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.

For Providers

Staging draft — proposed rewrite of the Providers page. Not published.

For licensed clinicians

Flore Clinical lets you prescribe a personalized probiotic with the same confidence you'd want from any clinical decision: an individually manufactured synbiotic, chosen by an intelligence engine built on nine years of longitudinal outcome data (18,000+ patients, 200+ conditions), reviewed by you before anything is made, and tracked over time in a clinical-grade record. It answers the question clinicians actually ask about probiotics — how do I know this will work for my patient? — and removes the operational barriers that usually keep a custom-supplement program out of a practice.

The clinical model

Flore is a compounding platform, not a catalog. A patient's microbiome data — from shotgun metagenomic sequencing run by an accredited lab — drives a formula compounded specifically for them, typically several strains at meaningful CFU dosing plus prebiotics, delivered as capsules or powder (never liquid). Multi-test context (microbiome, bloodwork, urinalysis) can be imported, and outcomes are followed across cycles so each formula is informed by the last.

How to start (step by step)

Request provider access — book a 15-minute onboarding call or apply via the concierge. License verified, account activated, no setup fee.
Onboard your portal — add patients, set target systems, and review formulas before manufacturing.
Test or import — send a microbiome kit or upload an existing accredited-lab report.
Review and approve — the Central Intelligence Engine proposes a formulation; you adjust systems and boosters and approve.
Flore manufactures and ships — made per patient, shipped direct, no inventory on your side.
Track and iterate — outcomes recorded in the Microbiome EHR inform the next cycle.

No inventory, no manufacturing, no logistics

You don't buy stock, hold lots, or ship product. Nothing to forecast, nothing to expire, no fulfillment to run. Your role stays clinical — identify candidates, set target systems, approve formulas — while Flore handles sequencing-lab coordination, GMP manufacturing, and direct-to-patient shipping.

Provider economics

Made-to-order means no upfront inventory purchase and no minimum stocking commitment to open an account. Flore Clinical uses a low monthly engagement threshold instead of a large buy-in: a $250 minimum per 30-day cycle, first 30 days free for new provider accounts. Test and custom-formula pricing is published on the pricing page; 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 and 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.

Flore doesn't run the lab — accredited labs do

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

Active clinical programs

Programs span common GI presentations (IBS, IBD, SIBO, dysbiosis) and the microbiota–gut–brain axis. Flore's autism work is published as a 2024 pilot open-label study in mSystems (Phan et al.) — a pilot study, not a randomized controlled trial — reporting increased microbiome diversity and improved GI symptoms; two randomized controlled trials are underway. Review the evidence →

Who Flore Clinical is

Flore Inc. acquired Sun Genomics in 2026 and operates the clinical channel for licensed providers. The platform is built on nine years of paired sequencing-and-outcome data, headquartered in Joliet, IL.

Provider onboarding

Book a 15-minute onboarding call through the concierge to verify your license and activate your portal. Talk to us →

Frequently asked questions

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.

Flore Clinical is intended for use by licensed healthcare providers.