Identification of pathogenic bacteria on the salted fish Lutjanus vivanus in Sorong City of West Papua

Aims: Fisheries-based food is needed by humans as a protein source, one of which is salted fish Lutjanus vivanus.Market demand for this product in Indonesia is quite high. The aim of the study was to identify pathogenic bacteria insalted fish L. vivanus.Methodology and results: The method used in this study was descriptive method including pathogenic test, bacterialgenomic DNA isolation based on 16 sRNA gene using prokaryotic specific primers, namely 63f forward primer (5′-CAGGCC TAA CAC ATG CAA GTC-3′) and reverse 1387r primer (5′-GGG CGG WGT GTA CAA GGC-3′). The results of thisstudy indicated pathogenic bacteria in salted fish L. vivanus with pathogenic activity of α hemolytic and β hemolytic. Thebacteria were identified as Serratia marcescens strain ZK2 16S for isolate KS and Bacillus altitudinis strains A-19 16Sfor isolate LG.Conclusion, significance and impact of study: In salted fish L. vivanus in the Sorong city, West Papua, it wasobtained Serratia marcescens strain ZK2 16S with total hemolytic activity and B. altitudinis A-19 16S strain with partialhemolytic activity.

Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression inStaphylococcus aureus

ABSTRACTInStaphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs inS. aureus, we generated updated GenBank files for three commonly usedS. aureusstrains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs inS. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome annotation inS. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression inS. aureusand demonstrate that the newly identifiedtsr25is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to theS. aureusresearch community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions.IMPORTANCEDespite a large number of studies identifying regulatory or small RNA (sRNA) genes inStaphylococcus aureus, their annotation is notably lacking in available genome files. In addition to this, there has been a considerable lack of cross-referencing in the wealth of studies identifying these elements, often leading to the same sRNA being identified multiple times and bearing multiple names. In this work, we have consolidated and curated known sRNA genes from the literature and mapped them to their position on theS. aureusgenome, creating new genome annotation files. These files can now be used by the scientific community at large in experiments to search for previously undiscovered sRNA genes and to monitor sRNA gene expression by transcriptome sequencing (RNA-seq). We demonstrate this application, identifying 39 new sRNAs and studying their expression duringS. aureusgrowth in human serum.