| The digestive system of ruminants is very special, the rumen microorganisms capable of degrading plant cellulose, provides essential nutrients that can be absorbed for the host animals. Once the ruminal microflora changes will directly affect physiological functions of animals and even lead to certain diseases. Research found that ration and animal breeds have impact on ruminal microbial diversity, But the research in the past lack a efficient, low cost method to detect microbial sequences.High-throughput sequencing can provide deep sequencing and get most microbial reads, the target of this research is use the latest miseq sequencing technology to compare the different within ration and breeds of goats.The experiment I use 2*2 lartin square design to grouping the six goats within complete feed and all forage ration,to compare the microbial diversity in rumen.each goat rearing in sigle cage,and free to drink,14d to adaption to dietary,7d for experiment,the last day of experiment to sampling,when the first experimental period is over,the AF group goats and CF group goats will exchange their dietary,then the goats will carry on next experimental period.Then extract the DNA of rumen samples,and take advantage of the miseq sequencing platform to sequencing the V4 region of 16S rRNA of rumen microorganism with bacterial/archeae primer 515f/806r, The sequencing results were analyzed using QIIME software,and found that Bacteroidetes and firmicutes is the major bacteria in rumen. The fibrolytic bacteria like Ruminococcus and Lachnospiracea_incertae_sedis etc. will rise as the fibre content in dietary increase,Conversely, when the protein and fat in dietary increase the Pseudomonas and Anaerovibrio etc. will increase. Although the composion of the microorganism in different dietary groups were significance different,but the core bacteria like prevotella, Butyrivibrio and Pseudobutyrivibrio etc. between the treatment groups were not significant different,it indicates that the change in dietary do not have effect on core bacteria in rumen. Weighted unifrac distance matrix shows that the similarities within the CF and AF groups are 62.76% and 67.94% respectively, similarity between the groups was 61.99%±7.08. PCoA cluster diagram shows the various samples generally depending on your own group and together with each other.Experiment II use high-throughput sequencing to compare the microbial diversity in rumen between two breeds of goat with the bacteria/archeae primers 515f/806r,Six boer goats(B group) and six nanjiang goat(N group) as our experimental animal, each goat rearing in sigle cage,and free to drink,ad libitum with perennial ryegrass,14d to adaption to dietary,7d for experiment,the last day of experiment to sampling,DNA extracting,sequencing and software analysis just the same with experimental I,The result indicate that there is no significant abundance difference between Bacteroidetes and Firmicutes is the major bacteria in rumen,conversely,the proteobacteria, Planctomycetes and Chloroflexi which have lower relative abundance were significant different, Futher study shows that the relative abundance in N group of Desulfovibrio, Ruminobacter and Stenotrophomonas were higher than B group,and the microorganism in Desulfovibrio and Stenotrophomonas mostly belong to opportunistic pathogen.But the relative abundance in all of them were low,there is no significant different in other core Fibrolytic bacteria and like prevotella, Clostridium,Butyrivibrio and Ruminococcus etc.,this also indicate that variety in breeds do not have significant effect on ruminal microorganism.In conclusion, the change in dietary and goat breeds can change the microorganisms in rumen, but the relative abundance in main genus as well as some important shared bacteria do not change very much. |
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