Evaluation of fecal microbiota of late gestation sows in relation to pelvic organ prolapse risk

Abstract

Introduction: Sow mortality in the U.S. swine industry has increased in recent years, for which pelvic organ prolapse (POP) is a major contributor, accounting for 21% of all sow mortality. Dysbiosis of microbial communities has been associated with disease and reproductive dysfunction in several species, and previous studies have shown changes in vaginal microbiota in sows with increased risk for POP during late gestation. However, there is insufficient knowledge surrounding the potential relationship between fecal microbiota and POP in sows. Therefore, the study objective was to identify differences in sow fecal microbiota and determine if fecal and vaginal microbial communities are correlated in relation to POP risk.

Methods: Sows were evaluated for POP risk using an established perineal scoring system, with a perineal score (PS) of 1 (PS1) presuming little to no risk of POP to a PS of 3 (PS3) presuming high risk of POP. In the current study, 2,864 sows were scored during gestation week 15, and 1.0%, 2.7%, and 23.4% of PS1, PS2, and PS3 sows, respectively, subsequently experienced POP. Fecal swabs (n = 215) were collected between gestation days 108-115, DNA was extracted, and 16S rRNA gene amplicon sequencing libraries were analyzed using mothur, phyloseq and SAS in reference to PS and POP outcome. Additionally, co-occurrence networks were constructed using CoNet to compare fecal and vaginal microbiota from the same cohort of sows and identify correlations between different taxa.

Results: Differences in fecal community composition (PERMANOVA; P < 0.05), structure (alpha diversity measurements; P < 0.05), and 13 individual operational taxonomic units (OTUs) were revealed between PS1 and PS3 assigned sows. No differences in fecal microbiota were detected as a result of POP outcome. However, the abundances of several taxa were correlated across sample collection sites, suggesting the fecal and vaginal microbial communities may be related to one another.

Discussion: Collectively, fewer differences in the fecal microbiota exist in sows with differing risk for POP compared to the vaginal microbiota, suggesting the vaginal microbiome may be more relevant in relation to POP outcome, although correlations between fecal and vaginal communities may provide insight for strategies to combat POP.

Keywords: fecal microbiota; pelvic organ prolapse; reproduction; sow; vaginal microbiota.

Figure 1

Fecal microbial community comparisons. Canonical analysis of principal coordinates (CAP) demonstrating the maximum variation of beta-diversity between fecal microbiota communities. The CAP from sows with assumed low (PS1, n = 96) or high (PS3, n = 117) risk for pelvic organ prolapse (POP) during gestation week 15 (days 108–115) from two separate farms (A and B). Farm A, PS1 (APS1; light blue), Farm A, PS3 (APS3; dark blue); Farm B, PS1 (BPS1; light red) and Farm B, PS3 (BPS3; dark red). Statistical differences (p < 0.01) were detected in overall microbial communities between perineal score (PS) and Farm using PERMANOVA.

Figure 2

Alpha diversity of fecal microbiota in late gestation sows. Comparison of alpha diversity measurements species evenness (Simpson), richness (number of species observed, Chao1), and diversity (Shannon) across the variables within this study. (A) Alpha diversity measurements for fecal microbiota of sows with low (PS1; grey, n = 96) or high (PS3; black, n = 117) risk for pelvic organ prolapse (POP) at gestation week 15 (days 108–115) revealed significant differences (p ≤ 0.01) in community structure between samples regarding Chao species richness and the number of observed species. (B) Alpha diversity measurements from sows that subsequently did (Yes; black, n = 28) or did not (No; grey, n = 185) experience POP revealed no differences (p ≥ 0.66) in community structure. (C) Alpha diversity measurements for PS3 sows that subsequently did (Yes; black, n = 28) or did not (No; grey, n = 89) experience POP revealed no differences (p ≥ 0.14) in community structure. (D) Alpha diversity measurements for fecal microbiota compared to vaginal microbiota of all sows at gestation week 15. Species evenness (Simpson), richness (number of species observed, Chao1), and diversity (Shannon) were different (p < 0.01) between body sites. Significance is noted by ^***p ≤ 0.05.

Figure 3

Microbial community comparison analyzing the fecal and vaginal microbiota of sows in relation to POP. (A) Venn diagram illustrating the similarities and differences between all vaginal microbiota (Kiefer et al., 2021b, purple) and all fecal microbiota (current study, grey). A total of 9,647 OTUs were shared across studies and an additional 234 were unique to the vaginal communities while 1,128 were unique to the fecal communities. (B) Principal coordinates analysis (PCoA) demonstrating differences in beta diversity of all vaginal microbial communities (purple dots) of sows compared to the fecal microbial communities (grey dots). All points represent Bray Curtis dissimilarity measures for each sample. Significant differences (p < 0.01) were detected based on sample type (vaginal or fecal).

Figure 4

Co-occurrence networks for the fecal and vaginal microbiota of late gestation sows. Co-occurrence networks created using the CoNet (v 1.1.1) application with Cytoscape showing the significant (p < 0.05) correlations between the top 100 most abundant OTUs from the fecal and vaginal microbiota of late gestation sows. Nodes represent each individual OTU, with the color representing taxonomy and the shape representing body site (Square = Vaginal, Diamond = Fecal). Edges in green are positive correlations while those in red are negative. (A) Evaluated correlations with Clostridium species, has 33 nodes correlated, connected by 71 edges. (B) 8 nodes were connected by 5 edges between Streptococcus species. (C) Treponema species were connected by 44 edges and included 30 nodes. (D) Veillonella taxa had only 7 nodes connected by 5 edges.