Characterization of fecal microbiota from a Salmonella endemic cattle herd as determined by oligonucleotide fingerprinting of rDNA genes

The gastrointestinal (GI) tract microbiota is composed of complex communities. For all species examined thus far, culture and molecular analyses show that these communities are highly diverse and individuals harbor unique consortia. The objective of the current work was to examine inter-individual diversity of cattle fecal microbiota and determine whether Salmonella shedding status correlated with community richness or evenness parameters. Using a ribosomal gene array-based approach, oligonucleotide fingerprinting of ribosomal genes (OFRG), we analyzed 1440 16S genes from 19 fecal samples obtained from a cattle herd with a history of salmonellosis. Identified bacteria belonged to the phyla Firmicutes (53%), Bacteroidetes (17%), and Proteobacteria (17%). Sequence analysis of 16S rDNA gene clones revealed that Spirochaetes and Verrucomicrobia were also present in the feces. The majority of Firmicutes present in the feces belonged to the order Clostridiales, which was verified via dot blot analysis. β-Proteobacteria represented 1.5% of the bacterial community as determined by real-time PCR. Statistical analysis of the 16S libraries from the 19 animals indicated very high levels of species richness and evenness, such that individual libraries represented unique populations. Finally, this study did not identify species that prevented Salmonella colonization or resulted from Salmonella colonization.