Bacterial Community In The Rumen Of Dairy Cows Fed Diets Differing In Forage And Protein Sources

In order to characterize the dynamic rumen bacterial community of cows fed three diets differing inforage and protein sources and to analysis dominance bacteria related to three diets. Forty-eight ChineseHolstein dairy cows with similar production performance (55±15DIM and33.22±4.57kg of milk/d)were randomly assigned to three treatments: MF diet (alfalfa hay, corn silage and soybean meal), CSAdiet (corn straw and soybean meal) and CSB diet (corn straw, cottonseed and rapeseed meal). MF dietand CSA diet are differing in forage source, while CSA diet and CSB diet are differing in protein source.The cows were fed their assigned diets twice daily for91d, after which all were shifted to the MF diet.Rumen contents were collected via an oral lavage and were performed before and after morning feedingon d31,61,91, and d107of the experiment. The samples were used to compare and validate the rumenbacteria from different forage and protein sources. The main contents are as follows:1. Characterization of the dynamics rumen bacterial community of cows fed different forage andprotein sources. Total DNA of rumen microbial were extracted. Bacterial community structures wereanalyzed using denaturing gradient gel electrophoresis (DGGE), with select DGGE bands beingsequenced. The DGGE profiles showed clear difference among the three diets after feeding for31d,with the overall similarity being only51%, and little difference were found between CSA and CSB diets.As expected, the MF diet resulted in more unique bands than the CSA and CSB diets. The DGGEfingerprints became less difference among three diets at d61and d91compared to d31, and thesimilarity were53%and59%respectively, suggesting gradual adaptation of rumen bacteria to the diets.Diversity indices showed that DGGE profiles had higher Shannon diversity index (P<0.05) at d31, d61after feeding and d91. The sequence results of DGGE bands showed that genera Vibrio and Prevotellaand some uncultured bacteria increased in MF group. The special band appeared in MF group wereidentified as uncultured bacteria, we named it R-UB. The other uncultured bacteria belonging to thephylum Bacteroidetes, Firmicutes, and Proteobacteria had some changes between the three groups.2. Verification of the special dominance bacteria related to types of forages. In order to getinformation of the uncultured bacteria (bacterium) R-UB appeared in MF group, The DNA wasrecoveried from the gel and was sequenced. Results showed that the distinct band appeared in the MFgroup had a90%similarity with Vibrio. Primers for qPCR were designed according to the16S rDNAsequence of R-UB. The qPCR detection was done using samples of d91and d107. The qPCRquantification showed that R-UB had a higher (P<0.001) abundance in the MF group than in the othertwo groups at d91, But after the three groups were all changed to the same MF diet, Statistical analysisshowed that DNA copy numbers of R-UB significantly increased in group CSA and CSB and had littledifference (P>0.05) among three groups.In conclusion, different forage source changed the structure and population of rumen bacterialcommunity, and there were little difference in bacteria diversity of cows fed different protein source.There was an unique bacterial community with high diversity in the rumen of dairy cows fed mixed forage. The uncultured bacteria R-UB had a higher abundence in mixed forage diet and a lowabundence in corn straw diet. The population of bacteria R-UB was correlated with different foragesources.