Molecular ıdentification of Nocardia Diversity in soil by multilocus sequence analysis

Year 2015, Volume: 8 Issue: 2, 122 - 133, 15.08.2015

Fadime Özdemirkoçak Kamil Işık

Abstract

Identification of Nocardia strains is difficult due to the failure of 16S rRNA sequence analysis, chemotaxonomical and biochemical tests. In this study, identification of the possible novel Nocardia isolates was made by Multilocus Sequence Analysis. Four multilocus gene regions, gyrase B, β subunit of DNA topoisomerase gyrB , 16S rRNA 16S rDNA , subunit A of SecA preprotein translocase secA1 , and RNA polymerase rpoB , were used to identify ten Nocardia strains isolated from different soil samples. The region of gyrB, 16S rRNA, secA1 and rpoB genes of ten isolates were compared with related type strains of Nocardia. Concatenate sequence analysis of 2.061 bp allowed differentiation of all isolates and type strains, with a range of interspecies similarity of 91.4-99.8%. Nocardia sp. FSN13, FSN14, FSN34 and FSN37 isolates shared 95.4- 96.4% of the concatenated gyrB-16S rRNA-secA1-rpoB sequences similarity with the type strain N. abscessus. FSN35, FMN06 and FMN15 Nocardia isolates were determined to be related with N. rhamnosiphila 97.9, 95.3 and 98.6% sequences similarity, respectively. It was determined that FSN27 isolate was closely related with N. takedensis and had 96.7% similarity, FGN17 and FGN19 isolates were determined to be related with N. speluncae the similarity of 95.5 and 95.3%., respectively

Keywords

16S rRNA, gyrB, rpoB, secA1, Nocardia

Multilokus dizi analizleri ile topraktaki Nocardia çeşitliliğinin moleküler tanımlaması

Abstract

Nocardia suşlarının tanımlanması 16S rRNA dizi analizleri, kemotaksonomik ve biyokimyasal testlerdeki hatalar nedeniyle zordur. Bu çalışmada, olası yeni Nocardia izolatlarının tanımlaması Multilokus Dizi Analizleri kullanılarak yapıldı. Dört multilokus gen bölgesi, giraz B, DNA topoisomerazın β altünitesi gyrB , 16S rRNA 16S rDNA , SecA preprotein translokazın A altünitesi secA1 ve RNA polymeraz β altünitesi rpoB , farklı toprak örneklerinden izole edilen on Nocardia suşunun tanımlanmasında kullanıldı. On izolatın gyrB, 16S rRNA, secA1 ve rpoB gen bölgeleri ilişkili Nocardia tip suşları ile karşılaştırıldı. 2.061 bp’in birleştirilmiş dizi analizleri tüm izolat ve tip suşlarının 91.4-99.8%. tür içi benzerlik oranı ile farklılaşmasını sağladı. Nocardia sp. FSN13, FSN14, FSN34 ve FSN37 isolatları N. abscessus tip suşu ile birleştirilmiş gyrB-16S rRNA-secA1-rpoB dizi benzerliği 95.4- 96.4% olduğu belirlendi. FSN35, FMN06 ve FMN15 Nocardia isolatlarının 97.9, 95.3 ve 98.6% dizi benzerliği ile N. rhamnosiphila’a akraba olduğu belirlendi. FSN27 izolatı N. takedensis ile yakın ilişkili olduğu belirlendi ve FGN17 ve FGN19 izolatlarınında N. speluncae ile 95.5 ve 95.3% benzerlik oranı ile ilişkili olduğu belirlendi

Keywords

16S rRNA, gyrB, rpoB, secA1, Nocardia

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