Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle

Feed-efficient animals have lower production costs and reduced environmental impact. Given that rumen microbial fermentation plays a pivotal role in host nutrition, the premise that rumen microbiota may contribute to host feed efficiency is gaining momentum. Since diet is a major factor in determining rumen community structure and fermentation patterns, we investigated the effect of divergence in phenotypic residual feed intake (RFI) on ruminal community structure of beef cattle across two contrasting diets. PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR) were performed to profile the rumen bacterial population and to quantify the ruminal populations of Entodinium spp., protozoa, Fibrobacter succinogenes, Ruminococcus flavefaciens, Ruminococcus albus, Prevotella brevis, the genus Prevotella, and fungi in 14 low (efficient)- and 14 high (inefficient)-RFI animals offered a low-energy, high-forage diet, followed by a high-energy, low-forage diet. Canonical correspondence and Spearman correlation analyses were used to investigate associations between physiological variables and rumen microbial structure and specific microbial populations, respectively. The effect of RFI on bacterial profiles was influenced by diet, with the association between RFI group and PCR-DGGE profiles stronger for the higher forage diet. qPCR showed that Prevotella abundance was higher (P < 0.0001) in inefficient animals. A higher (P < 0.0001) abundance of Entodinium and Prevotella spp. and a lower (P < 0.0001) abundance of Fibrobacter succinogenes were observed when animals were offered the low-forage diet. Thus, differences in the ruminal microflora may contribute to host feed efficiency, although this effect may also be modulated by the diet offered.     

Influence of Sire Breed on the Interplay among Rumen Microbial Populations Inhabiting the Rumen Liquid of the Progeny in Beef Cattle

This study aimed to evaluate whether the host genetic background impact the ruminal microbial communities of the progeny of sires from three different breeds under different diets. Eighty five bacterial and twenty eight methanogen phylotypes from 49 individuals of diverging sire breed (Angus, ANG; Charolais, CHA; and Hybrid, HYB), fed high energy density (HE) and low energy density (LE) diets were determined and correlated with breed, rumen fermentation and phenotypic variables, using multivariate statistical approaches. When bacterial phylotypes were compared between diets, ANG offspring showed the lowest number of diet-associated phylotypes, whereas CHA and HYB progenies had seventeen and twenty-three diet-associated phylotypes, respectively. For the methanogen phylotypes, there were no sire breed-associated phylotypes; however, seven phylotypes were significantly different among breeds on either diet (P<0.05). Sire breed did not influence the metabolic variables measured when high energy diet was fed. A correlation matrix of all pairwise comparisons among frequencies of bacterial and methanogen phylotypes uncovered their relationships with sire breed. A cluster containing methanogen phylotypes M16 (Methanobrevibacter gottschalkii) and M20 (Methanobrevibacter smithii), and bacterial phylotype B62 (Robinsoniella sp.) in Angus offspring fed low energy diet reflected the metabolic interactions among microbial consortia. The clustering of the phylotype frequencies from the three breeds indicated that phylotypes detected in CHA and HYB progenies are more similar among them, compared to ANG animals. Our results revealed that the frequency of particular microbial phylotypes in the progeny of cattle may be influenced by the sire breed when different diets are fed and ultimately further impact host metabolic functions, such as feed efficiency.     

Correlation of Particular Bacterial PCR-Denaturing Gradient Gel Electrophoresis Patterns with Bovine Ruminal Fermentation Parameters and Feed Efficiency Traits

The influence of rumen microbial structure and functions on host physiology remains poorly understood. This study aimed to investigate the interaction between the ruminal microflora and the host by correlating bacterial diversity with fermentation measurements and feed efficiency traits, including dry matter intake, feed conversion ratio, average daily gain, and residual feed intake, using culture-independent methods. Universal bacterial partial 16S rRNA gene products were amplified from ruminal fluid collected from 58 steers raised under a low-energy diet and were subjected to PCR-denaturing gradient gel electrophoresis (DGGE) analysis. Multivariate statistical analysis was used to relate specific PCR-DGGE bands to various feed efficiency traits and metabolites. Analysis of volatile fatty acid profiles showed that butyrate was positively correlated with daily dry matter intake (P < 0.05) and tended to have higher concentration in inefficient animals (P = 0.10), while isovalerate was associated with residual feed intake (P < 0.05). Our results suggest that particular bacteria and their metabolism in the rumen may contribute to differences in host feed efficiency under a low-energy diet. This is the first study correlating PCR-DGGE bands representing specific bacteria to metabolites in the bovine rumen and to host feed efficiency traits.A fundamental understanding of microbial ecology and relationships to ruminant physiology is essential for successful manipulation of ruminal microflora and subsequent improvement in animal production since rumen microflora play important roles in the nutrient and energy uptake of the host (25). Hence, principles such as niche occupancy, selective pressure, adaptation, and interactions among populations (42) as well as the kinetics of substrate utilization (18) have to be taken into account when evaluating the ruminal microflora and host interactions. Bacterial density in the rumen is high, with direct counts as high as 10 billion cells per gram of ruminal contents (19, 33). Due to the limited understanding of the complex nature of the microbial component and activities in the rumen, the mechanisms of host-microbe and microbe-microbe interactions and whether such interactions impact host biology have not been well established.Many recent studies have employed molecularly based culture-independent techniques to investigate bacterial profiles (11, 22, 24, 39). PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis has been applied to assess ruminal microbial diversity based upon PCR-amplified 16S rRNA fragments to study community interactions (34), monitor populations shifts (23), and screen clone libraries (10). The PCR-DGGE banding patterns are considered to be representative of the dominant bacterial groups (26) and can be applied to screen changes of dominant species in the microflora for large numbers of environmental samples. A new terminology of “microbiome” has been applied to the study of the rumen microbial community, and such studies have further confirmed the complexity of this environment (7). However, many questions remain unanswered. For example, how does the microbiome change in large numbers of animals in response to host, diet, environment, health, and other factors? Which is more important to the host, the whole microbiome or the core microbiome? What is the function of a particular microbiome? Therefore, defining the ruminal microbiome to study its functions and interactions with the host has been an immense challenge. The selection of the rumen microbiome with particular functions after screening by culture-independent methods such as PCR-DGGE, therefore, is essential for high-throughput sequence analysis.Feed efficiency is one of the most critical factors that impact feed utilization by cattle. We hypothesized that particular bacterial populations in the rumen are associated with fermentation metabolites, which can also influence host feed efficiency. A recent study suggested that the bacterial structure may be associated with cattle''s residual feed intake (14); however, the small number of animals used in this study did not provide a direct linkage between a particular microbial population and host feed efficiency traits. The rumen microbial community changes in response to the feeding time (20). Since previous studies have shown that the concentration of volatile fatty acids (VFA) at prefeeding had less variation by diet (31) or by feeding cycles (43) and because of limited access to rumen fluid sampling from the examined commercial population in this study, we centered on the characterization of prefeeding dynamics in the ruminal bacteria and in the fermentation metabolites in 58 steers to test our hypothesis. Therefore, we focused on investigating the associations between rumen bacteria and host feed efficiency traits using PCR-DGGE analysis, aiming to identify the functional rumen microflora. The traits evaluated were daily dry matter intake (DMI), average daily gain (ADG), feed conversion ratio (FCR) (feed/gain), and residual feed intake (RFI) to measure the feed efficiency of cattle (1, 2, 28). Furthermore, we developed a multivariate statistical analysis to correlate bacterial PCR-DGGE profiles with fermentation measurements such as VFA and ammonia-nitrogen (NH₃-N) in the rumen and with feed efficiency traits, including, DMI, FCR, ADG, and RFI.     

Comparative effects of feeding citrus pulp and grape pomace on nutrient digestibility and utilization in steers

Feedlot beef production in tropics and subtropics is being limited by shortage of feed ingredients due to prolonged droughts resulting in high prices of cereal grains and reduced profitability. To alleviate feed shortages and increase profitability for the feedlot industry, it is important to explore underutilized non-conventional resources such as fruit by-products. The current study compared the nutrient intake, digestibility and utilization effects of feeding either 150 g/kg of dried citrus pulp (DCP) or grape pomace (DGP) as alternative dietary fibre sources to 7 months-old Angus steers (281 ± 15.7 kg) under feedlot conditions. Twenty-four steers were assigned to three dietary treatments (8 steers/treatment) in a completely randomised design. Each steer was treated as an experimental unit. Steers were adapted to diets for 21 d followed by 7 d of sample collection during which nutrient intake, digestibility, rumen fermentation parameters, nitrogen retention and microbial N supply were determined. All the data were analysed using the GLIMMIX procedures. Overall, steers fed DGP had the greatest dry matter intake (DM), organic matter (OM) crude protein (CP), ash free neutral detergent fibre (aNDFom), ether extract (EE) and starch intake followed by DCP and control (CON) diets (P ≤ .05). Apparent digestibilities of DM, OM and aNDFom were higher (P ≤ .05) for DCP diet compared to DGP and CON diets. Feeding DCP and DGP diets increased ruminal concentrations of total volatile fatty acids, acetate and isovalerate, and acetate to propionate ratio, and reduced propionate concentrations compared to the CON diet (P ≤ .05). The steers fed the CON diet had the greatest urinary excretions of allantoin, uric acid and total purine derivatives followed by those fed the DCP and DGP diets (P ≤ .05). Nitrogen intake, faecal nitrogen (N), N retention and N efficiency utilization were in the order of DGP > DCP > CON diets (P ≤ .05). Overall, feeding DGP as alternative fibre source to wheat bran improved nutrient intake, retention and efficiency of N utilization but reduced apparent nutrient digestibility compared to DCP. Current finding suggests that DGP may be a better fibre substitute for wheat bran in beef diets than DCP.     

Assessing feed efficiency in beef steers through feeding behavior, infrared thermography and glucocorticoids

A better understanding of the factors regulating feed efficiency and their potential as predictors of feed efficiency in cattle is needed. Therefore, the potential of three classes of traits, namely, feeding behavior characteristics: daily time at feeder (TF; min/day), time per meal (TM; min), meal size (MS; g DM), eating rate (ER; g DM/min), number of daily meals (NM) and daily visits to the feeder (VF); infrared (IR) thermography traits (°C): eye (EY), cheek (CK), snout (SN), ribs (RB) and hind area (HA); and glucocorticoid levels: fecal cortisol metabolites (FCM; ng/g) and plasma cortisol (PC; ng/ml) as predictors of efficiency were evaluated in 91 steers (436 ± 37 kg) over 2 years (Y1 = 46; Y2 = 45). Additionally, the individual traits of each of these three classes were combined to define three single traits. Individual daily feed intake of a corn silage and high-moisture corn-based diet was measured using an automated feeding system. Body weight and thermographs were taken every 28 days over a period of 140 days. Four productive performance traits were calculated: daily dry matter intake (DMI), average daily gain (ADG), feed to gain ratio (F : G) and residual feed intake (RFI). Steers were also classified into three RFI categories (low-, medium- and high-RFI). Among the feeding behavior characteristics, MS and ER were correlated with all efficiency traits (range: 0.26 to 0.75). Low-RFI (more efficient steers) had smaller MS, lower ER and fewer VF in comparison to high-RFI steers. Less efficient steers (high-RFI) performed more VF during the nocturnal period than more efficient steers. More efficient steers had lower CK and SN temperatures than less efficient steers (28.1°C v. 29.2°C and 30.0°C v. 31.2°C), indicating greater energetic efficiency for low-RFI steers. In terms of glucocorticoids, PC was not correlated with efficiency traits. In contrast, more efficient steers had higher FCM in comparison to less efficient steers (51.1 v. 31.2 ng/g), indicating that a higher cortisol baseline is related to better feed efficiency. The overall evaluation of the three classes of traits revealed that feeding behavior, IR thermography and glucocorticoids accounted for 18%, 59% and 7% of the total variation associated with RFI, respectively. These classes of traits have usefulness in the indirect assessment of feed efficiency in cattle. Among them, IR thermography was the most promising alternative to screen cattle for this feed efficiency. These findings might have application in selection programs and in the better understanding of the biological basis associated with productive performance.     

Impact of adding nitrate or increasing the lipid content of two contrasting diets on blood methaemoglobin and performance of two breeds of finishing beef steers

Adding nitrate to the diet or increasing the concentration of dietary lipid are effective strategies for reducing enteric methane emissions. This study investigated their effect on health and performance of finishing beef cattle. The experiment was a two×two×three factorial design comprising two breeds (CHX, crossbred Charolais; LU, Luing); two basal diets consisting of (g/kg dry matter (DM), forage to concentrate ratios) 520 : 480 (Mixed) or 84 : 916 (Concentrate); and three treatments: (i) control with rapeseed meal as the main protein source replaced with either (ii) calcium nitrate (18 g nitrate/kg diet DM) or (iii) rapeseed cake (RSC, increasing acid hydrolysed ether extract from 25 to 48 g/kg diet DM). Steers (n=84) were allocated to each of the six basal diet×treatments in equal numbers of each breed with feed offered ad libitum. Blood methaemoglobin (MetHb) concentrations (marker for nitrate poisoning) were monitored throughout the study in steers receiving nitrate. After dietary adaptation over 28 days, individual animal intake, performance and feed efficiency were recorded for a test period of 56 days. Blood MetHb concentrations were low and similar up to 14 g nitrate/kg diet DM but increased when nitrate increased to 18 g nitrate/kg diet DM (P<0.001). An interaction between basal diet and day (P<0.001) indicated that MetHb% was consistently greater in Concentrate – than Mixed-fed steers at 18 g nitrate/kg diet DM. Maximum individual MetHb% was 15.4% (of total Hb), which is lower than considered clinically significant (30%). MetHb concentrations for individual steers remained consistent across time. Concentrate-fed steers were more efficient (lower residual feed intake (RFI) values) than Mixed-fed steers (P<0.01), with lower dry matter intake (DMI) (kg/day) (P<0.001) and similar average daily gain (ADG). CHX steers were more efficient (lower RFI; P<0.01) than LU steers with greater ADG (P<0.01), lower DMI (/kg BW; P<0.01) and lower fat depth (P<0.001). ADG, BW or DMI did not differ across dietary treatments (P>0.05). Neither basal diet nor treatment affected carcass quality (P>0.05), but CHX steers achieved a greater killing out proportion (P<0.001) than LU steers. Thus, adding nitrate to the diet or increasing the level of dietary lipid through the use of cold-pressed RSC, did not adversely affect health or performance of finishing beef steers when used within the diets studied.     

Temperament and dominance relate to feeding behaviour and activity in beef cattle: implications for performance and methane emissions

In beef cattle, feeding behaviour and activity are associated with feed efficiency and methane (CH₄) emissions. This study aimed to understand the underlying traits responsible for the contribution of cattle behaviour to individual differences in feed efficiency, performance and CH₄ emissions. A total of 84 steers (530±114 kg BW) of two different breeds (crossbreed Charolais and Luing) were used. The experiment was a 2×2×3 factorial design with breed, basal diets (concentrate v. mixed) and dietary treatments (no additive, calcium nitrate or rapeseed cake) as the main factors. The individual dry matter intake (DMI; kg) was recorded daily and the BW was measured weekly over a 56-day period. Ultrasound fat depth was measured on day 56. Based on the previous data, the indexes average daily gain, food conversion and residual feed intake (RFI) were calculated. The frequency of meals, the duration per visit and the time spent feeding per day were taken as feeding behaviour measures. Daily activity was measured using the number of steps, the number of standing bouts and the time standing per day. Agonistic interactions (including the number of contacts, aggressive interactions, and displacements per day) between steers at the feeders were assessed as indicators of dominance. Temperament was assessed using the crush score test (which measures restlessness when restrained) and the flight speed on release from restraint. Statistical analysis was performed using multivariate regression models. Steers that spent more time eating showed better feed efficiency (P=0.039), which can be due to greater secretion of saliva. Feeding time was longer with the mixed diet (P<0.001), Luings (P=0.009) and dominant steers (P=0.032). Higher activity (more steps) in the pen was associated with poorer RFI, possibly because of higher energy expenditure for muscle activity. Frequent meals contributed to a reduction in CH₄ emissions per kg DMI. The meal frequency was higher with a mixed diet (P<0.001) and increased in more temperamental (P=0.003) and dominant (P=0.017) steers. In addition, feed intake was lower (P=0.032) in more temperamental steers. This study reveals that efficiency increases with a longer feeding time and CH₄ emissions decrease with more frequent meals. As dominant steers eat more frequently and for longer, a reduction in competition at the feeder would improve both feed efficiency and CH₄ emissions. Feed efficiency can also be improved through a reduction in activity. Selection for calmer cattle would reduce activity and increase feed intake, which may improve feed efficiency and promote growth, respectively.     

Characterization of Variation in Rumen Methanogenic Communities under Different Dietary and Host Feed Efficiency Conditions,as Determined by PCR-Denaturing Gradient Gel Electrophoresis Analysis

Understanding ruminal methanogens is essential for greenhouse gas mitigation, as well as for improving animal performance in the livestock industry. It has been speculated that ruminal methanogenic diversity affects host feed efficiency and results in differences in methane production. This study examined methanogenic profiles in the rumen using culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis for 56 beef cattle which differed in feed efficiency, as well as diet (the cattle were fed a low-energy diet or a high-energy diet). The methanogenic PCR-DGGE profiles detected were greatly affected by diet, and the major pattern changed from a community containing predominantly Methanobrevibacter ruminantium NT7 with the low-energy diet to a community containing predominantly Methanobrevibacter smithii, Methanobrevibacter sp. AbM4, and/or M. ruminantium NT7 with the high-energy diet. For each diet, the methanogenic PCR-DGGE pattern was strongly associated with the feed efficiency of the host. Diet-associated bands for Methanobrevibacter sp. AbM4 and M. smithii SM9 and a feed efficiency-related band for M. smithii PS were identified. The abundance of total methanogens was estimated by determining the numbers of copies of the 16S rRNA genes of methanogens. However, the size of the methanogen population did not correlate with differences in feed efficiency, diet, or metabolic measurements. Thus, the structure of the methanogenic community at the species or strain level may be more important for determining host feed efficiency under different dietary conditions.Ruminal methanogens use methanogenesis pathways to maintain low hydrogen partial pressure and to facilitate fiber digestion in the rumen by converting hydrogen into methane gas (24, 37). However, although it is necessary, this process also has adverse effects because the released methane represents a significant loss of dietary energy for the host animal (14) and it constitutes a large proportion of the agricultural greenhouse gas emitted (4, 10). Many studies to obtain a better understanding of rumen methanogens have been conducted in order to improve the efficiency of ruminal function and to mitigate methane release. Assessments by both cultivation-dependent and cultivation-independent methods have found that members of the genus Methanobrevibacter account for the majority of the methanogens in the rumens of sheep and cattle (11, 18, 21-23, 28, 31, 33, 34). In addition, Methanosphaera stadtmanae, Methanobacterium species, and Methanosarcina barkeri have also been found in some studies (13, 32). Although the phylogenetic positions of the methanogens in the rumen are diverse, these organisms utilize only three major pathways for methanogenesis: the CO₂ reduction pathway, the C₁ compound (e.g., methanol and methylamine) conversion pathway, and the acetate fermentation pathway. Each methanogen species has a substrate preference, and most methanogens can use only one or two substrates (37).Previous studies of rumen methanogens focused primarily on determining the methanogen species composition in different samples and developing strategies to reduce the methane yield from ruminants. Recently, there has been a strong desire to understand the impact of methanogens on host biology. Two primary studies found that feedlot beef cattle with higher feed efficiency (designated “efficient” animals) produced about 20% less methane gas than animals with lower feed efficiency (designated “inefficient” animals) (8, 19). The methanogenic communities of efficient and inefficient animals fed a low-energy diet have been compared, and divergence between the two communities has been reported (36). However, it is not clear how the methanogens in the rumen of cattle change when the animals are fed a different diet.The aims of this study were to describe the methanogenic communities in 56 steers with different feed efficiencies that were fed two distinct diets (a low-energy diet and a high-energy diet) and to understand how methanogenic communities change in response to diet modification using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) and sequence analysis. Multivariate analysis was used to analyze the association of PCR-DGGE bands with the daily dry matter intake (DMI), average daily gain (ADG), feed conversion ratio (FCR), and residual feed intake (RFI). Methanogens that were associated with diet and with host feed efficiency were identified. In addition, the methanogen population of each rumen sample was examined by quantitative real-time PCR (qRT-PCR), and the results for different RFI groups and both diets were compared.     

Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

Fourteen Holstein cows of similar ages were monitored through their first two lactation cycles, during which ruminal solids and liquids, milk samples, production data, and feed consumption data were collected for each cow during early (76 to 82 days in milk [DIM]), middle (151 to 157 DIM), and late (251 to 257 DIM) lactation periods. The bacterial community of each ruminal sample was determined by sequencing the region from V6 to V8 of the 16S rRNA gene using 454 pyrosequencing. Gross feed efficiency (GFE) for each cow was calculated by dividing her energy-corrected milk by dry matter intake (ECM/DMI) for each period of both lactation cycles. Four pairs of cows were identified that differed in milk production efficiency, as defined by residual feed intake (RFI), at the same level of ECM production. The most abundant phyla detected for all cows were Bacteroidetes (49.42%), Firmicutes (39.32%), Proteobacteria (5.67%), and Tenericutes (2.17%), and the most abundant genera included Prevotella (40.15%), Butyrivibrio (2.38%), Ruminococcus (2.35%), Coprococcus (2.29%), and Succiniclasticum (2.28%). The bacterial microbiota between the first and second lactation cycles were highly similar, but with a significant correlation between total community composition by ruminal phase and specific bacteria whose relative sequence abundances displayed significant positive or negative correlation with GFE or RFI. These data suggest that the ruminal bacterial community is dynamic in terms of membership and diversity and that specific members are associated with high and low milk production efficiency over two lactation cycles.     

Analysis of the Rumen Bacterial Diversity under two Different Diet Conditions using Denaturing Gradient Gel Electrophoresis,Random Sequencing,and Statistical Ecology Approaches

Bacterial community structure and diversity in the rumen of steers in conditions of hay and corn diets was assessed by in vitro retrieval and analysis of the variable region (V3) of 16S rDNA. Two types of libraries were generated in this study: DGGE libraries, which further were analysed by excising, reamplification, and sequencing, and random shotgun sequence libraries. Phylogenetic and sequence similarity analyses of the resultant 68 clone sequences in DGGE libraries revealed the presence of 42 operational taxonomic units (OTUs) or phylotypes defined as having more than 97% of sequence similarity. One hundred and thirty four clone sequences in shotgun libraries were clustered into 72 phylotypes. The phylotype similarity, diversity, richness, and evenness in these libraries were estimated using a variety of diversity indices. In relation to diet, the corn-fed animals displayed more diverse and rich bacterial populations, which were mostly contributed by CFB-related phylotypes. Proteobacteria were also numerically prevalent on this diet (27%) but were represented by a few phylotypes thus diminishing the overall diversity and species richness values. On hay diet, the principal contributors to general diversity and species richness appeared to be low-G + C gram-positives. Although the ruminal Treponemaes were encountered only in hay-fed animals, their impact on species diversity on hay diet was low because of the limited number of phylotypes.     

Protein metabolism,body composition and oxygen consumption in young bulls divergent in residual feed intake offered two contrasting forage-based diets

Protein metabolism and body composition have been identified as major determinants of residual feed intake (RFI) in beef cattle fed high-starch fattening diets. This study aimed to evaluate if these two identified RFI determinants in beef cattle are the same across two contrasting silage-based diets. During two consecutive years, an 84-day feed efficiency test (Test A) immediately followed by a second 112-day feed efficiency test (Test B) was carried out using a total of 100 animals offered either one of two diets (either corn silage- or grass silage-based) over 196 days. At the end of Test A, the 32 animals most divergent for RFI (16 extreme RFI animals per diet, eight low RFI and eight high RFI) were identified and evaluated during Test B for their i) N use efficiency (NUE; N retention/N intake) calculated either from a 10-d nitrogen balance trial or from estimations based on body composition changes occurring during the whole experiment (Test A and Test B; 196 days), ii) carcass and whole-body protein turnover rates analysed through the 3-methyl-histidine urinary excretion and the N isotopic turnover rates of urine, respectively, and iii) body composition measured at the slaughterhouse at the end of Test B. Oxygen consumption was measured during Test B for the 100 animals by two GreenFeed systems. Irrespective of the diet, efficient RFI animals tended (P = 0.08) to improve their NUE when N retention was estimated for 196 days or when considering their lower urinary urea-N to total N ratio (P = 0.03). In contrast, NUE calculated during the 10-d N balance showed no differences (P = 0.65) across RFI groups suggesting that this method may not be suitable to capture small NUE differences. Efficient RFI individuals presented higher dressing percentage and muscle deposition in the carcass (P = 0.003) but lighter rumen (P = 0.001), and a trend for lower oxygen consumption (P = 0.08) than inefficient RFI animals irrespective of the diet. Lower protein degradation rates of skeletal muscle and lower protein synthesis rates of plasma proteins were found in efficient RFI cattle but only with the corn silage-based diet (RFI × Diet; P = 0.02). The higher insulinaemia associated with the corn silage-based diet (P = 0.001) seemed to be a key metabolic feature explaining the positive association between protein turnover and RFI only in this diet. Feed N was more efficiently used for growth by efficient RFI animals regardless of the diet but lower protein turnover rates in efficient RFI animals were only observed with corn silage-based diets.     

The genetic parameters of feed efficiency and its component traits in the turkey (Meleagris gallopavo)

Residual feed intake (RFI) and feed conversion ratio (FCR) can be incorporated into a breeding program as traits to select for feed efficiency. Alternatively, the direct measures used to calculate RFI and FCR can be analyzed to determine the underlying variation in the traits that impact overall efficiency. These constituent traits can then be appropriately weighted in an index to achieve genetic gain. To investigate feed efficiency in the turkey, feed intake and weight gain were measured on male primary breeder line turkeys housed in individual feeding cages from 15 to 19 weeks of age. The FCR and RFI showed moderate heritability values of 0.16 and 0.21, respectively. Feed intake, body weight, and weight gain were also moderately heritable (0.25, 0.35, and 0.18, respectively). Weight gain was negatively correlated to feed conversion ratio and was not genetically correlated to RFI. Body weight had a small and positive genetic correlation to RFI (0.09) and FCR (0.12). Feed intake was positively genetically correlated to RFI (0.62); however, there was no genetic correlation between feed intake and FCR. These estimates of heritability and the genetic correlations can be used in the development of an index to improve feed efficiency and reduce the cost of production.     

Digestibility contributes to between-animal variation in feed efficiency in beef cows

Residual feed intake (RFI) is an alternative measure of feed efficiency (FE) and is calculated as the difference between actual and expected feed intake. The biological mechanisms underlying animal-to-animal variation in FE are not well understood. The aim of this study was to investigate the digestive ability of beef cows selected for RFI divergence as heifers, using two contrasted diets. Fifteen 4-year-old beef cows were selected from a total of 69 heifers based on their RFI following the feedlot test. The selected heifers were ranked into high-RFI (+ 1.02 ± 0.28, n = 8) and low-RFI (−0.73 ± 0.28, n = 7), and a digestibility trial was performed after their first lactation. Both RFI groups were offered two different diets: 100% hay or a fattening diet which consisted of a DM basis of 67% whole-plant maize silage and 33% high starch concentrates over four experimental periods (two per diet). A diet effect was observed on feed intake and apparent digestibility, whereas no diet × RFI interaction was detected (P > 0.05). Intake and apparent digestibility were higher in cows fed the fattening diet than in those fed the hay diet (P < 0.0001). DM intake (DMI) and organic matter apparent digestibility (OMd) were repeatable and positively correlated between the two subsequent periods of measurements. For the hay and fattening diets, the repeatability between periods was r = 0.71 and r = 0.73 for DMI and r = 0.87 and r = 0.48 for OMd, respectively. Moreover, both intake (r = 0.55) and OMd (r = 0.54) were positively correlated (P < 0.05) between the hay and fattening diets. Significant differences between beef cows selected for divergence in RFI as heifers were observed for digestive traits (P < 0.05), DM and organic matter (OM) apparent digestibility being higher for low-RFI cows. Overall, this study showed that apparent digestibility contributes to between-animal variation in FE in beef cows.     

Linkage of microbial ecology to phenotype: correlation of rumen microbial ecology to cattle's feed efficiency

Linkage of rumen microbial structure to host phenotypical traits may enhance the understanding of host-microbial interactions in livestock species. This study used culture-independent PCR-denaturing gradient gel electrophoresis (PCR-DGGE) to investigate the microbial profiles in the rumen of cattle differing in feed efficiency. The analysis of detectable bacterial PCR-DGGE profiles showed that the profiles generated from efficient steers clustered together and were clearly separated from those obtained from inefficient steers, indicating that specific bacterial groups may only inhabit in efficient steers. In addition, the bacterial profiles were more likely clustered within a certain breed, suggesting that host genetics may play an important role in rumen microbial structure. The correlations between the concentrations of volatile fatty acids and feed efficiency traits were also observed. Significantly higher concentrations of butyrate (P < 0.001) and valerate (P = 0.006) were detected in the efficient steers. Our results revealed potential associations between the detectable rumen microbiota and its fermentation parameters with the feed efficiency of cattle.     

Comparative Analysis of Microbial Profiles in Cow Rumen Fed with Different Dietary Fiber by Tagged 16S rRNA Gene Pyrosequencing

The ruminal microbiome of cattle plays an important role not only in animal health and productivity but also in food safety and environment. Microbial profiles of rumen fluid obtained from dairy cows fed on three different fiber/starch diet compositions were characterized. Tagged 16S rRNA gene pyrosequencing and statistical analysis revealed that the dominant ruminal bacteria shared by all three sample groups belonged to phyla Bacteroidetes, Firmicutes, and Proteobacteria. However, the relative abundance of these bacterial groups was markedly affected by diet composition. In animals fed with a high fiber diet, the fibrolytic and cellulolytic bacteria Lachnospiraceae, Ruminococcaceae, and Fibrobacteraceae were found in highest abundance compared with animals fed other diets with lower fiber content. The polysaccharide-degrading Prevotellaceae and Flavobacteriaceae bacteria were most abundant in the rumen of cows fed on diet with the highest starch content. These data highlight the ruminal microbiome’s ability to adapt to feed composition and also provide a basis for the development of feed formulation systems designed to improve livestock productivity.     

Effects of Dietary Linseed Oil and Propionate Precursors on Ruminal Microbial Community,Composition, and Diversity in Yanbian Yellow Cattle

The rumen microbial ecosystem is a complex system where rumen fermentation processes involve interactions among microorganisms. There are important relationships between diet and the ruminal bacterial composition. Thus, we investigated the ruminal fermentation characteristics and compared ruminal bacterial communities using tag amplicon pyrosequencing analysis in Yanbian yellow steers, which were fed linseed oil (LO) and propionate precursors. We used eight ruminally cannulated Yanbian yellow steers (510 ± 5.8 kg) in a replicated 4 × 4 Latin square design with four dietary treatments. Steers were fed a basal diet that comprised 80% concentrate and 20% rice straw (DM basis, CON). The CON diet was supplemented with LO at 4%. The LO diet was also supplemented with 2% dl-malate or 2% fumarate as ruminal precursors of propionate. Dietary supplementation with LO and propionate precursors increased ruminal pH, total volatile fatty acid concentrations, and the molar proportion of propionate. The most abundant bacterial operational taxonomic units in the rumen were related to dietary treatments. Bacteroidetes dominated the ruminal bacterial community and the genus Prevotella was highly represented when steers were fed LO plus propionate precursors. However, with the CON and LO diet plus malate or fumarate, Firmicutes was the most abundant phylum and the genus Ruminococcus was predominant. In summary, supplementing the diets of ruminants with a moderate level of LO plus propionate precursors modified the ruminal fermentation pattern. The most positive responses to LO and propionate precursors supplementation were in the phyla Bacteriodetes and Firmicutes, and in the genus Ruminococcus and Prevotella. Thus, diets containing LO plus malate or fumarate have significant effects on the composition of the rumen microbial community.     

Effects of finishing diet sorting and digestibility on performance and feed efficiency in beef steers

The aim of this study was to test the hypotheses that differences in residual feed intake (RFI) of beef steers are related to diet sorting, diet nutrient composition, energy intake and apparent digestibility. To phenotype steers for RFI, 69 weaned Angus × Hereford steers were fed individually for 56 days. A finishing diet was fed twice daily on an ad libitum basis to maintain approximately 0.5 to 1.0 kg refusals. Diet offered and refused was measured daily, and DM intakes (DMI) were calculated by difference. Body weights were recorded at 14-day intervals following an 18-h solid feed withdrawal. The residual feed intake was determined as the residual of the regression of DMI versus mid-test metabolic BW (BW ^0.75) and average daily gain (ADG). Particle size distributions of diet and refusals were determined using the Penn State Particle Separator to quantify diet sorting. Sampling of diet, refusals and feces were repeated in four sampling periods which occurred during weeks 2, 4, 6 and 8 of the study. Particle size distributions of refusals and diet were analyzed in weeks 2, 4 and 6, and sampling for chemical analysis of refusals and feces occurred in all four periods. Indigestible neutral detergent fiber (288 h in situ) was used as an internal marker of apparent digestibility. We conclude that preference for the intakes of particles > 19 mm and 4 to 8 mm were negatively correlated to RFI and ADG, respectively. Although steers did sort to consume a different diet composition than offered, diet sorting did not impact intake energy, digestible energy or DM digestibility.     

Interaction Between Nickel and Protein Source in the Ruminant

Eighty growing steers were used to determine the effect of nickel supplementation on performance and metabolic parameters of steers fed corn silage-based diets supplemented with different crude protein sources. Crude protein sources examined included: (1) soybean meal, (2) blood meal, (3) urea, and (4) blood meal-urea (two-thirds of supplemental nitrogen from blood meal and one-third from urea). The protein sources differed in ruminal degradability, nitrogen solubility, and nickel content. Nickel was added within each protein treatment to supply either 0 or 5 ppm of supplemental nickel. The experiment was 84 d in duration and rumen fluid and blood samples were collected on days 42 and 80. Average daily gain and feed efficiency were not affected by nickel supplementation. The addition of 5 ppm supplemental nickel greatly increased rumen bacterial urease activity regardless of protein source. When samples were collected prior to feeding on day 80, nickel increased serum urea nitrogen concentrations in steers fed urea, but decreased circulating urea concentrations in animals fed blood meal or the blood meal-urea combination.Ad libitum intake of trace mineral salt was greatly reduced in steers receiving 5 ppm supplemental nickel. The present study suggests that the source of protein may influence ruminant responses to dietary nickel.     

Expression of candidate genes for residual feed intake in Angus cattle

Residual feed intake (RFI) has been adopted in Australia for the purpose of genetic improvement in feed efficiency in beef cattle. RFI is the difference between the observed feed intake of an animal and the predicted feed intake based on its size and growth rate over a test period. Gene expression of eight candidate genes (AHSG, GHR, GSTM1, INHBA, PCDH19, S100A10, SERPINI2 and SOD3), previously identified as differentially expressed between divergent lines of high‐ and low‐RFI animals, was measured in an unselected population of 60 steers from the Angus Society Elite Progeny Test Program using quantitative real‐time PCR. Results showed that the levels of gene expression were significantly correlated with RFI. The genes explain around 33.2% of the phenotypic variance in RFI, and prediction equations using the expression data are reasonably accurate estimators of RFI. The association of these genes with economically important traits, such as other feed efficiency‐related traits and fat, growth and carcass traits, was investigated as well. The expression of these candidate genes was significantly correlated with feed conversion ratio and daily feed intake, which are highly associated with RFI, suggesting a functional role for these genes in modulating feed utilisation. The expression of these genes did not show any association with average daily gain, eye muscle area and carcass composition.