Synergistic bacterial compositions and methods of production and use thereof
Inventors
Henn, Matthew R. • von Maltzahn, Geoffrey • D'Onofrio, Anthony Mario • Litcofsky, Kevin Daniel • Berry, David Arthur • Cook, David N. • Afeyan, Noubar B. • Aunins, John Grant
Assignees
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Publication Number
US-11389490-B2
Publication Date
2022-07-19
Expiration Date
Abstract
Provided are therapeutic compositions containing Ecobiotic™ populations for prevention, treatment and reduction of symptoms associated with a dysbiosis of a mammalian subject such as a human.
Core Innovation
The disclosed Ecobiotic™ bacterial spore/vegetative compositions include synergistic combinations of isolated bacterial species for preventing and treating gastrointestinal dysbiosis and for reducing growth and colonization of gastrointestinal pathogens, including Clostridium difficile. The compositions are defined using spore-forming bacterial fractions and specific bacterial mixture designs, including binary, ternary, and multi-type combinations, with defined selection and combining principles for the bacterial species.
The bacterial species are specified using 16S rRNA/16S rDNA identity requirements tied to SEQ ID NOs from a SEQUENCE LISTING. In the provided independent claim coverage, the composition includes Clostridium innocuum and Clostridium orbiscindens, wherein Clostridium orbiscindens comprises a 16S rDNA sequence that is at least 97% identical to SEQ ID NO: 548. The document further ties additional species identity requirements to respective SEQ ID NOs.
The document frames inhibitory performance using an assay framework, including a CivSim assay concept, and evaluates inhibitory combinations with quantified confidence-based ranking. The compositions and related disclosures further include co-administration with antibiotics and prebiotics, and formulation features such as lyophilized spore populations and enteric coatings, together with kit-based presentations.
Claims Coverage
The provided independent claims cover three inventive directions: treating recurrence of Clostridium difficile infection, treating dysbiosis, and producing a bacterial composition by combining two isolated species with specified 16S rDNA identity for Clostridium orbiscindens. Across these independent claims, the inventive content is centered on a two-species Ecobiotic™ bacterial composition defined by 16S rDNA sequence identity, and on the indicated therapeutic use or production action.
Treating or preventing recurrence of Clostridium difficile infection using a two-species isolated bacterium composition defined by 16S rDNA identity
A method of treating or preventing recurrence of Clostridium difficile infection in a subject in need thereof, comprising administering to the subject a composition comprising a first species of isolated bacterium and a second species of isolated bacterium, wherein the first species is Clostridium innocuum and the second species is Clostridium orbiscindens, wherein the Clostridium orbiscindens comprises a 16S rDNA sequence that is at least 97% identical to SEQ ID NO: 548.
Treating dysbiosis using a two-species isolated bacterium composition defined by 16S rDNA identity
A method of treating a dysbiosis in a subject in need thereof, comprising administering to the subject a composition comprising a first species of isolated bacterium and a second species of isolated bacterium, wherein the first species is Clostridium innocuum and the second species is Clostridium orbiscindens, wherein the Clostridium orbiscindens comprises a 16S rDNA sequence that is at least 97% identical to SEQ ID NO: 548.
Producing a bacterial composition by combining two isolated bacterium species defined by 16S rDNA identity
A method of producing a bacterial composition, comprising combining a first species of isolated bacterium and a second species of isolated bacterium, wherein the first species is Clostridium innocuum and the second species is Clostridium orbiscindens, wherein the Clostridium orbiscindens comprises a 16S rDNA sequence that is at least 97% identical to SEQ ID NO: 548.
The independent claim set provided centers on administering or producing a composition comprising Clostridium innocuum and Clostridium orbiscindens, with Clostridium orbiscindens defined by a 16S rDNA sequence identity of at least 97% relative to SEQ ID NO: 548. The recurrence-focused claim further targets recurrence of C. difficile infection, while the dysbiosis-focused claim targets dysbiosis, and the production claim targets producing the specified composition.
Stated Advantages
Treating or preventing recurrence of Clostridium difficile infection.
Treating dysbiosis.
Reducing growth and colonization of gastrointestinal pathogens, including C. difficile.
Documented Applications
Preventing and treating GI dysbiosis in a subject.
Treating or preventing recurrence of Clostridium difficile infection in a subject.
Reducing growth and colonization of GI pathogens, including C. difficile.
Producing a bacterial composition by combining Clostridium innocuum and Clostridium orbiscindens defined by 16S rDNA identity.
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