stool marker tracks this intervention specifically.

Food first: Bone broth and collagen are reasonable, generally safe protein-containing foods to include as part of an overall gut-supportive diet, but should be presented to clients as a traditional/palatability-driven food choice rather than a scientifically validated "leaky gut treatment."

When to see someone: Collagen supplements are generally very safe; the caution here is purely about honest expectation-setting -- don't oversell this one relative to what the (limited, and in the one controlled trial, null) evidence actually shows.

Typical range: Not applicable -- dosed in colony-forming units (CFU), typically billions per day, with no standardized "optimal" CFU count across all strains/purposes.

Food first: When recommending a probiotic, match the specific studied strain to the specific studied indication rather than recommending "a probiotic" generically -- this is the single most important honesty point to convey to clients until the dedicated probiotics file is built.

When to see someone: Generally very safe in healthy people; immunocompromised individuals and those with central lines/severe illness should use probiotics under medical supervision given rare case reports of bacteremia/fungemia in high-risk populations.

Typical range: No standardized blood/stool reference range for optimal butyrate levels -- see Fecal SCFA entry above for the measurement-noise caveat.

Food first: Fermentable fiber intake (see Fiber/Prebiotics entry above) is the primary lever for increasing colonic butyrate production -- this is not something supplemented directly in a meaningfully bioavailable oral form the way, say, vitamin D is, since oral butyrate is largely absorbed before reaching the colon in most delivery forms; fiber intake driving bacterial fermentation in situ is the validated pathway.

When to see someone: As above under Fiber/Prebiotics -- ramping up fermentable fiber too quickly to "boost butyrate" can cause bloating/gas, especially in someone with an already-disrupted gut (active IBS, recent SIBO). Gradual increases are better tolerated and just as effective over time.