Dynamic Distribution of Gut Microbiota in Goats at Different Ages and Health States

Abstract

The importance of the gut microbiota (GM) of animals is widely acknowledged because of its pivotal roles in metabolism, immunity, and health maintenance. The level of health can be reflected by the dynamic distribution of GM. In this study, high-throughput sequencing of the bacterial 16S rRNA gene was used to compare the microbial populations from feces in healthy and diarrheic kids, which reflected the dynamic shift of microbiota in kids and investigated differences from adult healthy goats. Healthy kids and goats not only displayed higher species richness but also exhibited higher bacterial diversity than diarrheic kids based on the results of the operational taxonomic unit analysis, alpha diversity, and beta diversity. Firmicutes and Bacteroidetes were the most dominant phyla in all samples. At the genus level, the differences in diversity and abundance between diarrheic kids and the other two groups were gradually observed. In the diarrheic kid intestine, Bacteroides remained the dominant species, and the proportion of Clostridium_sensu_stricto_1 and Paeniclostridium increased, whereas Rikenellaceae_RC9_gut_group, Ruminococcaceae_UCG-005, and Christensenellaceae_R-7_group were significantly reduced. The results showed the differences of GM in diarrheic kids and healthy kids were significant while in kids and goats were not obvious. Differences in the composition of intestinal microbiota may not be the cause of diarrhea, and some changes of bacterial richness may guide our interpretation of diarrhea. This study is the first to investigate the distribution of GM in Boer goats with different ages and health states. Furthermore, this study will provide a theoretical basis for the establishment of a prevention and treatment system for goat diarrhea.

Keywords: Boer goats; diarrheic kids; gut microbiota; health states; high-throughput sequencing.

FIGURE 1

DNA sequence data and microbial diversity index analysis. (A) Chao1 index. (B) Shannon index. (C) Venn diagram. The numbers in the figure represent the unique or common OTUs of each group. (D) ANOSIM analysis. “Between” represents the difference between the three groups, the closer the R-value is to 1, the greater the difference between the groups. “C,” “G,” and “GF” represent the different three groups.

FIGURE 2

Sample feasibility analysis. Each curve represents a sample. (A) Rank-Abundance curve. The abscissa indicates the OTU (species) abundance order, and the ordinate corresponds to the relative abundance ratio of OTU (species). (B) Rarefaction curves depicting the effect of sequences on the number of OTUs identified.

FIGURE 3

Differences in bacterial community structures. (A,B) Principal Coordinate Analysis (PCoA) of bacterial community structures of the GM in the three sample groups. Each blue point represents each sample. The distance between the two points represents the difference of GM.

FIGURE 4

Microbial composition of different samples. Each bar represents the average relative abundance of each bacterial taxon within a group. (A) Taxa assignments at Phylum level. (B) Taxa assignments at Family level. (C) Taxa assignments at Genus level.

FIGURE 5

Differences in bacterial abundance between the groups. The left side of the graph shows the abundance ratios of different strains in two samples. The middle graph shows the difference in bacterial abundance within the 95% confidence interval. The rightmost values are the P-values of the significance test. (A) Differences in species abundance between groups G and C. (B) Differences in species abundance between groups G and GF.