Microbiota Compositions and Methods for Treating Disorders Inulin-Based Cryoprotectants for Viable Gut Bacteria Therapies

This patent from Australian microbiome therapy company BiomeBank covers formulations for preserving live gut bacteria through freeze-drying and long-term storage, enabling cultured microbiome therapies to reach patients without losing the microbial viability on which their effectiveness depends.

The Problem

The human gut microbiota contains trillions of microorganisms from hundreds of bacterial species, performing functions ranging from digestion of complex carbohydrates and vitamin synthesis to pathogen suppression and immune modulation. Disruption of this microbiota, a state called dysbiosis, is associated with a growing range of conditions including recurrent Clostridioides difficile infection, inflammatory bowel disease, and metabolic disorders. Cultured microbiome therapies — compositions of defined microorganisms administered to a patient to restore or augment the gut microbiota — are emerging as a treatment class for these conditions. The central manufacturing challenge is preserving live, functional microorganisms through the storage, transport, and delivery chain. Freeze-drying (lyophilization) is the preferred long-term preservation method, but the freeze-thaw process imposes severe mechanical and osmotic stresses on bacterial cells. Without effective cryoprotectants, cell viability drops substantially, reducing both the dose that reaches the patient and the therapeutic efficacy of the product. Prior cryoprotectant efforts have largely failed to maintain both the structural integrity and the functional activity of the complex microbial communities used in microbiome therapies.

What This Invention Does

BiomeBank’s invention provides compositions comprising at least one strain of a microorganism (bacteria, yeast, or archaea) together with an excipient that acts as a cryoprotectant during lyophilization and reconstitution. The key cryoprotectant identified is inulin, a prebiotic fructo-oligosaccharide, used alone or in combination with maltodextrin (a glucose polymer), dextran, pectin, sucrose, or trehalose. The patent specifies the concentration ranges that produce the best outcomes, with combinations such as inulin at 5% w/v with maltodextrin at 5% w/v appearing as preferred embodiments. The composition is characterised not only by its chemical composition but by physical properties including moisture content (below 5% w/v preferred) and mechanical parameters (Young’s Modulus and maximum stress at fracture), providing measurable quality criteria for the dried product. The compositions can be administered to patients to treat or prevent diseases associated with microbiota disruption.

Key Features

• Inulin as the central cryoprotectant. The patent claims inulin and its analogs, covering a structural range from short fructo-oligosaccharides (2 fructose units) through to long-chain variants (up to 500 units), accommodating commercial inulin sources of varying chain length and providing broad coverage of the chemical space.
• Defined combination excipients. Eleven specific excipient combinations are described, including inulin alone, inulin/maltodextrin, inulin/dextran 70k, inulin/pectin, inulin/sucrose, inulin/trehalose, and three-component mixtures, each tested for cryoprotective performance.
• Physical property specifications. Claims covering Young’s Modulus (between 2 and 4 preferred) and maximum stress at fracture (20-30 kPa preferred) for the lyophilized cake provide objective quality attributes for manufacturing and regulatory purposes, translating biological efficacy into measurable physical metrics.
• Lyophilized and liquid dosage forms. Both freeze-dried and liquid formulations are claimed, giving flexibility in dosage form development and delivery route.
• Broad therapeutic application. The compositions are positioned for treating diseases and disorders associated with gut microbiota disruption, encompassing the range of conditions for which microbiome therapies are in clinical development.

Who Is Behind It?

The applicant is COST-BRY Pty Ltd, trading as BiomeBank, an Adelaide-based Australian biopharmaceutical company founded by gastroenterologist Dr Samuel Paul Costello. BiomeBank is one of Australia’s leading microbiome therapy companies, operating Australia’s first accredited stool bank and developing standardised cultured microbiome therapies for conditions including recurrent C. difficile infection and ulcerative colitis. The named inventors are Samuel Paul Costello, Alice Sarah Day, Garrett Grant Heiman, Reuben Zachary Wheeler, Sarah Haylock-Jacobs, and Remy Blair Young. This application is a divisional of AU 2024234064. The Australian patent attorney is FB Rice in Sydney.

Why It Matters

Microbiome therapeutics are moving from experimental to mainstream. The approval of faecal microbiota transplant-derived products for recurrent C. difficile in the United States has opened the path for a new class of regulated live biotherapeutic products. The manufacturing bottleneck for these products is precisely what this patent addresses: stable, long-shelf-life preparations that can be distributed through standard pharmaceutical supply chains rather than requiring fresh preparation and cold-chain logistics for every patient. For Australia, where BiomeBank is already operating a stool bank and supplying hospitals, this patent protects a key element of the company’s product manufacturing platform. As the microbiome therapeutics market grows globally, intellectual property around preservation formulations will be central to the competitive positioning of Australian-origin products against international entrants.

Related Concepts

BiomeBank’s cryoprotection work addresses one of the central manufacturing challenges for live biotherapeutic products – maintaining microbial viability through freeze-drying and storage. The use of inulin, a prebiotic polysaccharide, as a cryoprotectant reflects a growing interest in excipients that may also benefit the gut microenvironment after dosing.

The broader context is the emergence of gut microbiome therapeutics as a regulated pharmaceutical class, following early approvals for faecal microbiota transplant-based treatments for recurrent Clostridioides difficile infection. Stable, shelf-distributed formulations are a prerequisite for commercial-scale deployment of this new generation of microbial medicines.

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AU 2026201833 was published in the Australian Official Journal of Patents on 2 April 2026 and is open for public inspection. Patent applications represent inventions that are sought to be protected and do not necessarily reflect commercially available products.