Dynamic Change of Gut Microbiota During Porcine Epidemic Diarrhea Virus Infection in Suckling Piglets - PubMed (original) (raw)

Dynamic Change of Gut Microbiota During Porcine Epidemic Diarrhea Virus Infection in Suckling Piglets

Anni Huang et al. Front Microbiol. 2019.

Abstract

Porcine epidemic diarrhea (PED) is a disease that has a devastating effect on livestock. Currently, most studies are focused on comparing gut microbiota of healthy piglets and piglets with PED, resulting in gut microbial populations related to dynamic change in diarrheal piglets being poorly understood. The current study analyzed the characteristics of gut microbiota in porcine epidemic diarrhea virus (PEDV)-infected piglets during the suckling transition stage. Fresh fecal samples were collected from 1 to 3-week-old healthy piglets (n = 20) and PEDV infected piglets (n = 18) from the same swine farm. Total DNA was extracted from each sample and the V3-V4 hypervariable region of the 16S rRNA gene was amplified and sequenced using the Illumina MiSeq platform. Statistically significant differences were observed in bacterial diversity and richness between the healthy and diarrheal piglets. Principal coordinates analysis (PCoA) showed structural segregation between diseased and healthy groups, as well as among 3 different age groups. The abundance of Escherichia-Shigella, Enterococcus, Fusobacterium, and Veillonella increased due to dysbiosis induced by PEDV infection. Notably, there was a remarkable age-related increase in Fusobacterium and Veillonella in diarrheal piglets. Certain SCFA-producing bacteria, such as Ruminococcaceae_UCG-002, Butyricimonas, and Alistipes, were shared by all healthy piglets, but were not identified in various age groups of diarrheal piglets. In addition, significant differences were observed between clusters of orthologous groups (COG) functional categories of healthy and PEDV-infected piglets. Our findings demonstrated that PEDV infection caused severe perturbations in porcine gut microbiota. Therefore, regulating gut microbiota in an age-related manner may be a promising method for the prevention or treatment of PEDV.

Keywords: PEDV infection; SCFA-producing bacteria; core microbiota; gut microbiota; suckling piglets.

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Figures

FIGURE 1

FIGURE 1

Dynamic changes in gut microbial alpha diversity of PEDV-infected piglets determined by (A) Shannon index and (B) Chao1 index. Different letters above the bars denote a significant difference in alpha diversity index among the groups tested by paired sample Wilcoxon signed-rank test and adjusted for false discovery rate (FDR, p < 0.05).

FIGURE 2

FIGURE 2

Principal coordinates analysis (PCoA) was performed at the operational taxonomic unit (OTU) level based on unweighted UniFrac distance for all samples. Each group is represented in a different color and shape. (A) Scatterplot from PCoA showed a clear separation of diarrheal (D) from healthy (H) samples (p < 0.05, analysis of similarity (ANOSIM)); Principal coordinates 1 and 2 (PC1 and PC2) represent 18.99 and 11.61% of the variance, respectively (x and y axes). (B) PCoA scatterplot identified significant bacteria compositional difference among the three ages (p < 0.05, ANOSIM). Principal coordinates 1 and 2 (PC1 and PC2) represent 18.4 and 15.55% of the variance, respectively (x and y axes).

FIGURE 3

FIGURE 3

Relative abundance of sequences at the phylum and genus levels in diarrheal (D) and healthy (H) groups. (A) Collinear relation diagram between samples and bacterial phylum. (B) Heatmap analyses of abundant genera in each group. The heatmap plot depicts the relative percentage of each bacterial genus (variables clustering on the vertical-axis) within each group (horizon-axis clustering). The color of the spots in the right panel represents the relative values (lg) of the genera in each group.

FIGURE 4

FIGURE 4

Community bar-plot analysis shows relative abundance of sequences at (A) phylum and (B) genus levels in the three age groups. OTUs comprising less than 1% of the total abundance at both phylum and genus level are represented.

FIGURE 5

FIGURE 5

COG functional classification in (A) healthy and (B) diarrhea piglets. Boxes represent the interquartile range (IQR) between the first and third quartiles. The lines and spots inside the boxes represent the median and mean, respectively. Whiskers denote the lowest and highest values within 1.5 × IQR from the first and third quartiles, respectively. The ring above the box indicates the outliers.

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