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

Seres Therapeutics Inc

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 invention relates to a composition comprising a first species of isolated bacterium and a second species of isolated bacterium, together with a capsule that encapsulates the first species, the second species, or both. The first species is Lachnospiraceae_bacterium_5_1_57FAA and the second species is Clostridium orbiscindens. The bacterial species are defined by 16S rDNA sequence identity thresholds to specified reference sequences.

Lachnospiraceae_bacterium_5_1_57FAA comprises a 16S rDNA sequence that is at least 97% identical to the 16S rDNA sequence set forth in SEQ ID NO: 979. Clostridium orbiscindens comprises a 16S rDNA sequence that is at least 97% identical to SEQ ID NO: 548. The core concept links the defined two-species composition and the presence of a capsule to an inhibitory functional outcome against C. difficile.

The inhibition is measured by a CivSim assay, which is used as the stated basis for establishing that the first species and the second species are capable of inhibiting C. difficile growth. The claim set coverage further reflects dependent refinements that adjust CivSim inhibition performance, tighten 16S rDNA identity thresholds, and specify spore form and enteric coating.

Claims Coverage

The independent claim is focused on a two-species bacterial composition with capsule encapsulation, where both species are identity-defined by 16S rDNA similarity to specified SEQ ID references and are functionally defined by inhibiting C. difficile growth in a CivSim assay. The claim coverage includes 9 inventive features.

Overall, the claim set coverage centers on a capsule-encapsulated composition containing two specifically defined isolated bacterial species, each defined by 16S rDNA sequence identity to specified SEQ ID references, and functionally defined by inhibition of C. difficile growth measured by a CivSim assay. Dependent refinements further constrain the CivSim inhibition confidence interval, tighten 16S identity thresholds, specify spore form, and add enteric coating.

Stated Advantages

Documented Applications

No documented applications found