Ruminants are unique among livestock due to their ability to efficiently convert plant cell wall carbohydrates into meat and milk. This ability is a result of the evolution of an essential symbiotic association with a complex microbial community in the rumen that includes vast numbers of bacteria, methanogenic archaea, anaerobic fungi and protozoa. These microbes produce a diverse array of enzymes that convert ingested feedstuffs into volatile fatty acids and microbial protein which are used by the animal for growth. Recent advances in high-throughput sequencing and bioinformatic analyses have helped to reveal how the composition of the rumen microbiome varies significantly during the development of the ruminant host, and with changes in diet. These sequencing efforts are also beginning to explain how shifts in the microbiome affect feed efficiency. In this review, we provide an overview of how meta-omics technologies have been applied to understanding the rumen microbiome, and the impact that diet has on the rumen microbial community.

Future growth in demand for meat and milk, and the socioeconomic and environmental challenges that farmers face, represent a “grand challenge for humanity”. Improving the digestibility of crop residues such as straw could enhance the sustainability of ruminant production systems. Here, we investigated if transfer of rumen contents from bison to cattle could alter the rumen microbiome and enhance total tract digestibility of a barley straw-based diet. Beef heifers were adapted to the diet for 28 days prior to the experiment. After 46 days, ~70 percent of rumen contents were removed from each heifer and replaced with mixed rumen contents collected immediately after slaughter from 32 bison. This procedure was repeated 14 days later. Intake, chewing activity, total tract digestibility, ruminal passage rate, ruminal fermentation, and the bacterial and protozoal communities were examined before the first and after the second transfer. Overall, inoculation with bison rumen contents successfully altered the cattle rumen microbiome and metabolism, and increased protein digestibility and nitrogen retention, but did not alter fiber digestibility.

Demand for meat and milk is predicted to double by 2050, and meeting this increased demand represents a “grand challenge for humanity.” Sustainable production practices for ruminants will require more efficient utilization of feed, with a greater emphasis on the use of fibrous feedstuffs. Fibrolytic enzyme cocktails have the potential to improve the nutritional value of low quality forages, such as straw, and improve overall feed efficiency in ruminants. Available commercial fibrolytic enzymes are not specifically developed for use in ruminant livestock and have not consistently improved ruminal fiber digestion. “-Omics” including, metagenomics and metatranscriptomics, have improved our understanding of rumen microbes and the enzymes involved in deconstruction of plant cell walls. A better understanding of the enzymes that limit plant cell wall deconstruction in the rumen could lead to more effective fibrolytic enzyme additives for ruminants.

The objective of this study was to investigate the effects of adding engineered biocarbon to a high-forage diet on ruminal fermentation, nutrient digestion, and enteric methane (CH₄) production in a semi-continuous culture artificial rumen system (RUSITEC). The experiment was a completely randomized block design with four treatments assigned to sixteen fermentation vessels (four/treatment) in two RUSITEC apparatuses. The basal diet consisted of 60% barley silage, 27% barley grain, 10% canola meal, and 3% supplement (DM basis) with biocarbon added at 0, 0.5, 1, and 2% of substrate DM. The study period was 17 d, with a 10-d adaptation and 7-d sample collection period. Increasing biocarbon linearly increased (P < 0.05) disappearance of DM, OM, CP, ADF and NDF. Compared to control, increasing biocarbon enhanced (P < 0.01) production of total VFA, acetate, propionate, branch-chained VFAs, and tended to increase (P = 0.06) NH₃-N. Microbial protein synthesis linearly increased (P = 0.01) with increasing biocarbon. Addition of biocarbon reduced overall CH₄ production compared with the control (P ≤ 0.05). There were no differences (P > 0.05) in production of total gas, large or small peptides, or in the number of protozoa as a result of addition of biocarbon to the diet. Addition of biocarbon to a forage diet increased DM digestibility by up to 2%, while lowering enteric CH₄ production and enhancing microbial protein synthesis in in vitro semi- continuous culture fermenters.

The objective of this study was to examine the effect of a pine enhanced biochar (EB) on rumen fermentation, apparent total tract digestibility, methane (CH₄) emissions, and the rumen and fecal microbiome of Angus × Hereford heifers fed a barley silage-based diet. The experiment was a replicated 4 × 4 Latin square using 8 ruminally cannulated heifers (565 ± 35 kg initial BW). The basal diet contained 60% barley silage, 35% barley grain and 5% mineral supplement with EB added at 0% (control), 0.5, 1.0, or 2.0% (DM basis). Each period lasted 28 days, consisting of 14 days adaptation and 14 days of measurements. Samples for profiling of the microbiome in rumen liquid, solids and feces were collected on d 15 before feeding. Rumen samples for fermentation characterization were taken at 0, 3, 6, and 12 h post feeding. Total collection of urine and feces was conducted from days 18 to 22. Heifers were housed in open-circuit respiratory chambers on days 26–28 to estimate CH₄ emissions. Ruminal pH was recorded at 1-min intervals during CH₄ measurements using indwelling pH loggers. Data were analyzed with the fixed effects of dietary treatment and random effects of square, heifer within square and period. Dry matter intake was similar across treatments (P = 0.21). Ammonia N concentration and protozoa counts responded quadratically (P = 0.01) to EB in which both were decreased by EB included at 0.5 and 1.0%, compared to the control and 2.0% EB. Minimum pH was increased (P = 0.04), and variation of pH was decreased (P = 0.03) by 2.0% EB. Total tract digestibility, N balance and CH₄ production were not affected (P ≥ 0.17) by EB. Enhanced biochar decreased the relative abundance of Fibrobacter (P = 0.05) and Tenericutes (P = 0.01), and increased the relative abundance of Spirochaetaes (P = 0.01), Verrucomicrobia (P = 0.02), and Elusimicrobia (P = 0.02). Results suggest that at the examined concentrations, EB was ineffective at decreasing enteric CH₄ emissions, but did alter specific rumen microbiota.