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HOSPITAL-BASED FMT PRODUCTION PLATFORM

Standardizing microbiota therapy through automated capsule production.

A hospital-based production platform designed to turn complex FMT preparation into a controlled, reproducible workflow.

THE CHALLENGE

FMT works through biology. Delivering it reliably requires engineering.

FMT preparation involves donor screening, testing, processing, encapsulation, storage and clinical handling.

Gut in Balance is developing a system designed to bring these steps into a standardized hospital workflow.

The FMT cycle: 1 donor screening, 2 integrated processing in a closed bag system, 3 encapsulation of filtered FMT, 4 standardized FMT capsules, 5 oral administration and clinical outcome — 80% clinical cure in rCDI using a single dosage.
HOW THE SYSTEM WORKS

From Donor Material toHospital-Ready FMT Capsules

Follow the workflow behind hospital-based microbiota capsule production.

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STAGE 01

Donor screening

Suitable stool donors are screened according to clinical guidelines — medical history, physical examination, infectious disease testing and microbiome and virome characterization.

STAGE 02

Collection & testing

Stool is collected and tested for pathogens and intestinal health markers.

STAGE 03

Controlled storage & release

Finished FMT capsules are stored in quarantine for 3 months while all clinical test results are reviewed. After approval, the capsules are released for clinical use.

STAGE 04

Automated processing

Stool is homogenized, mixed, filtered and dosed in a closed processing bag system and filled directly into capsules using a capsule filling machine.

STAGE 05

Hospital storage & use

Standardized FMT capsules are stored at −80 °C in hospital facilities and used for approved clinical indications.

COMPLETE WORKFLOW

One controlled workflow.

From donor material to ready-to-use capsules.

Illustration: a clinician screens a stool donor — medical history, physical examination, infectious disease testing and microbiome and virome characterization.
Illustration: stool collection and laboratory testing for bacterial and viral pathogens, parasites, blood-borne infections, additional safety screening and intestinal health markers.
Illustration: capsules held in quarantine storage at −80 °C for 3 months, review of test results, then release for clinical use.
Illustration: automated processing — processing bag, capsule filling, cooling and collection, and transfer to −80 °C storage.
Illustration: capsules stored at −80 °C in hospital facilities, selected for the clinical indication and taken orally by the patient under clinical supervision.
Overview: hospital FMT laboratory (donor screening, stool collection and testing, FMT capsule storage) and the automated FMT capsule production platform with consumables supplied by technology partners and long-term storage at −80 °C.
  1. 01

    Donor screening

    Suitable stool donors are screened according to clinical guidelines — medical history, physical examination, infectious disease testing and microbiome and virome characterization.

    Illustration: a clinician screens a stool donor — medical history, physical examination, infectious disease testing and microbiome and virome characterization.
  2. 02

    Collection & testing

    Stool is collected and tested for pathogens and intestinal health markers.

    Illustration: stool collection and laboratory testing for bacterial and viral pathogens, parasites, blood-borne infections, additional safety screening and intestinal health markers.
  3. 03

    Controlled storage & release

    Finished FMT capsules are stored in quarantine for 3 months while all clinical test results are reviewed. After approval, the capsules are released for clinical use.

    Illustration: capsules held in quarantine storage at −80 °C for 3 months, review of test results, then release for clinical use.
  4. 04

    Automated processing

    Stool is homogenized, mixed, filtered and dosed in a closed processing bag system and filled directly into capsules using a capsule filling machine.

    Illustration: automated processing — processing bag, capsule filling, cooling and collection, and transfer to −80 °C storage.
  5. 05

    Hospital storage & use

    Standardized FMT capsules are stored at −80 °C in hospital facilities and used for approved clinical indications.

    Illustration: capsules stored at −80 °C in hospital facilities, selected for the clinical indication and taken orally by the patient under clinical supervision.
  6. —

    One controlled workflow.

    From donor material to ready-to-use capsules.

    Overview: hospital FMT laboratory (donor screening, stool collection and testing, FMT capsule storage) and the automated FMT capsule production platform with consumables supplied by technology partners and long-term storage at −80 °C.
THE SYSTEM

More than equipment. A complete production system.

TECHNOLOGY

The production platform

Automated, closed processing and standardized capsule filling — designed for hospital FMT laboratories.

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WHY HOSPITAL-BASED PRODUCTION

Production, where clinical expertise already exists.

Standardization

Controlled, hygienic workflows designed to reduce contamination risk, support consistent product quality, and increase production capacity.

Hospital autonomy

Production takes place within hospitals, where clinical expertise and patient care come together. Our platform is designed to enable local production, reduce costs and make FMT treatment more accessible and affordable for patients.

Traceability

A traceable workflow from donor to patient. Donors are screened and recruited through the hospital, FMT capsules are produced and stored under controlled conditions, and patients are treated within the clinical setting. This supports documentation, quality control and traceability throughout the treatment pathway.

Scalability

Moving from manual preparation towards automated production enables increased production capacity to meet growing clinical demand. As FMT capsules show potential for use across a wider range of diseases, our platform is designed to help hospitals scale production while maintaining controlled workflows and consistent quality.

Long-term storage

Laboratory-validated storage stability for up to four years at −80°C. This supports long-term storage of finished FMT capsules under controlled conditions, helping hospitals manage inventory and plan treatment availability.

CLINICAL EVIDENCE

Built on clinicalexperience.

Selected clinical and research work behind hospital-based microbiota production. Published evidence is presented separately from platform claims.

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SELECTED PUBLICATIONS
Resistant bacteria · ScienceDirectDecolonisation of a multidrug-resistant Escherichia coli and a vancomycin-resistant Enterococcus faecium after intervention with faecal microbiota transplantation Anorexia nervosa · PubMedImpact of a single fecal microbiome transplantation in adult women with anorexia nervosa: an open-label feasibility pilot trial rCDI · PubMedThe Efficacy of Faecal Microbiota Transplant and Rectal Bacteriotherapy in Patients with Recurrent Clostridioides difficile Infection: A Retrospective Cohort Study Crohn’s disease · Medical Research Archives · ESMEDFecal Microbiota Transplantation promotes disease remission in a patient with active Crohn’s disease: A Case Report
1,000+
rCDI PATIENTS TREATED
500
CAPSULE TREATMENTS / YEAR
2020
HOSPITAL PRODUCTION SINCE
REGULATION · EU SoHO

Designed for a changingregulatory environment.

The EU SoHO Regulation (EU 2024/1938) will apply from 7 August 2027, introducing a harmonised European framework for the quality and safety of substances of human origin, including intestinal microbiota. Gut in Balance is developing hospital-based production infrastructure with standardised processes, traceability and controlled workflows at its core, designed to support hospitals as they prepare for the evolving regulatory landscape.

DONORSCREENED
MATERIALTESTED
PROCESSCONTROLLED
CAPSULESTANDARDIZED
STORAGEDEFINED
TRACEABILITYEND-TO-END
GIB-FMT · EUROSTARS PROJECT E93692026 — 2028

Developing the next generationof automated FMT capsule manufacturing.

Explore the GIB-FMT project
CONSORTIUM
  • 1Health Gut Inn Balance ApSDK
  • Medesign Ltd.IE
  • Hvidovre HospitalDK
  • Harro HöfligerDE
2026
2027
2028
OUR STORY
Hengameh Chloe Lauridsen, founder of Gut in Balance
Hengameh Chloe Lauridsen
Founder, M.Sc., Ph.D., Senior Researcher Scientist

Built from a questionthat started with a patient.

Personal experience with Crohn’s disease led our founder to a long-term scientific focus on microbiology, biotechnology and the intestinal microbiome.

That focus developed into practical work on hospital-based microbiota production — and into Gut in Balance.

Our story

Developed with clinical, industrial and research partners.

  • Hvidovre Hospital
  • Medesign
  • Harro Höfliger
  • Danish Life Science Cluster
  • Novo Nordisk Foundation
  • Erhvervsministeriet
  • Innovationsfonden
  • Enterprise Ireland
  • Eureka Eurostars
  • Turku University Hospital
  • Australian Red Cross Lifeblood

Bring standardizedmicrobiota productioninto the hospital.

Talk with Gut in Balance about the production platform, clinical collaboration or the GIB-FMT development project.

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