MyMedR

Identification of three homologous latex-clearing protein (lcp) genes from the genome of Streptomyces sp. strain CFMR 7

Nanthini J, Ong SY, Sudesh K

Gene, 2017 Sep 10;628:146-155.

PMID: 28711667 DOI: 10.1016/j.gene.2017.07.039

Rubber materials have greatly contributed to human civilization. However, being a polymeric material does not decompose easily, it has caused huge environmental problems. On the other hand, only few bacteria are known to degrade rubber, with studies pertaining them being intensively focusing on the mechanism involved in microbial rubber degradation. The Streptomyces sp. strain CFMR 7, which was previously confirmed to possess rubber-degrading ability, was subjected to whole genome sequencing using the single molecule sequencing technology of the PacBio® RS II system. The genome was further analyzed and compared with previously reported rubber-degrading bacteria in order to identify the potential genes involved in rubber degradation. This led to the interesting discovery of three homologues of latex-clearing protein (Lcp) on the chromosome of this strain, which are probably responsible for rubber degrading activities. Genes encoding oxidoreductase α-subunit (oxiA) and oxidoreductase β-subunit (oxiB) were also found downstream of two lcp genes which are located adjacent to each other. In silico analysis reveals genes that have been identified to be involved in the microbial degradation of rubber in the Streptomyces sp. strain CFMR 7. This is the first whole genome sequence of a clear-zone-forming natural rubber- degrading Streptomyces sp., which harbours three Lcp homologous genes with the presence of oxiA and oxiB genes compared to the previously reported Gordonia polyisoprenivorans strain VH2 (with two Lcp homologous genes) and Nocardia nova SH22a (with only one Lcp gene).

Matched MeSH terms: Genome, Bacterial

Fulltext (GTG)5-PCR analysis and 16S rRNA sequencing of bacteria from Sarawak aquaculture environment

Kathleen, M.M., Samuel, L., Felecia, C., Ng K. H., Lesley, M.B., Kasing, A.

International Food Research Journal, 2014;21(3):915-920.

MyJurnal

(GTG)5 PCR is a type of repetitive extragenic palindromic (rep)-PCR which amplifies the (GTG)5 repetitive element that lays throughout the bacterial genome. In this study, fifty, thirty-nine and forty-nine unknown bacteria were isolated from aquaculture farms in Miri, Limbang and Lundu, respectively. (GTG)5 PCR was used to screen for clonal diversity among the isolates according to sampling sites. Banding profiles obtained from electrophoresed (GTG)5 PCR products were analyzed by RAPDistance Software to generate a dendrogram of neighbor joining tree (NJT) format. Based on the constructed dendrogram, representative isolates were selected for further identification. Conserved 16S rRNA region of the selected bacteria isolates were amplified and purified DNA products were sequenced. (GTG)5 PCR is useful in differentiation of unknown bacterial isolates and 16S rRNA analysis species identity of the bacteria in Sarawak aquaculture environment. The high diversity of bacteria in aquaculture environment may be caused by contamination from various sources.

Matched MeSH terms: Genome, Bacterial

Fulltext International links between Streptococcus pneumoniae vaccine serotype 4 sequence type (ST) 801 in Northern European shipyard outbreaks of invasive pneumococcal disease

Gladstone RA, Siira L, Brynildsrud OB, Vestrheim DF, Turner P, Clarke SC, et al.

Vaccine, 2022 Feb 11;40(7):1054-1060.

PMID: 34996643 DOI: 10.1016/j.vaccine.2021.10.046

BACKGROUND: Pneumococcal disease outbreaks of vaccine preventable serotype 4 sequence type (ST)801 in shipyards have been reported in several countries. We aimed to use genomics to establish any international links between them.

METHODS: Sequence data from ST801-related outbreak isolates from Norway (n = 17), Finland (n = 11) and Northern Ireland (n = 2) were combined with invasive pneumococcal disease surveillance from the respective countries, and ST801-related genomes from an international collection (n = 41 of > 40,000), totalling 106 genomes. Raw data were mapped and recombination excluded before phylogenetic dating.

RESULTS: Outbreak isolates were relatively diverse, with up to 100 SNPs (single nucleotide polymorphisms) and a common ancestor estimated around the year 2000. However, 19 Norwegian and Finnish isolates were nearly indistinguishable (0-2 SNPs) with the common ancestor dated around 2017.

CONCLUSION: The total diversity of ST801 within the outbreaks could not be explained by recent transmission alone, suggesting that harsh environmental and associated living conditions reported in the shipyards may facilitate invasion of colonising pneumococci. However, near identical strains in the Norwegian and Finnish outbreaks does suggest that transmission between international shipyards also contributed to those outbreaks. This indicates the need for improved preventative measures in this working population including pneumococcal vaccination.

Matched MeSH terms: Genome, Bacterial

Genetic dynamics of Salmonella typhi--diversity in clonality

Pang T

Trends Microbiol, 1998 Sep;6(9):339-42.

PMID: 9778724

Matched MeSH terms: Genome, Bacterial

Identification of polyunsaturated fatty acid and diterpenoid biosynthesis pathways from draft genome of Aureispira sp. CCB-QB1

Furusawa G, Lau NS, Shu-Chien AC, Jaya-Ram A, Amirul AA

Mar Genomics, 2015 Feb;19:39-44.

PMID: 25468060 DOI: 10.1016/j.margen.2014.10.006

The genus Aureispira consisting of two species, Aureispira marina and Aureispira maritima is an arachidonic acid-producing bacterium and produces secondary metabolites. In this study, we isolated a new Aureispira strain, Aureispira sp. CCB-QB1 from coastal area of Penang, Malaysia and the genome sequence of this strain was determined. The draft genome of this strain is composed of 185 contigs for 7,370,077 bases with 35.6% G+C content and contains 5911 protein-coding genes and 76 RNA genes. Linoleoyl-CoA desaturase, the key gene in arachidonic acid biosynthesis, is present in the genome. It was found that this strain uses mevalonate pathway for the synthesis of geranylgeranyl diphosphate (GGPP), which is precursor of diterpenoid, and novel pathway via futalosine for the synthesis of menaquinones. This is the first draft genome sequence of a member of the genus Aureispira.

Matched MeSH terms: Genome, Bacterial/genetics*

Comparative genome analysis of Ureaplasma parvum clinical isolates

Momynaliev K, Klubin A, Chelysheva V, Selezneva O, Akopian T, Govorun V

Res. Microbiol., 2007 May;158(4):371-8.

PMID: 17363224

Ureaplasma parvum colonizes human mucosal surfaces, primarily in the respiratory and urogenital tracts, causing a wide spectrum of diseases, from non-gonococcal urethritis to pneumonitis in immunocompromised hosts. Although the basis for these diverse clinical outcomes is not yet understood, more severe disease may be associated with strains harboring a certain set of strain-specific genes. To investigate this, whole genome DNA macroarrays were constructed and used to assess genomic diversity in 10 U. parvum clinical strains. We found that 7.6% of U. parvum genes were dispersed into one or more strains, thus defining a minimal functional core of 538 U. parvum genes. Most of the strain-specific genes (79%) were of unknown function and were unique to U. parvum. Four hypervariable plasticity regions were identified in the genome containing 93% of the variability in the gene pool (UU32-UU33, UU145-UU170, UU440-UU447 and UU527-UU529). We hypothesized that one of them (UU145-UU170) was a pathogenicity island in U. parvum and we characterized it. Thus, we propose that the clinical outcome of U. parvum infection is probably associated with this newly identified pathogenicity island.

Matched MeSH terms: Genome, Bacterial*

Fulltext Comparative Genomic Analysis Reveals a Possible Novel Non-Tuberculous Mycobacterium Species with High Pathogenic Potential

Choo SW, Dutta A, Wong GJ, Wee WY, Ang MY, Siow CC

PLoS One, 2016;11(4):e0150413.

PMID: 27035710 DOI: 10.1371/journal.pone.0150413

Mycobacteria have been reported to cause a wide range of human diseases. We present the first whole-genome study of a Non-Tuberculous Mycobacterium, Mycobacterium sp. UM_CSW (referred to hereafter as UM_CSW), isolated from a patient diagnosed with bronchiectasis. Our data suggest that this clinical isolate is likely a novel mycobacterial species, supported by clear evidence from molecular phylogenetic, comparative genomic, ANI and AAI analyses. UM_CSW is closely related to the Mycobacterium avium complex. While it has characteristic features of an environmental bacterium, it also shows a high pathogenic potential with the presence of a wide variety of putative genes related to bacterial virulence and shares very similar pathogenomic profiles with the known pathogenic mycobacterial species. Thus, we conclude that this possible novel Mycobacterium species should be tightly monitored for its possible causative role in human infections.

Matched MeSH terms: Genome, Bacterial*

Fulltext Agarolytic bacterium Persicobacter sp. CCB-QB2 exhibited a diauxic growth involving galactose utilization pathway

Furusawa G, Lau NS, Suganthi A, Amirul AA

Microbiologyopen, 2017 02;6(1).

PMID: 27987272 DOI: 10.1002/mbo3.405

The agarolytic bacterium Persicobacter sp. CCB-QB2 was isolated from seaweed (genus Ulva) collected from a coastal area of Malaysia. Here, we report a high-quality draft genome sequence for QB2. The Rapid Annotation using Subsystem Technology (RAST) annotation server identified four β-agarases (PdAgaA, PdAgaB, PdAgaC, and PdAgaD) as well as galK, galE, and phosphoglucomutase, which are related to the Leloir pathway. Interestingly, QB2 exhibited a diauxic growth in the presence of two kinds of nutrients, such as tryptone and agar. In cells grown with agar, the profiles of agarase activity and growth rate were very similar. galK, galE, and phosphoglucomutase genes were highly expressed in the second growth phase of diauxic growth, indicating that QB2 cells use galactose hydrolyzed from agar by its agarases and exhibit nutrient prioritization. This is the first report describing diauxic growth for agarolytic bacteria. QB2 is a potential novel model organism for studying diauxic growth in environmental bacteria.

Matched MeSH terms: Genome, Bacterial/genetics

Fulltext Metabolic potential of the moderate halophile Yangia sp. ND199 for co-production of polyhydroxyalkanoates and exopolysaccharides

Romero Soto L, Thabet H, Maghembe R, Gameiro D, Van-Thuoc D, Dishisha T, et al.

Microbiologyopen, 2021 01;10(1):e1160.

PMID: 33650793 DOI: 10.1002/mbo3.1160

Yangia sp. ND199 is a moderately halophilic bacterium isolated from mangrove samples in Northern Vietnam, which was earlier reported to grow on several sugars and glycerol to accumulate poly(hydroxyalkanoates) (PHA). In this study, the potential of the bacterium for co-production of exopolysaccharides (EPS) and PHA was investigated. Genome sequence analysis of the closely related Yangia sp. CCB-M3 isolated from mangroves in Malaysia revealed genes encoding enzymes participating in different EPS biosynthetic pathways. The effects of various cultivation parameters on the production of EPS and PHA were studied. The highest level of EPS (288 mg/L) was achieved using sucrose and yeast extract with 5% NaCl and 120 mM phosphate salts but with modest PHA accumulation (32% of cell dry weight, 1.3 g/L). Growth on fructose yielded the highest PHA concentration (85% of CDW, 3.3 g/L) at 90 mM phosphate and higher molecular weight EPS at 251 mg/L yield at 120 mM phosphate concentration. Analysis of EPS showed a predominance of glucose, followed by fructose and galactose, and minor amounts of acidic sugars.

Matched MeSH terms: Genome, Bacterial/genetics

Comparative genomic and phylogenetic analysis of a toxigenic clinical isolate of Corynebacterium diphtheriae strain B-D-16-78 from Malaysia

Hong KW, Asmah Hani AW, Nurul Aina Murni CA, Pusparani RR, Chong CK, Verasahib K, et al.

Infect Genet Evol, 2017 Oct;54:263-270.

PMID: 28711373 DOI: 10.1016/j.meegid.2017.07.015

In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile. In the context of CRISPR-Cas system, which confers adaptive immunity against re-invading DNA, 73 out of 86 spacer sequences were found to be unique to Malaysian strains which harboured only type-II-C and/or type-I-E-a systems. A total of 48 tox genes which code for the diphtheria toxin were retrieved from the 74 genomes and with the exception of one truncated gene, only nucleotide substitutions were detected when compared to the tox gene sequence of PW8. More than half were synonymous substitution and only two were nonsynonymous substitutions whereby H24Y was predicted to have a damaging effect on the protein function whilst T262V was predicted to be tolerated. Both toxigenic and non-toxigenic toxin-gene bearing strains have been isolated in Malaysia but the repeated isolation of toxigenic strains with the same MLST profile suggests the possibility of some of these strains may be circulating in the population. Hence, efforts to increase herd immunity should be continued and supported by an effective monitoring and surveillance system to track, manage and control outbreak of cases.

Matched MeSH terms: Genome, Bacterial*

Fulltext Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus

Steinig EJ, Andersson P, Harris SR, Sarovich DS, Manoharan A, Coupland P, et al.

BMC Genomics, 2015;16:388.

PMID: 25981586 DOI: 10.1186/s12864-015-1599-9

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-associated infection, but there is growing awareness of the emergence of multidrug-resistant lineages in community settings around the world. One such lineage is ST772-MRSA-V, which has disseminated globally and is increasingly prevalent in India. Here, we present the complete genome sequence of DAR4145, a strain of the ST772-MRSA-V lineage from India, and investigate its genomic characteristics in regards to antibiotic resistance and virulence factors.

Matched MeSH terms: Genome, Bacterial*

Fulltext Insights from the genome sequence of quorum-quenching Staphylococcus sp. strain AL1, isolated from traditional Chinese soy sauce brine fermentation

Chong TM, Tung HJ, Yin WF, Chan KG

J Bacteriol, 2012 Dec;194(23):6611-2.

PMID: 23144375 DOI: 10.1128/JB.01669-12

We report the draft genome sequence of Staphylococcus sp. strain AL1, which degrades quorum-sensing molecules (namely, N-acyl homoserine lactones). To the best of our knowledge, this is the first documentation that reports the whole genome sequence and quorum-quenching activity of Staphylococcus sp. strain AL1.

Matched MeSH terms: Genome, Bacterial*

Fulltext Genome sequence and comparative pathogenomics analysis of a Salmonella enterica Serovar Typhi strain associated with a typhoid carrier in Malaysia

Yap KP, Gan HM, Teh CS, Baddam R, Chai LC, Kumar N, et al.

J Bacteriol, 2012 Nov;194(21):5970-1.

PMID: 23045488 DOI: 10.1128/JB.01416-12

Salmonella enterica serovar Typhi is a human pathogen that causes typhoid fever predominantly in developing countries. In this article, we describe the whole genome sequence of the S. Typhi strain CR0044 isolated from a typhoid fever carrier in Kelantan, Malaysia. These data will further enhance the understanding of its host persistence and adaptive mechanism.

Matched MeSH terms: Genome, Bacterial*

Fulltext Genome sequence of the alkane-degrading bacterium Alcanivorax hongdengensis type strain A-11-3

Lai Q, Shao Z

J Bacteriol, 2012 Dec;194(24):6972.

PMID: 23209226 DOI: 10.1128/JB.01849-12

Alcanivorax hongdengensis A-11-3(T) was isolated from an oil-enriched consortium enriched from the surface seawater of Hong-Deng dock in the Straits of Malacca and Singapore. Strain A-11-3(T) can degrade n-alkane and produce a lipopeptide biosurfactant. Here we report the genome of A-11-3(T) and the genes associated with alkane degradation.

Matched MeSH terms: Genome, Bacterial*

Fulltext Genome sequence of multidrug-resistant Escherichia coli EC302/04, isolated from a human tracheal aspirate

Ho WS, Gan HM, Yap KP, Balan G, Yeo CC, Thong KL

J Bacteriol, 2012 Dec;194(23):6691-2.

PMID: 23144425 DOI: 10.1128/JB.01804-12

Escherichia coli is an important etiologic agent of lower respiratory tract infections (LRTI). Multidrug-resistant E. coli EC302/04 was isolated from a tracheal aspirate, and its genome sequence is expected to provide insights into antimicrobial resistance as well as adaptive and virulence mechanisms of E. coli involved in LRTI.

Matched MeSH terms: Genome, Bacterial*

Fulltext Draft genome sequence of Mycobacterium bolletii strain M24, a rapidly growing mycobacterium of contentious taxonomic status

Wong YL, Choo SW, Tan JL, Ong CS, Ng KP, Ngeow YF

J Bacteriol, 2012 Aug;194(16):4475.

PMID: 22843600 DOI: 10.1128/JB.00916-12

The whole-genome sequence of Mycobacterium bolletii M24, isolated from the bronchoalveolar lavage fluid of a Malaysian patient, is reported here. The circular chromosome of 5,507,730 bp helped to clarify the taxonomic position of this organism within the M. abscessus complex and revealed the presence of proteins potentially important for pathogenicity in a human host.

Matched MeSH terms: Genome, Bacterial*

Fulltext Complete genome and proteome of Acholeplasma laidlawii

Lazarev VN, Levitskii SA, Basovskii YI, Chukin MM, Akopian TA, Vereshchagin VV, et al.

J Bacteriol, 2011 Sep;193(18):4943-53.

PMID: 21784942 DOI: 10.1128/JB.05059-11

We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.

Matched MeSH terms: Genome, Bacterial*

Analysis of the genome of Mycobacterium abscessus strain M94 reveals an uncommon cluster of tRNAs

Choo SW, Wong YL, Leong ML, Heydari H, Ong CS, Ng KP, et al.

J Bacteriol, 2012 Oct;194(20):5724.

PMID: 23012295

Mycobacterium abscessus is a species of rapidly growing nontuberculous mycobacteria that is frequently associated with opportunistic infections in humans. Here, we report the annotated genome sequence of M. abscessus strain M94, which showed an unusual cluster of tRNAs.

Matched MeSH terms: Genome, Bacterial*

Genome sequence of Enterococcus sp. strain C1, an azo dye decolorizer

Chan GF, Gan HM, Rashid NA

J Bacteriol, 2012 Oct;194(20):5716-7.

PMID: 23012290

Enterococcus sp. strain C1 is a facultative anaerobe which was coisolated with Citrobacter sp. strain A1 from a sewage oxidation pond. Strain C1 could degrade azo dyes very efficiently via azo reduction and desulfonation in a microaerophilic environment. Here the draft genome sequence of Enterococcus sp. C1 is reported.

Matched MeSH terms: Genome, Bacterial*

Draft genome sequences of Helicobacter pylori isolates from Malaysia, cultured from patients with functional dyspepsia and gastric cancer

Gunaletchumy SP, Teh X, Khosravi Y, Ramli NS, Chua EG, Kavitha T, et al.

J Bacteriol, 2012 Oct;194(20):5695-6.

PMID: 23012278

Helicobacter pylori is the main bacterial causative agent of gastroduodenal disorders and a risk factor for gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. The draft genomes of 10 closely related H. pylori isolates from the multiracial Malaysian population will provide an insight into the genetic diversity of isolates in Southeast Asia. These isolates were cultured from gastric biopsy samples from patients with functional dyspepsia and gastric cancer. The availability of this genomic information will provide an opportunity for examining the evolution and population structure of H. pylori isolates from Southeast Asia, where the East meets the West.

Matched MeSH terms: Genome, Bacterial*

Displaying publications 101 - 120 of 177 in total