Methods and compositions relating to microbial treatment and diagnosis of disorders

Inventors

Cutcliffe, Colleen • Eid, John S. • Bullard, James H. • SCHICKLBERGER, Marcus F.

Assignees

Pendulum Therapeutics Inc

Abstract

The present disclosure provides methods, systems, compositions, and kits to address the need for microbiome-related treatment of health conditions and disease. The present disclosure provides for treatment of metabolic conditions using microbial compositions.

Core Innovation

The disclosure relates to microbial therapeutic compositions comprising microbes characterized by 16S rRNA sequences that have at least 97% sequence identity to a 16S rRNA sequence of Akkermansia muciniphila. The microbe in the composition is generated by growth on a plant-based culture medium, and the microbial approach is positioned within compositions that can include pharmaceutical formulation and delivery characteristics.

The document further describes plant-based culture media for generating such microbes, including growth media formulations with components such as PYGveg and/or other plant-based media components, yeast extract and hydrolysates, vitamins, salts, buffers, and additional ingredients, with anaerobic culturing used as described in the document. The purpose of the culture media description is to enable production of microbial strains and support desired characteristics in microbial preparations.

The document also describes pharmaceutical formulations and administration options for multi-strain consortia that can include Akkermansia muciniphila and other gut microbes, together with optional prebiotics such as inulin/starch. The described formulation options include oral enteric-coated forms for ileum/colon, lyophilized powders and tablets, and other routes, with additional discussion of stability testing and preclinical metabolic outcomes in diet-induced obese mice, including weight loss and glucose control.

Additionally, the document references microbiome testing and monitoring concepts, including a Complete Biome Test for strain-level profiling using long-read sequencing and machine-learning or algorithm-based scoring for disease status and therapy response, and refers to figures related to microbial preparation and analysis, including sequencing and strain classification, SCFA quantification, peak density, formulation stability, and metabolic study results.

Claims Coverage

The provided claim set identifies a central inventive focus on a microbe defined by 16S rRNA sequence identity to Akkermansia muciniphila and generated by growth on a plant-based culture medium. Dependent refinements add enteric coating, culturing-based generation, plant-based medium components including PYGveg, vitamins, salts, and a buffer, anaerobic culturing, and optional prebiotic selection from an enumerated group.

The claim coverage centers on a composition with a microbe having at least 97% 16S rRNA sequence identity to Akkermansia muciniphila and generated by growth on a plant-based culture medium. Additional claim features refine the composition with enteric coating, culturing conditions, plant-based medium components, and optional prebiotic selection.

Stated Advantages

Documented Applications