Patent Document ID: 10150982
Application ID: 14775722
Patent Flag: 1

Claim One:
1. A method for determining the effects of an agent on microbiota of a first subject, the method comprising: a) preparing a first reaction mixture that comprises a first portion of a sample from a first subject in contact with an agent and preparing a second reaction mixture that comprises a second portion of said sample, wherein said second reaction mixture does not comprise said agent, wherein said agent is an antibiotic, wherein said sample is from the gut of the first subject and/or comprises fecal or cecal material from the first subject, wherein said sample comprises microbiota of the first subject, and wherein the volumes of said first and second reaction mixtures are at most 1 milliliter (mL); b) obtaining an enumeration of the abundance of one or more microbial taxa in said first and second reaction mixtures, wherein said enumeration of the abundance comprises amplifying and sequencing DNA comprising the variable region of the 16S rRNA gene from said first and second reaction mixtures; c) determining the effects of the agent on the microbiota of the first subject, based on a comparison of the enumeration of the abundance of said one or more microbial taxa in said first and second reaction mixtures; d) performing a functionality assay on said first and second reaction mixtures, wherein said functionality assay comprises a cell viability assay, a barrier function assay, or a cytokine assay; e) determining the effects of the agent on the microbiota of the first subject, based on a comparison of the results of the functionality assays on the first and second reaction mixtures; and f) selecting said first subject and/or additional subjects for use of said agent in a method of treatment for a Clostridium difficile infection.