Search

Understanding host-microbial interactions in the rumen and its influence on desirable production traits may lead to potential microbiota manipulation or genetic selection for improved cattle feed efficiency. This study investigated the host transcriptome and its correlation with the rumen archaea and bacteria differential abundance of two pure beef cattle breeds (Angus and Charolais) and one composite beef hybrid (Kinsella) divergent for residual feed intake (RFI; low-RFI vs. high-RFI). Using RNA-Sequencing of rumen tissue and 16S rRNA gene amplicon sequencing, differentially expressed genes (FDR ≤ 0.05, |log2(Fold-change) >|2) and differentially abundant (p-value < 0.05) archaea and bacteria amplicon sequence variants (ASV) were determined. Significant correlations between gene expression and ASVs (p-value < 0.05) were determine using Spearman correlation. Interesting associations with muscle contraction and the modulation of the immune system were observed for the genes correlated with bacterial ASVs. Potential functional candidate genes for feed efficiency status were identified for Angus (CCL17, CCR3, and CXCL10), Charolais (KCNK9, GGT1 and IL6), and Kinsella breed (ESR2). The results obtained here provide more insights regarding the applicability of target host and rumen microbial traits for the selection and breeding of more feed efficient beef cattle. [ABSTRACT FROM AUTHOR]

A greater understanding of the rumen microbiota and its function may help find new strategies to improve feed efficiency in cattle. This study aimed to investigate whether the cattle breed affects specific ruminal taxonomic microbial groups and functions associated with feed conversion ratio (FCR), using two genetically related Angus breeds as a model. Total RNA was extracted from 24 rumen content samples collected from purebred Black and Red Angus bulls fed the same forage diet and then subjected to metatranscriptomic analysis. Multivariate discriminant analysis (sparse partial least square discriminant analysis (sPLS-DA)) and analysis of composition of microbiomes were conducted to identify microbial signatures characterizing Black and Red Angus cattle. Our analyses revealed relationships among bacterial signatures, host breeds and FCR. Although Black and Red Angus are genetically similar, sPLS-DA detected 25 bacterial species and 10 functions that differentiated the rumen microbial signatures between those two breeds. In Black Angus, we identified bacterial taxa Chitinophaga pinensis , Clostridium stercorarium and microbial functions with large and small subunits ribosomal proteins L16 and S7 exhibiting a higher abundance in the rumen microbiome. In Red Angus, nonetheless, we identified the poorly characterized bacterial taxon Oscillibacter valericigenes with a higher abundance and pathways related to carbohydrate metabolism. Analysis of composition of microbiomes revealed that C. pinensis and C. stercorarium exhibited a higher abundance in Black Angus compared to Red Angus associated with FCR, suggesting that these bacterial species may play a key role in the feed conversion efficiency of forage-fed bulls. This study highlights how the discovery of signatures of bacterial taxa and their functions can be used to harness the full potential of the rumen microbiome in Angus cattle. [ABSTRACT FROM AUTHOR]

The objective was to evaluate whether long-term addition of 3-nitrooxypropanol (NOP) to a beef cattle diet results in a sustained reduction in enteric CH4 emissions in beef cattle. Eight ruminally cannulated heifers (637 ± 16.2 kg BW) were used in a completely randomized design with 2 treatments: Control (0 g/d of NOP) and NOP (2 g/d of NOP). Treatments were mixed by hand into the total mixed ration (60% forage, DM basis) at feeding time. Feed offered was restricted to 65% of ad libitum DMI (slightly over maintenance energy intake) and provided once per day. The duration of the experiment was 146 d, including an initial 18-d covariate period without NOP use; a 112-d treatment period with NOP addition to the diet, divided into four 28-d time intervals (d 1 to 28, 29 to 56, 57 to 84, and 85 to 112); and a final 16-d recovery period without NOP use. During the covariate period and at the end of each interval and the end of the recovery period, CH4 was measured for 3 d using whole animal metabolic chambers. The concentration of VFA was measured in rumen fluid samples collected 0, 3, and 6 h after feeding, and the microbial population was evaluated using rumen samples collected 3 h after feeding on d 12 of the covariate period, d 22 of each interval within the treatment period, and d 8 of the recovery period. Average DMI for the experiment was 7.04 ± 0.27 kg. Methane emissions were reduced by 59.2% when NOP was used (9.16 vs. 22.46 g/kg DMI; P < 0.01). Total VFA concentrations were not affected (P = 0.12); however, molar proportion of acetate was reduced and that for propionate increased when NOP was added (P < 0.01), which reduced the acetate to propionate ratio (3.0 vs. 4.0; P < 0.01). The total copy number of the 16S rRNA gene of total bacteria was not affected (P = 0.50) by NOP, but the copy number of the 16S rRNA gene of methanogens was reduced (P < 0.01) and the copy number of the 18S rRNA gene of protozoa was increased (P = 0.03). The residual effect of NOP for most of the variables studied was not observed or was minimal during the recovery period. These results demonstrated that the addition of NOP to a diet for beef cattle caused a sustained decrease of methanogenesis, with no sign of adaptation, and that these effects were reversed once NOP addition was discontinued. [ABSTRACT FROM AUTHOR]

This study evaluated if 3-nitrooxypropanol reduces enteric methane (CH4) emissions when added to the diet of beef cattle. The effects of 3-nitrooxypropanol on related variables including diet digestibility, ruminai fermentation, and ruminai microorganisms were also investigated. Eight ruminally cannulated Angus heifers (549 ± 64.3 kg [mean BW ± SD]) were fed a high forage diet (backgrounding diet) supplemented with 4 levels of 3-nitrooxypropanol (0, 0.75, 2.25 and 4.50 mg/kg BW). The experiment was designed as a duplicated 4><4 Latin square with 2 groups of heifers and four 28-d periods. Methane emissions were measured during 3 consecutive days using metabolic chambers. Up to a 5.8% reduction in ad libitum DMI was observed when 2.5 mg/kg BW of 3-nitrooxypropanol was fed (P = 0.03). Increasing level of 3-nitrooxypropanol linearly (P < 0.001) reduced CH4, with 33% less CH4 (corrected for DMI) at the highest level of supplementation compared with the control. Feed energy lost as CH4 was also reduced when 3-nitrooxypropanol was supplemented (P < 0.001). Molar proportion of acetate was reduced (P < 0.001) and that for propionate increased (P < 0.001) with increasing dose of 3-nitrooxypropanol, which in turn led to a reduction in the acetate to propionate ratio (P < 0.001). Total copy numbers of 16S ribosomal RNA (rRNA) genes for bacteria, methanogens, and 18S rRNA genes for protozoa in ruminai contents were not affected by 3-nitrooxypropanol supplementation (P > 0.31). There was no effect of 3-nitrooxypropanol on DM (P = 0.1) digestibility in the total tract. The use of 4.5 mg/kg BW of 3-nitrooxypropanol in beef cattle consuming a backgrounding diet was effective in reducing enteric CH4 emissions without negatively affecting diet digestibility. [ABSTRACT FROM AUTHOR]

Fat deposition influences both meat quality and animal productivity. However, it is not clear how fat development is regulated in growing and fattening beef cattle. This study characterized proteomic changes in subcutaneous adipose tissue from steers fed a high-grain diet in an effort to understand the molecular mechanisms of fat development during feedlot production. Eight British-Continental crossbred steers had two subcutaneous adipose tissue biopsies at 12 and 15 mo of age. Protein expression in fat samples was profiled using liquid chromatography-tandem mass spectrometry (LC-MS/MS). During the finishing period, steers increased subcutaneous adipose tissue mass with concomitant changes in the proteome profile, but the nature of these changes varied among steers. The expression of 123 out of 627 identified proteins differed (P < 0.05) between 2 ages. Functional analyses on differentially expressed proteins revealed that 20.2% of them were associated with cellular growth and proliferation of adipose tissue. There were 17 out of 108 differentially expressed proteins associated with lipid metabolism, which were acyl-CoA synthetase mediumchain family member 1 (ACSMl),annexin A 1 (ANXA1), apolipoprotein C-III (APOC3), apolipoprotein H (beta- 2-glycoprotein I; APOH), EH-domain containing 1 (EHD1), coagulation factor II (thrombin; F2), gelsolin (GSN), lamin A/C (LMNA), mitogen-activated protein kinase kinase 1 (MAP2K1), myosin, heavy chain 9, non-muscle (MYH9), orosomucoid 1 (ORM1), protein disulfide isomerase family A, member 3 (PDIA3), retinol binding protein 4, plasma (RBP4), renin binding protein (RENBP), succinate dehydrogenase complex, subunit A, flavoprotein (Fp; SDHA), serpin peptidase inhibitor, clade C (antithrombin), member 1 (SERPINC1), and serpin peptidase inhibitor, clade G (Cl inhibitor), member 1 (SERPING1). Further analysis of the expression levels of proteins associated with lipid metabolism indicated a downregulation in the synthesis of fatty acids at the cellular level at 15 compared to 12 mo of age. These results suggest that even though adipose tissue expanded, fat anabolism was reduced in adipocytes during growth, revealing a coordinated balance between subcutaneous fat mass and the cellular abundance of lipogenic proteins to control the rate of fat deposition in growing beef cattle. The findings observed in this study expand our understanding on how proteome of bovine adipose tissue is regulated during growth, which might help the development in the future of new strategies to manipulate adiposity in beef cattle in a manner that improves meat quality and animal productivity. [ABSTRACT FROM AUTHOR]

This study investigated the variability of ruminal methanogen/protozoa among beef heifers (n =4) fed corn- or wheat-dried distillers' grain with solubles (DDGS). Polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis and quantitative real-time PCR were used to investigate variation in ruminal methanogenic communities, while protozoal communities were analyzed using light microscopy. Observed methanogen profiles were not affected by DDGS source, but were distinctive within individuals (GlobalR=0.87,P <0.01). Populations of total methanogens, total protozoa,Methanobrevibactersp. AbM4,Entodinium, andPolyplastronvaried among heifers and diets, while densities of totalMethanosphaera stadtmanae,Isotricha, andOstracodiniumonly differed among individual hosts. Responses in the ruminal methanogenic community to DDGS source were host dependent, suggesting that host biology should not be ignored if dietary strategies are used to alter ruminal methanogens to lower enteric methane emissions. [ABSTRACT FROM PUBLISHER]

The molecular mechanisms that regulate fat deposition in bovine adipose tissue have not been well studied. To elucidate the genes and gene networks involved in bovine fat development, transcriptional profiles of backfat (BF) tissues from Hereford x Aberdeen Angus (HEAN, a = 6) and Charolais x Red Angus (CHRA, a = 6) steers with high or low BF thickness were characterized by digital gene expression-tag profiling. Approximately 9.8 to 21.9 million tags were obtained for each library, and a total of 18,034 genes were identified. In total, 650 genes were found to be differentially expressed, with a greater than 1.5-fold difference between the 2 crossbreds (Benjamini-Hochberg false discovery rate ~ 0.05). The majority of differentially expressed genes that were more highly expressed in CHRA vs. HEAN were associated with development, whereas the differentially expressed genes with greater expression in HEAN vs. CHRA were overrepresented in biological processes such as metabolism and immune response. Thirty-six and 152 differentially expressed genes were detected between animals with high (n = 3) and low (n = 3) BF thickness in HEAN and CHRA, respectively (Benjamini-Hochberg false discovery rate ≤0.05). The differentially expressed genes between high and low groups in CHRA were related to cell proliferation and development processes. In addition, lipid metabolism was 1 of the top 5 molecular and cellular functions identified in both crossbreds. Ten and 17 differentially expressed genes were found to be involved in fat metabolism in HEAN and CHRA, respectively. Genes associated with obesity, such as PTX3 (pentraxin 3, long) and SERPINE1 (serpin peptidase inhibitor, dade E, member 1), were more highly expressed (P < 0.05) in the subset of CHRA animals with greater BF thickness. Our study revealed that the expression patterns of genes in BF tissues differed depending on the genetic background of the cattle. [ABSTRACT FROM AUTHOR]

Background: Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. Results: On average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P < 0.05) associated with immune and metabolic pathways. Conclusion: The most optimized RNA-Seq pipeline allowed for more accurate identification of SNPs, associated positional candidate genes, and significantly associated metabolic pathways in muscle and liver tissues, providing insight on the underlying genetic architecture of feed efficiency in beef cattle. [ABSTRACT FROM AUTHOR]

Breeding and management of animals to achieve improved feed efficiency is a significant priority for the beef industry. Feed conversion ratio (FCR) and residual feed intake (RFI) have become popular measurements for feed efficiency, although both have limitations and practical challenges. The identification of additional, cost-effective indicators of feed efficiency is needed to improve breeding programs. We hypothesized that volatile fatty acids (VFAs), the end products of rumen microbial fermentation and the primary energy source for ruminants, could potentially dictate feed utilization for growth and production. In this study, we tested whether residual VFA (rVFAs) could serve as a predictor of feed efficiency. Rumen content was collected from a total of 204 beef (Angus, Charolais, and Kinsella composite) steers raised under a Growsafe® system, and VFA concentrations (mol/L) were analyzed by gas chromatography. Microbial populations were estimated using total copy numbers of 16S rRNA genes for bacteria and archaea using quantitative PCR (qPCR). Animal phenotypic measures including body weight (BW), dry matter intake (DMI), average daily gain (ADG), feeding frequency, RFI, and carcass performances were collected. The feed was collected at the time of rumen sample collection, and its nutrient content was analyzed. VFA concentrations and production rates were predicted using the Molly mathematical model for each animal based on observed BW, DMI, and ration composition. Residual VFA concentrations were calculated as observed minus predicted VFA concentration. The relationships among digestion parameters and rVFA were tested using stepwise, backward linear regression, which was also used to test rVFA as a predictor of feed efficiency. Residual acetate (ResAc), propionate (ResPro), and total VFA concentrations were significantly correlated with BW, DMI, and breed. Residual butyrate (ResBu) was correlated only with DMI. Total bacterial copy number was negatively correlated with eating frequency (P < 0.05) and ResAc (P < 0.01) and positively associated with ResPro (P < 0.01) concentrations. Total archeal copy number was inversely related to ResPro. RFI was significantly affected by DMI (P < 0.01) and ResAc and showed a significant negative relationship with ResPr and ResBu (P < 0.05). Similarly, FCR was significantly affected by DMI, ADG, and breed. Both ResPr and ResBu had non-significant (P < 0.1), inverse relationships with FCR. Although the work needs to be independently evaluated, our preliminary results identified the potential of using rVFA concentrations to predict feed efficiency traits in beef steers. [ABSTRACT FROM AUTHOR]

The objective was to determine the effect of maternal nutrition management during mid-gestation on the skeletal muscle transcriptome in progeny using 3 dietary treatments. Springcalving, multiparous cows (n = 25) were limit-fed a common diet at three levels of intake to achieve 70% NRC requirement (70%REQ; 5.2 kg DMI), 100% NRC energy and protein requirements (REQ; 7.4 kg DMI), and 130% NRC requirements (130%REQ; 9.7 kg DMI). Diet composition included soy hulls, corn silage, and alfalfa haylage. Treatment diets were fed during mid-gestation (d 88 to 171 of gestation), and a common diet formulated to meet 100% NRC requirements was fed during the remainder of gestation. After calving, all cows and calves were managed similarly as a single contemporary group. Longissimus muscle biopsies were taken on 99 and 392 d of age. Extracted RNA was used in paired-end RNA sequencing on the Illumina HiSeq 2500 platform to analyze the transcriptome at d 99 and 392. Transcriptomic data were mapped to the UMD3.1.1 bovine reference genome and analyzed using a mixed model approach within the R-package limma. Over 7,000 expressed genes were included in weighted gene co-expression network analysis (WGCNA), which clustered genes into 11 modules including 4 that correlated to phenotypic measures. The largest module included over 2,000 co-expressed genes and was downregulated (P < 0.01) in progeny born to 130%REQ-fed compared with REQfed dams. The Dynamic Impact Approach annotated genes within this module to KEGG pathways. The pathways most impacted by maternal plane of nutrition were mainly lipid-associated including steroid and steroid hormone biosynthesis, sulfur metabolism, retinol metabolism, ketone synthesis and degradation, fat digestion and absorption, and PPAR signaling pathways. Module 7 (342 genes) was correlated positively with Warner-Bratzler shear force and negatively with marbling score. Major pathways in module 7 centered on glycolysis/gluconeogenesis, energy metabolism, and calcium signaling. These genes and associated pathways support increased glycolytic muscle fibers (type 2x) in progeny born to 130%REQfed compared with 70%REQ-fed dams. Results indicate the skeletal muscle transcriptome and associated metabolic functions prior to slaughter are affected by mid-gestation maternal plane of nutrition and may be regulated by epigenetic factors. [ABSTRACT FROM AUTHOR]

Current understanding regarding the impact of interactions between diet and host on the rumen microbiome is limited. The objectives of this study were to (i) investigate rumen microbial population dynamics in beef cattle fed grain-based (high starch content) and/or forage-based diets (rich in neutral detergent fiber, NDF) over two 80-day feeding periods (with a 20-day adaptation in between) and (ii) evaluate the rumen microbiota of cattle exhibiting different feed efficiencies. Sixty purebred Angus bulls (mean age: 249 ± 22 days; average body weight: 313.9 ± 32 kg; mean ± SD) were raised in confinement at the Glenlea Research Station (University of Manitoba, CA) and randomly assigned into four pens fed the following diets in periods one and two, respectively: pen 1, forage/forage; pen 2, forage/grain; pen 3, grain/forage; and pen 4, grain/grain. Microbial populations were estimated using quantitative PCR (qPCR) for bacteria, archaea, fungi, and protozoa from two rumen fluid samples collected per period using a Geishauser oral probe. Thereafter, individual hosts were classified into three groups based on the magnitude of the microbial population shift between each feeding period using log2-fold change (log2fc < -1, low; -1 < log2fc < 1, stable; and log2fc > 1, high) in 16S rRNA gene copy number for bacteria/archaea and 18S rRNA/ITS (internal transcribed spacer) for protozoa/fungi. The effects of starch/NDF intakes, feed conversion rate (FCR), and CH4 on the rumen microbes and their interactions with the three groups of host-microbial abundance variation were analyzed through log-normal generalized linear mixed models. Starch intake was associated with a marked decline in bacteria and fungi in the low group (P < 0.001 and P = 0.012, respectively), and NDF consumption increased bacteria and fungi only in the high group (P < 0.011), while no relationship was observed for archaea and protozoa across groups. Cattle in the low group produced more CH4 as bacteria density increased (P = 0.028), whereas bacterial abundance and CH4 remained constant in the stable and high groups. Bulls in the stable group were more efficient when linked to a higher bacterial abundance while bulls categorized in the low and high groups utilized the diet more efficiently when associated with the lowest bacteria densities. These findings suggest the potential use of the individualized rumen microbiota in host-tailored precision feeding systems, specially designed to improve feed efficiency in cattle. [ABSTRACT FROM AUTHOR]