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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 Gram-negative, filamentous aerobic bacterium designated as strain Mgbs1T was isolated on 12 April 2017 from the subsurface soil and leaf litter substrate at the base of a Koompassia malaccensis tree in a tropical peat swamp forest in the northern regions of the state of Selangor, Malaysia (3° 39′ 04.7′ N 101° 17′ 43.7′′ E). Phylogenetic analyses based on the full 16S rRNA sequence revealed that strain Mgbs1T belongs to the genus Chitinophaga with the greatest sequence similarity to Chitinophaga terrae KP01T (97.65 %), Chitinophaga jiangningensis DSM27406T (97.58 %), and Chitinophaga dinghuensis DHOC24T (97.17 %). The major fatty acids of strain Mgbs1T (>10 %) are iso-C15 : 0, C16 : 1 ω5c and iso-C17 : 0 3-OH while the predominant respiratory quinone is menaquinone-7. Strain Mgbs1T has a complete genome size of 8.03 Mb, with a G+C content of 48.5 mol%. The DNA–DNA hybridization (DDH) score between strain Mgbs1T and C. jiangningensis DSM27406T was 15.9 %, while in silico DDH values of strain Mgbs1T against C. dinghuensis DHOC24T and C. terrae KP01T were 20.0 and 19.10% respectively. Concurrently, Average Nucleotide Identity (ANI) scores between strain Mgbs1T against all three reference strains are 73.2 %. Based on the phenotypic, chemotaxonomic, and phylogenetic consensus, strain Mgbs1T represents a novel species of the genus Chitinophaga , for which the name Chitinophaga extrema sp. nov. is proposed (=DSM 108835T=JCM 33276T).

We characterized the draft genome of the potentially beneficial Bacillus tropicus strain UPM-CREST01, which was isolated from the bulk soil at a paddy cultivation area in Kampung Gajah, Perak, Malaysia. The final draft assembly of 5,252,705 bp, with a G+C content of 35.23%, was found to harbor 5,368 coding sequences, including several plant-growth-promoting genes.

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

Here, we present the complete mitochondrial genome of

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., Measurement(s)genome • sequence_assemblyTechnology Type(s)DNA sequencing • genome assemblySample Characteristic - OrganismSphingomonas paucimobilisSample Characteristic - Environmentoil contaminated soilSample Characteristic - LocationMalaysia Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.9971711

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.

Schizophrenia is a chronic mental disorder with marked symptoms of hallucination, delusion, and impaired cognitive behaviors. Although multidimensional factors have been associated with the development of schizophrenia, the principal cause of the disorder remains debatable. Microbiome involvement in the etiology of schizophrenia has been widely researched due to the advancement in sequencing technologies. This review describes the contribution of the gut microbiome in the development of schizophrenia that is facilitated by the gut-brain axis. The gut microbiota is connected to the gut-brain axis via several pathways and mechanisms, that are discussed in this review. The role of the oral microbiota, probiotics and prebiotics in shaping the gut microbiota are also highlighted. Lastly, future perspectives for microbiome research in schizophrenia are addressed.

Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12-week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over ten phyla were detected, with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in the compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum and Coprococcus. No methanogens were identified due to the bias in general 16S primers to eubacteria. The preponderance of anaerobic species in the compost and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile due to the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest that the presence of enzymes involved in degradation of polysaccharides such as glucoamylase, endoglucanase and arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples.

Parkinson&rsquo, s disease (PD) is a neurodegenerative disorder defined by progressive deterioration of dopaminergic neurons in the substantia nigra pars compacta (SNpc). Dental pulp stem cells (DPSCs) have been proposed to replace the degenerated dopaminergic neurons due to its inherent neurogenic and regenerative potential. However, the effective delivery and homing of DPSCs within the lesioned brain has been one of the many obstacles faced in cell-based therapy of neurodegenerative disorders. We hypothesized that DPSCs, delivered intranasally, could circumvent these challenges. In the present study, we investigated the therapeutic efficacy of intranasally administered DPSCs in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced mouse model of PD. Human deciduous DPSCs were cultured, pre-labelled with PKH 26, and intranasally delivered into PD mice following MPTP treatment. Behavioural analyses were performed to measure olfactory function and sensorimotor coordination, while tyrosine hydroxylase (TH) immunofluorescence was used to evaluate MPTP neurotoxicity in SNpc neurons. Upon intranasal delivery, degenerated TH-positive neurons were ameliorated, while deterioration in behavioural performances was significantly enhanced. Thus, the intranasal approach enriched cell delivery to the brain, optimizing its therapeutic potential through its efficacious delivery and protection against dopaminergic neuron degeneration.

Background The role of oral and gut microbiomes in the pathogenesis of schizophrenia has recently come to light with the advancement of sequencing technology. Recent studies have shown that schizophrenia patients have different gut and oral microbiome profiles than healthy people. The interaction of oral and gut microbiota with the brain is facilitated through the gut-brain axis. Several studies have profiled the gut microbiomes in the Malaysian population, however none has investigated its relationship with etiology of schizophrenia. The aim of this preliminary study is to therefore investigate the relationship between oral and gut microbiomes in pathogenesis of schizophrenia in the Malaysian population based on the total transcriptome profiles. Methods In this study, 15 schizophrenia patients and 15 healthy people (control) were recruited from the three major ethnic groups in Malaysia, namely Malay, Chinese and Indian. Throat swabs and stool samples were collected and subjected to total RNA extraction. Following this, ribosomal RNA depletion and cDNA conversion were performed prior to sequencing using Illumina platform. Bioinformatic tools will be used to analyse and compare the transcriptome profiles of microbiomes from schizophrenia and healthy subjects. Brain derived neurotrophic factor, serotonin and dopamine assays will be performed using their blood samples too. The results of the bioassays will be then correlated with the transcriptome profiles to identify possible mechanisms by which microbiota could promote schizophrenia Results The RNA sequencing results will reveal differences in gene expression profiles between the microbiomes of schizophrenic and healthy subjects. Based on the transcriptome profiles and bioassay results, the possible pathways and mechanisms by which these microbiota can cause schizophrenia will be identified. In addition, candidate biomarkers from the oral and/or gut microbiomes for diagnosis of schizophrenia can be identified. Discussion The first and second generations of schizophrenia treatments mostly are based on controlling the symptoms of the disease, whereas treatment based on microbiome dysbiosis correction can tackle the underlying mechanism leading to a precise treatment of the disease.The findings from this study will enable the identification of distinct schizophrenia associated bacteria, that may help in development of new treatments and novel diagnostics for schizophrenia via microbiome-targeted therapy including probiotics and prebiotic.

Microorganisms have been shown to have an adaptive ability for efficiently breaking down oxidized polymers. In the present study, we have developed a rapid and sensitive analytical technique using Fourier Transform Infrared coupled Attenuated Total Reflectance (FTIR-ATR) spectroscopy to quantify low density polyethylene (LDPE) biodegradation by microorganisms. In order to demonstrate the utility of this technique, LDPE biodegradation was performed using two bacterial strains, Microbacterium paraoxydans and Pseudomonas aeruginosa. Prior to quantification, these bacterial strains were acclimatized to nitric acid pretreated LDPE for 2 months. The acclimatized strains were then subjected to in vitro biodegradation assay with the pretreated LDPE as its sole carbon source for another 2 months. Subsequently, biodegradation quantification was performed with FTIR-ATR spectroscopy using various concentrations of LDPE standards for comparison. It was observed that the percentage of transmittance at 2920 cm−1 was directly proportional to the concentration of LDPE. Results indicated that M. paraoxydans degraded 61.0% of LDPE while P. aeruginosa degraded 50.5% in 2 months. In conclusion, we established a rapid and sensitive FTIR-ATR spectroscopy based technique to quantify LDPE biodegradation.