The partial 16S rRNA gene sequences (100 to 500 bp) were widely used to reveal rumen bacterial composition influenced by diets, while quantification of the changed uncultured bacteria was inconvenient due to difficult designing of specific primers based on short sequences. This study evaluated the effect of forage resources on rumen bacterial diversity and developed new strategy for primer design based on short sequences to quantify the changed uncultured bacteria. Denaturing gradient gel electrophoresis (DGGE) analysis and subsequent band sequencing were used to reveal the distinct rumen bacteria composition in cows fed with two forage sources (single corn stover vs. mixed forages including alfalfa hay and corn silage). The bacterial diversity in the rumen of dairy cows fed with corn stover was lower than that with mixed forages (P<0.05). The bacterium named R-UB affiliating to uncultured Succinivibrionaceae was identified, and it was abundant in the rumen of cows fed with mixed forages compared to corn stover. The full length 16S rRNA gene sequences with identity of >97% to the R-UB 16S rRNA gene sequence were obtained from GenBank and used to design specific primers to quantify uncultured bacterium R-UB. All sequences of amplicon from the new primers were of 100% identity to R-UB sequences indicating the high specificity of new primers. Quantitative PCR confirmed that abundance of R-UB in the rumen of cows fed with corn stover was lower than those fed with mixed forages (P<0.01). New strategy for designing primers based on partial 16S rRNA genes to quantify targeted uncultured bacteria was successfully developed. The rumen bacteria descending significantly in the cows fed corn stover compared to those fed mixed forages was identified as uncultured R-UB from Succinivibrionaceae.

Dairy cows undergo tremendous changes in physiological, metabolism and the immune function from pregnancy to lactation that are associated with cows being susceptible to metabolic and infectious diseases. The objective of this study is to investigate the changes of plasma proteome on 21 d before expected calving and 1 d after calving from dairy cows using an integrated proteomic approach consisting of minor abundance protein enrichment by ProteoMiner beads, protein labeling by isobaric tags for relative and absolute quantification, and protein identification by liquid chromatography coupled with tandem mass spectrometry. Nineteen proteins were changed around the time of calving. These proteins were associated with response to stress, including acute-phase response and defense response, based on the proteins annotation. In particular, three up-regulated proteins after calving including factor V, α2-antiplasmin and prothrombin were assigned into the complement and coagulation pathway. These results may provide new information in elucidating host response to lactation and parturition stress, and inflammatory-like conditions at the protein level. Differential proteins may serve as potential markers to regulate the lactation and parturition stress in periparturient dairy cows.

Protein phosphorylation is an important post-translational modification that regulates milk protein structure and function. The objective of this study was to analyze the presence of phosphorylated casein. Bovine milk proteins were first separated by SDS polyacrylamide gel electrophoresis. After in gels digestion and extraction, phosphorylated peptides were enriched by titanium dioxide and identified by ultra performance liquid chromatography coupled with nano electrospray ionization tandem mass spectrometry. This method ensured the identification of 20 phosphorylated peptides, including 7 phosphorylated forms of αs1-casein, 8 αs2-casein, and 5 β-casein. Eight phosphorylated sites derived from 3 αs1-caseins, 3 αs2-caseins, and 2 β-caseins were also identified, and localized on residues Ser61, Ser63 and Ser130 in αs1-casein; Thr145, Ser146 and Ser158 in αs2-casein; and Ser50 and Thr56 in β-casein. These findings provide valuable information for investigating casein phosphorylation of the bovine milk.