Using a multi-omics approach to explore potential associations with rumen content and serum of cows with different milk production levels based on genomic predicted transmitting ability for milk and phenotypic milk production.

This study aims to compare rumen microbiome and metabolites between second lactation dairy cows in the 75th percentile (n = 12; 57.2 ± 5.08 kg/d) of production according to genomic predicted transmitting ability for milk (GPTAM) and their counterparts in the 25th percentile (n = 12; 47.2 ± 8.61 kg/d). It was hypothesized that the metagenome and metabolome would differ between production levels. Cows were matched by days in milk (DIM), sire, occurrence of disease, and days open in previous lactation. For an additional comparison, the cows were also divided by phenotype into high (n = 6; 61.3 ± 2.8 kg/d), medium (n = 10; 55 ± 1.2 kg/d), and low (n = 8; 41.9 ± 5.6 kg/d) based on their milk production. Samples were collected 65 ± 14 DIM. Rumen content was collected using an oro-gastric tube and serum samples were collected from the coccygeal vessels. High-resolution liquid chromatography-mass spectrometry (LC-MS) was used for rumen and serum metabolite profiling. Shotgun metagenomics was used for rumen microbiome profiling. Microbiome sample richness and diversity were used to determine alpha and Bray-Curtis dissimilarity index was used to estimate beta diversity. Differences in metabolites were determined using t-tests or ANOVA. Pearson correlations were used to consider associations between serum metabolites and milk production. There was no evidence of a difference in rumen metabolites or microbial communities by GPTAM or phenotype. Cows in the phenotypic low group had greater serum acetate to propionate ratio and acetate proportion compared to the cows in the phenotypic medium group. Likewise, serum propionate proportion was greater in the medium compared to the low phenotypic group. Serum acetate, butyrate, and propionate concentrations had a weak positive correlation with milk production. When investigating associations between rumen environment and milk production, future studies must consider the impact of the ruminal epithelium absorption and post-absorption processes in relation to milk production.

Effects of partially replacing dietary corn with sugars in a dual-flow continuous culture system on the ruminal microbiome.

The objective of this study was to evaluate the effects of feeding sugars as a replacement for starch on the ruminal microbiome using a dual-flow continuous culture system. Four periods of 10 days each were conducted with 8 fermenters in a 4 × 4 replicated Latin square design. Treatments included: 1) control with corn-CON, 2) molasses-MOL, 3) untreated condensed whey permeate-CWP, and 4) CWP treated with a caustic agent-TCWP as a partial substitute for corn. Sugars were defined as the water-soluble carbohydrates (WSC) concentration. Diets were formulated by replacing 4% of the diet DM in the form of starch from corn with the sugars in byproducts. Microbial samples for DNA analysis were collected from the solid and liquid effluent containers at 3, 6, and 9 h after feeding. Bacterial community composition was analyzed with sequencing the V4 region of the 16S rRNA gene using Illumina MiSeq platform. Data were analyzed with R 4.1.3 packages vegan, lmer, and ggplot to determine the effects of treatment on the relative abundance of taxa in the solid and liquid fractions, as well as the correlation of Acetate: Propionate ratio and pH to taxa relative abundance. Treatments did not affect alpha or beta diversity. At the phylum level the relative abundance of Proteobacteria was increased in CON compared to sugars in the solid fraction. In the liquid fraction, Firmicutes had greater relative abundance in sugar treatments while Bacteroidota and Spirochaetota were present in lower relative abundance in CWP. For solid and liquid samples, the family Lachnospiraceae had greater relative abundance in sugar treatments compared to CON. The decreased relative abundance of Christensenellaceae and Rikenellaceae paired with the greater relative abundance of Selenomonadaceae in CWP could help explain greater propionate molar proportion and decreased ruminal pH previously observed for this treatment. The genera Olsenella a lactic acid-producing bacterium, had the greatest relative abundance in MOL. Incorporating TCWP or MOL as a partial replacement for starch was more conservative of fibrolytic bacterial taxa compared to CWP. Additionally, TCWP did not increase bacterial taxa associated with synthesis of lactate as compared to MOL. Overall, replacing starch with sugars is mostly conservative of the ruminal microbiome; however, changes observed coincide with differences observed in acetate and propionate proportions and ruminal pH.

Megasphaera elsdenii and Saccharomyces Cerevisiae as direct fed microbials during an in vitro acute ruminal acidosis challenge.

This study aimed to evaluate the effects of Saccharomyces cerevisiae and Megasphaera elsdenii as direct fed microbials (DFM) in beef cattle finishing diets to alleviate acute ruminal lactic acidosis in vitro. A dual-flow continuous culture system was used. Treatments were a Control, no DFM; YM1, S. cerevisiae and M. elsdenii strain 1; YM2, S. cerevisiae and M. elsdenii strain 2; and YMM, S. cerevisiae and half of the doses of M. elsdenii strain 1 and strain 2. Each DFM dose had a concentration of 1 × 108 CFU/mL. Four experimental periods lasted 11 days each. For the non-acidotic days (day 1-8), diet contained 50:50 forage to concentrate ratio. For the challenge days (day 9-11), diet contained 10:90 forage to concentrate ratio. Acute ruminal acidosis was successfully established. No differences in pH, D-, L-, or total lactate were observed among treatments. Propionic acid increased in treatments containing DFM. For N metabolism, the YMM treatment decreased protein degradation and microbial protein synthesis. No treatment effects were observed on NH3-N concentration; however, efficiency of N utilization by ruminal bacteria was greater than 80% during the challenge period and NH3-N concentration was reduced to approximately 2 mg/dL as the challenge progressed.

Effects of lignocellulolytic enzymes on the fermentation profile, chemical composition, and in situ ruminal disappearance of whole-plant corn silage.

The objective of this study was to examine the enzyme activities of an enzymatic complex produced by Pleurotus ostreatus in different pH and the effects of adding increased application rates of this enzymatic complex on the fermentation profile, chemical composition, and in situ ruminal disappearance of whole-plant corn silage (WPCS) at the onset of fermentation and 30 d after ensiling. The lignocellulolytic enzymatic complex was obtained through in vitro cultivation of P. ostreatus. In the first experiment, the activities of laccase, lignin peroxidase (LiP), manganese peroxidase, endo- and exo-glucanase, xylanase, and mannanase were determined at pH 3, 4, 5, and 6. In the second experiment, five application rates of enzymatic complex were tested in a randomized complete block design (0, 9, 18, 27, and 36 mg of lignocellulosic enzymes/kg of fresh whole-plant corn [WPC], corresponding to 0, 0.587, 1.156, 1.734, and 2.312 g of enzymatic complex/kg of fresh WPC, respectively). There were four replicates per treatment (vacuum-sealed bags) per opening time. Bags were opened 1, 2, 3, and 7 d after ensiling (onset of fermentation period) and 30 d after ensiling to evaluate the fermentation profile, chemical composition, and in situ dry matter and neutral fiber detergent disappearance of WPCS. Laccase had the greatest activity at pH 5 (P < 0.01), whereas manganese peroxidase and LiP had the greatest activity at pH 4 (P < 0.01; P < 0.01). There was no effect of the rate of application of enzymatic complex, at the onset of fermentation, on the fermentation profile (P > 0.21), and chemical composition (P > 0.36). The concentration of water-soluble carbohydrate quadratically decreased (P < 0.01) over the ensiling time at the onset of fermentation, leading to a quadratic increase of lactic acid (P = 0.02) and a linear increase of acetic acid (P = 0.02) throughout fermentation. Consequently, pH quadratically decreased (P < 0.01). Lignin concentration linearly decreased (P = 0.04) with the enzymatic complex application rates at 30 d of storage; however, other nutrients and fermentation profiles did not change (P > 0.11) with the enzymatic complex application rates. Addition of lignocellulolytic enzymatic complex from P. ostreatus cultivation to WPC at ensiling decreased WPCS lignin concentration 30 d after ensiling; however, it was not sufficient to improve in situ disappearance of fiber and dry matter.