Ruminal microbiome changes across lactation in primiparous Holstein cows with varying methane intensity: Heritability assessment.

Methane is a potent greenhouse gas produced during the ruminal fermentation and is associated with a loss of feed energy. Therefore, efforts to reduce methane emissions have been ongoing in the last decades. Methane production is highly influenced by factors such as the ruminal microbiome and host genetics. Previous studies have proposed to use the ruminal microbiome to reduce long-term methane emissions, as ruminal microbiome composition is a moderately heritable trait and genetic improvement accumulates over time. Lactation stage is another important factor that might influence methane production but potential associations with the ruminal microbiome have not been evaluated previously. This study sought to examine the changes in ruminal microbiome over the lactation period of primiparous Holstein cows differing in methane intensity and estimate the heritability of the abundance of relevant microorganisms. Ruminal content samples from 349 primiparous Holstein cows with 14 - 378 d in milk were collected from May 2018 to June 2019. Methane intensity (MI) of each cow was calculated as methane concentration/milk yield. Up to 64 taxonomic features (TF) from 20 phyla had a significant differential abundance between cows with low and high MI early in lactation, 16 TF during mid lactation, and none late in lactation. Taxonomical features within the Firmicutes, Proteobacteria, Melainabacteria, Cyanobacteria, Bacteroidetes and Actinobacteria phyla were associated to low MI, whereas eukaryotic TF and those within the Euryarchaeota, Verrucomicrobia, Kiritimatiellaeota, Lentisphaerae phyla were associated to high MI. Out of the 60 TF that were found to be differentially abundant between early and late lactation in cows with low MI, 56 TF were also significant when cows with low and high MI were compared in the first third of the lactation. In general, microbes associated with low MI were more abundant early in lactation (e.g., Acidaminococcus, Aeromonas and Weimeria genera) and showed low to moderate heritabilities (0.03 to 0.33). These results suggest some potential to modulate the rumen microbiome composition through selective breeding for lower MI. Differences in the ruminal microbiome of cows with extreme MI levels likely result from variations in the ruminal physiology of these cows and were more noticeable early in lactation probably due to important interactions between the host phenotype and environmental factors associated to that period. Our results suggest that the ruminal microbiome evaluated early in lactation may be more precise for MI difference, and hence, this should be considered to optimize sampling periods to establish a reference population in genomic selection scenarios.

The oral microbiome as a proxy for feed intake in dairy cattle.

Genetic material from rumen microorganisms can be found within the oral cavity, and hence there is potential in using the oral microbiome as a proxy of the ruminal microbiome. Feed intake (FI) influences the composition of rumen microbiota and might directly influence the oral microbiome in dairy cattle. Ruminal content samples (RS) from 29 cows were collected at the beginning of the study and also 42 d later (RS0 and RS42, respectively). Additionally, 18 oral samples were collected through buccal swabbing at d 42 (OS42) from randomly selected cows. Samples were used to characterize and compare the taxonomy and functionality of the oral microbiome using nanopore sequencing and to evaluate the feasibility of using the oral microbiome to estimate FI. Up to 186 taxonomical features were found differentially abundant (DA) between RS and OS42. Similar results were observed when comparing OS42 to RS collected on different days. Microorganisms associated with the liquid fraction of the rumen were less abundant in OS42 because these were probably swallowed after regurgitation. Up to 1,102 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were found to be DA between RS and OS42, and these results differed when comparing time of collection, but DA KEGG pathways were mainly associated with metabolism in both situations. Models based on the oral microbiome and rumen microbiome differed in their selection of microbial groups and biological pathways to predict FI. In the rumen, fiber-associated microorganisms are considered suitable indicators of FI. In contrast, biofilm formers like Gammaproteobacteria or Bacteroidia classes are deemed appropriate proxies for predicting FI from oral samples. Models from RS exhibited some predictive ability to estimate FI, but oral samples substantially outperformed them. The best lineal model to estimate FI was obtained with the relative abundance of taxonomical feature at genera level, achieving an average R2 = 0.88 within the training data, and a root mean square error of 3.46 ± 0.83 (±SD) kg of DM, as well as a Pearson correlation coefficient between observed and estimated FI of 0.48 ± 0.30 in the test data. The results from this study suggest that oral microbiome has potential to predict FI in dairy cattle, and it encourages validating this potential in other populations.

Effects of agroindustrial by-product supplementation on dairy goat milk characteristics, nutrient utilization, ruminal fermentation, and methane production.

The use of agroindustrial by-products, such as dried distillers grains with solubles (DDGS) and dried citrus pulp (DCP), has been widely investigated in dairy cows, but information on their effects in dairy goats is limited. The influence of feeding olive cake (a by-product of olive oil production) to dairy goats has been assessed in some studies, but exhausted olive cake (EOC) has been much less investigated. Twelve Murciano-Granadina goats were used in a crossover design trial with 2 periods to assess the effects of including agroindustrial by-products on nutrient digestibility, ruminal fermentation, methane production, urinary excretion of purine derivatives, and milk yield and composition. In each period, 6 goats received daily a control diet comprising 1 kg of alfalfa hay and 1 kg of high-cereal concentrate, and another 6 goats received a diet (BYP) comprising 1 kg of alfalfa hay and 1 kg of a concentrate including corn DDGS, DCP, and EOC in proportions of 180, 180, and 80 g/kg of concentrate (as-fed basis), respectively. Diet had no effect on total dry matter intake, but intake of alfalfa hay, CP, and fat was greater for the BYP group than for the control group. There were no differences between diets in nutrient apparent digestibility, with the exception of fat, which was greater for the BYP diet compared with the control diet. Although fecal N tended to be greater for the BYP diet, there were no differences in N utilization. Compared with the control diet, milk yield tended to be greater and daily production of milk CP, fat, whey protein, and TS as well as milk gross energy were greater for the BYP diet. The concentration of C12:0, C14:0, and C16:0 fatty acids (FA) was or tended to be lower and the concentration of polyunsaturated FA was greater in the milk of BYP-fed goats compared with goats fed the control diet. Diet had no effect on ruminal parameters (pH, volatile FA, and NH3-N concentrations) and methane emissions, but urinary excretion of total purine derivatives tended to be lower in BYP-fed goats than in those fed the control diet. A mixture of corn DDGS (180 g), DCP (180 g), and EOC (80 g) could replace 44% of cereal grains and protein feeds in the concentrate for dairy goats without compromising nutrient utilization, ruminal fermentation, or milk yield and led to a more unsaturated FA profile in milk.