World Journal of
Pharmaceutical and Life Sciences

HAPLOTYPE ANALYSIS OF 16S RIBOSOMAL RNA ISOLATED FROM CUTTING BOARDS AT DIFFERENT BOVINE MEAT RETAIL STORES

Ayman Sabry*, Abdullah Abdulhafith Aljaddawi and Salah Abo Aba

ABSTRACT

This work was carried out to present a comprehensive workflow of haplotype analysis using R for 16s rRNA sequences. Eleven bacterial samples were isolated from cutting boards at four different bovine meat retail stores. Phylogenetic analysis revealed presence of 8 different bacterial strains. Macrococcus caseolyticus was found in samples from the four locations. The length of sequences ranged from 1071 for M.caseolyticus in location VI to 1280 also for M. caseolyticus but in location II. The GC% content averaged 52.8, ranging from 51 to 55 % with no outlier. In this data set no common haplotype was noticed, meaning each haplotype was unique. The smallest distance between the haplotype pairs was 41 nucleotides between H7–H8, and 42 nucleotides between H1–H2, where the largest distance was 931 nucleotides between H10-H11. The haplotype difference (Hd) was 0.98 (±0.05) and the nucleotide difference (?) was 0.27. The average number of nucleotide differences (K) was 264 and the total variance of k (free recombination), V(k) was 106. Four conserved regions were detected. These 4 regions occupied the distance from nucleotide 701 to 1265. All 4 conserved regions were significant Based on results presented in this work, this haplotype analysis framework is found to be as efficient and straightforward.

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