A comparative study of the bacterial diversity and composition of nursery piglets’ oral fluid, feces, and housing environment

Abstract

The oral cavity is the portal of entry for many microorganisms that affect swine, and the swine oral fluid has been used as a specimen for the diagnosis of several infectious diseases. The oral microbiota has been shown to play important roles in humans, such as protection against non-indigenous bacteria. In swine, studies that have investigated the microbial composition of the oral cavity of pigs are scarce. This study aimed to characterize the oral fluid microbiota of weaned pigs from five commercial farms in Brazil and compare it to their respective fecal and environmental microbiotas. Bacterial compositions were determined by 16S rRNA gene sequencing and analyzed in R Studio. Oral fluid samples were significantly less diverse (alpha diversity) than pen floor and fecal samples (P < 0.01). Alpha diversity changed among farms in oral fluid and pen floor samples, but no differences were observed in fecal samples. Permutational ANOVA revealed that beta diversity was significantly different among sample types (P = 0.001) and farms (P = 0.001), with separation of sample types (feces, pen floor, and oral fluid) on the principal coordinates analysis. Most counts obtained from oral fluid samples were classified as Firmicutes (80.4%) and Proteobacteria (7.7%). The genera Streptococcus, members of the Pasteurellaceae family, and Veillonella were differentially abundant in oral fluid samples when compared to fecal samples, in which Streptococcus was identified as a core genus that was strongly correlated (SparCC) with other taxa. Firmicutes and Bacteroidota were the most relatively abundant phyla identified in fecal and pen floor samples, and Prevotella_9 was the most classified genus. No differentially abundant taxa were identified when comparing fecal samples and pen floor samples. We concluded that under the conditions of our study, the oral fluid microbiota of weaned piglets is different (beta diversity) and less diverse (alpha diversity) than the fecal and environmental microbiotas. Several differentially abundant taxa were identified in the oral fluid samples, and some have been described as important colonizers of the oral cavity in human microbiome studies. Further understanding of the relationship between the oral fluid microbiota and swine is necessary and would create opportunities for the development of innovative solutions that target the microbiota to improve swine health and production.