Porcine circovirus type 3 (PCV3) is a novel porcine circovirus species associated with several diseases such as porcine dermatitis and nephropathy syndrome (PDNS)-like clinical signs, reproductive failure, cardiac pathologies, and multisystemic inflammation in piglets and sows. Currently, many studies have focused on the interaction between microbiota composition and disease progression. However, dynamic changes in the composition of the gut microbiota following PCV3 infection are still unknown. In this study, alterations in gut microbiota in PCV3-inoculated and sham-inoculated piglets were analyzed at various time points [7, 14, 21, and 28 days post-inoculation (dpi)] using the Illumina MiSeq platform. Using principal coordinate analysis, obvious structural segregations were observed in bacterial diversity and richness between PCV3- and sham-inoculated piglets, as well as at the four different time points. The abundance of gut microbiota exhibited a remarkable time-related decrease in Clostridium_sensu_stricto_1 in PCV3-inoculated piglets. In addition, significant differences were observed in functional classification based on cluster of orthologous groups assignment, between PCV3- and sham-inoculated piglets. Our findings demonstrated that PCV3 infection caused dynamic changes in the gut microbiota community. Therefore, regulating gut microbiota community may be an effective approach for preventing PCV3 infection.

猪圆环病毒3型（PCV3）是一种新型猪圆环病毒，与多种疾病有关，如猪皮炎和肾病综合征（PDNS）的临床体征，生殖衰竭，心脏病理以及仔猪和母猪的多系统性炎症。当前，许多研究集中于微生物群组成与疾病进展之间的相互作用。但是，PCV3感染后肠道菌群组成的动态变化仍然未知。在这项研究中，使用Illumina MiSeq平台在不同时间点[接种后7、14、21和28天（dpi）]分析了PCV3接种和假接种的仔猪的肠道菌群变化。使用主坐标分析，在PCV3和假接种的仔猪之间以及在四个不同的时间点，在细菌多样性和丰富度方面观察到明显的结构性分离。肠道菌群的丰富度显示出与时间有关的显着下降Clostridium_sensu_stricto_1在接种PCV3的仔猪中。此外，PCV3和假接种的仔猪之间在基于直系同源基团分配簇的功能分类中观察到显着差异。我们的发现表明，PCV3感染引起肠道菌群群落的动态变化。因此，调节肠道菌群可能是预防PCV3感染的有效方法。