A cross-sectional study of the nasal and fecal microbiota of sows from different health status within six commercial swine farms

Abstract

Background: Cull sows are a unique population on swine farms, often representing poor producing or compromised animals, and even though recent studies have reported that the microbiome is associated with susceptibility to diseases, the microbiome of the cull sow population has not been explored. The main objective of this study was to investigate whether there were differences in fecal and upper respiratory tract microbiota composition for groups of sows of different health status (healthy, cull, and compromised/ clinical sows) and from different farms (1 to 6).

Methods: Six swine farms were visited once. Thirty individual fecal samples and nasal swabs were obtained at each farm and pooled by five across health status and farm. Samples underwent 16S rRNA gene amplicon sequencing and nasal and fecal microbiota were analyzed using QIIME2 v.2021.4.

Results: Overall, the diversity of the nasal microbiota was lower than the fecal microbiota (p < 0.01). No significant differences were found in fecal or nasal alpha diversity by sow's health status or by farm. There were significant differences in nasal microbial composition by farm and health status (PERMANOVA, p < 0.05), and in fecal microbiota by farm (PERMANOVA, p < 0.05), but not by health status. Lastly, at the L7 level, there was one differentially abundant taxa across farms for each nasal and fecal pooled samples.

Discussion: This study provided baseline information for nasal and fecal microbiota of sows under field conditions, and results suggest that farm of origin can affect microbial diversity and composition. Furthermore, sow's health status may have an impact on the nasal microbiota composition.

Keywords: Cull sows; Nasal and fecal microbiota; Swine; Swine health; Swine microbiota.

Figure 1. Sampling protocol with summarized sample processing steps (A) and relative locations (B) of the six participating farms.

Numbers represent farms 1 to 6. Actual map is not shown for confidentiality reasons.

Figure 2. Alpha diversity by farm and health status.

Microbial diversity (Shannon index) did not differ by farm or health status for pooled fecal samples and pooled nasal swabs. Median and quartiles are shown in the box and whiskers plots. Fecal samples were rarefied at 5600 reads and nasal samples were rarefied at 500 reads.

Figure 3. Nasal microbial communities (Bray Curtis) by (A) farm and (B) health status.

Nasal samples were rarefied to 500 reads and differed significantly by farm (PERMANOVA p = 0.002) and by health status (PERMANOVA p = 0.017). No pairwise comparisons were significant by farm. Healthy versus cull was significant (p = 0.033) by health status.

Figure 4. Fecal microbial communities (Bray Curtis) by (A) farm and (B) health status.

Fecal samples were rarefied to 5600 reads and differed significantly by farm (PERMANOVA p = 0.001) but not by health status (PERMANOVA p = 0.663). Pairwise comparisons were significant between all farms (p < 0.05) with the exception of farms 4 and 5 (p = 0.08) and farms 5 and 6 (p = 0.1). No significant differences were found based on health status (p = 0.663).

Figure 5. Microbial taxa bar plots at the phyla level in (A) nasal samples and (B) fecal samples.

Farm and health status of each sample is identified. All taxa with >1% abundance are included.