Animal board invited review: The effect of diet on rumen microbial composition in dairy cows

Ruminants play an important part in the food supply chain, and manipulating rumen microbiota is important to maximising ruminants' production. Rumen microbiota through rumen fermentation produces as major end products volatile fatty acids that provide animal's energy requirements, and microbial CP. Diet is a key factor that can manipulate rumen microbiota, and each variation of the physical and chemical composition creates a specific niche that selects specific microbes. Alteration in the chemical composition of forage, the addition of concentrates in the diet, or the inclusion of plant extract and probiotics, can induce a change in rumen microbiota. High-throughput sequencing technologies are the approaches utilised to investigate the microbial system. Also, the application of omics technologies allows us to understand rumen microbiota composition and these approaches are useful to improve selection programmes. The aim of this review was to summarise the knowledge about rumen microbiota, its role in nutrient metabolism, and how diet can influence its composition.

Relationship between the rumen microbiome and liver transcriptome in beef cattle divergent for feed efficiency

BACKGROUND

Feed costs account for a high proportion of the variable cost of beef production, ultimately impacting overall profitability. Thus, improving feed efficiency of beef cattle, by way of determining the underlying genomic control and selecting for feed efficient cattle provides a method through which feed input costs may be reduced whilst also contributing to the environmental sustainability of beef production. The rumen microbiome dictates the feed degradation capacity and consequent nutrient supply in ruminants, thus potentially impacted by feed efficiency phenotype. Equally, liver tissue has been shown to be responsive to feed efficiency phenotype as well as dietary intake. However, although both the rumen microbiome and liver transcriptome have been shown to be impacted by host feed efficiency phenotype, knowledge of the interaction between the rumen microbiome and other peripheral tissues within the body, including the liver is lacking. Thus, the objective of this study was to compare two contrasting breed types (Charolais and Holstein-Friesian) divergent for residual feed intake (RFI) over contrasting dietary phases (zero-grazed grass and high-concentrate), based on gene co-expression network analysis of liver transcriptome data and microbe co-abundance network of rumen microbiome data. Traits including RFI, dry matter intake (DMI) and growth rate (ADG), as well as rumen concentrations of volatile fatty acids were also included within the network analysis.

RESULTS

Overall, DMI had the greatest number of connections followed by RFI, with ADG displaying the fewest number of significant connections. Hepatic genes related to lipid metabolism were correlated to both RFI and DMI phenotypes, whilst genes related to immune response were correlated to DMI. Despite the known relationship between RFI and DMI, the same microbes were not directly connected to these phenotypes, the Succiniclasticum genus was however, negatively connected to both RFI and ADG. Additionally, a stepwise regression analysis revealed significant roles for both Succiniclasticum genus and Roseburia.faecis sp. in predicting RFI, DMI and ADG.

CONCLUSIONS

Results from this study highlight the interactive relationships between rumen microbiome and hepatic transcriptome data of cattle divergent for RFI, whilst also increasing our understanding of the underlying biology of both DMI and ADG in beef cattle.

Microbial Populations in Ruminal Liquid Samples from Beefmaster Steers at Both Extremes of RFI Values

The gut microbiota is involved in the productivity of beef cattle, but the impact of different analysis strategies on microbial composition is unclear. Ruminal samples were obtained from Beefmaster steers (n = 10) at both extremes of residual feed intake (RFI) values (5 with the lowest and 5 with the highest RFI) from two consecutive days. Samples were processed using two different DNA extraction methods. The V3 and V4 regions of the 16S rRNA gene were amplified using PCR and sequenced with a MiSeq instrument (Illumina). We analyzed 1.6 million 16S sequences from all 40 samples (10 steers, 2 time points, and 2 extraction methods). The abundance of most microbes was significantly different between DNA extraction methods but not between high-efficiency (LRFI) and low-efficiency (HRFI) animals. Exceptions include the genus Succiniclasticum (lower in LRFI, p = 0.0011), and others. Diversity measures and functional predictions were also mostly affected by DNA extraction methods, but some pathways showed significant differences between RFI levels (e.g., methylglyoxal degradation, higher in LRFI, p = 0.006). The results suggest that the abundance of some ruminal microbes is associated with feed efficiency and serves as a cautionary tale for the interpretation of results obtained with a single DNA extraction method.

Silage Mixtures of Alfalfa with Sweet Sorghum Alter Blood and Rumen Physiological Status and Rumen Microbiota of Karakul Lambs

The study investigated the effects of feeding mixtures of alfalfa (AF) and sweet sorghum (SS) at different ratios of silages in terms of the physiological status of blood and rumen, and rumen microbiota in lambs. A total of 30 four-month-old male Karakul lambs with 25.5 ± 1.4 kg mean initial body weight were randomly allocated to five groups, with six lambs in each group. Five experimental diets containing 40% of one of the five AF−SS mixed silages (containing 0%, 20%, 40%, 60%, and 80% AF on a fresh weight basis, respectively) and 60% of other ingredients were formulated. Overall, the results showed that the mixed silage with more AF tended to increase serum antioxidant capacity, dry matter (DM) intake, and rumen fermentation metabolites. The AF−SS mixed silages containing AF at 60% and 80% caused a significant linear increase (p < 0.05) in the activity of total antioxidant capacity. The superoxide dismutase in the Karakul lamb responded with significant linear and quadratic increases (p < 0.01) as the ratio of AF was increased in the AF−SS mixed silages. Feeding diets with AF in silage mixtures at the ratio of 60% significantly increased (p < 0.05) the concentration of ruminal total volatile fatty acids (tVFA), acetate, and ammonia-N. However, no statistical significance (p > 0.05) was found in the alpha diversity of rumen microbes among the tested groups (p > 0.05). Principal coordinates analysis could clearly discriminate the differences between the five groups (p = 0.001). The relative abundance of Firmicutes in the rumen were significantly higher with AF at 40% in the AF−SS silage-based diet than those with AF at 0%, and 20% ratios. The abundance of Ruminococcus_albus had a significant linear increase (p < 0.05), as the ratio of AF in the AF−SS mixed silages was increased. In conclusion, the best beneficial effect on the physiological status of the blood and rumen, DM intake, and rumen microbiota in lambs came from those that consumed the diet containing the AF−SS mixed silage with 60% AF.