Different feeding strategies can affect growth performance and rumen functions in Gangba sheep as revealed by integrated transcriptome and microbiome analyses

Abstract

Due to the harsh environment in the Tibetan Plateau, traditional grazing greatly limits the growth potential of local animals and causes severe ecosystem degradation. This is an urgent issue to be solved, which requires alternative strategies for grazing animals in the Tibetan alpine pastoral livestock systems. This study aimed to investigate the effects of different feeding strategies on growth performance and ruminal microbiota-host interactions in the local breed of sheep (Gangba sheep). Thirty 9-month old Gangba sheep (n = 10 per group) were assigned to natural grazing (G), semi-grazing with supplementation (T), and barn feeding (F) groups (supplementation of concentrate and oat hay) based on body weight. At the end of the experiment (75 d), all sheep were weighed, rumen fluid was obtained from six sheep per group, and ruminal epithelium was obtained from 3 sheep per group. The results showed that: (1) Compared with the G and T groups, the F group significantly increased dry matter intake, average daily gain, and feed conversion ratio of animals. Additionally, Gangba sheep in the F group had higher concentrations of ruminal short-chain volatile fatty acids (VFAs), especially propionate and butyrate (P <0.05) than sheep in the G and T groups. (2) The principal coordinates analysis indicated a significant difference in bacterial composition among different feed strategies. More specifically, the relative abundance of propionate (unidentified F082 and Succiniclasticum) and butyrate-producing (Eubacterium_coprostanoligenes_group) genera were also observed to be increased in the F group, in which unidentified F082 was identified as a differential biomarker among the three groups according to linear discriminant analysis effect size analysis. (3) The dynamics of the rumen epithelial transcriptome revealed that ECM-receptor interactions, focal adhesion, and PI3K-Akt signaling pathways, which are critical in mediating many aspects of cellular functions such as cell proliferation and motility, were upregulated in the F group. In conclusion, under harsh conditions in the Tibetan alpine meadow, barn feeding increased ruminal VFAs concentrations (especially propionate and butyrate), which stimulated gene expression related to cell proliferation in rumen epithelium, appearing to be superior to natural grazing and semi-grazing in gaining body weight of the local Gangba sheep.

Keywords: Gangba sheep; feeding strategies; growth performance; microbiome; transcriptome.

Figure 1

Effects of feeding strategies on ruminal microbiota of Gangba sheep. (A) The richness and diversity indices of rumen microbiota in Gangba sheep under different feeding strategies. (B) Principal coordinates analysis (PCoA) of the overall rumen microbiota in Gangba sheep based on unweighted UniFrac distance. G, natural grazing; T, semi-grazing with supplementation; F, barn feeding.

Figure 2

Comparisons of ruminal bacteria in Gangba sheep under different feeding strategies. (A) Relative abundances of bacterial communities at the phylum level. (B) Relative abundances of bacterial communities at the family level. (C) Relative abundances of bacterial communities at the genus level. G, natural grazing; T, semi-grazing with supplementation; F, barn feeding.

Figure 3

LEFSe (Linear discriminant analysis Effect Size) cladogram comparing microbial communities among the three feeding strategies. Differences are represented by color, indicating the group where taxa are most abundant: red = taxa abundant in F group, green = taxa abundant in G group, blue = taxa abundant in T group. G, natural grazing; T, semi-grazing with supplementation; F, barn feeding.

Figure 4

Correlation between the relative abundances of rumen bacteria and fermentation parameters. “*”, “**”, and “***” indicate the significance level at 0.05, 0.01 and 0.001, respectively.

Figure 5

Overview of Gangba sheep ruminal epithelium transcriptome under different feeding strategies. (A) PCA plots of transcripts identified by RNA-Seq of Gangba sheep under natural grazing (G), semi-grazing with supplementation (T), and barn feeding (F) conditions. (B) Number of individual transcripts significantly up- or down-regulated under different feeding strategies. (C) KEGG pathway enrichment analysis of DEGs in the Gangba sheep transcriptome under different feeding strategies. X-axis depicts richness factor (Richness factor = DEGs enriched in the pathway/background genes in the pathway). Y-axis represents the KEGG pathway terms. The color of each circle represents q-value. The area of each circle represents the number of DEGs enriched in this pathway. (D) Venn diagram of common and unique pathways presented in the Gangba sheep transcriptome under different feeding strategies.

Figure 6

The dynamics of the rumen epithelial transcriptomic analysis of significant DEGs in Profile 4 under different feeding strategies. The top 20 KEGG pathways for Profile 4 are listed on the right. X-axis depicts the richness factor (Richness factor = DEGs enriched in the pathway/background genes in the pathway). Y-axis represents the KEGG pathway terms. G, natural grazing; T, semi-grazing with supplementation; F, barn feeding.