Distinct Stage Changes in Early-Life Colonization and Acquisition of the Gut Microbiota and Its Correlations With Volatile Fatty Acids in Goat Kids

Abstract

In livestock, a comprehensive understanding of the early-life establishment and acquisition of commensal gut microbiota allow us to develop better husbandry management operations and manipulate the gut microbiota for young animals, improving the efficiency of animal production. Here, we collected 123 microbial samples of 11 healthy goat kids and their mothers to investigate the colonization and acquisition of the gut microbiota and their correlations with volatile fatty acids (VFAs) in goat kids from birth to day 56. An age-dependent increasing and more homogeneous diversity were observed for the feces of goat kids. Overall, Firmicutes, Bacteroidetes, and Proteobacteria were the predominant phyla in the fecal microbiota of goat kids, but their relative abundance varied considerably with age. Accordingly, the colonization of the fecal microbiota in goat kids was divided into three distinct stages: newborn (day 0), non-rumination stage (days 7-21), and transition stages (days 28-56). LEfSe analysis revealed a total of 49 bacterial biomarkers that are stage-specific (LDA score > 3, P < 0.05). Significant Spearman correlations (P < 0.05) were observed between the abundances of several bacterial biomarkers and the VFA concentrations. Furthermore, a substantial difference in the fecal microbiota composition was present between 56-day-old goat kids and mothers, whereas there was a moderate difference in the rumen microbiota between them. Among four body sites (i.e., feces, oral cavity, vagina, and breast milk) of mothers, the maternal vaginal and breast milk microbiota were the major source of the fecal microbiota of goat kids in the first 56 days after birth, although their contributions decreased with age and unknown sources increased after day 28. In summary, we concluded that the gut bacterial community in goat kids after birth was mainly acquired from the maternal vagina and breast milk. Its colonization showed three distinct phases with dramatic shifts of composition mainly driven by age and diet changes. Our results provide a framework for a better understanding of the roles of the gut microbiota in young ruminants.

Keywords: acquisition; early life; establishment; fecal microbiota; goat; rumen microbiota; volatile fatty acid.

FIGURE 1

Alpha and beta diversities in all the microbial samples. (A) Boxplot for the Shannon diversity index in each microbial sampling group. The fecal microbiota of goat kids was sampled on days 0 (FE-D0), 7 (FE-D7), 14 (FE-D14), 21 (FE-D21), 28 (FE-D28), 42 (FE-D42), and 56 (FE-D56). The microbiota in the four body sites of mothers included oral cavity (OR-M), breast milk (MI-M), feces (FE-M), and vagina (VA-M). The rumen microbial samples were obtained from 56-day-old goat kids (RU-56) and mothers (RU-M). (B) Principal coordinates analysis of all 123 microbial samples using the unweighted UniFrac distance. (C) Analysis of similarity (ANOSIM) of the bacterial community structure among the feces of goat kids in different age groups and their mothers. High ANOSIM R values indicate well-separated groups. The statistical significance (q-value < 0.05) is indicated by ^∗. (D) The ANOSIM of the bacterial community structure among four body sites of mothers.

FIGURE 2

Bacterial community composition at different taxonomic levels in the feces of goat kids in all the seven age groups. (A) The bacterial community composition at the phylum level in feces of goat kids in the seven age groups. The top 10 bacterial phyla are represented separately with different colors, whereas the “Others” proportion represented other known phyla with low abundances and unassigned taxa. (B) Longitudinal changes of the Firmicutes/Bacteroidetes ratio in feces of goat kids across seven age groups. Significant differences among groups were analyzed by one-way ANOVA and Duncan’s tests. (C) The bacterial community composition at the genus level in feces of goat kids in seven age groups. The “Others” proportion represented other known genera with <1% average relative abundance across all samples and unassigned taxa. Different letters above the whiskers of bars indicate significantly different.

FIGURE 3

The identified biomarkers in the feces of goat kids at three growth stages and their correlations with VFAs. (A) The identified biomarkers in fecal samples of goat kids at three growth stages using LEfSe analysis (LDA score >3 and P < 0.05). (B) Spearman correlations between stage-associated biomarkers and VFAs in fecal samples of goat kids in seven age groups. The blue color represents a positive correlation between the biomarkers and VFAs and the red color represents a negative correlation. The statistical significance (P < 0.05) is denoted by ^∗.

FIGURE 4

Proportion of each fecal microbiota sample in goat kids estimated to originate from different maternal body sites. (A) The bacterial community composition at the genus level in the four body sites of mothers. The “Others” proportion represented other remaining genera with <1% average relative abundance across all samples and unassigned taxa. (B) The differential proportion analysis of five bacterial genera that were highly abundant in the feces of goat kids among the four body sites of mothers. Significant differences among groups were analyzed by one-way ANOVA and Duncan’s tests. (C) Dynamic contributions of different microbial sources to gut microbiota in goat kids from birth to day 56 using SourceTracker. Different letters above the whiskers of bars indicate significantly different.

FIGURE 5

Bacterial community compositions at different taxonomic levels in the rumen fluids of the 56-day-old goat kids and mothers. (A) The bacterial community composition at the phylum level in the rumen fluids of the 56-day-old goat kids and mothers. The “Others” proportion represented other remaining phyla with low abundances. (B) The bacterial community composition at the genus level in the rumen fluids of the 56-day-old goat kids and mothers. The “Others” proportion represented other remaining genera with <1% average relative abundance across all samples.