Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase.
Ontology highlight
ABSTRACT:
SUBMITTER: Lourenco JM
PROVIDER: S-EPMC9227454 | biostudies-literature | 2022 May
REPOSITORIES: biostudies-literature
Publications
Fecal Microbiome Differences in Angus Steers with Differing Feed Efficiencies during the Feedlot-Finishing Phase.
Lourenco Jeferson M JM Welch Christina B CB Krause Taylor R TR Wieczorek Michael A MA Fluharty Francis L FL Rothrock Michael J MJ Pringle T Dean TD Callaway Todd R TR
Microorganisms 20220531 6
The gastrointestinal microbiota of cattle is important for feedstuff degradation and feed efficiency determination. This study evaluated the fecal microbiome of Angus steers with distinct feed efficiencies during the feedlot-finishing phase. Angus steers (<i>n</i> = 65), fed a feedlot-finishing diet for 82 days, had growth performance metrics evaluated. Steers were ranked based upon residual feed intake (RFI), and the 5 lowest RFI (most efficient) and 5 highest RFI (least efficient) steers were ...[more]
Similar Datasets
Project description:Feed is the greatest cost of animal production, so reducing it is critical to increase producer profits. In ruminants, the microbial population within the gastrointestinal tract (GIT) is critical to nutrient digestion and absorption in both the rumen and the hindgut. The objective of this study was to determine the bacterial taxonomic profile of the rumen, cecum, and feces of feedlot steers at slaughter in order to link feed efficiency and the GIT bacterial populations from these three locations. Twenty commercial Angus steers were selected and divided into two groups according to their residual feed intake (RFI) classification determined during the feedlot-finishing period: high-RFI (n = 10) and low-RFI (n = 10). After the ruminal, cecal, and fecal samples were collected at slaughter, DNA extraction and 16S rRNA gene sequencing were performed on them to determine their bacterial composition. One-way ANOVA was performed on the animal performance data, alpha diversities, and bacterial abundances using RFI classification as the fixed effect. Overall, the ruminal bacterial population was the most different in terms of taxonomic profile compared with the cecal and fecal populations as revealed by beta diversity analysis (P < 0.001). Moreover, bacterial richness (Chao1) was greatest (P = 0.01) in the rumen of the high-RFI group compared with the low-RFI group. In contrast, bacterial richness and diversity in the intestinal environment showed that Chao1 was greater (P = 0.01) in the cecum, and the Shannon diversity index was greater in both the cecum and feces of low-RFI compared with high-RFI steers (P = 0.01 and P < 0.001, respectively). Ruminococcaceae was more abundant in the low-RFI group in the cecum and feces (P = 0.01); fecal Bifidobacteriaceae was more abundant in high-RFI steers (P = 0.03). No correlations (P ≥ 0.13) between any ruminal bacterial family and RFI were detected; however, Ruminococcaceae, Mogibacteriaceae, Christensenellaceae, and BS11 were negatively correlated with RFI (P < 0.05) in the cecum and feces. Succinivibrionaceae in the cecum was positively correlated with RFI (P = 0.05), and fecal Bifidobacteriaceae was positively correlated with RFI (P = 0.03). Results collectively indicate that in addition to the ruminal bacteria, the lower gut bacterial population has a significant impact on feed efficiency and nutrient utilization in feedlot steers; therefore, the intestinal bacteria should also be considered when examining the basis of ruminant feed efficiency.
| S-EPMC7392532 | biostudies-literature
Project description:Numerous studies have examined the link between the presence of specific gastrointestinal bacteria and the feed efficiency of cattle. However, cattle undergo dietary changes during their productive life which can cause fluctuations in their microbial consortium. The objective of the present study was to assess changes in the fecal microbiome of beef steers genetically selected to be divergent in feedlot feed efficiency, to determine whether differences in their fecal microbiomes could be detected as early as weaning, and continued throughout the rearing process regardless of dietary changes. Fecal samples were collected at weaning, yearling age, and slaughter for a group of 63 steers. Based on their feedlot-finishing performance, the steers were selected and divided into two groups according to their residual feed intake (RFI): efficient steers (low-RFI; n = 7) and inefficient steers (high-RFI; n = 8). To ascertain the fecal microbial consortium and volatile fatty acid (VFA) content, 16S rRNA gene sequencing and VFA analysis were performed. Overall, bacterial evenness and diversity were greater at weaning compared to yearling and slaughter for both efficiency groups (P < 0.001). Feedlot RFI linearly decreased as both Shannon diversity and Ruminococcaceae abundance increased (R 2 = 65.6 and 60.7%, respectively). Abundances of Ruminococcaceae, Rikenellaceae, and Christensenellaceae were higher at weaning vs. yearling age and slaughter (P < 0.001); moreover, these families were consistently more abundant in the feces of the low-RFI steers (for most of the timepoints evaluated; P ≤ 0.05), compared to the high-RFI steers. Conversely, abundances of Bifidobacteriaceae were numerically higher in the feces of the high-RFI steers throughout their lifespan. Total VFA concentrations increased at slaughter compared to weaning and yearling for both efficiency groups (P < 0.001). The acetate:propionate ratio decreased linearly (P < 0.001) throughout the life of the steers regardless of their efficiency, reflective of dietary changes. Our results indicate that despite fluctuations due to animal age and dietary changes, specific bacterial families may be correlated with feed efficiency of steers. Furthermore, such differences may be identifiable at earlier stages of the production cycle, potentially as early as weaning.
| S-EPMC8275654 | biostudies-literature
Project description:BackgroundImproving feedlot performance, carcase weight and quality is a primary goal of the beef industry worldwide. Here, we used data from 3408 Australian Angus steers from seven years of birth (YOB) cohorts (2011-2017) with a minimal level of sire linkage and that were genotyped for 45,152 SNPs. Phenotypic records included two feedlot and five carcase traits, namely average daily gain (ADG), average daily dry matter intake (DMI), carcase weight (CWT), carcase eye muscle area (EMA), carcase Meat Standard Australia marbling score (MBL), carcase ossification score (OSS) and carcase subcutaneous rib fat depth (RIB). Using a 7-way cross-validation based on YOB cohorts, we tested the quality of genomic predictions using the linear regression (LR) method compared to the traditional method (Pearson's correlation between the genomic estimated breeding value (GEBV) and its associated adjusted phenotype divided by the square root of heritability); explored the factors, such as heritability, validation cohort, and phenotype that affect estimates of accuracy, bias, and dispersion calculated with the LR method; and suggested a novel interpretation for translating differences in accuracy into phenotypic differences, based on GEBV quartiles (Q1Q4).ResultsHeritability (h2) estimates were generally moderate to high (from 0.29 for ADG to 0.53 for CWT). We found a strong correlation (0.73, P-value < 0.001) between accuracies using the traditional method and those using the LR method, although the LR method was less affected by random variation within and across years and showed a better ability to discriminate between extreme GEBV quartiles. We confirmed that bias of GEBV was not significantly affected by h2, validation cohort or trait. Similarly, validation cohort was not a significant source of variation for any of the GEBV quality metrics. Finally, we observed that the phenotypic differences were larger for higher accuracies.ConclusionsOur estimates of h2 and GEBV quality metrics suggest a potential for accurate genomic selection of Australian Angus for feedlot performance and carcase traits. In addition, the Q1Q4 measure presented here easily translates into possible gains of genomic selection in terms of phenotypic differences and thus provides a more tangible output for commercial beef cattle producers.
| S-EPMC8474816 | biostudies-literature
Project description:BackgroundCastration is a common practice in beef cattle production systems to manage breeding and enhance meat quality by promoting intramuscular fat (IMF) deposition, known as marbling. However, the molecular mechanisms that are influenced by castration in beef cattle are poorly understood. The aim of this study was to identify differentially expressed genes (DEGs) and metabolic pathways that regulate IMF deposition in crossbred cattle by RNA sequencing (RNA-Seq) of skeletal muscle tissue. Six hundred and forty F1 Angus-Nellore bulls and steers (n = 320/group) were submitted to feedlot finishing for 180 days. Sixty Longissimus thoracis muscle samples were collected randomly from each group in the hot carcass (at slaughter) and 48 h post-mortem (at deboning), at between 12th and 13th thoracic vertebrae. Three muscle samples of each group were randomly selected for RNA-Seq analysis, while the post-deboning meat samples were submitted to determination of IMF content.ResultsSteers had a 2.7-fold greater IMF content than bulls (5.59 vs. 2.07%; P < 0.01). A total of 921 DEGs (FDR < 0.05) were identified in contrast between Bulls versus Steers; of these, 371 were up-regulated, and 550 were down-regulated. Functional transcriptome enrichment analysis revealed differences in biological processes and metabolic pathways related to adipogenesis and lipogenesis, such as insulin resistance, AMPK, cAMP, regulation of lipolysis in adipocytes, and PI3K-Akt signaling pathways. Candidate genes such as FOXO1, PPARG, PCK2, CALM1, LEP, ADIPOQ, FASN, FABP4, PLIN1, PIK3R3, ROCK2, ADCY5, and ADORA1 were regulated in steers, which explains the expressive difference in IMF content when compared to bulls.ConclusionsThe current findings suggest the importance of these pathways and genes for lipid metabolism in steers with greater IMF. Notably, this study reveals for the first time the involvement of the PI3K-Akt pathway and associated genes in regulating IMF deposition in F1 Angus-Nellore cattle. Castration influenced DEGs linked to energy metabolism and lipid biosynthesis, highlighting key molecular players responsible for IMF accumulation post-castration in beef cattle.
| S-EPMC11616301 | biostudies-literature
Project description:Abstract Although residual feed intake (RFI) is a moderately heritable trait that can be used as a selection tool, little is known about gene pathways and networks that affect it. Angus steers (n=1,460) from 72 contemporary groups (RFI: -6.44 to 7.52 kg/d) were genotyped with Illumina BovineHD or BovineSNP50 BeadChip assays. Significant SNP (P<0.05), identified by a genome-wide association analysis on RFI, were used as proxies for each of the annotated genes in the UMD3.1 bovine reference genome assembly. A gene set enrichment analysis-SNP was performed to identify gene sets and leading edge genes (LEG) and a network analysis was conducted to identify upstream and master regulators influencing RFI. Three enriched gene sets (normalized enrichment score>3.0) related to energy production and efficiency of energy usage (cellular respiration, GO:0045333, 20 LEG; Reactome respiratory electron transport, R-HSA-611105, 12 LEG; respiratory chain, GO:0070469, 12 LEG) were identified, corroborating evidence from RFI studies with cattle and other species. Additional enriched gene sets were synaptic vesicle (GO:0008021, 16 LEG), cell-cell junction (GO:0005911, 55 LEG), and protein localization to plasma membrane (GO:0072659, 20 LEG). Mediator complex subunit 30 (MED30) and RPTOR independent companion of MTOR complex 2 (RICTOR) were the most significant (P<10-10) upstream regulators. Part of the Mediator complex, MED30 plays a key role in transcription regulation and mediates lipid biosynthesis while RICTOR is a component of the mTOR complex, which regulates mitochondrial metabolism. Thyroid stimulating hormone receptor (TSHR), part of the hypothalamus-pituitary-thyroid axis that is essential for growth and metabolism and Ras homolog enriched in brain like 1 (RHEBL1), a gene that activates the mTOR complex in the brain, were the two most significant (P<10–14) master regulators. Gene set and pathway analyses suggest that biological processes related to energy metabolism and mitochondrial function play important roles in controlling RFI in cattle.
| S-EPMC6285512 | biostudies-literature
Project description:One hundred eight Angus × Hereford steers, originating from 7 cow-calf were obtained from an auction yard on d -2 and transported by road (800 km; 12 h) to an experimental feedlot facility. Upon arrival on d -1, shrunk BW was recorded and steers were grouped with free-choice access to grass hay, mineral supplement, and water. On d 0, steers were ranked by source and shrunk BW and assigned to 1 of 18 pens (6 steers/pen). Pens were allocated to 1) no immunomodulatory ingredient supplementation during feedlot receiving (CON), 2) supplementation with OmniGen-AF (OMN; 22 g/steer daily, as-fed basis; Phibro Animal Health Corp., Teaneck, NJ) from d 0 to 30, or 3) 2 oral capsules of Stocker Immune Primer on d 0 + 15 g/steer daily (as-fed basis) of Stocker Preconditioned Premix (Ramaekers Nutrition, Santa Cruz, CA) from d 7 to 30 (IPF). From d 0 to 80, steers had free-choice access to grass hay and water and received a corn-based concentrate. Feed DMI was recorded from each pen, and steers were assessed for bovine respiratory disease (BRD) signs daily. Steers were vaccinated against BRD pathogens on d 0 and 21. Final shrunk BW was recorded on d 81, and blood samples were collected on d 0, 3, 7, 10, 14, 21, 31, 42, 56, and 73. Steer ADG and final BW were greater ( ? 0.05) in CON steers than in OMN and IPF steers (1.23, 0.76, and 1.06 kg/d [SEM 0.06], respectively, and 320, 282, and 307 kg [SEM 4], respectively) and ( < 0.01) in IPF steers than in OMN steers. No treatment effects were detected ( ? 0.76) for BRD incidence (66 ± 4%) and DMI, whereas G:F was greater ( < 0.01) in OMN steers than in CON steers. Mean plasma cortisol concentration was greater ( = 0.01) in CON steers than in OMN and IPF steers. Plasma haptoglobin concentrations tended ( = 0.10) to be greater in CON steers than in IPF steers on d 3, were greater ( = 0.04) in IPF steers than in CON steers on d 7, and tended ( = 0.10) to be less in OMN steers than in IPF and CON steers on d 21. Blood mRNA expression of was greater ( ? 0.05) in OMN and IPF steers than in CON steers on d 3 and in OMN steers than in CON and IPF steers on d 14. Blood mRNA expression of was greater ( ? 0.05) in OMN and IPF steers than in CON steers on d 10. Plasma IGF-I concentrations, serum antibody titers to BRD pathogens, and blood mRNA expression of , , , and did not differ ( ? 0.21) among treatments. Collectively, the immunomodulatory feed ingredients evaluated herein impacted adrenocortical and innate immune responses but failed to mitigate BRD incidence and improve performance of receiving cattle.
| S-EPMC6292293 | biostudies-literature
Project description:Growing ruminants maintained under dietary restriction for extended periods will exhibit compensatory growth when reverted to ad libitum feeding. This period of compensatory growth is associated with increased feed efficiency, lower basal energy requirements, and changes in circulating concentrations of metabolic hormones. To identify genetic mechanisms contributing to these physiological changes, 8 month-old steers were fed either ad libitum (control; n = 6) or 60-70% of intake of control animals (feed-restricted; n=6) for a period of 12 weeks. All steers were then fed ad libitum for the remaining 8 weeks of the experiment (realimentation period). Liver was biopsied from each animal at days -14, +1 and +14 relative to realimentation for RNA extraction and gene expression analysis by microarray hybridization.
2008-10-01 | GSE12853 | GEO
Project description:Escherichia coli O157:H7 is a major foodborne human pathogen causing disease worldwide. Cattle are a major reservoir for this pathogen and those that shed E. coli O157:H7 at >104 CFU/g feces have been termed "super-shedders". A rich microbial community inhabits the mammalian intestinal tract, but it is not known if the structure of this community differs between super-shedder cattle and their non-shedding pen mates. We hypothesized that the super-shedder state is a result of an intestinal dysbiosis of the microbial community and that a "normal" microbiota prevents E. coli O157:H7 from reaching super-shedding levels. To address this question, we applied 454 pyrosequencing of bacterial 16S rRNA genes to characterize fecal bacterial communities from 11 super-shedders and 11 contemporary pen mates negative for E. coli O157:H7. The dataset was analyzed by using five independent clustering methods to minimize potential biases and to increase confidence in the results. Our analyses collectively indicated significant variations in microbiome composition between super-shedding and non-shedding cattle. Super-shedders exhibited higher bacterial richness and diversity than non-shedders. Furthermore, seventy-two operational taxonomic units, mostly belonging to Firmicutes and Bacteroidetes phyla, were identified showing differential abundance between these two groups of cattle. The operational taxonomic unit affiliation provides new insight into bacterial populations that are present in feces arising from super-shedders of E. coli O157:H7.
| S-EPMC4032279 | biostudies-literature
Project description:Increasing nutrient utilization efficiency is an important component of enhancing the sustainability of beef cattle production. The objective of this experiment was to determine the association of glucose metabolism and insulin resistance with dry matter intake (DMI), average daily gain (ADG), gain:feed ratio (G:F), and residual feed intake (RFI). Steers (n = 54; initial body weight = 518 ± 27.0 kg) were subjected to an intravenous glucose tolerance test (IVGTT) where glucose was dosed through a jugular catheter and serial blood samples were collected. Three days after the last group's IVGTT, steers began a 63-d DMI and ADG test. Body weight was measured on days 0, 1, 21, 42, 62, and 63, and DMI was measured using an Insentec Roughage Intake Control system (Hokofarm Group, Emmeloord, the Netherlands). To examine relationships between DMI, ADG, G:F, and RFI with IVGTT measurements, Pearson correlations were calculated using Proc Corr of SAS 9.4 (SAS Inst. Inc., Cary, NC). Additionally, cattle were classified based on DMI, ADG, RFI, and G:F, where the medium classification was set as mean ± 0.5 SD, the low classification was < 0.5 SD from the mean, and the high classification was > 0.5 SD from the mean. No associations between DMI and IVGTT parameters were observed, and no differences were detected when classifying cattle as having low, medium, or high DMI. Peak insulin concentration in response to the IVGTT tended to be correlated with ADG (r = 0.28; P = 0.07), indicating cattle with greater ADG tend to have a greater insulin release in response to glucose. Glucose nadir concentrations tended to be positively correlated with ADG (r = 0.26; P = 0.10). Additionally, the glucose nadir was greater in high-ADG steers (P = 0.003). The association of greater glucose nadir with high-ADG could indicate that high-ADG steers do not clear glucose as efficiently as low-ADG steers, potentially indicating increased insulin resistance. Further, RFI was not correlated with IVGTT measurements, but low RFI steers had a greater peak glucose concentration (P = 0.040) and tended to have a greater glucose area under the curve (P = 0.09). G:F was correlated with glucose area under the curve (r = 0.33; P = 0.050), glucose nadir (r = 0.35; P = 0.011), and insulin time to peak (r = 0.39; P = 0.010). These results indicate that glucose metabolism and insulin signaling are associated with growth and efficiency, but the molecular mechanisms that drive these effects need to be elucidated.
| S-EPMC10926941 | biostudies-literature
Project description:Our previous study suggested that supplementation of high-grain diets with ruminally protected and non-protected active dried yeast (ADY) may potentially reduce manure pathogen excretion by feedlot cattle. We hypothesized that feeding ruminally protected ADY might change the fecal bacterial community of finishing cattle. The objective of this study was to investigate the effects of feeding ruminally protected and non-protected ADY to finishing beef steers on their fecal bacterial community. Fresh fecal samples were collected on day 56 from 50 steers fed one of five treatments: 1) control (no monensin, tylosin, or ADY), 2) antibiotics (ANT, 330 mg monensin + 110 mg tylosin·steer-1d-1), 3) ADY (1.5 g·steer-1d-1), 4) encapsulated ADY (EDY; 3 g·steer-1d-1), and 5) a mixture of ADY and EDY (MDY; 1.5 g ADY + 3 g EDY·steer-1d-1). Bacterial DNA was extracted from fecal samples and sequenced using a MiSeq high-throughput sequencing platform. A total number of 2,128,772 high-quality V4 16S rRNA sequences from 50 fecal samples were analyzed, and 1,424 operational taxonomic units (OTU) were detected based on 97% nucleotide sequence identity among reads, with 769 OTU shared across the five treatments. Alpha diversity indices, including species observed, Chao estimate, abundance-based coverage estimator, Shannon, Simpson, and coverage, did not differ among treatments, and principal coordinate analysis revealed a high similarity among treatments without independent distribution. Bacteroidetes and Firmicutes were dominant phyla in the fecal bacterial community for all treatments, with a tendency (P < 0.10) for greater relative abundance of Bacteroidetes but lesser Firmicutes with ANT, EDY, and MDY compared with control steers. Prevotella was the dominant genus in all treatments and steers supplemented with ANT, EDY, and MDY had greater (P < 0.05) relative abundance of Prevotella than control steers, but lesser (P < 0.03) relative abundance of Oscillospira. No differences between ADY and control were observed for the aforementioned variables. Fecal starch contents were not different among treatments, but the relative abundance of Bacteroidetes, as well as Prevotella at genera level, tended (P < 0.06) to be positively correlated to fecal starch content. We conclude that supplementing ruminally protected or non-protected ADY or ANT had no effect on diversity and richness of fecal bacteria of finishing beef cattle, whereas feeding protected ADY or ANT to finishing beef steers altered the dominant fecal bacteria at phylum and genus levels. Therefore, supplementation of ruminally protected ADY may potentially improve intestinal health by stimulating the relative abundance of Prevotella.
| S-EPMC7105065 | biostudies-literature