Growth is frequently described as weight gain over time. Researchers have used this information in equations to predict carcass composition and estimate fat deposition. Diet, species, breed, and gender all influence fat deposition. Alterations in diets result in changes in fat deposition as well as the fatty acid profile of meat. Additionally, the amount and composition of the fat can affect lipid stability and flavor development upon cooking. Fat functions not only as a storage of energy and contributor of flavor compounds, but also participates in signaling that affects many aspects of the physiological functions of the animal. Transcription factors that are upregulated in response to excess energy to be stored are an important avenue of research to improve the understanding of fat deposition and thus, the efficiency of production. Additionally, further study of the inflammation associated with increased fat depots may lead to a better understanding of finishing animals, production efficiency, and overall health.

Although a number of common reproductive disorders in livestock involve bacterial infection, very little is known about their normal vaginal microbiota. Therefore, we sought to determine the species composition of sheep and cattle vaginal microbiota. Twenty Rambouillet ewes and twenty crossbred cows varying in age and reproductive status were sampled by ectocervicovaginal lavage. We amplified and sequenced the V3-V4 region of the 16S ribosomal RNA contents yielding a total of 907,667 high-quality reads. Good's Coverage estimates indicated that we obtained data on 98 +/- 0.01 % of the total microbial genera present in each sample. Cow and ewe vaginal microbiota displayed few differences. Cow microbiota exhibited greater (P ≤ 0.05) α-diversity compared to the ewe microbiota. Both livestock species differed (P ≤ 0.05) from all previously reported vaginal communities. While bacteria were numerically dominant, Archaea were detected in 95% of cow and ewe samples, mainly of the order Desulfurococcales. Both ewes and cows were predominately colonized by the bacterial phyla Bacteroidetes, Fusobacteria, and Proteobacteria. The most abundant genera were Aggregatibacter spp., and Streptobacillus spp. Lactobacillus ssp. were detected in 80% of ewe and 90% of cow samples, but only at very low abundances. Bacteria previously described from culture-based studies as common to the cow and ewe vaginal tract, except for Escherichia, were variably present, and only in low abundance. Ewe and cow pH differed (P ≤ 0.05), with means (+/- standard deviation) of 6.7 +/- 0.38 and 7.3 +/- 0.63, respectively. In conclusion, 16S rRNA sequencing of cow and ewe vaginal ectocervicovaginal lavages showed that cow and ewe vaginal microbiota differ from culture-led results, revealing a microbiota distinct from previously described vaginal ecosystems.

Background: One of the goals of livestock genomics research is to identify the genetic differences responsible for variation in phenotypic traits, particularly those of economic importance. Characterizing the genetic variation in livestock species is an important step towards linking genes or genomic regions with phenotypes. The completion of the bovine genome sequence and recent advances in DNA sequencing technology allow for in-depth characterization of the genetic variations present in cattle. Here we describe the whole-genome resequencing of two Bos taurus bulls from distinct breeds for the purpose of identifying and annotating novel forms of genetic variation in cattle. Results: The genomes of a Black Angus bull and a Holstein bull were sequenced to 22-fold and 19-fold coverage, respectively, using the ABI SOLiD system. Comparisons of the sequences with the Btau4.0 reference assembly yielded 7 million single nucleotide polymorphisms (SNPs), 24% of which were identified in both animals. Of the total SNPs found in Holstein, Black Angus, and in both animals, 81%, 81%, and 75% respectively are novel. In-depth annotations of the data identified more than 16 thousand distinct non-synonymous SNPs (85% novel) between the two datasets. Alignments between the SNP-altered proteins and orthologues from numerous species indicate that many of the SNPs alter well-conserved amino acids. Several SNPs predicted to create or remove stop codons were also found. A comparison between the sequencing SNPs and genotyping results from the BovineHD high-density genotyping chip indicates a detection rate of 91% for homozygous SNPs and 81% for heterozygous SNPs. The false positive rate is estimated to be about 2% for both the Black Angus and Holstein SNP sets, based on follow-up genotyping of 422 and 427 SNPs, respectively. Comparisons of read depth between the two bulls along the reference assembly identified 790 putative copy-number variations (CNVs). Ten randomly selected CNVs, five genic and five non-genic, were successfully validated using quantitative real-time PCR. The CNVs are enriched for immune system genes and include genes that may contribute to lactation capacity. The majority of the CNVs (69%) were detected as regions with higher abundance in the Holstein bull. Conclusions: Substantial genetic differences exist between the Black Angus and Holstein animals sequenced in this work and the Hereford reference sequence, and some of this variation is predicted to affect evolutionarily conserved amino acids or gene copy number. The deeply annotated SNPs and CNVs identified in this resequencing study can serve as useful genetic tools, and as candidates in searches for phenotype-altering DNA differences.

Several studies have revealed differences in rumen-located microbes between greatly efficient and inefficient animals; however, how the microbiota vary in the hind gastrointestinal tract (GIT) has only been sparsely explored and how they vary in the small intestine remains to be determined. We therefore sampled the microbiota of the duodenum, jejunum, ileum, colon, and colorectally-obtained feces, in addition to the rumen of 12 lambs that, in a residual feed intake trial, were found to be at either extreme of feed efficiency phenotypes. The 16S rRNA gene (V3-V4 region) profiles of all samples were analyzed and revealed unique microbiota in all GIT locations except the jejunum and ileum (ANOSIM R > 0.2, P < 0.001). Measures of β-diversity revealed greater dissimilarity between more anatomically distant GIT locations (e.g., Rumen–Duodenum, ANOSIM R = 0.365, P < 0.001; Rumen–Colon, ANOSIM R = 1, P < 0.001) with the nearest distal region typically more similar than the nearest proximal location. The relative abundances of 13 operational taxonomic units (OTUs) from the duodenum, jejunum, colon, and feces, as well as the rumen, differed between efficient and inefficient animals (Bonferroni corrected, P < 0.05), while another 2 OTUs trended toward significance. These OTUs were classified as taxa with known roles in fibrolysis (Fibrobacteres, Ruminococcaceae, and Saccharofermentans) and others that are commonly associated with health (Bifidobacteriaceae, and Christensenellaceae) and dysbiosis (Proteobacteria). Our findings show biospatial delineations of microbiota throughout the GIT and suggest that feed efficiency extends beyond the rumen, transcending these regions, and involves increases in both rumen- and colon-located fibrolytic taxa, increases in bifidobacterial species in the small intestine, and reductions in small intestine and distal GIT-located Proteobacteria.

Adipose tissue metabolism is an essential factor in establishment of a successful lactation, and we have a good understanding of changes in metabolic flux in relation to lactation, parity, and diet. However, the mechanisms of control of flux are less well understood. To continue our investigations into the control of adipose tissue metabolism, we conducted a transcriptomic analysis of adipose tissue of dairy cattle in late pregnancy and early lactation. Our objective was to determine the changes in gene expression in adipose tissue between 30 d prepartum and 14 d in milk in first-lactation animals, and to determine if changes in expression were related to practical production variables. Animals were Holstein heifers fed the same diet to National Research Council requirements, and adipose tissue was biopsied at 30 d prepartum and 14 DIM. Total RNA was extracted and used to determine gene expression on a bovine gene array. Genes that code for proteins controlling fatty acid transport were highly expressed including fatty acid binding proteins (FABP4 and FABP5) and lipoprotein lipase. Among those genes increasing in expression were those controlling lipolysis, including ADRB2 (52%) and LIPE (23%). Many genes coding for enzymes controlling lipogenesis decreased, including SREBP (-25%), TSHSP14 (-30.8%), LPL (-48.4%), and ACACA (-63.9%). This gene expression array analysis in adipose tissue of lactating dairy cattle identifies several key genes that are components of the adaptation to lactation that can be incorporated into models of nutritional efficiency and may be amenable to genetic or dietary manipulation.