Characterization of the Rumen Microbiota and Volatile Fatty Acid Profiles of Weaned Goat Kids under Shrub-Grassland Grazing and Indoor Feeding

Abstract

In this study, we conducted comparative analyses to characterize the rumen microbiota and volatile fatty acid (VFA) profiles of weaned Nanjiang Yellow goat kids under shrub-grassland grazing (GR), shrub-grassland grazing and supplementary feeding (SF), and indoor feeding (IF) systems. We observed significant differences (p < 0.05) in the concentrations of total VFA and the proportions of acetate and butyrate in the rumen fluid among the three groups, whereas the proportions of propionate and the acetate/propionate ratio did not differ substantially. Alpha diversity of the rumen bacterial and archaeal populations in the GR and SF kids was significantly higher (p < 0.05) than that in the IF goat kids, and significant differences (p < 0.05) in similarity were observed in the comparisons of GR vs. IF and SF vs. IF. The most predominant bacterial phyla were Bacteroidetes and Firmicutes across the three groups, and the archaeal community was mainly composed of Euryarchaeota. At the genus and species levels, the cellulose-degrading bacteria, including Lachnospiraceae, Ruminococcaceae and Butyrivibrio fibrisolvens, were abundant in the GR and SF groups. Furthermore, 27 bacterial and 11 unique archaeal taxa, such as Lachnospiraceae, Butyrivibrio fibrisolvens, and Methanobrevibacter ruminantium, were identified as biomarkers, and showed significantly different (p < 0.05) abundances among the three groups. Significant Spearman correlations (p < 0.05), between the abundances of several microbial biomarkers and the concentrations of VFAs, were further observed. In summary, our results demonstrated that the adaptation to grazing required more rumen bacterial populations due to complex forage types in shrub-grassland, although the rumen fermentation pattern did not change substantially among the three feeding systems. Some microbial taxa could be used as biomarkers for different feeding systems, particularly cellulose-degrading bacteria associated with grazing.

Keywords: 16S rRNA gene; goat; grazing; microbiota; rumen; volatile fatty acid.

Figure 1

Principal coordinate analysis (PCoA) plots of the bacterial and archaeal community compositions in the rumen fluid of the goat kids among the three feeding systems using an unweighted UniFrac metric. The percentages of variation explained by PC1 and PC2 are indicated on the axes. (A) The PCoA plot of the bacterial community composition; (B) the PCoA plot of the archaeal community composition.

Figure 2

Bacterial and archaeal community compositions at different taxon levels in the rumen fluid of the goat kids across the three feeding systems. (A) The composition of bacteria at the phylum level; (B) the Firmicutes/Bacteroidetes ratios among the three feeding systems; (C) the composition of bacteria at the genus level; (D) the composition of bacteria at the species level; (E) the composition of archaea at the phylum level; (F) the composition of archaea at the genus level. The “Others” proportion represents the known and unidentified taxa with low abundances at different taxon levels.

Figure 3

Bacterial taxa with significantly different abundances in each of the three feeding systems based on pairwise comparisons using linear discriminant analysis effect size (LEfSe) (linear discriminant analysis (LDA) score > 4 and p < 0.05). (A) Number of common and unique biomarkers between pairwise comparisons of the three feeding systems; (B) number of common and unique biomarkers in the supplementary feeding (SF) and shrub-grassland grazing (GR) groups based on the pairwise comparisons of GR vs. indoor feeding (IF) and SF vs. IF; (C) number of common and unique biomarkers in the IF group based on the pairwise comparisons of GR vs. IF and SF vs. IF; (D) the bacterial biomarkers identified in the pairwise comparison between GR and IF; (E) the bacterial biomarkers identified in the pairwise comparison between SF and IF; (F) the bacterial biomarkers identified in the pairwise comparison between GR and SF.

Figure 4

Archaeal taxa showing significantly different abundances in each of the three feeding systems based on pairwise comparisons using LEfSe (LDA score > 4 and p < 0.05). (A) Archaeal biomarkers identified in the pairwise comparison between GR and IF; (B) archaeal biomarkers identified in the pairwise comparison between SF and IF.

Figure 5

Spearman correlations between bacterial biomarkers and VFAs in the GR (A), IF (B), and SF (C) groups. Correlations with a threshold of statistical significance at p < 0.05 were visualized. The green color represents a positive correlation and the red color represents a negative correlation.