Interpretive Summary: Salmonella causes the most bacterial foodborne disease and death in the U.S. - an estimated 1.4 million illnesses per year that result in approximately 400 deaths. Controlling Salmonella in our food chain is difficult because it can live in food-producing animals (such as pigs, cows and chickens) without causing disease. These animals are called Salmonella-carrier animals, and they shed Salmonella in their feces without being detected since they do not have noticeable clinical symptoms. On the farm and in controlled experimental infections, Salmonella carriage and fecal shedding in pigs can vary greatly. To identify factors that may influence Salmonella gastrointestinal (GI) colonization and fecal shedding in pigs, we examined the bacteria residing in the pig intestinal tract. This “community” of bacteria, referred to as commensal bacteria or the GI microbiota, was analyzed in pigs before and after inoculation with Salmonella. Three discoveries indicate a significant correlation between changes in the GI microbiota and Salmonella shedding in pigs. 1) Prior to inoculating the pigs with Salmonella, the “will-be” low Salmonella-shedder pigs (LS pigs) and “will-be” high Salmonella-shedder pigs (HS pigs) had significantly different microbiotas, suggesting that the swine GI microbiota may affect subsequent Salmonella shedding status. 2) Early in the 3-week study, the HS pigs showed dramatic changes in their microbial communities compared to the LS pigs; in fact, the microbial community of the LS pigs was not significantly different from the pigs that were not inoculated with Salmonella (NI pigs) during the first week of acute infection. 3) By day 21 post-inoculation, the GI microbiota of the HS and LS pigs were no longer significantly different from one another, but both were significantly different from the NI pigs, suggesting that Salmonella induced comparable changes in the swine GI microbiota regardless of shedding status. Investigating the dynamics between the GI microbiota and Salmonella shedding in pigs will assist our research program in identifying and developing on-farm Salmonella intervention strategies, thereby providing the public with a safer food supply.

Technical Abstract:
Controlling Salmonella in the food chain is complicated by the ability of Salmonella to sub-clinically colonize livestock. These Salmonella-carrier animals are a significant reservoir for contamination of naïve animals, the environment, and our food supply. On the farm and in experimental infections, Salmonella colonization, carriage, and shedding in pigs varies greatly. To investigate the dynamics between the porcine intestinal microbiota and Salmonella shedding in swine, we temporally profiled the microbial communities of pigs retrospectively classified as low and high Salmonella-shedders. Piglets were collectively housed, fed and challenged with 109 Salmonella enterica serovar Typhimurium. Salmonella was bacteriologically quantitated from swine feces, and total fecal DNA was isolated for 16S rRNA-based ecological profiling. Pyrosequencing analysis revealed that prior to inoculation, the microbial communities of “will-be” low-shedder (LS) pigs were significantly different from “will-be” high-shedder (HS) pigs at the species level (97% similarity). Following S. Typhimurium challenge, significant differences were observed in the microbial profiles between HS and LS pigs at 2 and 7 days post-inoculation (d.p.i.) (p less than 0.05); no significant differences were detected between LS and non-inoculated (NI) pigs at those times. A significant decrease in Prevotella abundance and significant increases in various genera (e.g. Oscillibacter, Catenibacterium, Xylanibacter) were observed in HS pigs at 2 d.p.i. compared to either LS or NI pigs (p less than 0.05). By 21 d.p.i., the microbial communities of HS and LS pigs were no longer significantly different from one another, but were both significantly different from NI pigs, suggesting a similar Salmonella-induced alteration in maturation of the swine intestinal microbiota regardless of shedding status. Microbial community changes during the 21-day study occurred in the abundance of community members (evenness); no significant differences were observed in the overall number of unique species (richness). The data indicate a correlation between shifts in the intestinal microbiota and Salmonella shedding status in pigs.