Pig nasal and rectal microbiotas are involved in the antibody response to Glaesserella parasuis

Abstract

Vaccination stands as one of the most sustainable and promising strategies to control infectious diseases in animal production. Nevertheless, the causes for antibody response variation among individuals are poorly understood. The animal microbiota has been shown to be involved in the correct development and function of the host immunity, including the antibody response. Here, we studied the nasal and rectal microbiota composition in association with the antibody response against the pathobiont Glaesserella parasuis. The nasal and rectal microbiotas of 24 piglets were sampled in two farms before vaccination and in one unvaccinated farm (naturally exposed to the pathobiont) at similar time. Microbiota composition was inferred by V3V4 16S rRNA gene sequencing and bioinformatics analysis, and the antibody response was quantified using the variation between the levels before and after vaccination (normalized per farm). Piglets with higher antibody responses showed more diverse nasal and rectal microbial communities compared to piglets with lower responses. Moreover, swine nasal core microbiota colonizers were associated with higher antibody levels, such as several members from Bacteroidales and Clostridiales orders and genera including Moraxella, Staphylococcus, Fusobacterium and Neisseria. Regarding taxa found in the rectal microbiota, associations with antibody responses were detected only at order level, pointing towards a positive role for Clostridiales while negative for Enterobacteriales. Altogether, these results suggest that the microbiota is associated with the antibody response to G. parasuis (and probably to other pathogens) and serves as starting point to understand the factors that contribute to immunization in pigs.

Keywords: Antibody response; Microbiota; Pig; Swine; Vaccination.

Fig. 1

Correlation between nasal microbiota alpha diversity and antibody response. Spearman correlation between alpha diversity of the nasal microbiota (measured by Shannon index) and the antibody response (ΔAb, measured as the difference between the level of antibodies after and before vaccination or equivalent times in non-vaccinated piglets) are shown (A) in both farms vaccinated against G. parasuis (yellow and green triangles), (B) in the unvaccinated farm (red spheres) and (C) in the three farms together. Each tendency line depicted in the graphs (dashed lines) was generated using geom_smooth function (ggplot2) using linear model (lm) as the method.

Fig. 2

Correlations with the antibody response and nasal microbiota at order level. Scatter plots show the relative abundance versus ΔAb, measured as the difference between the level of antibodies after and before vaccination or equivalent times in non-vaccinated piglets. Only orders found significant with Maaslin2 are shown. Each tendency line depicted in the graphs was generated using geom_smooth function (ggplot2) using linear model (lm) as the method.

Fig. 3

Alpha and beta diversity of nasal microbiota from good (turquoise) and bad (mauve) responders. (A) Alpha diversity measured by Chao1 and Shannon indexes. (B) Beta diversity estimated through Bray–Curtis dissimilarity index. The shapes indicate different farms.

Fig. 4

Nasal microbiota taxa discriminating good responders. (A) At order level. (B) At genus level. (C) Relative abundance of the orders identified as associated with good responders (A) in the nasal microbiota. The analysis was done using Lefse. No taxa discriminating bad responders were found.