Metagenomic and metabolomic analyses reveal differences in rumen microbiota between grass- and grain-fed Sanhe heifers

Abstract

Introduction: The aim of this study was to investigate the effects of diets on the composition and function of rumen microbiome and metabolites in Sanhe heifers.

Methods: Metagenomic and metabolomic analyses were performed using rumen fluid samples collected from Sanhe heifers (n = 20) with similar body weights and ages from grass-fed and grain-fed systems.

Results: The grain-fed group exhibited more intensive rumen fermentation than the grass-fed group. However, the grass-fed group exhibited carbohydrate metabolism and methane production higher than that of the grain-fed group; these increases were observed as a higher abundance of various bacterial phyla (Firmicutes, Bacteroidetes, Actinobacteria, Lentisphaerae, and Verrucomicrobia), families (Lachnospiraceae, Eubacteriaceae, and Eggerthellaceae), and the archaeal family Methanobacteriaceae. A comparison of genes encoding carbohydrate-active enzymes, using Kyoto Encyclopedia of Genes and Genome profiles, revealed noteworthy differences in the functions of rumen microbiota; these differences were largely dependent on the feeding system.

Conclusion: These results could help manipulate and regulate feed efficiency in Sanhe cattle.

Keywords: Sanhe heifers; grain-fed; grass-fed; metabolites; microbiota.

Figure 1

Microbial compositional profiles of grain-fed and grass-fed Sanhe heifers. (A) Comparison of microbial domains between grain-fed and grass-fed Sanhe heifers, with significantly different domains tested using the Wilcoxon rank-sum test and an adjusted p value of <0.05. ** p < 0.01. (B) Bacterial compositional profiles of grain-fed and grass-fed Sanhe heifer samples based on species visualized using principal coordinate analysis (PCoA). (C) Archaeal compositional profiles of grain-fed and grass-fed Sanhe heifer samples, visualized based on species using PCoA. (D) Eukaryota compositional profiles of grain-fed and grass-fed Sanhe heifer samples, visualized on the species level using PCoA.

Figure 2

Compositional profiles of the rumen microbiome between grain-fed and grass-fed Sanhe heifers. Relative abundance of (A) phyla, (B) family, and (C) genus of bacterial species; Relative abundance of (D) phyla, (E) family, and (F) genus of archaeal species.

Figure 3

Comparative analysis of the composition of rumen bacteria and archaea between grain-fed and grass-fed Sanhe heifers. (A) Comparison of bacterial composition at phylum level. (B) Comparison of bacterial composition at family level. (C) Comparison of bacterial composition at species level. (D) Comparison of archaeal composition at phylum level. (E) Comparison of archaeal composition at family level. (F) Comparison of archaeal composition at species level. Statistical significance was assessed using the Wilcoxon rank-sum test, with an adjusted p value of < 0.05. ** p < 0.01.

Figure 4

The comparison of KEGG pathways and carbohydrate-active enzymes (CAZy) between grain-fed and grass-fed Sanhe heifers; (A) The top 15 KEGG pathways at the second level that were found to be significantly different between the two groups; (B) The top 15 of significantly different KEGG pathways at KEGG third-level; (C) The carbohydrate-active enzyme (CAZyme) profiles at the class level; (D) The top 15 of significantly different CAZyme profiles at the family level.

Figure 5

Spearman’s rank correlation constructed between the top 15 differential microbial species and metabolic pathways. Significant differences were determined using the Wilcoxon rank-sum test with an adjusted p value of < 0.05. ** p < 0.01.

Figure 6

Rumen metabolome comparison of grass-fed and grain-fed Sanhe heifers. (A) Scatter plots of the principal component analysis (PCA) model based on all identified metabolite features of rumen samples from the two groups (negative mode); (B) Scatter plots of the PCA model based on all identified metabolite features of rumen samples from the two groups (positive mode); (C) The pathway enrichment analysis conducted using the significantly different rumen metabolites between grass-fed and grain-fed Sanhe heifers; (D) The relationship between rumen fermentation parameters, the top 25 different rumen microbiota, and the top 25 significantly different rumen metabolites using Spearman’s rank correlations.