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Whole genome sequence of Brucella melitensisl local isolate from an infected goat in Malaysia
2016
Mohd Mokhtar Arshad | Ramlan Mohamed | Shuhaila Mat Sharani | Hardy Abu Daud | Omer Khazaal Sallou | Mohd Azam Khan Goriman Khan | Hirzahida Mohd. Padil
Brucellosis in goats is mainly caused by the bacterium Brucellamelitensis, which is one of the most important pathogenic species in the world. In Malaysia, the annual prevalence data of brucellosis was recorded in goats and the control strategy of the disease basedon test and cull of infected animals. This strategy has caused huge economic losses to farmers and government alike. Therefore, whole genome sequencing of B. melitensis local strain is essential forimproving the current vaccine. B. melitensis strain VRI 6530/11 wasobtained from veterinary research institute biobank, Ipoh. The strain was submitted for classical identification procedures and the total genomic DNA was extracted by using DNeasy blood and tissue kit(QIAGEN). The concentration and purity of DNA were determined by using agarose gel electrophoresis and spectrophotometer (DNA/RNA) assay respectively. The genome was sequenced by using IlluminaHiSeq platform with insert size ~200 bp. A total of 1.0 Gb data was generated from the sample. More than 95% of sequencing data was retained in the sample after quality filtering, this indicatethe sequencing reads are of high quality. Final assembly had 33 scaffolds with total size ~3.28 Mb, 44 contigs, GC content is 57.25%, N50 is 293,291. A total of 3,238 protein coding genes, 48 tRNAs and 3rRNAs were predicted and over 87% of the genes were functionally annotated. Genome sequencing of a local B. melitensis strain is the first of its kind in Malaysia and work from this study can contribute towards the development of a new effective vaccine for the control ofthe disease in the country.
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2016
Asad, S. | Bryden, W. L. | Maguire, A. | Faizah H. M. S. | Klive, A. V. | Li, X.
This study was conducted to investigate whether dietary enzymes alter the caecal microbial profile of broilers fed sorghum-based diets. Four sorghum-based diets (918 g sorghum/kg diet) were prepared. One was the control diet and three had enzymes (xylanase, phytase andprotease) added. Broilers, 35-day-old, were reared (8 birds/cage) in an environmentally controlled shed and randomly allocated to replicated (n=4) assay diets and free access to feed and water all time. On day-42, birds were euthanized and caecal contents collected, pooled on a per/pen basis and frozen (-20 °C). The DNA was extracted from caecal samples using a bead-beating protocol and the V2V3 regionof the bacterial 16S rRNA gene amplified by PCR. Amplicons were separated on sequence difference using Denaturing Gradient Gel Electrophoresis (DGGE) and microbial profiles generated and compared.The DGGE profiles, when analysed, indicated that there was approximately 80% similarity between caecal microflora in all types of the diet treatments. This suggests that there was no overalldifference between any of the profiles and therefore the addition of different types of feed enzymes in a sorghum-based diet had no impact on the overall composition of the broiler caecal microflora.
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