Embodiments of the invention include methods and/or compositions for analysis of samples for C. difficile infection to determine whether or not an individual is at risk for having recurrent C. difficile infection or a CDI misdiagnosis. Methods include characterization of microflora composition from the gut, wherein alterations of the microflora gut composition are indicative of recurrence of infection. Methods include analysis of nucleic acids from the gut, such as 16S rRNA as being identifying of a particular bacteria in the analysis of bacterial populations of the gut.