Displaying publications 121 - 140 of 634 in total

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  1. Haplotype-habitat associations of Coptotermes gestroi (Termitoidae: Rhinotermitidae) from mitochondrial DNA genes
    Cheng S, Thinagaran D, Mohanna SZ, Noh NA
    Environ Entomol, 2014 Aug;43(4):1105-16.
    PMID: 24915136 DOI: 10.1603/EN13318
    Coptotermes gestroi (Wasmann) or the Asian subterranean termite is a serious structural pest in urban settlements in Southeast Asia that has been introduced to other parts of the world through human commerce. Although mitochondrial DNA markers were previously used to shed light on the dispersal history of the Asian subterranean termite, there were limited attempts to analyze or include populations of the termite found in the wild in Southeast Asia. In this study, we analyzed the 16S ribosomal RNA (16S rRNA) and cytochrome c oxidase subunit 1 (cox1) genes of Asian subterranean termite colonies found in mangrove swamps, beach forests, plantations, and buildings in semi-urban and urban areas to determine the relationship between colonies found in the wild and the urban habitat, and to investigate the possibility of different ecotypes of the termite in Peninsular Malaysia. Our findings show that the 16S rRNA haplotypes recovered from this study clustered into eastern, western, and southern populations of the termite, while the cox1 haplotypes were often specific to an area or site. The 16S rRNA and cox1 genes or haplotypes showed that the most abundant haplotype occupied a wide range of environments or habitats. In addition, the cox1 tree showed evidence of historical biogeography where basal haplotypes inhabited a wide range of habitats, while apical haplotypes were restricted to mangrove swamps and beach forests. Information on the haplotype-habitat association of C. gestroi will enable the prediction of habitats that may harbor or be at risk of invasion in areas where they have been introduced.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics; RNA, Ribosomal, 16S/metabolism
  2. Refinement of a low-resolution crystal structure to better understand erythromycin interactions on large ribosomal subunit
    Wahab HA, Yam WK, Samian MR, Najimudin N
    J Biomol Struct Dyn, 2008 Aug;26(1):131-46.
    PMID: 18533733
    Macrolides are a group of diverse class of naturally occurring and synthetic antibiotics made of macrocyclic-lactone ring carrying one or more sugar moieties linked to various atoms of the lactone ring. These macrolides selectively bind to a single high affinity site on the prokaryotic 50S ribosomal subunit, making them highly effective towards a wide range of bacterial pathogens. The understanding of binding between macrolides and ribosome serves a good basis in elucidating how they work at the molecular level and these findings would be important in rational drug design. Here, we report refinement of reconstructed PDB structure of erythromycin-ribosome system using molecular dynamics (MD) simulation. Interesting findings were observed in this refinement stage that could improve the understanding of the binding of erythromycin A (ERYA) onto the 50S subunit. The results showed ERYA was highly hydrated and water molecules were found to be important in bridging hydrogen bond at the binding pocket during the simulation time. ERYA binding to ribosome was also strengthened by hydrogen bond network and hydrophobic interactions between the antibiotic and the ribosome. Our MD simulation also demonstrated direct interaction of ERYA with Domains II, V and with C1773 (U1782EC), a residue in Domain IV that has yet been described of its role in ERYA binding. It is hoped that this refinement will serve as a starting model for a further enhancement of our understanding towards the binding of ERYA to ribosome.
    Matched MeSH terms: RNA, Ribosomal, 23S/metabolism*; RNA, Ribosomal, 23S/chemistry*
  3. Fulltext Lactococcus lactis M4, a potential host for the expression of heterologous proteins
    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/metabolism; RNA, Ribosomal, 16S/chemistry
  4. Isolation and mode of action of bacteriocin BacC1 produced by nonpathogenic Enterococcus faecium C1
    Goh HF, Philip K
    J Dairy Sci, 2015 Aug;98(8):5080-90.
    PMID: 26004828 DOI: 10.3168/jds.2014-9240
    Lactic acid bacteria are present in fermented food products and help to improve shelf life and enhance the flavor of the food. They also produce metabolites such as bacteriocins to prevent the growth of undesirable or pathogenic bacteria. In this study, Enterococcus faecium C1 isolated from fermented cow milk was able to produce bacteriocin BacC1 and inhibit the growth of selected food-spoilage bacteria. The bacteriocin was purified through 4 steps: ammonium sulfate precipitation, hydrophobic interaction column, a series of centrifugal steps, and finally reversed-phase HPLC. A membrane permeability test using SYTOX green dye (Invitrogen, Grand Island, NY) showed that the bacteriocin caused significant disruptions to the test bacterial membrane, as shown by transmission electron microscopy. The molecular weight of the BacC1 obtained from SDS-PAGE was around 10kDa, and N-terminal sequencing revealed a partial amino acid sequence of BacC1: GPXGPXGP. The bacterial strain was nonhemolytic and not antibiotic resistant. Therefore, it has high potential for application in the food industry as an antimicrobial agent to extend the shelf life of food products.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics*; RNA, Ribosomal, 16S/metabolism
  5. Fulltext Isolation and characterization of cyclo-(tryptophanyl-prolyl) and chloramphenicol from Streptomyces sp. SUK 25 with antimethicillin-resistant Staphylococcus aureus activity
    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/genetics*; RNA, Ribosomal, 16S/chemistry
  6. Fulltext In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas
    Tran PN, Savka MA, Gan HM
    Front Microbiol, 2017;8:1296.
    PMID: 28747902 DOI: 10.3389/fmicb.2017.01296
    The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans-P. oryzihabitans, and P. kilonensis- P. brassicacearum, that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.
    Matched MeSH terms: RNA, Ribosomal, 16S
  7. Fulltext Identification of Escherichia spp. strains in street-vended beverages and associated preparation surfaces using 16S rRNA analysis
    Chong, S. Y., Rao, P. V., Soon, J. M.
    International Food Research Journal, 2017;24(4):1811-1818.
    MyJurnal
    Street-vended beverages are commonly prepared by mechanical extraction of the pulp, usually
    unpasteurised and requires multiple handling steps. Foodborne pathogens transmitted via skin of
    street vendors or via faecal-oral route may contaminate the preparation surfaces and beverages.
    The aim of this study is to identify Escherichia spp. strains of street-vended beverages and their
    associated preparation surfaces using 16s rRNA analysis. The hygienic practice of vendors was represented by Staphylococcus spp. analysis and Staphylococcus aureus is not detected in beverages and associated preparation surfaces. A total of 80 samples (18 beverages, 15 swab
    samples and 47 direct film samples) were collected followed by enumeration of microbial load.
    Polymerase Chain Reaction (PCR) amplification and 16S ribosomal ribonucleic acid (rRNA)
    sequencing were carried out. Results of 16S rRNA sequence analysis indicated that three gram-negative isolates were identified as Escherichia coli RM9387 (Accession no. CP009104.1),
    Escherichia coli c164 (Accession no. JQ781646.1) and Escherichia fergusonii E10 (Accession no. KJ626264.1) with similarity value of 99% respectively.
    Matched MeSH terms: RNA, Ribosomal, 16S
  8. Low-dissolved-oxygen nitrification in tropical sewage: an investigation on potential, performance and functional microbial community
    How SW, Lim SY, Lim PB, Aris AM, Ngoh GC, Curtis TP, et al.
    Water Sci Technol, 2018 May;77(9-10):2274-2283.
    PMID: 29757179 DOI: 10.2166/wst.2018.143
    Intensive aeration for nitrification is a major energy consumer in sewage treatment plants (STPs). Low-dissolved-oxygen (low-DO) nitrification has the potential to lower the aeration demand. However, the applicability of low-DO nitrification in the tropical climate is not well-understood. In this study, the potential of low-DO nitrification in tropical setting was first examined using batch kinetic experiments. Subsequently, the performance of low-DO nitrification was investigated in a laboratory-scale sequential batch reactor (SBR) for 42 days using real tropical sewage. The batch kinetic experiments showed that the seed sludge has a relatively high oxygen affinity. Thus, the rate of nitrification was not significantly reduced at low DO concentrations (0.5 mg/L). During the operation of the low-DO nitrification SBR, 90% of NH4-N was removed. The active low-DO nitrification was mainly attributed to the limited biodegradable organics in the sewage. Fluorescence in-situ hybridisation and 16S rRNA amplicon sequencing revealed the nitrifiers were related to Nitrospira genus and Nitrosomonadaceae family. Phylogenetic analysis suggests 47% of the operational taxonomic units in Nitrospira genus are closely related to a comammox bacteria. This study has demonstrated active low-DO nitrification in tropical setting, which is a more sustainable process that could significantly reduce the energy footprint of STPs.
    Matched MeSH terms: RNA, Ribosomal, 16S
  9. Fulltext 16S rRNA Gene Sequencing for Deciphering the Colorectal Cancer Gut Microbiome: Current Protocols and Workflows
    Osman MA, Neoh HM, Ab Mutalib NS, Chin SF, Jamal R
    Front Microbiol, 2018;9:767.
    PMID: 29755427 DOI: 10.3389/fmicb.2018.00767
    The human gut holds the densest microbiome ecosystem essential in maintaining a healthy host physiology, whereby disruption of this ecosystem has been linked to the development of colorectal cancer (CRC). The advent of next-generation sequencing technologies such as the 16S rRNA gene sequencing has enabled characterization of the CRC gut microbiome architecture in an affordable and culture-free approach. Nevertheless, the lack of standardization in handling and storage of biospecimens, nucleic acid extraction, 16S rRNA gene primer selection, length, and depth of sequencing and bioinformatics analyses have contributed to discrepancies found in various published studies of this field. Accurate characterization of the CRC microbiome found in different stages of CRC has the potential to be developed into a screening tool in the clinical setting. This mini review aims to concisely compile all available CRC microbiome studies performed till end of 2016 and to suggest standardized protocols that are crucial in developing a gut microbiome screening panel for CRC.
    Matched MeSH terms: RNA, Ribosomal, 16S
  10. Tumbuhan etnoperubatan sebagai perumah aktinomiset endofit yang bersifat bioaktif
    Nurul ‘Izzah Mohd Sarmin, Noraziah M. Zin, Nik Marzuki Sidik, Franco CM, Ng KT, Kaewkla O
    Sains Malaysiana, 2012;41:547-551.
    Sembilan aktinomiset endofit telah berjaya dipencilkan daripada pokok yang mempunyai nilai ubatan dari beberapa tempat di Semenanjung Malaysia. Pencilan tersebut telah dikenalpasti melalui pemerhatian morfologi, amplifikasi gen 16S rRNA dan analisis penjujukan 16S rRNA. Saringan awal terhadap aktiviti antimikrob telah dilakukan dengan menggunakan teknik calitan plat. Pembentukan miselium substrat dan aerial, warna jisim spora, pigmen larut dan morfologi rantai spora pada semua pencilan menyerupai Streptomyces sp. dan Microbispora sp. Analisis filogenetik jujukan separa 16S rRNA mendapati pencilan SUK 08, SUK 10 dan SUK 15 saling berkaitan dengan Streptomyceseurythermus ATCC 14975T. Walau bagaimanapun pencilan ini telah dipencilkan dari tumbuhan yang berbeza. Pencilan ini didapati mempunyai aktiviti antimikrob terhadap bakteria dan kulat kajian. Empat pencilan aktif iaitu SUK 08, SUK10, SUK 12 dan SUK 15 berupaya untuk membunuh dan merencat sehingga 100% satu atau lebih organisma patogen seperti Bacillus subtilis, Aspergillus fumigatus, Aspergillus niger, Fusarium solani, Rhizoctonia solani dan Trichoderma viride. Kajian ini mengesahkan bahawa tumbuhan etnoperubatan adalah sumber pencarian aktinomiset endofit bioaktif yang berupaya menjadi sumber novel dalam pencarian agen antibakteria dan antimikotik.
    Matched MeSH terms: RNA, Ribosomal, 16S
  11. In vitro and in vivo evaluation of streptomyces suppressions against anthracnose in chili caused by colletotrichum
    Shahbazi P, Md Yusoff Musa, Tan AGY, Farhat Ahmadi Avin, Teo AWF, Sabaratnam V
    Sains Malaysiana, 2014;43:697-705.
    The isolation of 66 streptomycetes from rhizosphere soil of chili plants was done for their inhibitory activities against three different dominant species of Colletotrichum namely C. acutatum, C. gloeosporioides and C. capsici. Twenty one streptomycetes strains were active against at least one of the Colletotrichum species. In addition, ten strains that inhibited the in vitro growth of Colletotrichum species showed chitinase activity. Strain P42, which displayed the highest inhibitory activity against all three anthracnose fungi species and high chitinase activity was tested as biological control agent in a greenhouse study. The strain successfully controlled chili anthracnose disease by significantly reducing the disease severity. Phylogenetic analysis of the 16S rRNA gene sequences showed that strain P42 belongs to the Streptomyces rochei clade. The results of the current study showed that rhizosphere-derived soil of chili plants is an important source of bioactive streptomycetes which are antagonistic against Colletotrichum.
    Matched MeSH terms: RNA, Ribosomal, 16S
  12. Molecular characterization of Malaysian marine fish species using partial sequence of mitochondrial DNA 12S and 16S rRNA markers
    Nur Haslindawaty Abd Rashid, Siti Farah Quraisha, Sundararajulu Panneerchelvam, Zafarina Zainuddin
    Sains Malaysiana, 2015;44:1119-1123.
    This study was conducted to characterize the selected marine fish species using partial sequence of mtDNA 12S and 16S rRNA gene. PCR amplification of 12S and 16S rRNA generated PCR amplicons at 350 and 440 bp lengths, respectively. Sequence analysis was performed using BioEdit software. Phylogenetic tree was constructed using MEGA software. Two reference species have been used namely Gobio gobio (AB239596 and EF112528) and Pentapodus caninus (DQ533268 and DQ532933). Based on the result obtained, mtDNA 12S and 16S rRNA were found to be useful as molecular markers for fish species identification. These markers will provide correct identification of fish species when considered along with morphological characteristics.
    Matched MeSH terms: RNA, Ribosomal, 16S
  13. Characterization and utilization of pulp and paper mill sludge digesting thermophilic bacteria in composting process
    Le Van Thien, Ngo Thi Tuong Chau, Pham Thi Ngoc Lan, Hiroyuki Futamata
    Sains Malaysiana, 2018;47:1051-1060.
    Pulp and paper mill sludge (PPMS) was found to be poorly colonised with thermophilic microorganisms. However,
    evidence to support the need for inoculation to facilitate PPMS composting has only been demonstrated in one instance.
    In this study, we aimed to: screen and identify PPMS digesting thermophilic bacterial strains; investigate effects of the
    mixture of selected thermophilic bacterial strains on PPMS digestion; and utilize this mixture as start inoculum in PPMS
    composting and assess the quality of compost product. The results showed that eleven thermophilic bacterial strains were
    isolated from Bai Bang PPMS by the enrichment culture method. Among these, three strains which reflected high growth
    rates on the plates of Minimal Media Agar supplemented with Bai Bang PPMS and showed hydrolytic and ligninolytic
    activities on the agar plates containing appropriate inductive substrates were selected. Based on the morphological,
    biochemical characteristics and 16S rRNA gene sequencing, they were identified as Bacillus subtilis. The inoculation
    with the mixture of selected strains enhanced remarkably Bai Bang PPMS digestion. The dry weight decrease, volatile
    suspended solids removal, dehydrogenase and protease activities in the inoculated sludge were 2.1-, 1.5-, 1.3- and 1.2-
    fold higher, respectively, compared to the non-inoculated sludge. The assessment of compost quality based on stability
    using the alkaline trap method and maturity using the germination and root elongation test showed that the inoculated
    compost was stable and mature while the non-inoculated compost was unstable and immature. These thermophilic
    bacterial strains therefore have great potential for Bai Bang PPMS composting.
    Matched MeSH terms: RNA, Ribosomal, 16S
  14. Fulltext Leptospiral Culture without 5'-Fluorouracil Revealed Improved Leptospira Isolation from Febrile Patients in North-Eastern Malaysia
    Mohamad Safiee AW, Ali MRM, Fauzi MH, Besari AM, Yean CY, Neela VK, et al.
    Int J Environ Res Public Health, 2020 02 18;17(4).
    PMID: 32085530 DOI: 10.3390/ijerph17041307
    Objectives: Isolation of Leptospira by culture represents a definitive growth and confirmation of the disease, yet it is hampered with its nature of slow growth. With slight modification of culture method, the study aims to isolate and characterize Leptospira spp. from patients with acute febrile illness. Methods: A total of 109 blood samples were collected from patients with acute febrile illness that presented at the Emergency Department of Hospital Universiti Sains Malaysia, Malaysia. Clinical samples were subjected to Leptospira IgM Rapid test, microscopic agglutination test (MAT), isolation by culture method, and direct real-time PCR test. For leptospiral isolation, the samples (whole blood and deposit from spun plasma) were cultured into modified Ellinghausen McCullough Johnson Harris (EMJH) media with and without 5'-fluorouracil (5-FU). In every culture positive sample, partial 16S rRNA gene sequencing was performed for molecular identification of the isolates. Phylogenetic analysis was carried out to determine the genetic relatedness among the isolates. An inhibition of 5-FU study was performed on Leptospirainterrogans serovar Canicola with different concentrations to compare the growth detection of the tested Leptospira with or without 5-FU within 7 days of incubation. Results: Leptospirosis was diagnosed in 14.7% of patients with acute febrile illness. Two Leptospira spp. (n = 2/109, 1.85%) were successfully isolated from whole blood and deposit from spun plasma samples. B004 and B208 samples were positive at day 11 and day 7, respectively, in EMJH media without addition of 5-FU. Sample B004 was identified as Leptospira interrogans and B208 as Leptospira weilli. Phylogenetic analysis confirmed that both of them were within pathogenic group and they were not related. The 5-FU inhibition study revealed that additional of 5-FU at final concentration of 200 µg/mL to EMJH media demonstrated an inhibitory effect on the growth of the tested strain Conclusion: Isolation of Leptospira spp. using EMJH media without addition of 5'-fluorouracil resulted in a better outcome. Two pathogenic Leptospira isolates were successfully cultivated from patients with acute febrile illness that were genetically not related.
    Matched MeSH terms: RNA, Ribosomal, 16S
  15. Discovery of the westernmost population of the genus Ansonia Stoliczka (Anura, Bufonidae) with the description of a new species from the Shan Plateau of eastern Myanmar
    Quah ESH, Grismer LL, Wood PLJ, Thura MK, Oaks JR, Lin A
    Zootaxa, 2019 Aug 14;4656(3):zootaxa.4656.3.11.
    PMID: 31716818 DOI: 10.11646/zootaxa.4656.3.11
    A new species of Ansonia is described from the Shan Plateau of Myanmar based on an integrative taxonomic analysis that differentiates it from all other congeners. Molecular phylogenetic analyses based on the mitochondrial genes 12S and 16S rRNA and tRNA-val recover A. kyaiktiyoensis sp. nov. as the sister species to A. inthanon from Thailand but differs from it and other congeners by at least a 5.0% sequence divergence. It is further differentiated by the following combination of morphological characters: (1) maximum SVL 24 mm in males and females; (2) first finger shorter than second; (3) absence of interorbital and tarsal ridges; (4) presence of light-coloured interscapular spot; (5) presence of yellow rictal tubercle; (6) absence of wide, light-coloured patch below eye; (7) presence of large, discrete, bright-yellow submandibular spots along the underside of lower jaw; (8) iris yellow-gold; (9) presence of markings on the snout consisting of streaks below the eye to the lip, and on the canthus rostralis to the nostril; (10) dorsum grey-brown with orange-beige spots, a dark-brown X-shaped marking on the back surrounding the interscapular spot, and dark-coloured markings on rump; (11) fore- and hind limbs with orange-beige cross-bars; and (12) venter light-gray with yellow spotting, especially near flanks and underside of hind limbs. Ansonia kyaiktiyoensis sp. nov. is the westernmost known record for the genus and the only species west of the Salween Basin. Its discovery echoes the increasing number of herpetological discoveries being made in upland regions fringing the Ayeyarwady and Salween Basins.
    Matched MeSH terms: RNA, Ribosomal, 16S
  16. Fulltext Metagenomic data of bacterial community from different land uses at the river basin, Kelantan
    Rupert R, Lie GJCW, John DV, Annammala KV, Jani J, Rodrigues KF
    Data Brief, 2020 Dec;33:106351.
    PMID: 33072827 DOI: 10.1016/j.dib.2020.106351
    The data provided in the article includes the sequence of bacterial 16S rRNA gene from a high conservation value forest, logged forest, rubber plantation and oil palm plantation collected at Kelantan river basin. The logged forest area was previously notified as a flooding region. The total gDNA of bacterial community was amplified via polymerase chain reaction at V3-V4 regions using a pair of specific universal primer. Amplicons were sequenced on Illumina HiSeq paired-end platform to generate 250 bp paired-end raw reads. Several bioinformatics tools such as FLASH, QIIME and UPARSE were used to process the reads generated for OTU analysis. Meanwhile, R&D software was used to construct the taxonomy tree for all samples. Raw data files are available at the Sequence Read Archive (SRA), NCBI and data information can be found at the BioProject and BioSample, NCBI. The data shows the comparison of bacterial community between the natural forest and different land uses.
    Matched MeSH terms: RNA, Ribosomal, 16S
  17. Genome analysis of cellulose and hemicellulose degrading Micromonospora sp. CP22
    Chen SJ, Lam MQ, Thevarajoo S, Abd Manan F, Yahya A, Chong CS
    3 Biotech, 2020 Apr;10(4):160.
    PMID: 32206494 DOI: 10.1007/s13205-020-2148-z
    In this study, a bacterial strain CP22 with ability to produce cellulase, xylanase and mannanase was isolated from the oil palm compost. Based on the 16S rRNA gene analysis, the strain was affiliated to genus Micromonospora. To further investigate genes that are related to cellulose and hemicellulose degradation, the genome of strain CP22 was sequenced, annotated and analyzed. The de novo assembled genome of strain CP22 featured a size of 5,856,203 bp with G + C content of 70.84%. Detailed genome analysis on lignocellulose degradation revealed a total of 60 genes consisting of 47 glycoside hydrolase domains and 16 carbohydrate esterase domains predicted to be involved in cellulolytic and hemicellulolytic deconstruction. Particularly, 20 genes encode for cellulases (8 endoglucanases, 3 exoglucanases and 9 β-glucosidases) and 40 genes encode for hemicellulases (15 endo-1,4-β-xylanase, 3 β-xylosidase, 3 α-arabinofuranosidase, 10 acetyl xylan esterase, 6 polysaccharide deacetylase, 1 β-mannanase, 1 β-mannosidase and 1 α-galactosidase). Thirty-two genes encoding carbohydrate-binding modules (CBM) from six different families (CBM2, CBM4, CBM6, CBM9, CBM13 and CBM22) were present in the genome of strain CP22. These CBMs were found in 27 cellulolytic and hemicellulolytic genes, indicating their potential role in enhancing the substrate-binding capability of the enzymes. CBM2 and CBM13 are the major CBMs present in cellulases and hemicellulases (xylanases and mannanases), respectively. Moreover, a GH10 xylanase was found to contain 3 CBMs (1 CBM9 and 2 CBM22) and these CBMs were reported to bind specifically to xylan. This genome-based analysis could facilitate the exploration of this strain for lignocellulosic biomass degradation.
    Matched MeSH terms: RNA, Ribosomal, 16S
  18. Fulltext Indoor microbiome, environmental characteristics and asthma among junior high school students in Johor Bahru, Malaysia
    Fu X, Norbäck D, Yuan Q, Li Y, Zhu X, Hashim JH, et al.
    Environ Int, 2020 05;138:105664.
    PMID: 32200316 DOI: 10.1016/j.envint.2020.105664
    Indoor microbial diversity and composition are suggested to affect the prevalence and severity of asthma by previous home microbiome studies, but no microbiome-health association study has been conducted in a school environment, especially in tropical countries. In this study, we collected floor dust and environmental characteristics from 21 classrooms, and health data related to asthma symptoms from 309 students, in junior high schools in Johor Bahru, Malaysia. The bacterial and fungal composition was characterized by sequencing 16s rRNA gene and internal transcribed spacer (ITS) region, and the absolute microbial concentration was quantified by qPCR. In total, 326 bacterial and 255 fungal genera were characterized. Five bacterial (Sphingobium, Rhodomicrobium, Shimwellia, Solirubrobacter, Pleurocapsa) and two fungal (Torulaspora and Leptosphaeriaceae) taxa were protective for asthma severity. Two bacterial taxa, Izhakiella and Robinsoniella, were positively associated with asthma severity. Several protective bacterial taxa including Rhodomicrobium, Shimwellia and Sphingobium have been reported as protective microbes in previous studies, whereas other taxa were first time reported. Environmental characteristics, such as age of building, size of textile curtain per room volume, occurrence of cockroaches, concentration of house dust mite allergens transferred from homes by the occupants, were involved in shaping the overall microbial community but not asthma-associated taxa; whereas visible dampness and mold, which did not change the overall microbial community for floor dust, was negatively associated with the concentration of protective bacteria Rhodomicrobium (β = -2.86, p = 0.021) of asthma. The result indicates complex interactions between microbes, environmental characteristics and asthma symptoms. Overall, this is the first indoor microbiome study to characterize the asthma-associated microbes and their environmental determinant in the tropical area, promoting the understanding of microbial exposure and respiratory health in this region.
    Matched MeSH terms: RNA, Ribosomal, 16S
  19. Fulltext Review of clinical aspects, epidemiology and diagnosis of haemotropic Mycoplasma ovis in small ruminants: current status and future perspectives in tropics focusing on Malaysia
    Paul BT, Jesse FFA, Chung ELT, Che-Amat A, Mohd Lila MA, Hashi HA, et al.
    Trop Anim Health Prod, 2020 Nov;52(6):2829-2844.
    PMID: 32712811 DOI: 10.1007/s11250-020-02357-9
    Mycoplasma ovis (formerly Eperythrozoon ovis) is an epierythrocytic parasitic bacterium of small ruminants known as haemotropic mycoplasma, which is transmitted mechanically by biting flies and contaminated instruments. Acute mycoplasmosis causes severe haemolytic anaemia and mortality in young animals. At the same time, chronic disease may produce mild anaemia and varying degrees of morbidity depending on several factors, including age, reproductive status, the plane of nutrition, immunological status and the presence of concurrent infection. Haemotropic Mycoplasma ovis is currently recognised as an emerging zoonotic pathogen which is widely distributed in the sheep and goat producing areas of tropics and subtropics, where the disease is nearly endemic. Human infection has been reported in pregnant women, immunocompromised patients and people exposed to animals and arthropods. The current diagnosis of haemoplasma relies on microscopic evaluation of Giemsa-stained blood smear and PCR. Although there are few published reports on the incidence of haemotropic Mycoplasma ovis infection of small ruminants in Malaysia, information on its prevalence, risk factors, severity and economic impacts is grossly inadequate. Therefore, a large-scale survey of small ruminant flocks is necessary to elucidate the current seroprevalence status and molecular characteristics of haemotropic M. ovis infection in Malaysia using ELISA and PCR sequencing technologies. In the future, surveillance programs, including vector forecast, quarantine, monitoring by periodic surveys and public enlightenment, will limit the internal and transboundary spread of M. ovis, enhance control efforts and mitigate production losses in Malaysia.
    Matched MeSH terms: RNA, Ribosomal, 16S
  20. Fulltext The complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) from Peninsular Malaysia
    Rosli N, Sitam FT, Rovie-Ryan JJ, Gan HM, Lee YP, Hartini Ithnin, et al.
    Mitochondrial DNA B Resour, 2019 Jul 13;4(2):2535-2536.
    PMID: 33365614 DOI: 10.1080/23802359.2019.1640085
    Here, we present the first complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) inferred using next-generation sequencing. The mitogenome is 16,367 bp in length with the structural organization of a typical bovine mitochondrial arrangement comprising 13 protein-coding genes, 21 tRNAs, and 2 rRNAs. No internal stop codon was found in the protein-coding genes. Phylogenetic tree analysis revealed that Malayan gaur is more closely related to Burmese banteng instead of gaur.
    Matched MeSH terms: RNA, Ribosomal
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