Associations among dietary non-fiber carbohydrate, ruminal microbiota and epithelium G-protein-coupled receptor, and histone deacetylase regulations in goats

Abstract

Background: Diet-derived short-chain fatty acids (SCFAs) in the rumen have broad effects on the health and growth of ruminants. The microbe-G-protein-coupled receptor (GPR) and microbe-histone deacetylase (HDAC) axes might be the major pathway mediating these effects. Here, an integrated approach of transcriptome sequencing and 16S rRNA gene sequencing was applied to investigate the synergetic responses of rumen epithelium and rumen microbiota to the increased intake of dietary non-fiber carbohydrate (NFC) from 15 to 30% in the goat model. In addition to the analysis of the microbial composition and identification of the genes and signaling pathways related to the differentially expressed GPRs and HDACs, the combined data including the expression of HDACs and GPRs, the relative abundance of the bacteria, and the molar proportions of the individual SCFAs were used to identify the significant co-variation of the SCFAs, clades, and transcripts.

Results: The major bacterial clades promoted by the 30% NFC diet were related to lactate metabolism and cellulose degradation in the rumen. The predominant functions of the GPR and HDAC regulation network, under the 30% NFC diet, were related to the maintenance of epithelium integrity and the promotion of animal growth. In addition, the molar proportion of butyrate was inversely correlated with the expression of HDAC1, and the relative abundance of the bacteria belonging to Clostridum_IV was positively correlated with the expression of GPR1.

Conclusions: This study revealed that the effects of rumen microbiota-derived SCFA on epithelium growth and metabolism were mediated by the GPR and HDAC regulation network. An understanding of these mechanisms and their relationships to dietary components provides better insights into the modulation of ruminal fermentation and metabolism in the promotion of livestock production.

Keywords: Dietary modulation; Epithelium physiology; G-protein-coupled receptors; Histone deacetylases; Microbe–host interactions; Rumen microbiota.

Fig. 1

a Comparisons of the concentrations of individual SCFAs (acetate, propionate, and butyrate) between the groups. b Comparisons of the concentrations of total SCFA between the groups. c Comparisons of the concentrations of rumen pH between the groups. d Comparisons of the molar proportions of the individual SCFAs between the groups. The molar proportions of the individual SCFAs for ruminal fluid sampled at 8 h after matinal feeding were presented here; 0 h indicates the sampling time just before matinal feeding, and other numbers indicate the sampling time after matinal feeding. Asterisk indicates a p value < 0.05 in the t test

Fig. 2

a Venn diagram showing the coincidence of phyla between the groups. b Phylum-level comparison of bacterial OTUs between the groups. c Venn diagram showing the overlap of genera between groups. d Genus-level comparison of bacterial OTUs between the groups

Fig. 3

Maximum likelihood tree of 27 detectable OTUs (the relative abundance > 1% in the given sample). The complete 16S rRNA gene sequences of the corresponding species in the RDP database were used to construct the tree. Triangle indicates the OTUs in the MC group, and the circle indicates the OTUs in the LC group. Only the OTUs with significant differences (p < 0.05) in relative abundance are shown behind the branches. The size of the symbol indicates the relative abundance of OTUs. Red indicates a significant increase (p < 0.05) of the relative abundance of the OTU under the 30% NFC diet, and blue indicates a significant reduction (p < 0.05) in the relative abundance of the OTU under a 15% NFC diet. Only those bootstrap values greater than 60 are shown on the tree. The solid black circles at the nodes stand for a bootstrap value of 100

Fig. 4

GPR and HDAC co-regulation network related to epithelium growth. The functions of the first neighbors were predicted by the KEGG pathway analysis. The genes colored in red were the genes that were significantly upregulated after 4 weeks of 30% NFC feeding, and the genes colored in blue were the significantly downregulated genes after 4 weeks of 30% NFC feeding. The signaling pathways regulating the same functions are given with the same line shapes in connection with the corresponding functions. Blue lines indicate that the largest number of signaling pathways was regulated by PLCG1

Fig. 5

GPR and HDAC co-regulation network related to epithelium metabolism. The functions of the first neighbors were predicted by the KEGG pathway analysis. The genes colored in red were the genes that were significantly upregulated after 4 weeks of 30% NFC feeding, and the genes colored in blue were the significantly downregulated genes after 4 weeks of 30% NFC feeding. The lines in the same color indicate the genes regulating the same metabolic function. The lines in the same shape indicate that the low-level metabolism was grouped in the same high-level metabolism by KEGG annotation

Fig. 6

Constrained correspondence analysis revealing the correlations of the relative abundance of the specific microbes (SCC > 0.085 and p < 0.01 in a Spearman correlation analysis of the relative abundance of the microbes and the molar proportions of the individual SCFAs), the molar proportions of the individual SCFAs, and the expression of the significantly different HDACs and GPRs