Alteration of the pig intestinal microbiome when vaccinated against or inoculated with porcine circovirus 2 using a multivariate analysis model

This study assessed the effect of porcine circovirus 2 (PCV2) vaccination compared with inoculation on the intestinal microbiome of piglets. Ninety-six weaned barrows (age 27 to 40 d and 7.1 kg BW) were either vaccinated for PCV2 (VAC) or inoculated with PCV2 (PCV) on d 0. Fecal samples were collected at d 0, 14, and 28 (n = 6/treatment). Microbial community structure was analyzed using Ion Torrent technology by sequencing the 16S rRNA gene. No differences (P > 0.10) were detected at the genus level between d 0 samples. Prevotella spp. decreased from d 14 to 28 in VAC pigs (P < 0.05) and was reduced compared with PCV at d 28 (P < 0.10). A core set of 383 operational taxonomic units (OTU), present in >80% of samples, were analyzed using a multivariate analysis by linear models. A total of 58 OTU were correlated with at least 1 phenotypic trait or fixed effect, that is, BW, day, or PCV status (P < 0.05, q < 0.05). Of these, 15 OTU were determined to be of the genus Prevotella. Abundances of Prevotella stercorea (r = 0.21) and Solitalea koreensis (r = 0.41) were shown to be associated with serum IgG concentration, whereas Intestinimonas butyriciproducens (r = –0.07) and Oscillibacter valericigenes (r = –0.09) were inversely associated with serum IgM concentration. Presence of P. stercorea (r = –0.11) was negatively associated with VAC pigs by d 28, whereas Ruminiclostridium ther-mosuccinogenes (r = 0.11) presence increased. These data suggest that Prevotella spp. flourish during a PCV challenge, irrespective of PCV status (vaccinated or inoculated), but decreased sooner in VAC pigs than PCV pigs. However, an age-dependent shift in the microbiome may also play a role.