Displaying publications 61 - 80 of 452 in total

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  1. Rediscovery of Micryletta inornata (Boulenger, 1890) from Sumatra: redescription, molecular identity, and taxonomic implications
    Alhadi F, Hamidy A, Farajallah A, Munir M, Atmaja VY, Garg S, et al.
    Zootaxa, 2019 Jun 04;4613(1):zootaxa.4613.1.5.
    PMID: 31716427 DOI: 10.11646/zootaxa.4613.1.5
    Micryletta inornata (Boulenger 1890), the type species of the genus Micryletta, was originally described from the island of Sumatra in Indonesia. Subsequently, this species has been widely reported from Sundaland (Sumatra and Malay Peninsula), Indo-China, Northeast India and South Andaman, up to southern China and Taiwan. However, since the original description there has been no further report of this species from the type locality or the island. During a herpetofaunal survey in Sumatra, several specimens that are morphologically concordant with the original description and the syntypes of M. inornata were found, and thus the species was rediscovered after 125 years. Here, we provide a redescription of the species based on the freshly collected specimens, along with a detailed morphological and molecular comparison with known congeners. Further, using molecular data from the mitochondrial 16S rRNA gene, our study recovered the Sumatran M. inornata as a phylogenetically distinct lineage from all other populations previously referred to this species. This confirms that all known Micryletta 'inornata' populations from regions outside Sumatra constitute several other lineages representing either new species or previously available names currently considered as synonyms, consequently requiring taxonomic validation in the future.
    Matched MeSH terms: RNA, Ribosomal, 16S
  2. Plasmid localization of sole rrn operon in genomes of Oecophyllibacter saccharovorans (Acetobacteraceae)
    Chua KO, See-Too WS, Yong HS, Song SL, Yin WF, Chan KG
    Plasmid, 2021 03;114:102559.
    PMID: 33476637 DOI: 10.1016/j.plasmid.2021.102559
    The bacterium Oecophyllibacter saccharovorans of family Acetobacteraceae is a symbiont of weaver ant Oecophylla smaragdina. In our previous study, we published the finding of novel O. saccharovorans strains Ha5T, Ta1 and Jb2 (Chua et al. 2020) but their plasmid sequences have not been reported before. Here, we demonstrate for the first time that the sole rrn operon of their genomes was detected on a 6.6 kb circular replicon. This replicon occurred in high copy number, much smaller size and lower G + C content than the main chromosome. Based on these features, the 6.6 kb circular replicon was regarded as rrn operon-containing plasmid. Further restriction analysis on the plasmids confirmed their circular conformation. A Southern hybridization analysis also corroborated the presence of 16S rRNA gene and thus the rrn operon on a single locus in the genome of the O. saccharovorans strains. However, similar genome architecture was not observed in other closely related bacterial strains. Additional survey also detected no plasmid-borne rrn operon in available genomes of validly described taxa of family Acetobacteraceae. To date, plasmid localization of rrn operon is rarely documented. This study reports the occurrence of rrn operon on the smallest bacterial plasmid in three O. saccharovorans strains and discusses its possible importance in enhancing their competitive fitness as bacterial symbiont of O. smaragdina.
    Matched MeSH terms: RNA, Ribosomal, 16S
  3. Shedding and Genetic Diversity of Leptospira spp. From Urban Stray Dogs in Klang Valley, Malaysia
    Goh SH, Khor KH, Radzi R, Lau SF, Khairani-Bejo S, Abdul Rahman MS, et al.
    Top Companion Anim Med, 2021 Nov;45:100562.
    PMID: 34271178 DOI: 10.1016/j.tcam.2021.100562
    Leptospirosis is an endemic zoonoses of global proportions. Stray dogs have been postulated to play a role in disease transmission; however, supporting information are still limited. Roaming behavior may not only predispose the dogs to infection, but could also contribute to disease spread. In this study, the susceptibility of urban stray dogs in shedding Leptospira spp. was determined. Blood, urine, and tissue samples of kidney and liver were collected from 100 dogs from 2 animal control facilities. Serological testing using microscopic agglutination test (MAT) were performed on blood against 20 leptospiral serovars with a cut-off titre of ≥ 1:100. Samples were cultured onto semi-solid Ellinghausen and McCullough modified by Johnson and Harris (EMJH) media. Isolates were identified using molecular polymerase chain reaction (PCR) using 2 primers (16s rRNA and LipL32) and hyperimmune serum (HIS) MAT. The seroprevalence for the dogs positive for leptospirosis was 32% (n=32/100) with the following detected serovars: Javanica (n=13), Bataviae (n=10), Icterohaemorrhagiae (n=3), Autumnalis (n=2), Canicola (n=1), Pyrogenes (n=1), Copenhageni (n=1), and Australis (n=1). Six Leptospira spp. isolated were procured from urine (n=2), kidney (n=2) and liver (n=2). All 6 isolates belonged to L. interrogans, a pathogenic variant of Leptospira spp. Serotyping and phylogenetic analysis suggested serovar Bataviae (n=5) and serovar Canicola (n=1). Presence of vaccinal serovars (Icterohaemorrhagiae and Canicola) suggested potential post-vaccination antibodies but the predominance of non-vaccinal serovars (Javanica and Bataviae) indicate the possibility of current infection or post-exposure. Isolation of Leptospira spp. directly from urine sample not only suggested an active infection but highlighted the potential shedding capability among these stray dogs. These findings further strengthen speculations that urban stray dogs could play a role in transmission and dissemination of leptospirosis through their constant movement. The urine of infected dogs may contaminate the environment, posing a major public health threat.
    Matched MeSH terms: RNA, Ribosomal, 16S
  4. Fulltext Four new species of Ctenodrilus, Raphidrilus, and Raricirrus (Cirratuliformia, Annelida) in Japanese waters, with notes on their phylogenetic position
    Jimi N, Fujimoto S, Fujiwara Y, Oguchi K, Miura T
    PeerJ, 2022;10:e13044.
    PMID: 35282276 DOI: 10.7717/peerj.13044
    Four new species of annelids, Ctenodrilus japonicus sp. nov., Raphidrilus misakiensis sp. nov., Raphidrilus okinawaensis sp. nov., and Raricirrus anubis sp. nov., are described based on specimens collected from Japanese waters. Ctenodrilus japonicus sp. nov. inhabits the interstitial environment and can be distinguished from the other congeners by the following features: (i) total of 16 chaetigers, (ii) chaetigers 1-3 with stout hooks, (iii) minute body (approximately 1 mm in length), (iv) all parapodia with the same number of chaetae (two notochaetae; two neurochaetae), and (v) presence of dorsal and ventral papillae. Raphidrilus misakiensis sp. nov. lives under intertidal stones and can be distinguished from other congeners by having pectinate neurochaetae. Raphidrilus okinawaensis sp. nov. inhabits the interstitial environment and can be distinguished from other congeners by: (i) absence of annulation on the peristomium and achaetous segment and (ii) presence of a heart body in chaetigers 4-5. Raricirrus anubis sp. nov. inhabits whale bones and can be distinguished from other congeners by the following features: (i) presence of a heart body in chaetigers 9-14, (ii) presence of capillary neurochaetae on chaetiger 1, and (iii) presence of simple curved spines. A phylogenetic tree based on partial sequences of cytochrome c oxidase subunit I and 16S rRNA from the new species and other cirratulid worms showed that Raphidrilus is included in Cirratuliformia. This is the first record of Raphidrilus and Raricirrus from Japanese waters.
    Matched MeSH terms: RNA, Ribosomal, 16S
  5. [Not Available]
    Al-Zergani F, Ronit A, Theilgaard ZP, Ronayne A, Nielsen HV, Porskrog A
    Ugeskr Laeger, 2023 Oct 02;185(40).
    PMID: 37873999
    Scrub typhus is caused by the mite-borne bacterium Orientia tsutsugamushi. Imported cases have been suspected in Denmark but no diagnostic method has yet been available to confirm the diagnosis. This is a case report of a 38-year-old male admitted to hospital with high fever, severe malaise and headache after returning from Malaysia. Scrub typhus was suspected and the patient recovered after one week of doxycycline treatment. The pathogen was identified by use of microbiome 16S/18S rRNA next-generation sequencing on ethylenediamine tetraacetic acid (EDTA) blood, which in the future may serve an important role in the investigation of travel-associated infections.
    Matched MeSH terms: RNA, Ribosomal, 16S
  6. Effects of elevated temperature and different crystal structures of TiO2 nanoparticles on the gut microbiota of mussel Mytilus coruscus
    Li Z, Li L, Sokolova I, Shang Y, Huang W, Khor W, et al.
    Mar Pollut Bull, 2024 Feb;199:115979.
    PMID: 38171167 DOI: 10.1016/j.marpolbul.2023.115979
    Coastal habitats are exposed to increasing pressure of nanopollutants commonly combined with warming due to the seasonal temperature cycles and global climate change. To investigate the toxicological effects of TiO2 nanoparticles (TiO2 NPs) and elevated temperature on the intestinal health of the mussels (Mytilus coruscus), the mussels were exposed to 0.1 mg/L TiO2 NPs with different crystal structures for 14 days at 20 °C and 28 °C, respectively. Compared to 20 °C, the agglomeration of TiO2 NPs was more serious at 28 °C. Exposure to TiO2 NPs led to elevated mortality of M. coruscus and modified the intestinal microbial community as shown by 16S rRNA sequence analysis. Exposure to TiO2 NPs changed the relative abundance of Bacteroidetes, Proteobacteria and Firmicutes. The relative abundances of putative mutualistic symbionts Tenericutes and Fusobacteria increased in the gut of M. coruscus exposed to anatase, which have contributed to the lower mortality in this group. LEfSe showed the combined stress of warming and TiO2 NPs increased the risk of M. coruscus being infected with potential pathogenic bacteria. This study emphasizes the toxicity differences between crystal structures of TiO2 NPs, and will provides an important reference for analyzing the physiological and ecological effects of nanomaterial pollution on bivalves under the background of global climate change.
    Matched MeSH terms: RNA, Ribosomal, 16S
  7. Fulltext Comparative genomic analysis of Mycobacterium iranicum UM_TJL against representative mycobacterial species suggests its environmental origin
    Tan JL, Ngeow YF, Wee WY, Wong GJ, Ng HF, Choo SW
    Sci Rep, 2014;4:7169.
    PMID: 25417557 DOI: 10.1038/srep07169
    Mycobacterium iranicum is a newly reported mycobacterial species. We present the first comparative study of M. iranicum UM_TJL and other mycobacteria. We found M. iranicum to have a close genetic association with environmental mycobacteria infrequently associated with human infections. Nonetheless, UM_TJL is also equipped with many virulence genes (some of which appear to be the consequence of transduction-related gene transfer) that have been identified in established human pathogens. Taken all together, our data suggest that M. iranicum is an environmental bacterium adapted for pathogenicity in the human host. This comparative study provides important clues and forms the basis for future functional studies on this mycobacterium.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics; RNA, Ribosomal, 16S/chemistry
  8. Phylogeography illuminates maternal origins of exotic Coptotermes gestroi (Isoptera: Rhinotermitidae)
    Jenkins TM, Jones SC, Lee CY, Forschler BT, Chen Z, Lopez-Martinez G, et al.
    Mol Phylogenet Evol, 2007 Mar;42(3):612-21.
    PMID: 17254806
    Coptotermes gestroi, the Asian subterranean termite (AST), is an economically important structural and agricultural pest that has become established in many areas of the world. For the first time, phylogeography was used to illuminate the origins of new found C. gestroi in the US Commonwealth of Puerto Rico; Ohio, USA; Florida, USA; and Brisbane, Australia. Phylogenetic relationships of C. gestroi collected in indigenous locations within Malaysia, Thailand, and Singapore as well as from the four areas of introduction were investigated using three genes (16S rRNA, COII, and ITS) under three optimality criteria encompassing phenetic and cladistic assumptions (maximum parsimony, maximum likelihood, and neighbor-joining). All three genes showed consistent support for a close genetic relationship between C. gestroi samples from Singapore and Ohio, whereas termite samples from Australia, Puerto Rico, and Key West, FL were more closely related to those from Malaysia. Shipping records further substantiated that Singapore and Malaysia were the likely origin of the Ohio and Australia C. gestroi, respectively. These data provide support for using phylogeography to understand the dispersal history of exotic termites. Serendipitously, we also gained insights into concerted evolution in an ITS cluster from rhinotermitid species in two genera.
    Matched MeSH terms: RNA, Ribosomal, 16S/analysis; RNA, Ribosomal, 16S/genetics
  9. Fulltext Comparative genome sequencing and analyses of Mycobacterium cosmeticum reveal potential for biodesulfization of gasoline
    Wee WY, Dutta A, Jayaraj J, Choo SW
    PLoS One, 2019;14(4):e0214663.
    PMID: 30964891 DOI: 10.1371/journal.pone.0214663
    Mycobacterium cosmeticum is a nontuberculous Mycobacterium recovered from different water sources including household potable water and water collected at nail salon. Individual cases of this bacterium have been reported to be associated with gastrointestinal tract infections. Here we present the first whole-genome study and comparative analysis of two new clinically-derived Mycobacterium sp. UM_RHS (referred as UM_RHS after this) and Mycobacterium sp. UM_NYF (referred as UM_NYF after this) isolated from patients in Indonesia and Malaysia respectively to have a better understanding of the biological characteristic of these isolates. Both strains are likely Mycobacterium cosmeticum as supported by the evidence from molecular phylogenetic, comparative genomic and Average Nucleotide Identity (ANI) analyses. We found the presence of a considerably large number of putative virulence genes in the genomes of UM_RHS and UM_NYF. Interestingly, we also found a horizontally transferred genomic island carrying a putative dsz operon proposing that they may have potential to perform biodesulfization of dibenzothiophene (DBT) that may be effective in cost reduction and air pollution during fuel combustion. This comparative study may provide new insights into M. cosmeticum and serve as an important reference for future functional studies of this bacterial species.
    Matched MeSH terms: RNA, Ribosomal, 16S/classification; RNA, Ribosomal, 16S/genetics
  10. 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
  11. 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
  12. 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
  13. 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
  14. Microtetraspora malaysiensis sp. nov., isolated from Malaysian primary dipterocarp forest soil
    Nakajima Y, Ho CC, Kudo T
    J Gen Appl Microbiol, 2003 Jun;49(3):181-9.
    PMID: 12949699
    The taxonomic position of three actinomycete strains isolated from Malaysian soil was established by using a polyphasic approach. The isolates formed chains composed of four spores on the tip of sporophores branching from the aerial mycelium, and their chemotaxonomic properties were common to those of members of the family Streptosporangiaceae. These phenotypic properties as well as a phylogenetic analysis based on 16S rRNA gene sequences indicated that they should be classified in the genus Microtetraspora. The three isolates showed a unique pattern of cultural, physiological and biochemical properties that distinguished them from previously described species of the genus Microtetraspora. The isolates showed more than 72% DNA relatedness to each other, but only 58% or less relatedness to any previously described species. On the basis of the data presented, a new species of the genus Microtetraspora, Microtetraspora malaysiensis, is proposed. The type strain of the new species is strain H47-7(T) (=JCM 11278(T)=DSM 44579(T)).
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics; RNA, Ribosomal, 16S/chemistry
  15. Fulltext A novel strain of acetic acid bacteria Gluconobacter oxydans FBFS97 involved in riboflavin production
    Noman AE, Al-Barha NS, Sharaf AM, Al-Maqtari QA, Mohedein A, Mohammed HHH, et al.
    Sci Rep, 2020 08 11;10(1):13527.
    PMID: 32782276 DOI: 10.1038/s41598-020-70404-4
    A novel bacterial strain of acetic acid bacteria capable of producing riboflavin was isolated from the soil sample collected in Wuhan, China. The isolated strain was identified as Gluconobacter oxydans FBFS97 based on several phenotype characteristics, biochemicals tests, and 16S rRNA gene sequence conducted. Furthermore, the complete genome sequencing of the isolated strain has showed that it contains a complete operon for the biosynthesis of riboflavin. In order to obtain the maximum concentration of riboflavin production, Gluconobacter oxydans FBFS97 was optimized in shake flask cultures through response surface methodology employing Plackett-Burman design (PBD), and Central composite design (CCD). The results of the pre-experiments displayed that fructose and tryptone were found to be the most suitable sources of carbon and nitrogen for riboflavin production. Then, PBD was conducted for initial screening of eleven minerals (FeSO4, FeCl3, KH2PO4, K2HPO4, MgSO4, ZnSO4, NaCl, CaCl2, KCl, ZnCl2, and AlCl3.6H2O) for their significances on riboflavin production by Gluconobacter oxydans strain FBFS97. The most significant variables affecting on riboflavin production are K2HPO4 and CaCl2, the interaction affects and levels of these variables were optimized by CCD. After optimization of the medium compositions for riboflavin production were determined as follows: fructose 25 g/L, tryptone 12.5 g/L, K2HPO4 9 g/L, and CaCl2 0.06 g/L with maximum riboflavin production 23.24 mg/L.
    Matched MeSH terms: RNA, Ribosomal, 16S/analysis; RNA, Ribosomal, 16S/genetics
  16. Misidentification of Burkholderia pseudomallei as Burkholderia cepacia by the VITEK 2 system
    Zong Z, Wang X, Deng Y, Zhou T
    J Med Microbiol, 2012 Oct;61(Pt 10):1483-1484.
    PMID: 22820689 DOI: 10.1099/jmm.0.041525-0
    A previously healthy Chinese male returned from working in the Malaysian jungle with a fever. A blood culture grew Gram-negative bacilli that were initially identified as Burkholderia cepacia by the VITEK 2 system but were subsequently found to be Burkholderia pseudomallei by partial sequencing of the 16S rRNA gene. The identification of B. pseudomallei using commercially available automated systems is problematic and clinicians in non-endemic areas should be aware of the possibility of melioidosis in patients with a relevant travel history and blood cultures growing Burkholderia spp.
    Matched MeSH terms: RNA, Ribosomal, 16S/classification; RNA, Ribosomal, 16S/genetics
  17. Fulltext Genome Sequence of Fusobacterium nucleatum Strain W1481, a Possible New Subspecies Isolated from a Periodontal Pocket
    Ang MY, Dymock D, Tan JL, Thong MH, Tan QK, Wong GJ, et al.
    Genome Announc, 2014;2(1).
    PMID: 24526626 DOI: 10.1128/genomeA.00009-14
    Fusobacterium nucleatum is a bacterial species commonly detected in dental plaque within the human oral cavity, with some strains associated with periodontal disease, one of the most common clinical bacterial infections in the human body. The exact mechanisms of its pathogenesis are still not completely understood. In this study, we present the genome sequence and annotation of F. nucleatum strain W1481, isolated from a periodontal pocket of a dental patient at the University of Bristol, United Kingdom, the 16S rRNA gene sequencing of which showed it to be markedly different from the five previously named subspecies.
    Matched MeSH terms: RNA, Ribosomal, 16S
  18. Fulltext Supporting data for identification of biosurfactant-producing bacteria isolated from agro-food industrial effluent
    Fulazzaky MA, Abdullah S, Salim MR
    Data Brief, 2016 Jun;7:834-8.
    PMID: 27077083 DOI: 10.1016/j.dib.2016.03.058
    The goal of this study was to identify the biosurfactant-producing bacteria isolated from agro-food industrial effluet. The identification of the potential bacterial strain using a polymerase chain reaction of the 16S rRNA gene analysis was closely related to Serratia marcescens with its recorded strain of SA30 "Fundamentals of mass transfer and kinetics for biosorption of oil and grease from agro-food industrial effluent by Serratia marcescens SA30" (Fulazzaky et al., 2015) [1]; however, many biochemical tests have not been published yet. The biochemical tests of biosurfactant production, haemolytic assay and cell surface hydrophobicity were performed to investigate the beneficial strain of biosurfactant-producing bacteria. Here we do share data collected from the biochemical tests to get a better understanding of the use of Serratia marcescens SA30 to degrade oil, which contributes the technical features of strengthening the biological treatment of oil-contaminated wastewater in tropical environments.
    Matched MeSH terms: RNA, Ribosomal, 16S
  19. 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
  20. 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
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