Analysis of Fecal Microbial Changes in Young Calves Following Bovine Rotavirus Infection

Abstract

The objective of the present study was to identify changes in fecal microbiota and predict the functional features of healthy calves and those infected with rotavirus over time. Six Holstein calves (average body weight 43.63 ± 1.19 kg, age-matched within 5-7 d) were randomly selected and distributed into two groups which contained three calves each. Fecal samples were taken 3 days before inoculation and on days 1 and 7 post-inoculation. The 16S rRNA gene amplicon sequencing was performed. Bacterial diversity tended to decrease in the rota group, as indicated by the alpha (evenness, p = 0.074 and Shannon, p = 0.055) and beta (Bray-Curtis dissimilarity, p = 0.099) diversity at 1 day post-inoculation. Differences in the bacterial taxa between healthy and rota-infected calves were detected using a linear discriminant analysis effect size (LDA > 2.0, p < 0.05). Rota calves had a higher abundance of certain bacterial taxa, such as Enterococcus, Streptococcus, and Escherichia-Shigella, and a lower abundance of bacteria that contribute to the production of short-chain fatty acids, such as Alistipes, Faecalibacterium, Pseudoflavonifractor, Subdoligranulum, Alloprevotella, Butyricicoccus, and Ruminococcus, compared to the healthy calves. The observed changes in the fecal microbiota of the rota-infected group compared to the healthy group indicated potential dysbiosis. This was further supported by significant differences in the predicted functional metagenomic profiles of these microbial communities. We suggest that calves infected with bovine rotavirus had bacterial dysbiosis, which was characterized by lower diversity and fewer observed genera than the fecal microbiota of healthy calves.

Keywords: bovine rotavirus; fecal microbiota; holstein calves; metataxonomic.

Figure 1

Change in the fecal bacterial community structure in Holstein calves. PCoA plot was generated based on (A) Bray–Curtis dissimilarity and (B) Weighted UniFrac distance in fecal bacterial communities determined via 16S rRNA gene amplicon sequencing for respective ages; 3 days before inoculation, 1 day post-inoculation, and 7 days post-inoculation. Individual points in each plot represent individual animals. Colors indicate the groups; healthy (orange) and rota (blue). p values were calculated using PERMANOVA test (n = 9999).

Figure 2

Fecal bacterial compositional profiles of Holstein calves. (A) Relative abundance of major bacteria phyla (relative abundance ≥ 0.1% in more than 50% animals) for all individuals. (B) Relative abundance of major bacteria genera (relative abundance ≥ 0.1% in more than 50% animals) for all individuals.

Figure 3

Venn diagrams showing the genera of fecal microbiota shared between the healthy and rota groups. (A) 3 days before inoculation, (B) 1 day post-inoculation, (C) 7 days post-inoculation, (D) Healthy group, and (E) Rota group.

Figure 4

Differentially abundant fecal microbial taxa between healthy and rota groups detected using LEfSe with an LDA effect size > 2. Only classified prevalent taxa (each detected in at least 50% of the samples) were visualized. Data points represent individual animals. LDA: linear discriminant analysis; LEfSe: LDA effect size.

Figure 5

Differentially abundant KEGG pathways between healthy and rota groups detected using LEfSe with an LDA effect size > 2. Only classified prevalent taxa (each detected in at least 50% of the samples) were visualized. KEGG: Kyoto Encyclopedia of Genes and Genomes; LDA: linear discriminant analysis; LEfSe: LDA effect size.