Temporal Changes in Fecal Swine Microbiome are Predominantly Reflective of Salmonella Typhimurium Challenge Combined With Poor Sanitary Housing Conditions Despite Functional Amino Acid Supplementation

Joao Carlos Gomes-Neto^1,2,3*Antonio Diego Brandão Melo⁴Graziela Alves da Cunha Valini⁴Qinnan Yang^2,3Marllon José Karpeggiane De Oliveira⁴Danilo Alves Marçal⁴Pedro Righetti Arnaut⁴Ismael França⁴Cleslei Alisson Silva⁴Nate Korth^2,3Natasha Pavlovikj⁵Paulo Henrique Reis Furtado Campos⁶Henrique Gastmann Brand⁷John Htoo⁸Andrew Benson^2,3Luciano Hauschild⁴

• ¹Center for Food Animal Health, College of Food, Agricultural, and Environmental Sciences, The Ohio State University, Wooster, Ohio, United States
• ²Department of Food Science and Technology, College of Agricultural Sciences and Natural Resources, University of Nebraska-Lincoln, Lincoln, Nebraska, United States
• ³Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Delaware, United States
• ⁴Faculty of Agricultural and Veterinary Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
• ⁵Holland Computer Center, University of Nebraska-Lincoln, Lincoln, United States
• ⁶Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
• ⁷Evonik Brazil Ltda, São Paulo, Brazil
• ⁸Evonik Operations GmbH,, Hannu, Germany

Nutrition has a major impact on the gastrointestinal (GI) microbiome which can affect pig metabolism, nutrient absorption, biomolecule synthesis and bioavailability (bile acids, short-chain fatty acids, etc), colonization resistance to GI pathogens, and disease tolerance as a whole through immune maturation and regulation. The purpose of the study was to assess the impact of functional amino acid supplementation, in pigs allocated into GOOD vs. POOR sanitary condition (SC), on the fecal microbiome over time using 16S rRNA data. One hundred and twenty female growing pigs were randomly assigned in a 2 × 2 factorial arrangement (n = 30/treatment), consisting of two sanitary conditions (GOOD vs. POOR) and two diets (control (CN; 100% NRC, 2012) vs. supplemented with AA (Trp, Thr, and Met+Cys:Lys ratios increased to 20% higher than CN). Pigs were allocated to the GOOD SC group were sham-inoculated and barn was kept clean, whereas pig housed under POOR SC were challenged with Salmonella Typhimurium, in addition to the spreading fecal material from a commercial farm undergoing poor growth performance. Fecal samples were collected at day post-challenge (DPC) 0, 10, and 21, and extracted DNA were sequenced for 16S rRNA data analysis. Although alpha-diversity analysis demonstrated minor significant changes between groups, beta-diversity analysis demonstrated a significant separation between communities based on sanitary condition at DPC 21. Based on that, the most important taxa differentiating the two groups were based on the enrichment of the following taxa in the POOR group at DPC 21: Clostridium sensu stricto 1, Dorea, Intestinibacter, Lactobacillus, Romboutsia, Ruminococcus torques, Subdoligranulum, Terrisporobacter, and Turicibacter. Network and a correlation structural analysis further revealed a sub-structuring of the data with positive correlation formed in the POOR SC group: Sub-cluster 1 (Romboutsia, Turicibacter, Clostridium sensu stricto 1, Terrisporobacter, and Intestinibacter) and Sub-cluster 2 (Dorea, Subdoligranulum, Ruminococcus torques, Blautia, Holdemanella, and Solobacterium). In conclusion, temporal changes in fecal swine microbiome of growing pigs were reflective of S. Typhimirium challenge and poor sanitary status despite dietary surplus of functional amino acids.