The microbiome
Gut health (GI Effects).
A comprehensive stool analysis that maps the bacteria, the barrier, and the immune signal in one collection.
By Genova Diagnostics · 48 biomarkers
Why it matters
The gut houses roughly 70% of your immune system, synthesizes critical nutrients and neurotransmitter precursors, and regulates gene expression through the metabolites your microbes produce. Read the system directly and you find what is driving symptoms across the rest of the body: autoimmunity, mood, skin, fatigue, and metabolic dysfunction. Genova GI Effects is the most clinically useful gut panel I order. Collection is an at-home stool kit shipped to you. This is a Genova specialty test; it is not run by LabCorp or Quest.
Most stool tests answer one question. GI Effects answers three at once. It reads how well you digest and absorb food, whether the gut wall is inflamed, and what the microbial ecosystem actually looks like, down to specific organisms. That combination is why a single collection can explain symptoms that have been chased in five different directions.
What I read for
Microbial diversity first. Then the presence of keystone beneficial species and any opportunistic overgrowth. Calprotectin and secretory IgA for inflammation and immune tone. Pancreatic elastase for digestion. Each marker points to a different lever.
I do not read this test as a list of red flags. I read it as five separate questions, each with its own answer and its own fix:
- Is food being broken down? (digestion)
- Is the gut wall inflamed? (inflammation)
- Is the microbial ecosystem balanced? (dysbiosis)
- Are the right metabolites being produced? (the short-chain fatty acids your microbes make)
- Are pathogens present? (infection)
What it measures
Genova organizes the panel around three functions of gut health: digestion and absorption, inflammation and immunology, and the gut microbiome itself.
Digestion and absorption. How completely you break down protein and fat, and whether your pancreas is producing enough enzyme. Pancreatic elastase is the standard marker of pancreatic output. Products of protein breakdown and fecal fat tell me where digestion is failing.
Inflammation and immunology. Calprotectin flags neutrophil-driven inflammation and helps separate inflammatory bowel disease from irritable bowel syndrome. Eosinophil protein X (EPX) tracks allergic and parasitic inflammation. Secretory IgA reads the strength of your mucosal immune barrier. A fecal occult blood test screens for hidden bleeding.
The gut microbiome. This is the depth that sets GI Effects apart. It uses three methods together. PCR (DNA-based) measures 24 commensal genera and species mapped across 7 major bacterial phyla. Culture grows living organisms and tests their sensitivity to both prescription and natural agents, so any treatment is targeted rather than guessed. Microscopy examines for parasites directly, which remains the standard for many of them. The report also generates an Inflammation-Associated Dysbiosis score and a Methane Dysbiosis score, plus metabolic readouts including short-chain fatty acids (the fuel your colon cells run on) and beta-glucuronidase (a marker tied to how well you clear used hormones and toxins).
See all 48 biomarkers
Digestion and absorption
- Pancreatic Elastase-1
- Products of Protein Breakdown (Valerate, Isovalerate, Isobutyrate)
- Fecal Fats (total, triglycerides, long-chain fatty acids, cholesterol, phospholipids)
Inflammation and immunology
- Calprotectin
- Eosinophil Protein X (EPX)
- Fecal Secretory IgA (sIgA)
- Fecal Occult Blood
Gut metabolism
- Short-Chain Fatty Acids (total)
- n-Butyrate (concentration and percentage)
- Acetate (percentage)
- Propionate (percentage)
- Beta-Glucuronidase
Microbiome composition (PCR)
- 24 commensal genera and species across 7 major phyla, reported against a healthy reference population
- Inflammation-Associated Dysbiosis score
- Methane Dysbiosis score
Culture and sensitivities
- Bacterial culture with identification (MALDI-TOF)
- Mycology (yeast) culture with identification
- Sensitivities for any pathogenic or potentially pathogenic organisms, including effective prescription and natural agents
Parasitology
- Microscopic exam for ova and parasites (O&P)
- PCR for 6 protozoal targets: Blastocystis, Cryptosporidium, Cyclospora, Dientamoeba fragilis, Entamoeba histolytica, and Giardia
Optional add-ons (available on request)
- Helicobacter pylori antigen
- Clostridium difficile (toxin)
- Campylobacter
- Shiga toxin E. coli
- Fecal Lactoferrin
- Zonulin Family Peptide
- Macroscopic exam for worms
- KOH prep for yeast
- IgG Food Antibodies (87 foods, finger-stick bloodspot)
Who this is for
GI Effects is the right test when there are symptoms pointing at the gut, or when systemic symptoms have a plausible gut origin and nothing else has explained them.
Common reasons I order it
- Gas, bloating, reflux, abdominal pain or cramping
- Diarrhea, constipation, or both
- Irritable bowel syndrome or inflammatory bowel disease workup
- Food reactions and suspected sensitivities
- Skin conditions like eczema and atopic dermatitis
- Mood changes, brain fog, and fatigue with no clear cause elsewhere
- Autoimmune or metabolic conditions where the gut may be an upstream driver
It is also a baseline test. You do not need to be sick to learn something useful from reading your microbiome against a healthy reference population.
How collection works
- 1
We decide it is the right test.
I review your history and symptoms and confirm GI Effects is the panel that answers your question. A one-day collection is standard. If there is real suspicion of a parasite, I order the three-day collection, which improves detection.
- 2
You collect at home.
The kit includes step-by-step instructions and collection videos. The process is private and takes a few minutes.
- 3
You ship it back.
Use the prepaid FedEx materials provided.
- 4
We read it together.
Results come back to me, and we sit down with them to build the correction plan. The findings translate directly into what to remove, what to support, and what to repair.
How to prepare
A few medications and supplements can shift specific markers. The goal is a clean baseline, so some are paused before collection. Never stop a medication you need without clearing it with me first.
Probiotics: stop 2 to 4 weeks before collection. They alter the bacteria and metabolite readings.
Antibiotics, antifungals, antiparasitics: stop 14 days before. They suppress the very organisms we are trying to read.
Antacids and acid blockers (PPIs, H2 blockers): generally hold 2 to 14 days. If we are testing for H. pylori, PPIs come off for a full 14 days.
Aspirin and NSAIDs: hold 2 days. They can shift the inflammation markers.
Digestive enzymes and betaine HCl: these change digestion markers. We pause them unless we are specifically testing how well they work.
Bismuth, bentonite clay, activated charcoal, mineral or castor oil, laxatives, suppositories, enemas: these interfere with the microscope exam and stool density. Hold per the kit instructions.
Wait 4 weeks after a colonoscopy or barium study before collecting.
Do not collect during an acute stomach illness.
What you get
A results review with me, and a written Precision Health Plan that turns the panel into action. Not a printout of numbers. A specific sequence: what to remove, what to replace, what to reintroduce, and what to repair, in the order that matters. If an organism needs treatment, the culture sensitivities tell us exactly which agent will work, so we are not guessing.
The microbiome is one of the most informative systems you can measure, and one of the most responsive. Diet, targeted supplements, and a few well-chosen interventions move these numbers. We measure, we compare to optimal, and we rebalance. Then we recheck and confirm it worked.
Questions
This is a cash-pay test ordered through the practice. Genova provides CPT codes you can submit to a commercial insurer for possible reimbursement, but coverage varies and is not guaranteed.
No. It is an at-home stool collection. The optional IgG food antibody add-on uses a simple finger-stick bloodspot.
One day is standard and adequate for most people. Three days is used when there is a real index of suspicion for a parasite, because parasites shed intermittently.
GI Effects combines DNA-based microbiome analysis with live culture and direct microscopy. Culture is what lets us test an organism against specific treatments. Most consumer kits report DNA only, which tells you what is present but not what will clear it.
Microbiomix is a metagenomic add-on that sequences the entire microbiome and its functional potential, detecting a far wider range of species and the metabolites they can produce. For complex or unresolved cases, the wider net is worth it. We decide together based on your situation.
Yes, with interpretation adjusted for age. Some markers like calprotectin and secretory IgA run higher in young children as a normal feature of a developing microbiome. C. difficile add-on testing is not available under age 2.
How to order this
Part of the Precision Partnership baseline. Lab fee at vendor cost. I interpret the results into your written Plan.