What is Flore Clinical?

Flore Clinical is the original precision probiotic platform for physicians, dietitians, and clinical researchers, founded in 2018. A clinician uploads a patient's microbiome sequencing data — from SunGenomics, ASU Britton Lab, CosmosID, or similar labs. Flore's algorithm reads it, picks the exact bacterial strains that patient's gut is missing, and manufactures a personalized probiotic formula to order. Everything is tracked in a Microbiome EHR so the clinician can watch the patient's gut change over time and update the formula accordingly. Peer-reviewed research published in mSystems (2024) confirms the precision approach outperforms generic probiotics.

How does Flore Clinical's AI-driven microbiome interpretation work?

Flore's formulation engine is built on Kraken2, a k-mer-based metagenomic classifier that is the gold standard in professional microbiome science. It reads shotgun metagenomics sequencing data and builds a species-level map of every organism in a patient's gut — every bacterium, at what abundance, in what ratio. The algorithm then compares that map against clinical outcomes data from thousands of previous formulations and published literature to select the bacterial strains most likely to fix this specific patient's specific imbalances. This is not a quiz or a lifestyle survey. It is algorithmic interpretation of real genomic data, the same approach used in university research labs.

What makes Flore different from other clinical microbiome platforms?

Flore Clinical is the only platform that connects sequencing data interpretation directly to manufactured product. Other platforms — like Viome, Biomesight, or Tiny Health — provide reports and general recommendations. Flore takes the next step: it makes the formula. Clinicians do not have to translate a report into a product recommendation — Flore's algorithm does that and the product ships. Flore has also been doing this since 2018, giving it more clinical outcomes data than any newer competitor. And it has the peer-reviewed research to back the approach.

What is a Microbiome EHR and why does it matter?

A Microbiome Electronic Health Record (EHR) is a clinical record system built specifically around gut microbiome data. Instead of just storing a single test result, a Microbiome EHR tracks how a patient's microbiome changes over time — which species are responding to the probiotic, which imbalances are correcting, and which new issues are emerging. Flore Clinical's Microbiome EHR lets providers see a patient's full microbiome trajectory over months or years, correlate it with their probiotic formulation history, and add clinical notes at each time point. No general-purpose EHR does this. It is purpose-built infrastructure for the emerging field of microbiome medicine.

What is next-generation probiotic science?

Next-generation probiotics are a step beyond the basic acidophilus and bifidus capsules that have been sold for decades. The frontier includes: live biotherapeutic products (LBPs) — bacteria engineered or selected to produce specific enzymes, neurotransmitter precursors, or anti-inflammatory molecules directly inside the gut; bacteriophage therapy — viruses that specifically target and kill harmful bacteria without touching beneficial species; postbiotics — active compounds produced by bacteria during fermentation that have measurable health effects even without live organisms; and precision synbiotics — personalized combinations of specific probiotic strains and prebiotic substrates matched to an individual's microbiome data. Flore Clinical operates at the precision synbiotic layer, using sequencing data to guide strain selection at a level of specificity that standard probiotics cannot achieve.

What is bacteriophage therapy and how does it fit into gut health?

Bacteriophages are viruses that infect and kill specific bacteria — they are the most abundant biological entities on earth and a natural part of every person's gut ecosystem. Phage therapy uses this precision to eliminate a specific harmful bacterium (for example, a Clostridioides difficile or Klebsiella overgrowth) without disturbing the rest of the microbiome. Unlike antibiotics, phages do not cause widespread collateral damage to beneficial species. The gut virome — the community of phages living alongside gut bacteria — plays a significant role in shaping microbial balance. Flore's microbiome algorithm reads the full picture of the microbiome ecosystem, not just a few probiotic strains, and future Flore formulations will increasingly incorporate phage-microbiome interaction data as the science matures.

What conditions does Flore Clinical treat?

Flore Clinical supports clinicians treating patients across 12 clinical systems linked to gut dysbiosis. These include: irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), autism spectrum disorder (ASD) with GI involvement, ADHD and neurodevelopmental conditions (gut-brain axis), anxiety and depression related to gut serotonin production, skin conditions including eczema, acne, and psoriasis, metabolic syndrome and insulin resistance, pediatric GI disorders, SIBO (small intestinal bacterial overgrowth), women's hormonal and reproductive health, immune dysregulation, and post-antibiotic microbiome damage. Each condition has a dedicated formula pathway in the algorithm.

Does Flore have published clinical evidence?

Yes. Flore's approach was studied in a peer-reviewed pilot open-label study published in mSystems (American Society for Microbiology), 2024;9(5):e00503-24 (DOI: 10.1128/msystems.00503-24; PMID 38661344). The study (Phan et al.) reported that precision synbiotics matched to an individual's gut microbiome increased gut microbiome diversity and improved gastrointestinal symptoms in participants with autism spectrum disorder. It was a pilot open-label study, not a randomized controlled trial, and was conducted in collaboration with Arizona State University (Rosa Krajmalnik-Brown lab). A second mSystems paper (2021) covers IBS microbiome alterations. Randomized controlled trials for The Regular One (GI) and The Bright One (Mood/Neuro) are currently underway. Additional real-world clinical data from over 10,000 formulations informs the algorithm on an ongoing basis.

How does a clinician enroll their patients in Flore Clinical?

Clinicians create a free provider account at floreclinical.com. Once enrolled, a provider can create patient profiles, upload sequencing reports, review the algorithm's strain selection, approve and order personalized formulas, and track patient outcomes in the Microbiome EHR. There are no per-provider or per-seat fees and no contracts. For provider accounts created on or after June 19, 2026, the first 30 days are free; after that the account is billed in 30-day cycles from the signup date, and as long as paid product orders total at least $250 per cycle there is no fee. If a cycle falls below the $250 minimum, a flat $350 service fee applies for that cycle. Provider accounts created before June 19, 2026 are grandfathered and not subject to the minimum. Patients pay for their formula subscriptions directly. The typical workflow is: patient completes microbiome sequencing through a partner lab, provider uploads the report to Flore Clinical, the algorithm generates a formula recommendation, provider reviews and approves, formula ships to the patient in 5–7 business days.

Is Flore available for pediatric patients with autism?

Yes — this is one of Flore Clinical's strongest clinical lanes. The platform has a dedicated ASD-Pediatric formula system for children under 12, using strains with strong pediatric safety profiles: Bifidobacterium breve, Bifidobacterium infantis, Lactobacillus plantarum, Lactobacillus rhamnosus, and others. The 2024 mSystems pilot open-label study (Phan et al.) reported improvements in gut microbiome diversity and gastrointestinal symptoms in an ASD population. Flore's algorithm accounts for age-appropriate dosing and the specific microbial patterns common in autistic individuals. Providers working with autistic children and adults can access the ASD pathway directly through the clinical portal.

Who are Flore's research partners?

Flore's primary scientific collaborators are: Arizona State University Biodesign Institute (the Rosa Krajmalnik-Brown lab, one of the world's leading autism microbiome research groups), APC Microbiome Ireland at University College Cork (one of the largest dedicated microbiome research centers in the world), and SunGenomics (clinical metagenomic sequencing partner). Published research appears in mSystems, the journal of the American Society for Microbiology. ORCID: 0009-0001-6794-5346.

Providers – Flore Clinical

The Clinical Model

Three linked capabilities, one stratified decision path.

Partner Data Ingestion

Flore Clinical does not run a lab. We partner with microbiome testing firms and receive your patient's raw metagenomic data directly from the partner — no wet-lab work on our side.

Clinical Analysis

Partner data is analyzed and returned as a clinical-decision report — delivered to your provider portal for review.

Matched Formulation

Where indicated, a formulation matched to the patient profile. Repeat partner data tracks the change over time.

What the Portal Does for Your Practice

Order Intake

Patient completes a standardized intake — symptoms, GI, neuro, medications, diet — routed to your dashboard for review and authorization.

Partner Routing

We connect the order to your chosen microbiome testing partner. Raw data is returned to Flore for analysis — you stay in one portal throughout.

Stratified Reporting

Functional-state classification plus cohort-referenced deviation metrics and likely mechanism calls — clinical decision support, not a taxa list.

Formulation

Where indicated, a precision synbiotic matched to the patient profile. Dispensed as a clinical product under your authorization.

Longitudinal Follow-up

Repeat partner data at 3–6 months quantifies the mechanistic shift. Supports outcome tracking and payer documentation.

Under Your License

All patient contact, reports, and prescriptions flow through the provider account. Patients do not self-refer or self-prescribe.

Active Clinical Programs

Autism Spectrum Disorder

Diagnosis and targeted microbiome-mediated intervention for early-onset ASD, building on the 2024 mSystems pilot with ASU Biodesign (n=296 ASD + 123 controls, 3-month precision synbiotic).

Open the autism program →

Irritable Bowel Syndrome

Microbial signature characterization in IBS plus probiotic engraftment quantification. Anchored in the 2021 mSystems study with APC Microbiome Ireland (Paul Cotter).

Read the IBS evidence →

Who Flore Clinical Is

Flore Clinical is the clinical arm of Flore Inc., a C-corporation registered in Joliet, Illinois. The company is the successor to Sun Genomics (San Diego), whose 2021 IBS and 2024 autism precision-synbiotics studies established the mechanistic framework the clinic now deploys.

Founder and CEO Craig J. Rouskey, MSc (ORCID 0009-0001-6794-5346) trained in molecular microbiology, biochemistry, and immunology — with research experience at Amsterdam's Academisch Medisch Centrum, Saint Louis University School of Medicine, Life Technologies, and Novartis Biomedical Research. Peer-reviewed publications in Cancer Research (2013) and Vaccine (2007). Flore Clinical applies that translational-science foundation to the analysis layer of the gut microbiome.

How a Clinician Starts

From provider access to tracked outcomes — six steps, no inventory.

Step 1

Request provider access

Book a 15-minute onboarding call or apply via the concierge. Your license is verified and your account is activated with no setup fee.

Step 2

Onboard your portal

Add patients, set target systems, and review formulas before anything is manufactured.

Step 3

Test or import data

Send a microbiome sequencing kit or upload an existing report from an accredited lab.

Step 4

Review and approve

The Central Intelligence Engine proposes a formulation; adjust target systems and boosters and approve.

Step 5

Flore manufactures and ships

The formula is manufactured per patient as capsules or powder and shipped directly, with no inventory held by the practice.

Step 6

Track and iterate

Outcomes are recorded in the Microbiome EHR to inform the next cycle.

Flore Doesn't Run the Lab — Accredited Labs Do

A clean line of accountability between the diagnostic and the therapy.

Flore is the formulation and outcomes platform, not the testing laboratory. Sequencing is performed by independent CLIA-certified, CAP-accredited laboratories using shotgun metagenomic sequencing. That separation gives a clean line of accountability: an accredited diagnostic, and a platform that acts on it to compound and track therapy.

Your patient's raw metagenomic data is returned to Flore from the accredited partner lab — no wet-lab work happens on our side. Flore analyzes that data, proposes a matched formulation for your review, and follows outcomes across cycles.

No Inventory. No Manufacturing. No Logistics.

Your role stays clinical. Flore runs everything operational behind it.

No Inventory

You don't buy stock, hold lots, or forecast demand. Every formula is made-to-order, so there is nothing to expire on your shelf.

No Manufacturing

Flore handles GMP manufacturing of each per-patient synbiotic — capsules or powder, never liquid. No compounding burden falls on your practice.

No Logistics

Flore coordinates the sequencing lab and ships direct to your patient. No fulfillment, no packing, no shipping to run.

Provider Economics

A low monthly engagement threshold instead of a large buy-in.

Made-to-order means no upfront inventory purchase and no minimum stocking commitment to open an account. Flore Clinical uses a $250 minimum per 30-day cycle, with the first 30 days free for new provider accounts. Test and custom-formula pricing is published on the pricing page, and the Test-to-Treat pathway credits a patient's microbiome test toward their custom formula. Your concierge reviews current provider terms during onboarding.

See pricing →

White-Label & Clinic Programs

The provider portal is, in effect, a microbiome-testing-and-probiotic program that runs under your clinic's care — your patients, your protocols, your follow-up — with Flore supplying the lab coordination, the engine, and the manufactured formulas behind it. Practices wanting deeper co-branding or a tailored clinic program can scope that with the concierge.

The deliverable is never a re-labeled stock supplement; it's a formula compounded from each patient's data.

Provider FAQ

How do I start offering Flore to my patients?

Request provider access, get your license verified, and your portal activates. Then add patients, order or import a microbiome test, approve the engine's formula, and track outcomes. No inventory required.

Do I have to hold inventory or manufacture anything?

No. Every formula is manufactured per patient and shipped direct. The practice holds no stock and runs no fulfillment.

What does it cost to open a provider account?

No inventory buy-in. A $250-per-30-day-cycle minimum applies, with the first 30 days free for new accounts; test and formula pricing is on the pricing page.

Is this a white-label program?

It functions as a clinic-run microbiome-and-probiotic program under your care, but the product is compounded per patient from their data, not a re-labeled stock formula. Deeper co-branding can be scoped with the concierge.

Who runs the microbiome test?

Independent CLIA-certified, CAP-accredited laboratories using shotgun metagenomic sequencing. Flore formulates and tracks outcomes from that accredited data.

What form do formulas take?

Capsules or powder — never liquid.

What evidence supports it?

Nine years of longitudinal outcomes plus a 2024 pilot open-label study in mSystems (Phan et al.) — a pilot, not an RCT; two RCTs are underway.

Provider Onboarding

Provider access is reviewed case-by-case. Book a 15-minute onboarding call and we'll walk you through the portal, the partner-data workflow, and how onboarding works for your practice.

Schedule onboarding call →

Or email support@flore.com

Microbiome medicine. Practice-ready.