PSVI-7 A traceable signature for a recovery microbiome composition after a dysbiosis caused by a sanitary challenge in pigs

Abstract Recent insights continue to point to a causal role of the gastrointestinal (GI) microbiome in digestion, nutrient absorption, and host metabolism. The GI microbiome may be a frequent target of perturbation since some challenges (i.e., high density, temperature and air quality fluctuations, presence of endemic enteric pathogens) faced by pigs may altogether create a spectrum of contrasting sanitary conditions. Therefore, our study investigated the influence of increased dietary tryptophan, threonine, and methionine supplementation in pigs from “good” vs. “poor” sanitary conditions, on the GI microbiome over time. For that purpose, female growing pigs were randomly assigned in a 2 × 2 factorial design (n = 30/treatment), consisting of two sanitary conditions (“good” vs. “poor”) and two diets control (CN) vs. supplemented with specific amino acids (Trp, Thr, and Met+Cys:Lys ratios increased to 20% greater than CN. Pigs allocated to the “good” sanitary condition treatment were sham-inoculated with pure BHI broth and the barn was cleaned twice a day and disinfected once a week. Whereas, “poor” sanitary condition comprised of all pigs being inoculated with 2 x 109 CFU of Salmonella Typhimurium (ST), in addition to spreading fecal material from a commercial farm under sanitary challenge, followed by leaving the barn uncleaned throughout the study (poor + ST). Fecal samples (n = 11) were collected at day post-challenge (DPC) 0, 10, and 21, and were sequenced for 16S rRNA data analysis of community diversity (alpha and beta) and taxonomic changes over time. Our results demonstrated that both alpha (Shannon and Simpson) and beta diversity metrics were significantly altered at DPC 21 by differentiating “good” vs “poor + ST” treatments, despite amino acids supplementation in the diet. Bacterial taxonomic analysis further captured community level alterations by a marked dysbiosis occurring on pigs allocated under “poor + ST” sanitary conditions. “ST + poor” sanitary conditions altered community structure as measured by co-occurrence networks, which was particularly pointed out at DPI 21. Specifically, Clostridium sensu stricto 1, Intestinibacter, Rombustsia, Terrisporobacter, and Megasphaera were five taxa between others co-enriched in fecal samples from pigs allocated under “poor + ST” sanitary conditions at DPC 21. These putative SCFA-producing bacteria were positively straighter correlated between them (Figure 1), which suggests a traceable signature for a recovery microbiome composition after a dysbiosis. In conclusion, temporal changes in fecal swine microbiome of growing pigs may be reflective of sanitary status despite dietary supplementation of specific amino acids.