From nose to systemic disease: Nasal bacteria community alterations in nursery piglets infected with Streptococcus suis serotype 9.

Streptococcus suis (S. suis) causes systemic disease in piglets mainly at the nursery phase. In Brazil, an increase in outbreaks caused by serotype 9 strains has been a challenge in the last few years. As the nasal cavity is the first line of defense against respiratory agents, this study aimed to characterize the nasal microbiota of piglets systemically infected with S. suis. Nasal swabs were collected from two groups (healthy and diseased piglets) from three farms. After the DNA extraction, the V4 region of 16S rRNA was amplified and submitted to metabarcoding sequencing. A series of bioinformatic analyses was performed to investigate the diversity and composition of the nasal bacterial community and metabolic pathways associated with both groups. Histopathological and bacteriological examination confirmed that all diseased animals had systemic infection by S. suis serotype 9. The diseased group showed significantly lower alpha diversity and distinct beta diversity compared to the healthy group. The nasal microbiota of the diseased group was enriched by Streptococcaceae family and Streptococcus genus. Conversely, gut-associated bacteria were enriched in the healthy group (Bacteroidota, Lachnospiraceae, Prevotellaceae, and Ruminococcaceae). Four metabolic pathways were enriched in the diseased group (Phosphomannomutase, Phenylacetyl-CoA 1,2-epoxidase, Ferrochelatase, and Membrane alanyl aminopeptidase) and could be associated with S. suis infection. In conclusion, this study brings the identification of a nasal dysbiotic profile associated with systemic S. suis serotype 9 infection and an unexpected enrichment of gut-associated taxa in healthy pigs.