Integrating heterogeneous across-country data for proxy-based random forest prediction of enteric methane in dairy cattle.

Direct measurements of methane (CH4) from individual animals are difficult and expensive. Predictions based on proxies for CH4 are a viable alternative. Most prediction models are based on multiple linear regressions (MLR) and predictor variables that are not routinely available in commercial farms, such as dry matter intake (DMI) and diet composition. The use of machine learning (ML) algorithms to predict CH4 emissions from across-country heterogeneous data sets has not been reported. The objectives were to compare performances of ML ensemble algorithm random forest (RF) and MLR models in predicting CH4 emissions from proxies in dairy cows, and assess effects of imputing missing data points on prediction accuracy. Data on CH4 emissions and proxies for CH4 from 20 herds were provided by 10 countries. The integrated data set contained 43,519 records from 3,483 cows, with 18.7% missing data points imputed using k-nearest neighbor imputation. Three data sets were created, 3k (no missing records), 21k (missing DMI imputed from milk, fat, protein, body weight), and 41k (missing DMI, milk fat, and protein records imputed). These data sets were used to test scenarios (with or without DMI, imputed vs. nonimputed DMI, milk fat, and protein), and prediction models (RF vs. MLR). Model predictive ability was evaluated within and between herds through 10-fold cross-validation. Prediction accuracy was measured as correlation between observed and predicted CH4, root mean squared error (RMSE) and mean normalized discounted cumulative gain (NDCG). Inclusion of DMI in the model improved within and between-herd prediction accuracy to 0.77 (RMSE = 23.3%) and 0.58 (RMSE = 31.9%) in RF and to 0.50 (RMSE = 0.327) and 0.13 (RMSE = 42.71) in MLR, respectively than when DMI was not included in the predictive model. When missing DMI records were imputed, within and between-herd accuracy increased to 0.84 (RMSE = 18.5%) and 0.63 (RMSE = 29.9%), respectively. In all scenarios, RF models out-performed MLR models. Results suggest routinely measured variables from dairy farms can be used in developing globally robust prediction models for CH4 if coupled with state-of-the-art techniques for imputation and advanced ML algorithms for predictive modeling.

Effect of strategy for harvesting regrowth grass silage on performance in dairy cows.

The objective of this study was to evaluate the effects of feeding lactating dairy cows with regrowth silages from different 2- and 3-cut harvesting systems on milk production, efficiency of N, and energy utilization. Thirty Nordic Red cows were offered 5 experimental diets containing regrowth silages, crimped barley, and canola meal in replicated incomplete 5 × 4 Latin squares with four 21-d periods consisting of 14 d of feed adaptation and 7 d of sampling. Four second-cut silage diets were examined in a 2 × 2 factorial arrangement, enabling evaluation of effect of harvest time of the early or late first cut on second-cut silages, short or long regrowth interval within second cut, and their interaction on dairy cow performance. The third-cut silage diet harvested from early first cut and short regrowth interval of second-cut ley was compared with the second-cut silage diets to evaluate the difference in dairy cow performance between second- and third-cut silages. Postponing the first cut and extending the regrowth interval decreased dry matter intake (DMI), energy-corrected milk (ECM) yield, nutrient digestibility, and urinary energy output, but improved N efficiency (milk N/N intake). Postponing the first cut also decreased the efficiency of metabolizable energy use for lactation, but increased CH4 yield (CH4/DMI). Extending the regrowth interval decreased feed efficiency (ECM/DMI) and increased CH4 intensity (CH4/ECM). Thus, feeding regrowth silages in 2- or 3-cut systems harvested after an early first cut and short regrowth interval promoted better dairy performance and feed intake, and higher efficiency of feed and energy utilization, but with poorer N efficiency. Feeding third-cut silage improve milk yield and feed efficiency compared with second-cut silages.

Equations to predict nitrogen outputs in manure, urine and faeces from beef cattle fed diets with contrasting crude protein concentration.

Accurately predicting nitrogen (N) outputs in manure, urine and faeces from beef cattle is crucial for the realistic assessment of the environmental footprint of beef production and the development of sustainable N mitigation strategies. This study aimed to develop and validate equations for N outputs in manure, urine and faeces for animals under diets with contrasting crude protein (CP) concentrations. Measurements from individual animals (n = 570), including bodyweight, feed intake and chemical composition, and N outputs were (i) analysed as a merged database and also (ii) split into three sub-sets, according to diet CP concentration (low CP, 84-143 g/kg dry matter, n = 190; medium CP, 144-162 g/kg dry matter, n = 190; high CP, 163-217 g/kg dry matter, n = 190). Prediction equations were developed and validated using residual maximum likelihood analysis and mean prediction error (MPE), respectively. In low CP diets the lowest MPE for N outputs in manure, urine and faeces was 0.244, 0.594 and 0.263, respectively; diet CP-specific equations improved accuracy in certain occasions, by 4.9% and 18.3% for manure N output and faeces N output respectively, while a reduction by 5.7% in the prediction accuracy for urinary N output was noticed. In medium CP diets the lowest MPE for N outputs in manure, urine and faeces was 0.227, 0.391 and 0.394, respectively; diet CP-specific equations improved accuracy by 13.2%, 41.2% and 16.8% respectively. In high CP diets the lowest MPE for N outputs in manure, urine and faeces was 0.120, 0.154 and 0.144, respectively; diet CP-specific equations improved accuracy in certain occasions by 5.8%, 9.1% and 6.3% respectively. This study demonstrated that for improved prediction accuracy of N outputs in manure, urine and faeces from beef cattle, the use of dietary CP concentration is essential while dietary starch, fat, and metabolisable energy concentrations can be used to further improve accuracy. In beef cattle fed low CP concentration diets, using diet CP-specific equations improves prediction accuracy when feed intake or dietary CP concentration are not known. However, in beef cattle fed medium or high CP concentration diets, using equations that have been developed from animals fed similar CP concentration diets, substantially improves the prediction accuracy of N outputs in manure, urine and faeces in most cases.

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks.

BACKGROUND: Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks (Bos grunniens) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level. RESULTS: The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including Christensenellaceae_R-7_group, Ruminococcus_1, Romboutsia, Alloprevotella, Eubacterium coprostanoligenes, Clostridium, Streptococcus, and Treponema were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks. CONCLUSIONS: Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.

Increasing roughage quality by using alfalfa hay as a substitute for concentrate mitigates CH4 emissions and urinary N and ammonia excretion from dry ewes.

Twelve Hu sheep × thin-tail Han crossbred dry ewes with an average body weight of 32.6 ± 0.68 kg and an age of 3 years were arranged in a 3 × 3 Latin square design, with each experimental period of 24 d to evaluate the effect of substituting alfalfa hay in a portion of concentrate on nutrient intake, digestibility, N utilisation efficiency and methane emissions. The ratios of corn straw to alfalfa to concentrate for 3 diet treatments were 60:0:40, 60:15:25 and 60:30:10, respectively. Intake and digestibility were measured for each of the ewes, which were housed in individual metabolism crates for 6 d after an adaptation period of 14 d, and the feed was offered at 1.2 MEm to ensure approximately 10% orts. Methane emissions were determined in a respiration chamber for 2 consecutive d. An increase in the levels of alfalfa as a substitute for concentrate significantly increased the roughage, NSC and ADF intake and faecal N output as a proportion of N intake and manure N output. Furthermore, this increase in alfalfa input levels decreased DE, ME and N intake; nutrient digestibility; DE/GE, ME/GE and CH4 emissions per day; CH4 output expressed as a portion of the DM, OM and GE intake; and urinary N and ammonia N output, especially between extreme treatments. Alfalfa input levels had no effect on the BW, DM and GE intake; the EB or EB/GE intake; and the retained N. This study indicated that increasing alfalfa input as a substitute for concentrate could significantly decrease the digestibility, CH4 emissions and urinary N and NH4 + -N outputs; and shift the N excretion from urine to faeces; and could sustain a similar DM intake.

Assessment of cutting time on nutrient values, in vitro fermentation and methane production among three ryegrass cultivars.

OBJECTIVE: The 3×3 factorial arrangement was used to investigate if either high watersoluble carbohydrates (WSC) cultivars or suitable time of day that the grass cut could improve nutrient values and in vitro fermentation characteristics. METHODS: The 3 cultivars were mowed at 3 diurnal time points and included a benchmark WSC ryegrass cultivar 'Premium', and 2 high WSC cultivars AberAvon and AberMagic, which contained, on average, 157, 173, and 193 g/kg dry matter (DM) of WSC, and 36.0, 36.5, and 34.1 g/kg DM of N during 7th regrowth stage, respectively. The fermentation jars were run at 39°C with gas production recorded and sampled at 2, 5, 8, 11, 14, 17, 22, 28, 36, and 48 h. The rumen liquid was collected from 3 rumen fistulated cows grazing on ryegrass pasture. RESULTS: High WSC cultivars had significantly greater WSC content, in vitro DM digestibility (IVDMD) and total gas production (TGP), and lower lag time than Premium cultivar. Methane production for AberMagic cultivar containing lower N concentration was marginally lower than that for AberAvon and Premium cultivars. Grass cut at Noon or PM contained greater WSC concentration, IVDMD and TGP, and lower N and neutral detergent fiber (NDF) contents, but CH4 production was also increased, compared to grass cut in AM. Meanwhile, the effects of diurnal cutting time were influenced by cultivars, such as in vitro CH4 production for AberMagic was not affected by cutting time. The IVDMD and gas production per unit of DM incubated were positively related to WSC concentration, WSC/N and WSC/NDF, respectively, and negatively related to N and NDF concentrations. CONCLUSION: These results imply either grass cut in Noon or PM or high WSC cultivars could improve nutrient values, IVDMD and in vitro TGP, and that AberMagic cultivar has a slightly lower CH4 production compared to AberAvon and Premium. Further study is necessary to determine whether the increase of CH4 production response incurred by shifting from AM cutting to Noon and/or PM cutting could be compensated for by high daily gain from increased WSC concentration and DM digestibility.

Rumen bacterial diversity of Tibetan sheep (Ovis aries) associated with different forage types on the Qinghai-Tibetan Plateau.

Diet is the great determinant of bacterial composition in the rumen. However, little is known about the rumen bacterial community of Tibetan sheep living in the special ecological environment of the Qinghai-Tibetan Plateau (QTP) of China. In the present study, we used high-throughput sequencing to investigate the rumen bacterial community of Tibetan sheep associated with two primary diets: alpine pasture diet (a continuation of the sheep's natural grazing diet) and oat (Avena sativa) hay diet on the QTP. The results showed that bacterial community richness and species diversity of the oat hay diet group were significantly greater than that of the native pasture diet group (p < 0.05). Principal co-ordinate analysis and analysis of similarities revealed that the bacterial community of the oat hay diet group was distinctly different from that of the native pasture diet group (p < 0.05). Bacteroidetes and Firmicutes were the predominant microbial phyla in the rumen. The rumen of oat-hay-fed sheep had higher proportions of Proteobacteria and novel bacteria species than the rumen of native-pasture-fed sheep. Actinobacteria, an uncommon bacterial phylum, occurred only in the oat-hay-fed group. At the genus level, Komagataeibacter, Ruminococcaceae_UCG-014, and Ruminococcaceae_NK4A214 showed significantly higher relative abundance in the oat-hay-fed sheep than in the native-pasture-fed sheep (p < 0.05). This study is the first of the QTP to employ high-throughput sequencing to examine the influence of diet on the rumen microbiome of Tibetan sheep.

Relationship between the structure and composition of rumen microorganisms and the digestibility of neutral detergent fibre in goats.

OBJECTIVE: This experiment was conducted to compare the structure and composition of ruminal microorganisms in goats with high and low neutral detergent fibre (NDF) digestibility. METHODS: Nineteen crossbred goats were used as experimental animals and fed the same total mixed rations during the 30-day pre-treatment and 6-day digestion trialperiods. All faeces were collected during the digestion period for measuring the NDF digestibility. Then, high and the low NDF digestibility individuals were chosen for the high NDF digestibility group (HFD) and low NDF digestibility group (LFD), respectively. Rumen contents were collected for total microbial DNA extraction. The V4 region of the bacterial 16S rRNA gene was amplified using universal primers of bacteria and sequenced using high-throughput sequencer. The sequences were mainly analysed by QIIME 1.8.0. RESULTS: A total of 18,694 operational taxonomic units were obtained, within 81.98% belonged to bacteria, 6.64% belonged to archaea and 11.38% was unassigned microorganisms. Bacteroidetes, Firmicutes, and Proteobacteria were the predominant microbial phyla in both groups. At the genus level, the relative abundance of fifteen microorganisms were significantly higher (p<0.05) and six microorganisms were extremely significantly higher (p<0.01) in LFD than HFD. Overall, 176 core shared genera were identified in the two groups. The relative abundance of 2 phyla, 5 classes, 10 orders, 13 families and 15 genera had a negative correlation with NDF digestibility, but only the relative abundance of Pyramidobacter had a positive correlation with NDF digestibility. CONCLUSION: There were substantial differences in NDF digestibility among the individual goats, and the NDF digestibility had significant correlation with the relative abundance of some ruminal microorganisms.

Effect of substituting fresh-cut perennial ryegrass with fresh-cut white clover on bovine milk fatty acid profile.

BACKGROUND: Including forage legumes in dairy systems can help address increasing environmental/economic concerns about perennial ryegrass monoculture pastures. This work investigated the effect of substituting fresh-cut grass with increasing quantities of fresh-cut white clover (WC) on milk fatty acid (FA) profile and transfer efficiency of dietary linoleic (LA) and α-linolenic (ALNA) acids to milk fat. Three groups of three crossbred dairy cows were used in a 3 × 3 crossover design. Dietary treatments were 0 g kg-1 WC + 600 g kg-1 grass, 200 g kg-1 WC + 400 g kg-1 grass, and 400 g kg-1 WC + 200 g kg-1 grass. All treatments were supplemented with 400 g kg-1 concentrates on a dry matter basis. Cows had a 19-day adaptation period to the experimental diet before a 6-day measurement period in individual tie stalls. RESULTS: Increasing dietary WC did not affect dry matter intake, milk yield or milk concentrations of fat, protein or lactose. Milk polyunsaturated FA concentrations (total n-3, total n-6, LA and ALNA) and transfer efficiency of LA and ALNA were increased with increasing dietary WC supply. CONCLUSION: Inclusion of WC in pastures may increase concentrations of nutritionally beneficial FA, without influencing milk yield and basic composition, but any implications on human health cannot be drawn. © 2018 The Authors. Journal of the Science of Food and Agriculture published by JohnWiley & Sons Ltd on behalf of Society of Chemical Industry.

Appropriate level of alfalfa hay in diets for rearing Simmental crossbred calves in dryland China.

OBJECTIVE: In dryland areas of China, alfalfa hay (AH) is a possible substitute for concentrate feed for beef cattle. To evaluate the potential benefits of this substitution, we studied the effect of the ratio of AH intake to total dry matter (DM) intake on average daily body-weight gain (ADG), dietary energy utilization status, and economic benefit in Gansu province. METHODS: In each of two feeding trials in 2016 (trial 1 [T1], July 3 to 17; trial 2 [T2], August 15 to September 23), crossbred male Simmental calves were allocated to low AH (LA), medium AH (MA), and high AH (HA) feeding groups (n = 4 per group). The target ADG was set as 1 kg for both trials. In a one-way-layout design based on conventional feeding practices in the province, calves received diets containing the different AH amounts, with a constant ratio of corn stover:total DM and decreasing rations of concentrate feed proportional to the increase in AH. Calves in T1 received AH at 15% (T1-LA), 23% (T1-MA), or 31% (T1-HA) of their dietary DM allowances; those in T2 received 9% (T2-LA), 24% (T2-MA), or 34% (T2-HA) AH. RESULTS: Among the T1 groups, both ADG and economic benefit were highest in T1-LA; whereas in T2, they were higher in the T2-LA and T2-MA groups than in T2-HA. Energy digestibility did not significantly differ among the groups in either trial. The dietary AH inclusion ratios of 14% in the warm season and 8% to 21% in the cool season appeared to yield optimal ADG, metabolizable energy intake, and economic benefit. CONCLUSION: Low-level inclusion of AH, ranging from 8% to 21%, is a practical approach for beef cattle feeding. This modified feeding regimen likely will promote increased growth performance during the fattening stage of beef steers in dryland areas of Gansu province, China.

Prediction of metabolisable energy concentrations of fresh-cut grass using digestibility data measured with non-pregnant non-lactating cows.

Pasture-based ruminant production systems are common in certain areas of the world, but energy evaluation in grazing cattle is performed with equations developed, in their majority, with sheep or cattle fed total mixed rations. The aim of the current study was to develop predictions of metabolisable energy (ME) concentrations in fresh-cut grass offered to non-pregnant non-lactating cows at maintenance energy level, which may be more suitable for grazing cattle. Data were collected from three digestibility trials performed over consecutive grazing seasons. In order to cover a range of commercial conditions and data availability in pasture-based systems, thirty-eight equations for the prediction of energy concentrations and ratios were developed. An internal validation was performed for all equations and also for existing predictions of grass ME. Prediction error for ME using nutrient digestibility was lowest when gross energy (GE) or organic matter digestibilities were used as sole predictors, while the addition of grass nutrient contents reduced the difference between predicted and actual values, and explained more variation. Addition of N, GE and diethyl ether extract (EE) contents improved accuracy when digestible organic matter in DM was the primary predictor. When digestible energy was the primary explanatory variable, prediction error was relatively low, but addition of water-soluble carbohydrates, EE and acid-detergent fibre contents of grass decreased prediction error. Equations developed in the current study showed lower prediction errors when compared with those of existing equations, and may thus allow for an improved prediction of ME in practice, which is critical for the sustainability of pasture-based systems.

Evaluation of composition and individual variability of rumen microbiota in yaks by 16S rRNA high-throughput sequencing technology.

The Yak (Bos grunniens) is a unique species of ruminant animals that is important to agriculture of the Tibetan plateau, and has a complex intestinal microbial community. The objective of the present study was to characterize the composition and individual variability of microbiota in the rumen of yaks using 16S rRNA gene high-throughput sequencing technique. Rumen samples used in the present study were obtained from grazing adult male yaks (n = 6) in a commercial farm in Ganzi Autonomous Prefecture of Sichuan Province, China. Universal prokaryote primers were used to target the V4-V5 hypervariable region of 16S rRNA gene. A total of 7200 operational taxonomic units (OTUs) were obtained after sequence filtering and chimera removal. Within these OTUs, 0.56% belonged to Archaea (40 OTUs), 7.19% to unassigned species (518 OTUs), and the remaining OTUs (6642) in all samples were of bacterial origin. When examining the community structure of bacteria, we identified 23 phyla within 159 families after taxonomic summarization. Bacteroidetes and Firmicutes were the predominant phyla accounting for 39.68% (SD = 0.05) and 45.90% (SD = 0.06), respectively. Moreover, 3764 OTUs were identified as shared OTUs (i.e. represented in all yaks) and belonged to 35 genera, exhibiting highly variable abundance across individual samples. Phylogenetic placement of these genera across individual samples was examined. In addition, we evaluated the distance among the 6 rumen samples by adding taxon phylogeny using UniFrac, representing 24.1% of average distance. In summary, the current study reveals a shared rumen microbiome and phylogenetic lineage and presents novel information on composition and individual variability of the bacterial community in the rumen of yaks.

Effects of a High-Concentrate Diet on the Blood Parameters and Liver Transcriptome of Goats.

The objective of this study was to determine the effect of high-concentrate diets on the blood parameters and liver transcriptome of goats. Eighteen goats were allocated into three dietary treatments: the high level of concentrate (HC) group, the medium level of concentrate (MC) group, and the low level of concentrate (LC) group. The blood parameters and pathological damage of the gastrointestinal tract and liver tissues were measured. In hepatic portal vein blood, HC showed higher LPS, VFAs, and LA; in jugular vein blood, no significant differences in LPS, VFAs, and LA were recorded among groups (p > 0.05). Compared to the LC and MC groups, the HC group showed significantly increased interleukin (IL)-1ß, IL-10, TNF-α, and diamine oxidase in jugular vein blood (p < 0.05). Liver transcriptome analysis discovered a total of 1269 differentially expressed genes (DEGs) among the three groups and most of them came from the HC vs. LC group. There were 333 DEGs up-regulated and 608 down-regulated in the HC group compared to the LC group. The gene ontology enrichment analysis showed that these DEGs were mainly focused on the regulation of triacylglycerol catabolism, lipoprotein particle remodeling, and cholesterol transport. The Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that the liver of the HC group enhanced the metabolism of nutrients such as VFAs through the activation of AMPK and other signaling pathways and enhanced the clearance and detoxification of LPS by activating the toll-like receptor signaling pathway. A high-concentrate diet (HCD) can significantly promote the digestion of nutrients; the liver enhances the adaptability of goats to an HCD by regulating the expression of genes involved in nutrient metabolism and toxin clearance.

Modulation of feed digestibility, nitrogen metabolism, energy utilisation and serum biochemical indices by dietary Ligularia virgaurea supplementation in Tibetan sheep.

Ligularia virgaurea is the most widely functional native herbage in the alpine meadow pastures of the Qinghai-Tibet Plateau (QTP) and has multiple pharmacological and biological activities. The effect of L. virgaurea as a dietary component on the digestion and metabolism of sheep was evaluated by conducting feeding trials in metabolic cages. Thirty-two Tibetan yearling rams (29 ± 1.56 kg BW) were randomly allotted to four groups included in a completely randomised design with eight animals per treatment. Sheep were fed a basal diet (freshly native pasture) without the addition of L. virgaurea (control) or with the addition of L. virgaurea (100, 200, or 300 mg/kg BW per day) for 45 days. Addition of L. virgaurea to the diet of Tibetan sheep was found to influence the average daily gain (quadratic [Q], P < 0.001), feed conversion ratio (Q, P = 0.002), CH4 emissions (linear [L], P = 0.029), DM (Q, P = 0.012), neutral detergent fibre (Q, P = 0.017), acid detergent fibre (ADF) (Q, P = 0.027), and ether extract (EE) intake (Q, P = 0.026). Apparently, different levels of L. virgaurea affected the digestibility coefficients of DM, ADF, and EE (L, P > 0.05; Q, P < 0.05). The nitrogen (N) intake (Q, P = 0.001), retained nitrogen (Q, P < 0.001), and N utilisation efficiency (L, P > 0.05; Q, P ≤ 0.001) were also affected by the dietary inclusion of L. virgaurea. Effects of L. virgaurea feeding were also witnessed on methane energy (CH4-E) (L, P = 0.029), gross energy (GE) (Q, P = 0.013), digestible energy (DE) (Q, P = 0.015), and metabolisable energy (ME) intake (Q, P = 0.015). Energy utilisation efficiency expressed as a proportion of GE intake (DE/GE intake, ME/GE intake, ME/DE intake, FE/GE intake, and CH4-E/GE intake) manifested quadratic changes (P < 0.05) with the increase in the L. virgaurea supplementation level. The addition of L. virgaurea increased the activity of superoxide dismutase (Q, P = 0.026) and glutathione peroxidase activity (Q, P = 0.039) in the serum. Overall, the greatest improvement of feed digestibility, N retention, energy utilisation, and antioxidant capacity of Tibetan sheep was yielded by the inclusion of 200 mg/kg BW per day of L. virgaurea. Therefore, the addition of an appropriate amount of L. virgaurea to the diet of Tibetan sheep is safe and natural, and may enhance the sustainability of small ruminant production systems in QTP areas.

Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis aries) To Adapt to the Cold Season.

The dynamics of ruminant-rumen microbiome symbiosis associated with feeding strategies in the cold season were examined. Twelve pure-grazing adult Tibetan sheep (Ovis aries) (18 months old; body weight, 40 ± 0.23 kg) were transferred from natural pasture to two indoor feedlots and fed either a native-pasture diet (NPF group) or an oat hay diet (OHF group) (n = 6 per treatment), and then the flexibility of rumen microbiomes to adapt to these compositionally different feeding strategies was examined. Principal-coordinate analysis and similarity analysis indicated that the rumen bacterial composition correlated with altered feeding strategies. Microbial diversity was higher in the grazing group than in those fed with native pasture and an oat hay diet (P < 0.05). The dominant microbial phyla were Bacteroidetes and Firmicutes, and the core bacterial taxa comprised mostly (42.49% of shared operational taxonomic units [OTUs]) Ruminococcaceae (408 taxa), Lachnospiraceae (333 taxa), and Prevotellaceae (195 taxa), which were relatively stable across different treatments. Greater relative abundances of Tenericutes at the phylum level, Pseudomonadales at the order level, Mollicutes at the class level, and Pseudomonas at the genus level were observed in a grazing period than in the other two treatments (NPF and OHF) (P < 0.05). In the OHF group, due to the high nutritional quality of the forage, Tibetan sheep can produce high concentrations of short-chain fatty acids (SCFAs) and NH3-N by increasing the relative abundances of key bacteria in the rumen, such as Lentisphaerae, Negativicutes, Selenomonadales, Veillonellaceae, Ruminococcus 2, Quinella, Bacteroidales RF16 group, and Prevotella 1, to aid in nutrients degradation and energy utilization. The levels of beneficial bacteria were increased by the oat hay diet; these microbiotas are likely to help improve and maintain host health and metabolic ability in Tibetan sheep to adapt to cold environments. The rumen fermentation parameters were significantly influenced by feeding strategy in the cold season (P < 0.05). Overall, the results of this study demonstrate the strong effect of feeding strategies on the rumen microbiota of Tibetan sheep, which provided a new idea for the nutrition regulation of Tibetan sheep grazing in the cold season on the Qinghai-Tibetan Plateau. IMPORTANCE During the cold season, like other high-altitude mammals, Tibetan sheep have to adapt their physiological and nutritional strategies, as well as the structure and function of their rumen microbial community, to the seasonal variation of lower food availability and quality. This study focused on the changes and adaptability in the rumen microbiota of Tibetan sheep when they adapted from grazing to a high-efficiency feeding strategy during the cold season by analyzing the rumen microbiota of Tibetan sheep raised under the different management systems, and it shows the linkages among the rumen core and pan-bacteriomes, nutrient utilization, and rumen short-chain fatty acids. The findings from this study suggest that the feeding strategies potentially contribute to variations in the pan-rumen bacteriome, together with the core bacteriome. Fundamental knowledge on the rumen microbiomes and their roles in nutrient utilization furthers our understanding of how rumen microbial adaptation to harsh environments may function in hosts. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of feeding strategy on nutrient utilization and rumen fermentation in harsh environments.

Dietary supplementation with xylooligosaccharides and exogenous enzyme improves milk production, energy utilization efficiency and reduces enteric methane emissions of Jersey cows.

BACKGROUND: Sustainable strategies for enteric methane (CH4) mitigation of dairy cows have been extensively explored to improve production performance and alleviate environmental pressure. The present study aimed to investigate the effects of dietary xylooligosaccharides (XOS) and exogenous enzyme (EXE) supplementation on milk production, nutrient digestibility, enteric CH4 emissions, energy utilization efficiency of lactating Jersey dairy cows. Forty-eight lactating cows were randomly assigned to one of 4 treatments: (1) control diet (CON), (2) CON with 25 g/d XOS (XOS), (3) CON with 15 g/d EXE (EXE), and (4) CON with 25 g/d XOS and 15 g/d EXE (XOS + EXE). The 60-d experimental period consisted of a 14-d adaptation period and a 46-d sampling period. The enteric CO2 and CH4 emissions and O2 consumption were measured using two GreenFeed units, which were further used to determine the energy utilization efficiency of cows. RESULTS: Compared with CON, cows fed XOS, EXE or XOS + EXE significantly (P < 0.05) increased milk yield, true protein and fat concentration, and energy-corrected milk yield (ECM)/DM intake, which could be reflected by the significant improvement (P < 0.05) of dietary NDF and ADF digestibility. The results showed that dietary supplementation of XOS, EXE or XOS + EXE significantly (P < 0.05) reduced CH4 emission, CH4/milk yield, and CH4/ECM. Furthermore, cows fed XOS demonstrated highest (P < 0.05) metabolizable energy intake, milk energy output but lowest (P < 0.05) of CH4 energy output and CH4 energy output as a proportion of gross energy intake compared with the remaining treatments. CONCLUSIONS: Dietary supplementary of XOS, EXE or combination of XOS and EXE contributed to the improvement of lactation performance, nutrient digestibility, and energy utilization efficiency, as well as reduction of enteric CH4 emissions of lactating Jersey cows. This promising mitigation method may need further research to validate its long-term effect and mode of action for dairy cows.

Dietary supplementation of Allium mongolicum modulates rumen-hindgut microbial community structure in Simmental calves.

Compared to traditional herbage, functional native herbage is playing more important role in ruminant agriculture through improving digestion, metabolism and health of livestock; however, their effects on rumen microbial communities and hindgut fermentation are still not well understood. The objective of present study was to evaluate the effects of dietary addition of Allium mongolicum on bacterial communities in rumen and feces of claves. Sixteen 7-month-old male calves were randomly divided into four groups (n = 4). All calves were fed a basal ration containing roughage (alfalfa and oats) and mixed concentrate in a ratio of 60:40 on dry matter basis. In each group, the basal ration was supplemented with Allium mongolicum 0 (SL0), 200 (SL200), 400 (SL400), and 800 (SL800) mg/kg BW. The experiment lasted for 58 days. Rumen fluid and feces in rectum were collected, Rumen fluid and hindgut fecal were collected for analyzing bacterial community. In the rumen, Compared with SL0, there was a greater relative abundance of phylum Proteobacteria (p < 0.05) and genera Rikenellaceae_RC9_gut_group (p < 0.01) in SL800 treatment. In hindgut, compared with SL0, supplementation of A. mongolicum (SL200, SL400, or SL800) decreased in the relative abundances of Ruminococcaceae_UCG-014 (p < 0.01), Ruminiclostridium_5 (p < 0.01), Eubacterium_coprostanoligenes_group (p < 0.05), and Alistipes (p < 0.05) in feces; Whereas, the relative abundances of Christensenellaceae_R-7_group (p < 0.05), and Prevotella_1 (p < 0.01) in SL800 were higher in feces, to maintain hindgut stability. This study provided evidence that A. mongolicum affects the gastrointestinal of calves, by influencing microbiota in their rumen and feces.

Recent advances in research in the rumen bloat of ruminant animals fed high-concentrate diets.

Rumen bloat is the most common digestive disorder in fattening ruminants, which is responsible for around 2-3 % of deaths in the ruminants industry and is therefore considered to be a serious threat to ruminant farming. The root cause of rumen bloat caused by feeding high concentrate dies would be attributed to the production of a large amount of stable foam during the fattening period. The exact mechanism of rumen foam formation has yet to be investigated. Proteins, polysaccharides and carboxylates derived from feed, and synthesized by microbes during the rumen fermentation may act as foaming agents or stabilizers in the formation progress of rumen foam. Supplementation of condensed tannins and other additives can be an effective way to prevent feedlot bloat induced by feeding high concentrate diets.

Implications of Organic Dairy Management on Herd Performance and Milk Fatty Acid Profiles and Interactions with Season.

Interest in organic cows' milk has increased due to the perceived superior nutritional quality and improved sustainability and animal welfare. However, there is a lack of simultaneous assessments on the influence of organic dairy practices and dietary and breed drivers on productivity, feed efficiency, health parameters, and nutritional milk quality at the herd level. This work aimed to assess the impact of organic vs. conventional management and month on milk yield and basic composition, herd feed efficiency, health parameters, and milk fatty acid (FA) composition. Milk samples (n = 800) were collected monthly from the bulk tanks of 67 dairy farms (26 organic and 41 conventional) between January and December 2019. Data on breed and feeding practices were gathered via farm questionnaires. The samples were analyzed for their basic composition and FA profile using Fourier transform infrared spectroscopy (FTIR) and gas chromatography (GC), respectively. The data were analyzed using a linear mixed model, repeated measures design and multivariate redundancy analysis (RDA). The conventional farms had higher yields (kg/cow per day) of milk (+7.3 kg), fat (+0.27 kg), and protein (+0.25 kg) and higher contents (g/kg milk) of protein, casein, lactose, and urea. The conventional farms produced more milk (+0.22 kg), fat (+8.6 g), and protein (+8.1 g) per kg offered dry matter (DM). The organic farms produced more milk per kg of offered non-grazing and concentrate DM offered, respectively (+0.5 kg and +1.23 kg), and fat (+20.1 g and +51 g) and protein (+17 g and +42 g). The organic milk had a higher concentration of saturated fatty acid (SFA; +14 g/kg total FA), polyunsaturated fatty acid (PUFA; +2.4 g/kg total FA), and nutritionally beneficial FA alpha linolenic acid (ALNA; +14 g/kg total FA), rumenic acid (RA; +14 g/kg total FA), and eicosapentaenoic acid (EPA; +14 g/kg total FA); the conventional milk had higher concentrations of monounsaturated FA (MUFA; +16 g/kg total FA). Although the conventional farms were more efficient in converting the overall diet into milk, fat, and protein, the organic farms showed better efficiency in converting conserved forages and concentrates into milk, fat, and protein as a result of reduced concentrate feeding. Considering the relatively small differences in the FA profiles between the systems, increased pasture intake can benefit farm sustainability without negatively impacting consumer nutrition and health.

The Effects of Dietary Crude Protein Level on Ammonia Emissions from Slurry from Lactating Holstein-Friesian Cows as Measured in Open-Circuit Respiration Chambers.

The effect of dietary crude protein (CP) level on ammonia (NH3) emissions from slurry from lactating Holstein-Friesian cows was studied. Twenty-four-hour total collections of faeces and urine were made from 24 lactating Holstein-Friesian cows fed four total mixed rations containing 141, 151, 177, and 201 g CP/kg DM (6 cows/diet). The collected urine and faeces from each cow were combined to form 2 kg duplicate slurry samples (weight/weight; fresh basis) according to the proportions in which they were excreted. NH3 emissions from the slurry samples were measured, during 0-24 and 24-48 h intervals in six open-circuit respiration chambers maintained at two temperatures (8 or 18 °C). NH3 emissions for the 0-24 and 0-48 h intervals, as well as the average daily emissions, increased linearly with increasing dietary CP level. Increasing the temperature from 8 to 18 °C positively affected NH3 emissions, but only for the 0-24 h interval. In situations where direct measurements are impossible, NH3 emissions from slurry can be predicted accurately using equations based on dietary CP level supported by either urinary nitrogen, faeces nitrogen, or both. In summary, increasing dietary CP level linearly increased average daily NH3 emissions from slurry, with a 5.4 g increase for each 10 g increase in dietary CP.