Ruminant production systems face significant challenges currently, driven by heightened awareness of their negative environmental impact and the rapidly rising global population. Recent findings have underscored how the composition and function of the rumen microbiome are associated with economically valuable traits, including feed efficiency and methane emission. Although omics-based technological advances in the last decade have revolutionized our understanding of host-associated microbial communities, there remains incongruence over the correct approach for analysis of large omic data sets. A global approach that examines host/microbiome interactions in both the rumen and the lower digestive tract is required to harness the full potential of the gastrointestinal microbiome for sustainable ruminant production. This review highlights how the ruminant animal production community may identify and exploit the causal relationships between the gut microbiome and host traits of interest for a practical application of omic data to animal health and production.

Periodic feed restriction is used in cattle production to reduce feed costs. When normal feed levels are resumed, cattle catch up to a normal weight by an acceleration of normal growth rate, known as compensatory growth, which is not yet fully understood. Illumina Miseq Phylogenetic marker amplicon sequencing of DNA extracted from rumen contents of 55 bulls showed that restriction of feed (70% concentrate, 30% grass silage) for 125 days, to levels that caused a 60% reduction of growth rate, resulted in a large increase of relative abundance of Methanobrevibacter gottschalkii clade (designated as OTU-M7), and a large reduction of an uncharacterised Succinivibrionaceae species (designated as OTU-S3004). There was a strong negative Spearman correlation (ρ = -0.72, P = <1x10-20) between relative abundances of OTU-3004 and OTU-M7 in the liquid rumen fraction. There was also a significant increase in acetate:propionate ratio (A:P) in feed restricted animals that showed a negative Spearman correlation (ρ = -0.69, P = <1x10-20) with the relative abundance of OTU-S3004 in the rumen liquid fraction but not the solid fraction, and a strong positive Spearman correlation with OTU-M7 in the rumen liquid (ρ = 0.74, P = <1x10-20) and solid (ρ = 0.69, P = <1x10-20) fractions. Reduced A:P ratios in the rumen are associated with increased feed efficiency and reduced production of methane which has a global warming potential (GWP 100 years) of 28. Succinivibrionaceae growth in the rumen was previously suggested to reduce methane emissions as some members of this family utilise hydrogen, which is also utilised by methanogens for methanogenesis, to generate succinate which is converted to propionate. Relative abundance of OTU-S3004 showed a positive Spearman correlation with propionate (ρ = 0.41, P = <0.01) but not acetate in the liquid rumen fraction.

Enrichment of calf diets with exogenous butyrate has shown promise as a promotor of calf growth and intestinal development. However, the impact of dietary derived butyrate on the gut microbiota and their potential role, in turn, as mediators of its effect on calf growth and development is not known. Here, the effects of butyrate supplementation on rumen and hindgut microbiota and fermentation profiles were assessed in 16 Holstein-Friesian bull calves randomly assigned to one of two groups: Control (CON) fed conventional milk replacer or Sodium-Butyrate (SB – added to milk replacer) from days 7 to 56 of life. In the colon, total short chain fatty acid (SCFA), propionate and acetate concentrations were increased by SB (P < 0.05). 16S rRNA gene amplicon sequencing showed cecal abundance of butyrate producers Butyrivibrio and Shuttleworthia were decreased by SB (P < 0.05), while that of the propionate producer Phascolarctobacterium was higher (P < 0.05). Mogibacterium is associated with impaired gut health and was reduced in the cecum of SB calves (P < 0.05). These data show that the beneficial effects of SB on growth and performance occur in tandem with changes in the abundance of important SCFA producing and health-associated bacteria in the hindgut in milk-fed calves.

The present study investigated whether delaying the first feeding of colostrum affected ileum and colon mucosa-associated microbiota in calves. Twenty-seven male Holstein calves were randomly assigned to 1 of 3 groups, fed colostrum at 45 min, 6 h, and 12 h after birth, respectively. Ileum and colon mucosa were collected at 51 h after birth, and their associated microbial profiles were assessed using amplicon sequencing. Both ileum and colon mucosa-associated microbiota were predominated by genus Escherichia-Shigella. The negative correlation between the molar proportion of shortchain fatty acids (SCFA) and ileum mucosa-associated opportunistic pathogens, and the positive correlation between the molar proportion of SCFA and colon mucosa-associated beneficial bacteria, suggest that SCFA might play an important role in maintaining the gut health of 2-d-old calves. A higher relative abundance of ileum mucosa-associated Enterococcus and Streptococcus was detected when the first colostrum feeding was delayed for 12 h. The relative abundance of colon mucosa-associated Lactobacillus tended to be lower in calves fed colostrum 12 h than those under the other 2 treatments, whereas that of Faecalibacterium tended to be lower in calves fed colostrum immediately after birth than those fed colostrum 6 and 12 h after birth, respectively. Our findings suggest that delayed first colostrum feeding affects the establishment of ileum and colon mucosa-associated bacteria, which may have long-term effects on gut health of calves.