22 results on '"Kian Mau Goh"'
Search Results
2. Genome sequence of an uncharted halophilic bacterium Robertkochia marina with deciphering its phosphate-solubilizing ability
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Chun Shiong Chong, Adibah Yahya, Ming Quan Lam, Sye Jinn Chen, Kian Mau Goh, Mohd Shahir Shamsir, and Fazilah Abd Manan
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Bacterial, Fungal and Virus Molecular Biology - Short Communication ,Sequence analysis ,Pseudogene ,Phosphatase ,Microbiology ,Genome ,Phosphates ,03 medical and health sciences ,Phylogenetics ,RNA, Ribosomal, 16S ,Media Technology ,Pyrophosphatases ,Gene ,Phylogeny ,030304 developmental biology ,Genetics ,Whole genome sequencing ,0303 health sciences ,Whole Genome Sequencing ,biology ,030306 microbiology ,Agriculture ,Sequence Analysis, DNA ,biology.organism_classification ,Solubility ,Phosphodiesterase I ,Flavobacteriaceae ,Genome, Bacterial ,Bacteria - Abstract
The wide use of whole-genome sequencing approach in the modern genomic era has opened a great opportunity to reveal the prospective applications of halophilic bacteria. Robertkochia marina CC-AMO-30D(T) is one of the halophilic bacteria that was previously taxonomically identified without any inspection on its biotechnological potential from a genomic aspect. In this study, we present the whole-genome sequence of R. marina and demonstrated the ability of this bacterium in solubilizing phosphate by producing phosphatase. The genome of R. marina has 3.57 Mbp and contains 3107 predicted genes, from which 3044 are protein coding, 52 are non-coding RNAs, and 11 are pseudogenes. Several phosphatases such as alkaline phosphatases and pyrophosphatases were mined from the genome. Further genomic study (phylogenetics, sequence analysis, and functional mechanism) and experimental data suggested that the alkaline phosphatase produced by R. marina could potentially be utilized in promoting plant growth, particularly for plants on saline-based agricultural land. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42770-020-00401-2.
- Published
- 2020
3. Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures
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Kok Jun Liew, Chee Hung Liang, Yee Ting Lau, Amira Suriaty Yaakop, Kok-Gan Chan, Saleha Shahar, Mohd Shahir Shamsir, and Kian Mau Goh
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Multidisciplinary ,Hot Temperature ,Bacteria ,Glycoside Hydrolases ,Biofilms ,RNA, Ribosomal, 16S ,Microbial Consortia ,Carbohydrates ,Metagenome ,Biodiversity ,Archaea ,Lignin ,Phylogeny - Abstract
The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-l-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.
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- 2021
4. Draft Genome Sequences of Longimonas halophila KCTC 42399 and Longibacter salinarum KCTC 52045
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Kian Mau Goh, Mohd Shahir Shamsir, Seng Chong Teo, and Kok Jun Liew
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0106 biological sciences ,Longibacter salinarum ,Genetics ,0303 health sciences ,Halophila ,biology ,Genome Sequences ,Genome project ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Genome ,Gene mining ,03 medical and health sciences ,Immunology and Microbiology (miscellaneous) ,Longimonas halophila ,Molecular Biology ,Bacteria ,030304 developmental biology - Abstract
Longimonas halophila and Longibacter salinarum are type strains of underexplored genera affiliated with Salisaetaceae. Herein, we report the draft genome sequences of two strains of these bacteria, L. halophila KCTC 42399 and L. salinarum KCTC 52045, with the intent of broadening knowledge of this family. Genome annotation and gene mining revealed that both bacteria exhibit amylolytic abilities.
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- 2019
5. Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy
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Kar-Wai Hong, Kok-Gan Chan, Lorena Buono, Ida Romano, Barbara Nicolaus, Javier Pascual, Luigi Leone, Annarita Poli, Pierangelo Orlando, Vincenza Mastascusa, and Kian Mau Goh
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DNA, Bacterial ,0301 basic medicine ,030106 microbiology ,red coral ,DNA, Ribosomal ,Microbiology ,03 medical and health sciences ,Bacterial Proteins ,RNA, Ribosomal, 16S ,Procida island ,Animals ,Molecular Biology ,Phylogeny ,Vibrio ,Base Composition ,Oxidase test ,Phylogenetic tree ,Strain (chemistry) ,biology ,Fatty Acids ,General Medicine ,Anthozoa ,16S ribosomal RNA ,biology.organism_classification ,Halophile ,Bacterial Typing Techniques ,Housekeeping gene ,Mucus ,030104 developmental biology ,Italy ,Bacteria - Abstract
Strain Corallo1T was isolated from mucus of red coral (Corallium rubrum) at Punta Pizzaco (Procida island, Naples, Italy). It was characterised as a Gram-stain negative, motile, rod-shaped bacterium. Strain Corallo1T was found to show positive responses for cytochrome-c oxidase, catalase, reduction of nitrate and nitrite, β-galactosidase activity and hydrolysis of starch, xylan, peptone, Tween 40, Tween 80 and casein. Strain Corallo1T was found to be mesophilic, neutrophilic to alkalophilic and slightly halophilic. According to analysis of the almost-complete 16S rRNA gene, strain Corallo1T is closely related to Vibrio celticus (100% sequence similarity), Vibrio gigantis (100%), Vibrio crassostreae (99.7%), Vibrio artabrorum (99.7%) and Vibrio pomeroyi (99.6%). MLSA of five housekeeping genes (atpA, pyrH, recA, rpoA and rpoD) was performed to refine the phylogenetic relationships of strain Corallo1T. A draft genome sequence of strain Corallo1T was obtained. The DNA G+C content of this strain was determined to be 44.5 mol %. The major cellular fatty acids of strain Corallo1T are C16:1, n-C16:0 and C18:1, and the major isoprenoid ubiquinone is Q8. ANI indexes, in silico estimations of DDH values and wet lab DDH values demonstrated that strain Corallo1T represents an independent genomospecies. Based on a polyphasic taxonomic characterisation, strain Corallo1T is concluded to represent a novel species of the genus Vibrio, for which the name Vibrio coralliirubri sp. nov. is proposed. The type strain is Corallo1T (= DSM 27495T = CIP 110630T).
- Published
- 2018
6. Characterizing a Halo-Tolerant GH10 Xylanase from Roseithermus sacchariphilus Strain RA and Its CBM-Truncated Variant
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Kian Mau Goh, Mohd Shahir Shamsir, Kok Jun Liew, Seng Chong Teo, Kok-Gan Chan, Chun Shiong Chong, and Neil C. Bruce
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0106 biological sciences ,0301 basic medicine ,Static Electricity ,01 natural sciences ,Article ,Catalysis ,Substrate Specificity ,Inorganic Chemistry ,lcsh:Chemistry ,03 medical and health sciences ,chemistry.chemical_compound ,Hydrolysis ,Protein Domains ,010608 biotechnology ,Xylobiose ,Glycoside hydrolase ,glycoside hydrolase ,Amino Acid Sequence ,Enzyme kinetics ,Physical and Theoretical Chemistry ,CBM truncation ,Molecular Biology ,lcsh:QH301-705.5 ,Phylogeny ,Spectroscopy ,carbohydrate-binding module ,xylanase ,Endo-1,4-beta Xylanases ,Bacteria ,Strain (chemistry) ,Organic Chemistry ,Genetic Variation ,Salt Tolerance ,General Medicine ,Xylan ,Recombinant Proteins ,Computer Science Applications ,Kinetics ,030104 developmental biology ,chemistry ,Biochemistry ,lcsh:Biology (General) ,lcsh:QD1-999 ,Xylanase ,Mutant Proteins ,Xylans ,Carbohydrate-binding module ,xylan hydrolysis ,halo-tolerant - Abstract
A halo-thermophilic bacterium, Roseithermus sacchariphilus strain RA (previously known as Rhodothermaceae bacterium RA), was isolated from a hot spring in Langkawi, Malaysia. A complete genome analysis showed that the bacterium harbors 57 glycoside hydrolases (GHs), including a multi-domain xylanase (XynRA2). The full-length XynRA2 of 813 amino acids comprises a family 4_9 carbohydrate-binding module (CBM4_9), a family 10 glycoside hydrolase catalytic domain (GH10), and a C-terminal domain (CTD) for type IX secretion system (T9SS). This study aims to describe the biochemical properties of XynRA2 and the effects of CBM truncation on this xylanase. XynRA2 and its CBM-truncated variant (XynRA2&Delta, CBM) was expressed, purified, and characterized. The purified XynRA2 and XynRA2&Delta, CBM had an identical optimum temperature at 70 °, C, but different optimum pHs of 8.5 and 6.0 respectively. Furthermore, XynRA2 retained 94% and 71% of activity at 4.0 M and 5.0 M NaCl respectively, whereas XynRA2&Delta, CBM showed a lower activity (79% and 54%). XynRA2 exhibited a turnover rate (kcat) of 24.8 s&minus, 1, but this was reduced by 40% for XynRA2&Delta, CBM. Both the xylanases hydrolyzed beechwood xylan predominantly into xylobiose, and oat-spelt xylan into a mixture of xylo-oligosaccharides (XOs). Collectively, this work suggested CBM4_9 of XynRA2 has a role in enzyme performance.
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- 2019
7. Vitellibacter aquimaris sp. nov., a marine bacterium isolated from seawater
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Chitra Selvaratnam, Kar-Wai Hong, Kian Mau Goh, Suganthi Thevarajoo, Xin Yue Chan, Chun Shiong Chong, and Kok-Gan Chan
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DNA, Bacterial ,0301 basic medicine ,Biology ,Microbiology ,03 medical and health sciences ,Genus ,RNA, Ribosomal, 16S ,Seawater ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Base Composition ,Strain (chemistry) ,Pigmentation ,Phosphatidylethanolamines ,DNA–DNA hybridization ,Fatty Acids ,Malaysia ,Nucleic Acid Hybridization ,Vitamin K 2 ,Sequence Analysis, DNA ,General Medicine ,16S ribosomal RNA ,biology.organism_classification ,Flavobacteriaceae ,Bacterial Typing Techniques ,genomic DNA ,030104 developmental biology ,Glycolipids ,Bacteria - Abstract
A Gram-staining-negative, aerobic, yellow–orange-pigmented, rod-shaped bacterium designated D-24T was isolated from seawater from sandy shoreline in Johor, Malaysia. The 16S rRNA gene sequence analysis revealed that strain D-24T is affiliated with the genus Vitellibacter . It shared more than 96 % sequence similarity with the types of some of the validly published species of the genus: Vitellibacter vladivostokensis KMM 3516T (99.5 %), Vitellibacter soesokkakensis RSSK-12T (97.3 %), Vitellibacter echinoideorum CC-CZW007T (96.9 %), Vitellibacter nionensis VBW088T (96.7 %) and Vitellibacter aestuarii JCM 15496T (96.3 %). DNA–DNA hybridization and genome-based analysis of average nucleotide identity (ANI) of strain D-24T versus V. vladivostokensis KMM 3516T exhibited values of 35.9±0.14 % and 89.26 %, respectively. Strain D-24T showed an even lower ANI value of 80.88 % with V. soesokkakensis RSSK-12T. The major menaquinone of strain D-24T was MK-6, and the predominant fatty acids were iso-C15 : 0 and iso-C17 : 0 3-OH. Strain D-24T contained major amounts of phosphatidylethanolamine, two lipids and two aminolipids, and a phosphoglycolipid that was different to that of other species of the genus Vitellibacter . The genomic DNA G+C content was 40.6 mol%. On the basis of phenotypic properties, DNA–DNA relatedness, ANI value and chemotaxonomic analyses, strain D-24T represents a novel species of the genus Vitellibacter , for which the name Vitellibacter aquimaris sp. nov. is proposed. The type strain is D-24T (=KCTC 42708T=DSM 101732T).
- Published
- 2016
8. Heterologous expression, purification and biochemical characterization of a new endo-1,4-β-xylanase from Rhodothermaceae bacterium RA
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Kok Jun Liew, Mohd Shahir Shamsir, Chen Yi Ngooi, Chun Shiong Chong, Kian Mau Goh, and Rajesh K. Sani
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0106 biological sciences ,Signal peptide ,Genetic Vectors ,Gene Expression ,Rhodothermus ,medicine.disease_cause ,01 natural sciences ,Substrate Specificity ,03 medical and health sciences ,chemistry.chemical_compound ,Bacterial Proteins ,010608 biotechnology ,Escherichia coli ,medicine ,Xylobiose ,Amino Acid Sequence ,Phylogeny ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Endo-1,4-beta Xylanases ,biology ,Chemistry ,biology.organism_classification ,Recombinant Proteins ,Amino acid ,Enzyme ,Biochemistry ,Xylanase ,Heterologous expression ,Sequence Alignment ,Bacteria ,Biotechnology - Abstract
Xylanases (EC 3.2.1.8) are essential enzymes due to their applications in various industries such as textile, animal feed, paper and pulp, and biofuel industries. Halo-thermophilic Rhodothermaceae bacterium RA was previously isolated from a hot spring in Malaysia. Genomic analysis revealed that this bacterium is likely to be a new genus of the family Rhodothermaceae. In this study, a xylanase gene (1140 bp) that encoded 379 amino acids from the bacterium was cloned and expressed in Escherichia coli BL21(DE3). Based on InterProScan, this enzyme XynRA1 contained a GH10 domain and a signal peptide sequence. XynRA1 shared low similarity with the currently known xylanases (the closest is 57.2–65.4% to Gemmatimonadetes spp.). The purified XynRA1 achieved maximum activity at pH 8 and 60 °C. The protein molecular weight was 43.1 kDa XynRA1 exhibited an activity half-life (t1/2) of 1 h at 60 °C and remained stable at 50 °C throughout the experiment. However, it was NaCl intolerant, and various types of salt reduced the activity. This enzyme effectively hydrolyzed xylan (beechwood, oat spelt, and Palmaria palmata) and xylodextrin (xylotriose, xylotetraose, xylopentaose, and xylohexaose) to produce predominantly xylobiose. This xylanase is the first functionally characterized enzyme from the bacterium, and this work broadens the knowledge of GH10 xylanases.
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- 2019
9. Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities
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Kok-Gan Chan, Mohd Shahir Shamsir, Kok Jun Liew, Chun Shiong Chong, Seng Chong Teo, Rajesh K. Sani, and Kian Mau Goh
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0301 basic medicine ,Whole genome sequencing ,biology ,Xylanase ,030106 microbiology ,Rhodothermus ,Cellulase ,Environmental Science (miscellaneous) ,biology.organism_classification ,Agricultural and Biological Sciences (miscellaneous) ,Genome ,Genome Report ,Halophile ,Rhodothermaceae ,03 medical and health sciences ,Metabolic pathway ,030104 developmental biology ,Biochemistry ,biology.protein ,Gene ,Bacteria ,GC-content ,Biotechnology - Abstract
Rhodothermaceae bacterium RA is a halo-thermophile isolated from a saline hot spring. Previously, the genome of this bacterium was sequenced using a HiSeq 2500 platform culminating in 91 contigs. In this report, we report on the resequencing of its complete genome using a PacBio RSII platform. The genome has a GC content of 68.3%, is 4,653,222 bp in size, and encodes 3711 genes. We are interested in understanding the carbohydrate metabolic pathway, in particular the lignocellulosic biomass degradation pathway. Strain RA harbors 57 glycosyl hydrolase (GH) genes that are affiliated with 30 families. The bacterium consists of cellulose-acting (GH 3, 5, 9, and 44) and hemicellulose-acting enzymes (GH 3, 10, and 43). A crude cell-free extract of the bacterium exhibited endoglucanase, xylanase, β-glucosidase, and β-xylosidase activities. The complete genome information coupled with biochemical assays confirms that strain RA is able to degrade cellulose and xylan. Therefore, strain RA is another excellent member of family Rhodothermaceae as a repository of novel and thermostable cellulolytic and hemicellulolytic enzymes. Electronic supplementary material The online version of this article (10.1007/s13205-018-1391-z) contains supplementary material, which is available to authorized users.
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- 2018
10. Direct Cellulase Gene Amplification From Hot Spring Using the Guidance of 16S rRNA Amplicon Metagenomics
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Kok Jun Liew, Kian Mau Goh, Kwek Yan Wei, Kok-Gan Chan, Chia Chiu Lim, Rajesh K. Sani, Chia Sing Chan, and Madihah Md. Salleh
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Genetics ,biology ,Metagenomics ,Thermophile ,biology.protein ,Environmental DNA ,Computational biology ,Cellulase ,Amplicon ,16S ribosomal RNA ,biology.organism_classification ,Gene ,Bacteria - Abstract
Thermostable cellulase plays an important role in the process of converting lignocellulosic waste to biofuel. A culture-dependent approach may not effectively discover new thermostable cellulase, hemicellulase, or lignin-acting enzymes, since many thermophiles are not culturable in general laboratory setups. Due to this limitation, culture-independent techniques—for instance, the metagenomic approach—may be a good technique for finding novel genes. This current chapter demonstrates a method to amplify complete genes from a hot spring complex metagenome without the need to isolate bacterium or perform a clonal library. To achieve this, one needs to perform sampling (water, sediment, or biofilm from hot spring), extract the environmental DNA material, and perform 16S rRNA amplicon sequencing using a next-generation sequencer. From the microbial population data, we can then identify the genera of interest and their cellulase genes, followed by the designing of specific or degenerate primers, and finally amplification of the genes of interest using conventional PCR. This methodology will likely be an economic and powerful approach to discover novel genes that are present in complex environments. This chapter also describes the challenges of using such an approach. Using this method, an interesting heat-tolerant enzyme for biomass degradation was cloned, expressed, and purified. The enzyme exhibited optimum activity at a pH of 5.5 and at 90°C, a much higher temperature than other known enzyme counterparts. This enzyme is highly active on complex polysaccharide carboxymethyl cellulose. This technique will be useful for any gene amplification from hot springs using the guidance of 16S rRNA amplicon metagenomics.
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- 2018
11. Genome sequence of Roseivirga sp. strain D-25 and its potential applications from the genomic aspect
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Kok-Gan Chan, Joseph P. Bennett, Chun Shiong Chong, Kian Mau Goh, Suganthi Thevarajoo, Robson Ee, and Chitra Selvaratnam
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0301 basic medicine ,Whole genome sequencing ,Genetics ,food.ingredient ,biology ,Strain (chemistry) ,Bacteroidetes ,030106 microbiology ,Malaysia ,Sequence Analysis, DNA ,Aquatic Science ,biology.organism_classification ,Roseivirga ,03 medical and health sciences ,030104 developmental biology ,food ,Bioremediation ,Seawater ,Genome size ,Gene ,Genome, Bacterial ,Bacteria - Abstract
Roseivirga sp. strain D-25 is an aerobic marine bacterium isolated from seawater collected from Desaru beach, Malaysia. To date, the genus Roseivirga consists of only four species with no genome sequence reported. Here, we present the genome sequence of Roseivirga sp. strain D-25 (=KCTC 42709=DSM 101709), with a genome size of approximately 4.08Mbp and G+C content of 39.18%. Genome sequence analysis of strain D-25 revealed the presence of genes related to petroleum hydrocarbon degradation, 2,4,6-trinitrotoluene detoxification, heavy metals bioremediation and production of carotenoids, which shed light on the potential application of this strain.
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- 2016
12. Draft Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum copahuensis Strain CINDEFI1 Isolated from the Geothermal Copahue System, Neuquén, Argentina
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Kok-Gan Chan, Chia Sing Chan, Graciana Willis Poratti, Adrian Tan-Guan-Sheng, M. Sofía Urbieta, Amira Suriaty Yaakop, Edgardo Ruben Donati, Kian Mau Goh, and Robson Ee
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0301 basic medicine ,Whole genome sequencing ,Strain (biology) ,fungi ,Química ,Biology ,biology.organism_classification ,Microbiology ,03 medical and health sciences ,030104 developmental biology ,Genetics ,Desulfotomaculum ,Prokaryotes ,Molecular Biology ,Bacteria ,Genoma - Abstract
Desulfotomaculum copahuensis strain CINDEFI1 is a novel spore-forming sulfate-reducing bacterium isolated from the Copahue volcano area, Argentina. Here, we present its draft genome in which we found genes related with the anaerobic respiration of sulfur compounds similar to those present in the Copahue environment., Centro de Investigación y Desarrollo en Fermentaciones Industriales
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- 2016
13. ISOLATION AND CHARACTERIZATION OF BIOTECHNOLOGY RELEVANT BACTERIA FROM MARINE ENVIRONMENT
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Zaharah Ibrahim, Fazilah Abd Manan, Kian Mau Goh, Suganthi Thevarajoo, Chun Shiong Chong, and Chitra Selvaratnam
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Marinomonas ,biology ,Pseudomonas ,General Engineering ,Micrococcus ,Kanamycin ,biology.organism_classification ,Shewanella ,Microbiology ,Pseudoalteromonas ,Marine bacteriophage ,medicine ,Bacteria ,medicine.drug - Abstract
Marine environment remained as largely unexplored source for researchers to discover marine microorganisms with novel properties. This study aims to isolate marine bacteria from the seashore of Desaru, Malaysia. Totally, six bacterial strains were successfully obtained and were identified by complete 16S rRNA sequencing. The characterizations of bacterial strains were performed based on morphological tests, Gram-staining, biochemical tests, and antibiotic sensitivity. The 16S rRNA sequence of D-2, D-4, D-7, D-15, D-31, and D-33 revealed a high identity of 97 to 99% with taxa belong to genera of Pseudomonas, Marinomonas, Exiquobacterium, Micrococcus, Pseudoalteromonas, and Shewanella respectively. Strain D-31 exhibited higher tolerance towards antibiotics kanamycin, ampicillin, and erythromycin while the growth of other strains were retarded by at least two of these antibiotics. We further characterized strain D-4 and D-31 that belonged to Marinomonas sp. and Pseudoalteromonas sp.. Both genera are interesting as earlier researchers have discovered new antibacterial substances, industrial enzymes and unique secondary metabolites.
- Published
- 2015
14. Meiothermus sp. SK3-2: A potential source for the production of trehalose from maltose
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Kian Mau Goh, Yen Yen Chai, Charles Voon, and Rosli Md. Illias
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chemistry.chemical_classification ,biology ,Thermophile ,chemistry.chemical_element ,Maltose ,Calcium ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Trehalose ,Amino acid ,chemistry.chemical_compound ,chemistry ,Biochemistry ,Genetics ,Ammonium chloride ,Agronomy and Crop Science ,Molecular Biology ,Bacteria ,Biotechnology ,Meiothermus - Abstract
Trehalose has similar chemical formula as maltose. In terms of price, trehalose is much more expensivethan maltose. A pink-pigmented bacterium identified as Meiothermus sp. SK3-2 was found to be able to convert maltose to trehalose. Based on fatty acids analysis, the Meiothermus sp. SK3-2 may be a new strain that produce trehalose synthase (TreS). Meiothermus sp. SK3-2 achieved a better biomass growth in MM medium containing maltose. Besides that, TreS activity yield was also higher in MM medium, approximately 3.5, 1.8 and 0.3 fold than that in PY medium, thermophilic Bacillus medium and Castenholz medium, respectively. The optimum working temperature and pH for Meiothermus sp. SK3-2 TreS was 65°C and pH 6.0, respectively. Ammonium chloride at 10 mM increased the activity significantly, while calcium chloride at 5 mM decreased the activity by about 80% and the activity wasfully retarded by 10 mM CaCl2. It was found that the product specificity of this TreS was influenced by factors like temperature, pH and buffer system used. Analysis of the nucleotide sequence revealed the presence of an open reading frame of 2,890 bp which encoded a 963 amino acid protein. In conclusion, Meiothermus sp. SK3-2 TreS could serve as an alternative source to trehalose production.
- Published
- 2011
15. Microbial diversity of thermophiles with biomass deconstruction potential in a foliage‐rich hot spring
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Kok-Gan Chan, Chun Shiong Chong, Geok Yuan Annie Tan, Chia Sing Chan, Kian Mau Goh, Li Sin Lee, and Wai-Fong Yin
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0301 basic medicine ,Hot Temperature ,food.ingredient ,Glycoside Hydrolases ,030106 microbiology ,Biomass ,Acidimicrobium ,Microbiology ,Hot Springs ,03 medical and health sciences ,food ,Bacterial Proteins ,Botany ,Cellulose ,Phylogeny ,Original Research ,Meiothermus ,cellulase ,thermophile ,Hot spring ,hot spring ,Bacteria ,biology ,Chemistry ,Biofilm ,Thermophile ,Original Articles ,biomass degradation ,Biodiversity ,biology.organism_classification ,Chloroflexus ,030104 developmental biology ,Microbial population biology ,biofuel ,Thermoanaerobacter - Abstract
The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y‐shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y‐shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.
- Published
- 2018
16. Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil
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Amira Suriaty Yaakop, Kian Mau Goh, Han Ming Gan, Kok-Gan Chan, Wen-Si Tan, Chia Sing Chan, and Robson Ee
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Whole genome sequencing ,Jeotgalibacillus soli ,biology ,Homoserine ,macromolecular substances ,biology.organism_classification ,Genome ,Microbiology ,chemistry.chemical_compound ,chemistry ,Genetics ,lipids (amino acids, peptides, and proteins) ,Glycoside hydrolase ,Jeotgalibacillus species ,Prokaryotes ,Molecular Biology ,Bacteria - Abstract
Jeotgalibacillus soli , a bacterium capable of degrading N -acyl homoserine lactone, was isolated from a soil sample in Portugal. J. soli constitutes the only Jeotgalibacillus species isolated from a non-marine source. Here, the draft genome, several interesting glycosyl hydrolases, and its putative N -acyl homoserine lactonases are presented.
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- 2015
17. Draft Genome Sequence of Erythrobacter vulgaris Strain O1, a Glycosyl Hydrolase-Producing Bacterium
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Ummirul Mukminin Kahar, Chia Sing Chan, Kok-Gan Chan, Amira Suriaty Yaakop, Kian Mau Goh, and Robson Ee
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Whole genome sequencing ,Genetics ,biology ,Strain (biology) ,Erythrobacter ,biology.organism_classification ,Genome ,Halophile ,Microbiology ,chemistry.chemical_compound ,chemistry ,Hydrolase ,Glycosyl ,Prokaryotes ,human activities ,Molecular Biology ,geographic locations ,Bacteria - Abstract
Erythrobacter vulgaris strain O1, a moderate halophile, was isolated from a beach in Johor, Malaysia. Here, we present the draft genome and suggest potential applications of this bacterium.
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- 2015
18. Complete genome of Jeotgalibacillus malaysiensis D5(T) consisting of a chromosome and a circular megaplasmid
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Kok-Gan Chan, Amira Suriaty Yaakop, Robson Ee, and Kian Mau Goh
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Genetics ,Base Composition ,Salinity ,Base Sequence ,Molecular Sequence Data ,Adaptation, Biological ,Chromosome ,Bacillus ,Bioengineering ,General Medicine ,Sequence Analysis, DNA ,Biology ,biology.organism_classification ,Applied Microbiology and Biotechnology ,Genome ,DNA sequencing ,Marine bacteriophage ,Planococcaceae ,Jeotgalibacillus ,Bacteria ,Genome, Bacterial ,Biotechnology ,Plasmids - Abstract
Jeotgalibacillus spp. are halophilic bacteria within the family Planococcaceae. No genomes of Jeotgalibacillus spp. have been reported to date, and their metabolic pathways are unknown. How the bacteria survive in hypertonic conditions such as seawater is yet to be discovered. As only few studies have been conducted on Jeotgalibacillus spp., potential applications of these bacteria are unknown. Here, we present the complete genome of J. malaysiensis D5(T) (=DSM 28777(T) =KCTC 33350(T)), which is invaluable in identifying interesting applications for this genus.
- Published
- 2015
19. Draft genome of Jeotgalibacillus campisalis SF-57T, a moderate halophilic bacterium isolated from marine saltern
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Han Ming Gan, Kok-Gan Chan, Amira Suriaty Yaakop, and Kian Mau Goh
- Subjects
DNA, Bacterial ,Whole genome sequencing ,biology ,Jeotgalibacillus campisalis ,Genus Jeotgalibacillus ,Aquatic Science ,biology.organism_classification ,C content ,Genome ,Halophile ,Microbiology ,Planococcaceae ,Genetics ,Seawater ,Genome, Bacterial ,Bacteria - Abstract
Jeotgalibacillus campisalis SF-57(T) (=KCCM 41644(T), JCM 11810(T)) is a moderate halophilic bacterium isolated from a Korean marine saltern. In this study, we describe the high-quality draft genome of strain SF-57(T), which was assembled into 24 contigs containing 3,650,490bp with a G+C content of 41.06%. Availability of the genome sequence of J. campisalis SF-57(T) will contribute to a better understanding of the genus Jeotgalibacillus.
- Published
- 2015
20. Draft genome sequence of Vitellibacter vladivostokensis KMM 3516T: A protease-producing bacterium
- Author
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Chitra Selvaratnam, Kok-Gan Chan, Chun Shiong Chong, Kian Mau Goh, and Suganthi Thevarajoo
- Subjects
Genetics ,Whole genome sequencing ,chemistry.chemical_classification ,Protease ,biology ,Bacteroidetes ,Phylum ,medicine.medical_treatment ,Proteolytic enzymes ,Gene Expression Regulation, Bacterial ,Aquatic Science ,biology.organism_classification ,Genome ,Gene Expression Regulation, Enzymologic ,Enzyme ,Bacterial Proteins ,chemistry ,medicine ,bacteria ,Gene ,Genome, Bacterial ,Peptide Hydrolases - Abstract
Type strain Vitellibacter vladivostokensis KMM 3516(T) (=NBRC 16718(T)) belongs to the phylum Cytophaga-Flavobacterium-Bacteroides. To date, no genomes of the Vitellibacter spp. have been reported, and their metabolic pathways are unknown. This study reports the draft genome sequence of V. vladivostokensis. Moreover, mining of genes associated with proteolytic enzymes was performed to provide insights for further enzyme characterization.
- Published
- 2015
21. Thermophiles in the genomic era: Biodiversity, science, and applications
- Author
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M. Sofía Urbieta, Saleha Shahar, Lee Li Sin, Kian Mau Goh, Edgardo Ruben Donati, and Kok-Gan Chan
- Subjects
Hot Temperature ,Archaeal Proteins ,Bioengineering ,Applied Microbiology and Biotechnology ,Ciencias Biológicas ,Industrial Microbiology ,Bacterial Proteins ,Crenarchaeota ,THERMOPHILES ,Hot spring ,APPLICATIONS ,biology ,Bacteria ,Ecology ,Thermophile ,Ecología ,biology.organism_classification ,Archaea ,Hyperthermophile ,Enzymes ,EXTREMOPHILES ,Biodegradation, Environmental ,Metagenomics ,Aquificae ,Biofuels ,Thermotogae ,Sulfolobus solfataricus ,Metagenome ,BIODIVERSITY ,CIENCIAS NATURALES Y EXACTAS ,Biotechnology - Abstract
Thermophiles and hyperthermophiles are present in various regions of the Earth, including volcanic environments, hot springs, mud pots, fumaroles, geysers, coastal thermal springs, and even deep-sea hydrothermal vents. They are also found in man-made environments, such as heated compost facilities, reactors, and spray dryers. Thermophiles, hyperthermophiles, and their bioproducts facilitate various industrial, agricultural, and medicinal applications and offer potential solutions to environmental damages and the demand for biofuels. Intensified efforts to sequence the entire genome of hyperthermophiles and thermophiles are increasing rapidly, as evidenced by the fact that over 120 complete genome sequences of the hyperthermophiles Aquificae, Thermotogae, Crenarchaeota, and Euryarchaeota are now available. In this review, we summarise the major current applications of thermophiles and thermozymes. In addition, emphasis is placed on recent progress in understanding the biodiversity, genomes, transcriptomes, metagenomes, and single-cell sequencing of thermophiles in the genomic era. Fil: Urbieta, María Sofía. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - la Plata. Centro de Investigación y Desarrollo En Fermentaciones Industriales. Universidad Nacional de la Plata. Facultad de Cs.exactas. Centro de Investigación y Desarrollo En Fermentaciones Industriales; Argentina Fil: Donati, Edgardo Ruben. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - la Plata. Centro de Investigación y Desarrollo En Fermentaciones Industriales. Universidad Nacional de la Plata. Facultad de Cs.exactas. Centro de Investigación y Desarrollo En Fermentaciones Industriales; Argentina Fil: Chan, Kok Gan. University of Malaya; Malasia Fil: Shahar, Saleha. Universiti Teknologi Malaysia; Malasia Fil: Sin, Lee Li. Universiti Teknologi Malaysia; Malasia Fil: Goh, Kian Mau. Universiti Teknologi Malaysia; Malasia
- Published
- 2014
22. Draft genome sequence of Vitellibacter aquimaris D-24T isolated from seawater
- Author
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Chun Shiong Chong, Kok-Gan Chan, Chitra Selvaratnam, Kian Mau Goh, and Suganthi Thevarajoo
- Subjects
0301 basic medicine ,Whole genome sequencing ,biology ,030106 microbiology ,lcsh:QR1-502 ,Proteases ,biology.organism_classification ,Microbiology ,Genome ,Halophile ,lcsh:Microbiology ,03 medical and health sciences ,030104 developmental biology ,Vitellibacter aquimaris ,Genome sequence ,Denitrification ,Extremophile ,Seawater ,Gene ,Genome size ,Bacteria - Abstract
Vitellibacter aquimaris D-24T (=KCTC 42708T = DSM 101732T), a halophilic marine bacterium, was isolated from seawater collected from Desaru beach, Malaysia. Here, we present the draft genome sequence of D-24T with a genome size of approximately 3.1 Mbp and G + C content of 39.93%. The genome of D-24T contains genes involved in reducing a potent greenhouse gas (N2O) in the environment and the degradation of proteinaceous compounds. Genome availability will provide insights into potential biotechnological and environmental applications of this bacterium.
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