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 (rRNA) 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 spp. 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 (±SD) 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.

BackgroundOne 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.ResultsThe 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.ConclusionsSubstantial 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.

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Abundant evidence from the medical, veterinary, and animal science literature demonstrates that there is substantial room for improvement of the clarity, completeness, and accuracy of reporting of intervention studies. More rigorous reporting guidelines are needed to improve the quality of data available for use in comparisons of outcomes (or meta-analyses) of multiple studies. Because of the diversity of factors that affect reproduction and the complexity of interactions between these, a systematic approach is required to design, conduct, and analyze basic and applied studies of dairy cattle reproduction. Greater consistency, clarity, completeness, and correctness of design and reporting will improve the value of each report and allow for greater depth of evaluation in meta-analyses. Each of these benefits will improve understanding and application of current knowledge and better identify questions that require additional modeling or primary research. The proposed guidelines and checklist will aid in the design, conduct, analysis, and reporting of intervention studies. We propose an adaptation of the REFLECT (Reporting Guidelines for Randomized Controlled Trials for Livestock and Food Safety) statement to provide guidelines and a checklist specific to reporting intervention studies in dairy cattle reproduction. Furthermore, we provide recommendations that will assist investigators to produce studies with greater internal and external validity that can more often be included in systematic reviews and global meta-analyses. Such studies will also assist the development of models to describe the physiology of reproduction.