Displaying all 14 publications

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  1. Tan JL, Ngeow YF, Wee WY, Wong GJ, Ng HF, Choo SW
    Sci Rep, 2014;4:7169.
    PMID: 25417557 DOI: 10.1038/srep07169
    Mycobacterium iranicum is a newly reported mycobacterial species. We present the first comparative study of M. iranicum UM_TJL and other mycobacteria. We found M. iranicum to have a close genetic association with environmental mycobacteria infrequently associated with human infections. Nonetheless, UM_TJL is also equipped with many virulence genes (some of which appear to be the consequence of transduction-related gene transfer) that have been identified in established human pathogens. Taken all together, our data suggest that M. iranicum is an environmental bacterium adapted for pathogenicity in the human host. This comparative study provides important clues and forms the basis for future functional studies on this mycobacterium.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  2. Shukor MY, Husin WS, Rahman MF, Shamaan NA, Syed MA
    J Environ Biol, 2009 Jan;30(1):129-34.
    PMID: 20112874
    Sodium dodecyl sulfate (SDS) is one of the main components in the detergent and cosmetic industries. Its bioremediation by suitable microorganism has begun to receive greater attention as the amount of SDS usage increases to a point where treatment plants would not be able to cope with the increasing amount of SDS in wastewater. The purpose of this work was to isolate local SDS-degrading bacteria. Screening was carried out by the conventional enrichment-culture technique. Six SDS-degrading bacteria were isolated. Of these isolates, isolate S14 showed the highest degradation of SDS with 90% degradation after three days of incubation. Isolate S14 was tentatively identified as Klebsiella oxytoca strain DRY14 based on carbon utilization profiles using Biolog GN plates and partial 16S rDNA molecular phylogeny. SDS degradation by the bacterium was optimum at 37 degrees 0. Ammonium sulphate; at 2.0 g l(-1), was found to be the best nitrogen source for the growth of strain DRY14. Maximum growth on SDS was observed at pH 7.25. The strain exhibited optimum growth at SDS concentration of 2.0 g l(-1) and was completely inhibited at 10 g l(-1) SDS. At the tolerable initial concentration of 2.0 g l(-1), almost 80% of 2.0 g l(-1) SDS was degraded after 4 days of incubation concomitant with increase in cellular growth. The K(m(app) and V(max(app)) values calculated for the alkylsulfatase from this bacterium were 0.1 mM SDS and 1.07 micromol min(-1) mg(-1) protein, respectively.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  3. Shukor MY, Gusmanizar N, Ramli J, Shamaan NA, MacCormack WP, Syed MA
    J Environ Biol, 2009 Jan;30(1):107-12.
    PMID: 20112871
    The presence of acrylamide in the environment poses a threat due to its well known neurotoxic, carcinogenic and teratogenic properties. Human activities in various geographical areas are the main anthropogenic source of acrylamide pollution. In this work, an acrylamide-degrading bacterium was isolated from Antarctic soil. The physiological characteristics and optimum growth conditions of the acrylamide-degrading bacteria were investigated. The isolate was tentatively identified as Pseudomonas sp. strain DRYJ7 based on carbon utilization profiles using Biolog GN plates and partial 16S rDNA molecular phylogeny. The results showed that the best carbon sources for growth was glucose and sucrose with no significant difference in terms of cellular growth between the two carbon sources (p>0.05). This was followed by fructose and maltose with fructose giving significantly higher cellular growth compared to maltose (p<0.05). Lactose and citric acid did not support growth. The optimum acrylamide concentration as a nitrogen source for cellular growth was at 500 mgl(-1). At this concentration, bacterial growth showed a 2-day lag phase before degradation took place concomitant with an increase in cellular growth. The isolate exhibited optimum growth in between pH 7.5 and 8.5. The effect of incubation temperature on the growth of this isolate showed an optimum growth at 15 degrees C. The characteristics of this isolate suggest that it would be useful in the bioremediation of acrylamide.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  4. Alshaibani MM, Jalil J, Sidik NM, Edrada-Ebel R, Zin NM
    Drug Des Devel Ther, 2016;10:1817-27.
    PMID: 27330275 DOI: 10.2147/DDDT.S101212
    BACKGROUND: Zingiber spectabile, commonly known as Beehive Ginger, is used as an ethnobotanical plant in many countries as an appetizer or to treat stomachache, toothache, muscle sprain, and as a cure for swelling, sores and cuts. This is the first report of isolation of Streptomyces strain from the root of this plant. Strain Universiti Kebangsaan 25 (SUK 25) has a very high activity to produce secondary metabolites against methicillin-resistant Staphylococcus aureus (MRSA), which is associated with high morbidity and mortality rates due to acquired multidrug resistance genes and causes medication failure in some clinical cases worldwide. Phylogenetic analysis based on the 16S ribosomal RNA gene sequence exhibited that the most closely related strain was Streptomyces omiyaensis NBRC 13449T (99.0% similarity).

    AIM: This study was conducted to carry out the extraction, identification, and biological evaluation of active metabolites isolated from SUK 25 against three MRSA strains, namely, MRSA ATCC 43300, MRSA ATCC 33591, and MRSA ATCC 49476.

    MATERIALS AND METHODS: The production of secondary metabolites by this strain was optimized through Thronton's media. Isolation, purification, and identification of the bioactive compounds were carried out using reversed-phase high-performance liquid chromatography, high-resolution mass spectrometry, Fourier transform infrared, and one-dimensional and two-dimensional nuclear magnetic resonance.

    RESULTS: During screening procedure, SUK 25 exhibited good antimicrobial potential against several strains of MRSA. The best biological activity was shown from fraction number VII and its subfractions F2 and F3 with minimum inhibitory concentration values at 16 µg/mL and 8 µg/mL, respectively. These two subfractions were identified as diketopiperazine cyclo-(tryptophanyl-prolyl) and chloramphenicol.

    CONCLUSION: On the basis of obtained results, SUK 25 isolated from Z. spectabile can be regarded as a new valuable source to produce secondary metabolites against bacteria, especially MRSA.

    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  5. Noreen N, Hooi WY, Baradaran A, Rosfarizan M, Sieo CC, Rosli MI, et al.
    Microb Cell Fact, 2011;10:28.
    PMID: 21518457 DOI: 10.1186/1475-2859-10-28
    Many plasmid-harbouring strains of Lactococcus lactis have been isolated from milk and other sources. Plasmids of Lactococcus have been shown to harbour antibiotic resistance genes and those that express some important proteins. The generally regarded as safe (GRAS) status of L. lactis also makes it an attractive host for the production of proteins that are beneficial in numerous applications such as the production of biopharmaceutical and nutraceutical. In the present work, strains of L. lactis were isolated from cow's milk, plasmids were isolated and characterised and one of the strains was identified as a potential new lactococcal host for the expression of heterologous proteins.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  6. Shukor MY, Dahalan FA, Jusoh AZ, Muse R, Shamaan NA, Syed MA
    J Environ Biol, 2009 Jan;30(1):145-50.
    PMID: 20112877
    A diesel-degrading bacterium has been isolated from a diesel-polluted site. The isolate was tentatively identified as Staphylococcus aureus strain DRY11 based on partial 16S rDNA molecular phylogeny and Biolog GP microplate panels and Microlog database. Isolate 11 showed an almost linear increase in cellular growth with respect to diesel concentrations with optimum growth occurring at 4% (v/v) diesel concentration. Optimization studies using different nitrogen sources showed that the best nitrogen source was potassium nitrite. Sodium nitrite was optimum at 1.2 g l(-1) and higher concentrations were strongly inhibitory to cellular growth. The optimal pH that supported growth of the bacterium was between 7.5 to 8.0 and the isolate exhibited optimal broad temperature supporting growth on diesel from 27 to 37 degrees C. An almost complete removal of diesel components was seen from the reduction in hydrocarbon peaks observed using Solid Phase Microextraction Gas Chromatography analysis after 5 days of incubation. The characteristics of this bacterium suggest that it is suitable for bioremediation of diesel spills and pollutions in the tropics.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  7. Nakajima Y, Ho CC, Kudo T
    J Gen Appl Microbiol, 2003 Jun;49(3):181-9.
    PMID: 12949699
    The taxonomic position of three actinomycete strains isolated from Malaysian soil was established by using a polyphasic approach. The isolates formed chains composed of four spores on the tip of sporophores branching from the aerial mycelium, and their chemotaxonomic properties were common to those of members of the family Streptosporangiaceae. These phenotypic properties as well as a phylogenetic analysis based on 16S rRNA gene sequences indicated that they should be classified in the genus Microtetraspora. The three isolates showed a unique pattern of cultural, physiological and biochemical properties that distinguished them from previously described species of the genus Microtetraspora. The isolates showed more than 72% DNA relatedness to each other, but only 58% or less relatedness to any previously described species. On the basis of the data presented, a new species of the genus Microtetraspora, Microtetraspora malaysiensis, is proposed. The type strain of the new species is strain H47-7(T) (=JCM 11278(T)=DSM 44579(T)).
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  8. Yeap BK, Othman AS, Lee VS, Lee CY
    J Econ Entomol, 2007 Apr;100(2):467-74.
    PMID: 17461072
    The phylogenetic relationship of Coptotermes gestroi (Wasmann) and Coptotermes vastator Light (Isoptera: Rhinotermitidae) was determined using DNA sequence comparisons of mitochondrial genes. Partial sequences of the ribosomal RNA small subunit 12S, ribosomal RNA large subunit 16S, and mitochondrial COII were obtained from nine populations of C. gestroi from South East Asia (Malaysia, Singapore, Thailand, and Indonesia) and four populations of C. vastator from the Philippines and Hawaii. In addition, four populations of Coptotermes formosanus Shiraki and Globitermes sulphureus (Haviland) were used as the outgroups. Consensus sequences were obtained and aligned. C. vastator and C. gestroi are synonymous, based on high sequence homology across the 12S, 16S, and COII genes. The interspecific pairwise sequence divergence, based on Kimura 2-parameter model between C. gestroi and C. vastator, varied only up to 0.80%. Morphometric measurements of 16 characteristics revealed numerous overlaps between the examined individuals of both species. Based on the molecular phylogenetics and morphometric data, it is proposed that C. vastator is a junior synonym of C. gestroi.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  9. Zokaeifar H, Balcázar JL, Kamarudin MS, Sijam K, Arshad A, Saad CR
    J Antibiot (Tokyo), 2012 Jun;65(6):289-94.
    PMID: 22491136 DOI: 10.1038/ja.2012.17
    In this study, potential probiotic strains were isolated from fermented pickles based on antagonistic activity against two shrimp pathogens (Vibrio harveyi and Vibrio parahaemolyticus). Two strains L10 and G1 were identified by biochemical tests, followed by16S ribosomal RNA gene sequence analysis as Bacillus subtilis, and characterized by PCR amplification of repetitive bacterial DNA elements (Rep-PCR). Subsequently, B. subtilis L10 and G1 strains were tested for antibacterial activity under different physical conditions, including culture medium, salinity, pH and temperature using the agar well diffusion assay. Among the different culture media, LB broth was the most suitable medium for antibacterial production. Both strains showed the highest level of antibacterial activity against two pathogens at 30 °C and 1.0% NaCl. Under the pH conditions, strain G1 showed the greatest activity against V. harveyi at pH 7.3-8.0 and against V. parahaemolyticus at pH 6.0-8.0, whereas strain L10 showed the greatest activity against two pathogens at pH 7.3. The cell-free supernatants of both strains were treated with four different enzymes in order to characterize the antibacterial substances against V. harveyi. The result showed considerable reduction of antibacterial activity for both strains, indicating the proteinaceous nature of the antibacterial substances. A wide range of tolerance to NaCl, pH and temperature was also recorded for both strains. In addition, both strains showed no virulence effect in juvenile shrimp Litopenaeus vannamei. On the basis of these results and safety of strains to L. vannamei, they may be considered for future challenge experiments in shrimp as a very promising alternative to the use of antibiotics.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  10. Horn M, Fritsche TR, Linner T, Gautom RK, Harzenetter MD, Wagner M
    Int J Syst Evol Microbiol, 2002 Mar;52(Pt 2):599-605.
    PMID: 11931173 DOI: 10.1099/00207713-52-2-599
    All obligate bacterial endosymbionts of free-living amoebae currently described are affiliated with the alpha-Proteobacteria, the Chlamydiales or the phylum Cytophaga-Flavobacterium-Bacteroides. Here, six rod-shaped gram-negative obligate bacterial endosymbionts of clinical and environmental isolates of Acanthamoeba spp. from the USA and Malaysia are reported. Comparative 16S rDNA sequence analysis demonstrated that these endosymbionts form a novel, monophyletic lineage within the beta-Proteobacteria, showing less than 90% sequence similarity to all other recognized members of this subclass. 23S rDNA sequence analysis of two symbionts confirmed this affiliation and revealed the presence of uncommon putative intervening sequences of 146 bp within helix-25 that shared no sequence homology to any other bacterial rDNA. In addition, the 23S rRNA of these endosymbionts displayed one polymorphism at the target site of oligonucleotide probe BET42a that is conserved in all other sequenced beta-Proteobacteria. Intra-cytoplasmatic localization of the endosymbionts within the amoebal host cells was confirmed by electron microscopy and fluorescence in situ hybridization with a specific 16S rRNA-targeted oligonucleotide probe. Based on these findings, the provisional name 'Candidatus Procabacter acanthamoebae' is proposed for classification of a representative of the six endosymbionts of Acanthamoeba spp. studied in this report. Comparative 18S rDNA sequence analysis of the Acanthamoeba host cells revealed their membership with either Acanthamoeba 18S rDNA sequence type T5 (Acanthamoeba lenticulata) or sequence type T4, which comprises the majority of all Acanthamoeba isolates.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  11. Loke MF, Chua EG, Gan HM, Thulasi K, Wanyiri JW, Thevambiga I, et al.
    PLoS One, 2018;13(12):e0208584.
    PMID: 30576312 DOI: 10.1371/journal.pone.0208584
    Colorectal cancer (CRC) is ranked the third most common cancer in human worldwide. However, the exact mechanisms of CRC are not well established. Furthermore, there may be differences between mechanisms of CRC in the Asian and in the Western populations. In the present study, we utilized a liquid chromatography-mass spectrometry (LC-MS) metabolomic approach supported by the 16S rRNA next-generation sequencing to investigate the functional and taxonomical differences between paired tumor and unaffected (normal) surgical biopsy tissues from 17 Malaysian patients. Metabolomic differences associated with steroid biosynthesis, terpenoid biosynthesis and bile metabolism could be attributed to microbiome differences between normal and tumor sites. The relative abundances of Anaerotruncus, Intestinimonas and Oscillibacter displayed significant relationships with both steroid biosynthesis and terpenoid and triterpenoid biosynthesis pathways. Metabolites involved in serotonergic synapse/ tryptophan metabolism (Serotonin and 5-Hydroxy-3-indoleacetic acid [5-HIAA]) were only detected in normal tissue samples. On the other hand, S-Adenosyl-L-homocysteine (SAH), a metabolite involves in methionine metabolism and methylation, was frequently increased in tumor relative to normal tissues. In conclusion, this study suggests that local microbiome dysbiosis may contribute to functional changes at the cancer sites. Results from the current study also contributed to the list of metabolites that are found to differ between normal and tumor sites in CRC and supported our quest for understanding the mechanisms of carcinogenesis.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  12. Matsui M, Kuraishi N, Eto K, Hamidy A, Nishikawa K, Shimada T, et al.
    Mol Phylogenet Evol, 2016 09;102:305-19.
    PMID: 27374495 DOI: 10.1016/j.ympev.2016.06.009
    A fanged frog Limnonectes kuhlii was once thought to be wide-ranging in Southeast Asia, but is now confined to its type locality Java through recent phylogenetic studies, which clarified heterospecific status of non-Javanese populations, and monophyly of Bornean populations. However, large genetic differences among Bornean populations suggest occurrence of cryptic species, which we test using dense geographic sampling. We estimated the phylogenetic relationships among samples of Bornean populations together with their putative relatives from the continental Southeast Asia, using 2517bp sequences of the 12S rRNA, tRNA(val), and 16S rRNA of mitochondrial DNA, and 2367bp sequences of the NCX1, POMC, and RAG1 of nuclear genes. In the mtDNA trees, Bornean L. kuhlii-like frogs formed a monophyletic group split into 18 species lineages including L. hikidai, with the deepest phylogenetic split separating L. cintalubang from the remaining species. Almost all of these lineages co-occur geographically, and two to three lineages were found syntopically in each locality. Co-occurrence of more than one lineage may be maintained by differential morphology and microhabitat selection. These syntopic lineages should be regarded as distinct species. Our results clearly indicate that taxonomic revision is urgent to clarify many evolutionary problems of Bornean L. kuhlii-like frogs.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  13. Chua PK, Corkill JE, Hooi PS, Cheng SC, Winstanley C, Hart CA
    Emerg Infect Dis, 2005 Feb;11(2):271-7.
    PMID: 15752446
    An obligate intracellular bacterium was isolated from urine samples from 7 (3.5%) of 202 fruit bats (Eonycteris spelaea) in peninsular Malaysia. The bacterium produced large membrane-bound inclusions in human, simian, and rodent cell lines, including epithelial, fibroblastlike, and lymphoid cells. Thin-section electron microscopy showed reticulate bodies dividing by binary fission and elementary bodies in the inclusions; mitochondria surrounded the inclusions. The inclusions were positive for periodic acid-Schiff stain but could not be stained by fluorescein-labeled anti-Chlamydia trachomatis major outer membrane protein monoclonal antibody. The bacterium was resistant to penicillin and streptomycin (MICs > 256 mg/L) but susceptible to tetracycline (MIC = 0.25 mg/L) and chloramphenicol (MIC = 0.5 mg/L). Sequence analysis of the 16SrRNA gene indicated that it was most closely related to 2 isolates of Waddlia chondrophila (94% and 96% identity). The 16S and 23S rRNA gene signatures were only 91% identical. We propose this novel bacterium be called W. malaysiensis.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
  14. Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, et al.
    Nat Commun, 2014;5:3112.
    PMID: 24473108 DOI: 10.1038/ncomms4112
    Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.
    Matched MeSH terms: RNA, Ribosomal, 16S/chemistry
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