Question 1

What is Flore Clinical?

Accepted Answer

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.

Question 2

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

Accepted Answer

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.

Question 3

What makes Flore different from other clinical microbiome platforms?

Accepted Answer

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.

Question 4

What is a Microbiome EHR and why does it matter?

Accepted Answer

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.

Question 5

What is next-generation probiotic science?

Accepted Answer

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.

Question 6

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

Accepted Answer

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.

Question 7

What conditions does Flore Clinical treat?

Accepted Answer

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.

Question 8

Does Flore have published clinical evidence?

Accepted Answer

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.

Question 9

How does a clinician enroll their patients in Flore Clinical?

Accepted Answer

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 fees. 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.

Question 10

Is Flore available for pediatric patients with autism?

Accepted Answer

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.

Question 11

Who are Flore's research partners?

Accepted Answer

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.

Craig J. Rouskey, MSc

About Craig Rouskey

Credentials & expertise

Education

Role

Experience

Peer-reviewed publication

Work with the team behind Flore Clinical