We characterized the complete genome of the lytic Enterococcus faecalis phage EFKL, which was isolated from a sewage treatment plant in Kuala Lumpur, Malaysia. The phage, which was classified in the genus Saphexavirus, has a 58,343-bp double-stranded DNA genome containing 97 protein-encoding genes and shares 80.60% nucleotide similarity with Enterococcus phage EF653P5 and Enterococcus phage EF653P3.
A lytic bacteriophage EF_RCK infecting Enterococcus faecalis was isolated from a water sample collected in a raw cockle storage container at Taman Ria market, Sungai Petani, Malaysia. The phage has a 57,848-bp double-stranded DNA genome harboring 107 protein-encoding genes and shares 90.9% nucleotide similarity with Enterococcus phage EFKL (Saphexavirus genus).
We characterized the complete genome sequence of the lytic Salmonella enterica bacteriophage PRF-SP1, isolated from Penang National Park, a conserved rainforest in northern Malaysia. The novel phage species from the Autographiviridae family has a 39,966-bp double-stranded DNA (dsDNA) genome containing 49 protein-encoding genes and shares 90.96% similarity with Escherichia phage DY1.
Complete genomes of xenobiotic-degrading microorganisms provide valuable resources for researchers to understand molecular mechanisms involved in bioremediation. Despite the well-known ability of Sphingomonas paucimobilis to degrade persistent xenobiotic compounds, a complete genome sequencing is lacking for this organism. In line with this, we report the first complete genome sequence of Sphingomonas paucimobilis (strain AIMST S2), an organophosphate and hydrocarbon-degrading bacterium isolated from oil-polluted soil at Kedah, Malaysia. The genome was derived from a hybrid assembly of short and long reads generated by Illumina HiSeq and MinION, respectively. The assembly resulted in a single contig of 4,005,505 bases which consisted of 3,612 CDS and 56 tRNAs. An array of genes involved in xenobiotic degradation and plant-growth promoters were identified, suggesting its' potential role as an effective microorganism in bioremediation and agriculture. Having reported the first complete genome of the species, this study will serve as a stepping stone for comparative genome analysis of Sphingomonas strains and other xenobiotic-degrading microorganisms as well as gene expression studies in organophosphate biodegradation.
Salmonella infections across the globe are becoming more challenging to control due to the emergence of multidrug-resistant (MDR) strains. Lytic phages may be suitable alternatives for treating these multidrug-resistant Salmonella infections. Most Salmonella phages to date were collected from human-impacted environments. To further explore the Salmonella phage space, and to potentially identify phages with novel characteristics, we characterized Salmonella-specific phages isolated from the Penang National Park, a conserved rainforest. Four phages with a broad lytic spectrum (kills >5 Salmonella serovars) were further characterized; they have isometric heads and cone-shaped tails, and genomes of ~39,900 bp, encoding 49 CDSs. As the genomes share a <95% sequence similarity to known genomes, the phages were classified as a new species within the genus Kayfunavirus. Interestingly, the phages displayed obvious differences in their lytic spectrum and pH stability, despite having a high sequence similarity (~99% ANI). Subsequent analysis revealed that the phages differed in the nucleotide sequence in the tail spike proteins, tail tubular proteins, and portal proteins, suggesting that the SNPs were responsible for their differing phenotypes. Our findings highlight the diversity of novel Salmonella bacteriophages from rainforest regions, which can be explored as an antimicrobial agent against MDR-Salmonella strains.