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Characterization of microbial community structure during Salmonella shedding in beef cattle
Food animals are a major reservoir for zoonotic transmission of Salmonella through contaminated foods. In particular, asymptomatic carriers play an important role in Salmonella propagation in cattle and in contaminated foods because they are not easily identified and isolated. Minimizing the number of such animals would have a significant impact on lowering incidence of Salmonella contamination in beef in a production setting. Depending on the serotype and other unknown factors, Salmonella can cause either a symptomatic infection in cattle or the organism can colonize the animals asymptomatically, converting the animal to a carrier state where the organism can be dispersed quite efficiently throughout the environment. We hypothesize that competition between pathogens and non-pathogens for nutrient resources is important for limiting disease incidence and pathogen colonization. Therefore, competitive exclusion may be a viable strategy to reduce or control pathogenic Salmonella populations. However, our knowledge about the fecal microbial community is limited as 99% of the bacteria in the rumen or feces have not been cultured or isolated, hindering the opportunity to identify competitor. As a first step toward identifying competitor microbial species, we used selective microbiological culture methods and molecular methods to identify Salmonella high-shedders and low-shedders among 225 beef steers over 4 time periods. Based on shedding numbers 48 high-shedders (>103 Salmonella cfu/g of feces) and 48 low shedders (<102 cfu/g of feces) were phenotyped for gut microbial composition using 16s rRNA based amplicon sequencing. A total of ~10,000,000 high-quality DNA sequences generated through Ion Torrent semi-conductor based sequencing was used to evaluate microbial community composition. Bioinformatic analysis of the sequences from high-shedders and low-shedders indicated significant variations in microbiome composition between high and low shedders. It was revealed that members of the phylum Bacteroidetes were more abundant in the high-shedders, while members of the phylum Firmicutes were more abundant in the low-shedding animals. Furthermore, the analysis showed that 8 operational taxonomic units (OTUs) were significantly more abundant in low-shedders than in high-shedders. These OTUs represented candidate members of the microbiome that can be used as direct fed microbials (DFM) to reduce Salmonella shedding. These results provide new insight into bacterial populations that are present in the feces of Salmonella shedding cattle.
Keywords: 16S bacterial community, Salmonella, dysbiosis