Background: Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predict performance traits or traits related to environmental impact, such as enteric methane emissions. Metagenome profiles were generated from 3139 rumen samples, collected from 1200 dual purpose ewes, using restriction enzyme-reduced representation sequencing (RE-RRS). Phenotypes were available for methane (CH4) and carbon dioxide (CO2) emissions, the ratio of CH4 to CH4 plus CO2 (CH4Ratio), feed efficiency (residual feed intake: RFI), liveweight at the time of methane collection (LW), liveweight at 8 months (LW8), fleece weight at 12 months (FW12) and parasite resistance measured by faecal egg count (FEC1). We estimated the proportion of phenotypic variance explained by host genetics and the rumen microbiome, as well as prediction accuracies for each of these traits. Results: Incorporating metagenome profiles increased the variance explained and prediction accuracy compared to fitting only genomics for all traits except for CO2 emissions when animals were on a grass diet. Combining the metagenome profile with host genotype from lambs explained more than 70% of the variation in methane emissions and residual feed intake. Predictions were generally more accurate when incorporating metagenome profiles compared to genetics alone, even when considering profiles collected at different ages (lamb vs adult), or on different feeds (grass vs lucerne pellet). A reference-free approach to metagenome profiling performed better than metagenome profiles that were restricted to capturing genera from a reference database. We hypothesise that our reference-free approach is likely to outperform other reference-based approaches such as 16S rRNA gene sequencing for use in prediction of individual animal performance. Conclusions: This paper shows the potential of using RE-RRS as a low-cost, high-throughput approach for generating metagenome profiles on thousands of animals for improved prediction of economically and environmentally important traits. A reference-free approach using a microbial relationship matrix from log ₁₀ proportions of each tag normalized within cohort (i.e., the group of animals sampled at the same time) is recommended for future predictions using RE-RRS metagenome profiles.

This study aimed to assess the potential use of increasing levels of murumuru cake (Astrocaryum murumuru var. murumuru, M art.) (MC) in sheep diets as a replacement for Mombasa grass (Panicum maximum Jacq). Metabolic tests were performed with 20 castrated male sheep at Embrapa Amazônia Oriental, Belém, Pará, during 26 days. The experiment was arranged in a completely randomized design, with five diets and four replications. MC0: 100% grass; MC10: 10% MC and 90% grass; MC20: 20% MC and 80% grass; MC40: 40% MC and 60% grass; and MC60: 60% MC and 40% grass. The intake and the coefficient of apparent digestibility of dry matter (DMI and CDDM), organic matter (OMI and CDOM), crude protein (CPI and CDCP), neutral detergent fiber (NDFI and CDNDF), acid detergent fiber (ADFI and CDADF), ether extract (EEI and CDEE), cellulose (CELI and CDCEL), hemicellulose (HEMI and CDHEM), and nitrogen balance (NB) of experimental diets were determined. The intake of mineral material (MMI) and lignin (LIGI) were also determined. The DMI, OMI, MMI, CPI, NDFI, and ADFI displayed a decreasing linear effect with the replacement of Mombasa grass by MC in the diet. The EEI and the LIGI presented quadratic effects according to the replacement levels of MC in the diet. The CDDM, CDOM, and CDHEM displayed increasing linear effects, between MC0 and MC60. The CDEE, CDNDF, CDADF, and CDCEL displayed a quadratic effect, with optimum replacement levels of 56.65%, 41%, 31.33%, and 27.46%, respectively. The nitrogen balance presented a negative linear effect in the range of 0% to 60% of murumuru cake. One can conclude that murumuru cake is an alternative to the dietary supplementation of ruminants in replacing the Mombasa grass because it provides an increase in the digestibility of nutrients for sheep. However, a limited replacement level must be implemented, considering that from 27.46%, 31.33%, 41%, and 56.65% replacement, a decline occurs in the CDCEL, CDADF, CDNDF, and CDEE, respectively, although a negative nitrogen balance does not occur.

The greatest source of global anthropogenic methane (CH₄) emissions is from ruminant livestock. Multiple mitigation strategies in livestock are currently being explored. Of these breeding for lower CH₄ emitting ruminants has the advantage of being permanent and cumulative and universally applicable to all classes of livestock. Here, we show that methane emissions can be predicted by the complex community of microbiota sampled from rumens enabling evaluation of systems and individuals. Furthermore, there is evidence that the microbial community is controlled not only be the feed substrate but also by the host itself and that selecting hosts that favour a microbial fermentation with lowered methane emissions changes the energy source to the animal, and in turn both rumen physiology and body composition. Current methods for obtaining microbial DNA and subsequent sequencing of an animal’s microbiome, however, are too expensive to implement in commercial selection programs. A methodology that offers fast, low-cost, high throughput profiling of rumen microbiomes using Genotyping-by-sequencing (GBS) has been developed using an unbiased reference free approach to group microbiota. To date, this has been applied to over 4000 sheep samples and validated in cattle. Results show that microbial profiles are heritable and correlated with methane emissions and feed intake. This research is part of a flagship program funded by the global research alliance to disseminate global access to technologies that lower greenhouse gas emissions in ruminant livestock.

In order to evaluate the feeding behavior of sheep fed with diets containing different levels of palm kernel meal (PKM) substituted for corn silage, a metabolic assay was performed on 20 ewes (5 treatments × 4 replicates) over 25 d. The animals received corn silage diets with the addition of increasing levels of PKM (0, 15, 30, 45, and 60%). The following parameters were evaluated: dry matter (DM) intake, neutral detergent fiber (NDF) intake, feeding time, rumination time, idle time, number of merycism mastications per bolus, time spent ruminating each bolus, DM and NDF per bolus, number of ruminated boluses per day, feeding and rumination efficiency, total chewing time, and number of merycism mastications per day. The daily intake of both DM and NDF increased linearly (P < 0.05), and when sheep were fed diets of at least 43.18 and 39.15% PKM, respectively, the consumption values were significantly different than when sheep were fed diets with 0% PKM (P < 0.05). In contrast, feeding time declined linearly, and in response to diets with at least 28.05% PKM, the sheep exhibited significantly different feeding times from those of sheep fed 0% PKM, with a reduction of 0.0613 percentage points per 1% increase in PKM. Idle time, rumination time, and rumination time per bolus each exhibited quadratic responses (P < 0.05), and the minimum rumination time per bolus was 44.37 s with 35.19% PKM. A quadratic response was also observed for total chewing time and both measures of merycism mastications (P < 0.05). Therefore, we concluded that the inclusion of PKM in the diets of sheep improves some parameters of feeding behavior, and the use of PKM is recommended at DM percentages of up to 40%.