Displaying publications 1 - 20 of 447 in total

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  1. γ-Aminobutyric acid production by selected lactic acid bacteria isolate of an Indonesian indigenous fermented buffalo milk (dadih) origin
    Harnentis H, Nurmiati N, Marlida Y, Adzitey F, Huda N
    Vet World, 2019 Aug;12(8):1352-1357.
    PMID: 31641319 DOI: 10.14202/vetworld.2019.1352-1357
    Aim: This study aimed at optimizing γ-aminobutyric acid (GABA) production using lactic acid bacteria (LAB) of an Indonesian indigenous fermented buffalo milk (dadih) origin. This study utilized LAB previously cultured from dadih that has the ability to produce GABA.

    Materials and Methods: The study started with the identification of selected LAB by 16S rRNA, followed by optimization of GABA production by culture conditions using different initial pH, temperature, glutamate concentration, incubation time, carbon, and nitrogen sources. 16S rRNA polymerase chain reaction and analysis by phylogenetic were used to identify Lactobacillus plantarum (coded as N5) responsible for the production of GABA.

    Results: GABA production by high-performance liquid chromatography was highest at pH of 5.5, temperature of 36°C, glutamate concentration of 500 mM, and incubation time of 84 h. Peptone and glucose served as the nitrogen and carbon sources, respectively, whereas GABA was produced at optimum fermentation condition of 211.169 mM.

    Conclusion: Production of GABA by L. plantarum N5 was influenced by initial pH of 5.5, glutamic acid concentration, nitrogen source, glucose as carbon source, and incubation temperature and time.

    Matched MeSH terms: RNA, Ribosomal, 16S
  2. Fulltext pH dominates variation in tropical soil archaeal diversity and community structure
    Tripathi BM, Kim M, Lai-Hoe A, Shukor NA, Rahim RA, Go R, et al.
    FEMS Microbiol Ecol, 2013 Nov;86(2):303-11.
    PMID: 23773164 DOI: 10.1111/1574-6941.12163
    Little is known of the factors influencing soil archaeal community diversity and composition in the tropics. We sampled soils across a range of forest and nonforest environments in the equatorial tropics of Malaysia, covering a wide range of pH values. DNA was PCR-amplified for the V1-V3 region of the 16S rRNA gene, and 454-pyrosequenced. Soil pH was the best predictor of diversity and community composition of Archaea, being a stronger predictor than land use. Archaeal OTU richness was highest in the most acidic soils. Overall archaeal abundance in tropical soils (determined by qPCR) also decreased at higher pH. This contrasts with the opposite trend previously found in temperate soils. Thaumarcheota group 1.1b was more abundant in alkaline soils, whereas group 1.1c was only detected in acidic soils. These results parallel those found in previous studies in cooler climates, emphasizing niche conservatism among broad archaeal groups. Among the most abundant operational taxonomic units (OTUs), there was clear evidence of niche partitioning by pH. No individual OTU occurred across the entire range of pH values. Overall, the results of this study show that pH plays a major role in structuring tropical soil archaeal communities.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  3. [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
  4. Fulltext Whole genome sequencing data of a clinical Enterococcus gallinarum strain EGR748 from Sabah, Malaysia
    Mastor NN, Subbiah VK, Bakar WNWA, Begum K, Alam MJ, Hoque MZ
    Data Brief, 2020 Dec;33:106370.
    PMID: 33102652 DOI: 10.1016/j.dib.2020.106370
    Enterococcus gallinarum is a gram positive facultatively anaerobic bacteria that is typically found in mammalian intestinal tracts. It is generally not considered pathogenic to humans and is rarely reported. Here, we present the draft genome sequence data of Enterococcus gallinarum strain EGR748 isolated from a human clinical sample, and sequenced using the Illumina HiSeq 4000 system. The estimated whole genome size of the strain was 3,730,000 bp with a G + C content of 40.43%. The de novo assembly of the genome generated 55 contigs with an N50 of 208,509 bp. In addition, the Maximum Likelihood phylogenetic analysis based on the 16S rRNA sequence data accurately clustered EGR748 with other E. gallinarum strains. The data may be useful to demonstrate the capacity of this enterococcal species becoming the causal agents of nosocomial blood-stream infections. The genome dataset has been deposited at DDBJ/ENA/GenBank under the accession number JAABOR000000000.
    Matched MeSH terms: RNA, Ribosomal, 16S
  5. Whole genome sequence of moderate halophilic marine bacterium Marinobacter litoralis SW-45: Abundance of non-coding RNAs
    Musa H, Kasim FH, Gunny AAN, Gopinath SCB, Chinni SV, Ahmad MA
    Int J Biol Macromol, 2019 Jul 15;133:1288-1298.
    PMID: 31055112 DOI: 10.1016/j.ijbiomac.2019.05.003
    A report on the de novo Whole Genome Sequence (WGS) of Marinobacter litoralis SW-45, a moderately salt-tolerant bacterium isolated from the seawater in Malaysia is presented. The strain has a genome size of 3.45 Mb and is capable of producing halophilic lipase, protease and esterase enzymes. Computational prediction of non-coding RNA (ncRNA) genes in M. litoralis SW-45 was performed using standalone software known as the non-coding RNA characterization (nocoRNAc). In addition, a phylogenetic tree showing the evolutionary relationship between the strain and other members of the genus Marinobacter was constructed using 16SrRNA sequence information. A total of 385 ncRNA transcripts, 1124 terminator region, and 2350 Stress Induced Duplex Destabilization sites were predicted. The current WGS shotgun project has provided the relevant genetic information that may be useful for the strain's improvement studies. This manuscript gives the first description of M. litoralis with a complete genome.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  6. Vitellibacter aquimaris sp. nov., a marine bacterium isolated from seawater
    Thevarajoo S, Selvaratnam C, Goh KM, Hong KW, Chan XY, Chan KG, et al.
    Int J Syst Evol Microbiol, 2016 Sep;66(9):3662-3668.
    PMID: 27334651 DOI: 10.1099/ijsem.0.001248
    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: Vitellibactervladivostokensis KMM 3516T (99.5 %), Vitellibactersoesokkakensis RSSK-12T (97.3 %), VitellibacterechinoideorumCC-CZW007T (96.9 %), VitellibacternionensisVBW088T (96.7 %) and Vitellibacteraestuarii JCM 15496T (96.3 %). DNA-DNA hybridization and genome-based analysis of average nucleotide identity (ANI) of strain D-24T versus V.vladivostokensisKMM 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).
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  7. Vishniacozyma pseudocarnescens sp. nov., a new anamorphic tremellomycetous yeast species
    Zhu HY, Wei YH, Guo LC, Wei XY, Li JN, Zhang RP, et al.
    Int J Syst Evol Microbiol, 2023 Oct;73(10).
    PMID: 37847534 DOI: 10.1099/ijsem.0.006076
    Three strains belonging to the basidiomycetous yeast genus Vishniacozyma were isolated from marine water samples collected from intertidal zones in Liaoning province, northeast China. Phylogenetic analyses based on the sequences of the small subunit (SSU) ribosomal DNA (rDNA), the D1/D2 domain of the large subunit (LSU) ribosomal DNA (rDNA), the internal transcribed spacer region (ITS), the two subunits of DNA polymerase II (RPB1 and RPB2), the translation elongation factor 1-α (TEF1), and the mitochondrial gene cytochrome b (CYTB) showed that these strains together with 20 strains from various geographic and ecological origins from other regions of the world represent a novel species in the genus Vishniacozyma. We propose the name Vishniacozyma pseudocarnescens sp. nov. (holotype CGMCC 2.6457) for the new species, which differs phenotypically from its close relatives V. carnescens, V. tephrensis, and V. victoriae by its ability to grow at 30 °C and on 50 % (w/v) glucose-yeast extract agar.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  8. Vibrio coralliirubri sp. nov., a new species isolated from mucus of red coral (Corallium rubrum) collected at Procida island, Italy
    Poli A, Romano I, Mastascusa V, Buono L, Orlando P, Nicolaus B, et al.
    Antonie Van Leeuwenhoek, 2018 Jul;111(7):1105-1115.
    PMID: 29299771 DOI: 10.1007/s10482-017-1013-5
    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).
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  9. Fulltext Using metabarcoding to compare the suitability of two blood-feeding leech species for sampling mammalian diversity in North Borneo
    Drinkwater R, Schnell IB, Bohmann K, Bernard H, Veron G, Clare E, et al.
    Mol Ecol Resour, 2019 Jan;19(1):105-117.
    PMID: 30225935 DOI: 10.1111/1755-0998.12943
    The application of high-throughput sequencing (HTS) for metabarcoding of mixed samples offers new opportunities in conservation biology. Recently, the successful detection of prey DNA from the guts of leeches has raised the possibility that these, and other blood-feeding invertebrates, might serve as useful samplers of mammals. Yet little is known about whether sympatric leech species differ in their feeding preferences, and whether this has a bearing on their relative suitability for monitoring local mammalian diversity. To address these questions, we collected spatially matched samples of two congeneric leech species Haemadipsa picta and Haemadipsa sumatrana from lowland rainforest in Borneo. For each species, we pooled ~500 leeches into batches of 10 individuals, performed PCR to target a section of the mammalian 16S rRNA locus and undertook sequencing of amplicon libraries using an Illumina MiSeq. In total, we identified sequences from 14 mammalian genera, spanning nine families and five orders. We found greater numbers of detections, and higher diversity of OTUs, in H. picta compared with H. sumatrana, with rodents only present in the former leech species. However, comparison of samples from across the landscape revealed no significant difference in mammal community composition between the leech species. We therefore suggest that H. picta is the more suitable iDNA sampler in this degraded Bornean forest. We conclude that the choice of invertebrate sampler can influence the detectability of different mammal groups and that this should be accounted for when designing iDNA studies.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  10. Unusually high genetic diversity in the Bornean Limnonectes kuhlii-like fanged frogs (Anura: Dicroglossidae)
    Matsui M, Kuraishi N, Eto K, Hamidy A, Nishikawa K, Shimada T, et al.
    Mol Phylogenet Evol, 2016 09;102:305-19.
    PMID: 27374495 DOI: 10.1016/j.ympev.2016.06.009
    A fanged frog Limnonectes kuhlii was once thought to be wide-ranging in Southeast Asia, but is now confined to its type locality Java through recent phylogenetic studies, which clarified heterospecific status of non-Javanese populations, and monophyly of Bornean populations. However, large genetic differences among Bornean populations suggest occurrence of cryptic species, which we test using dense geographic sampling. We estimated the phylogenetic relationships among samples of Bornean populations together with their putative relatives from the continental Southeast Asia, using 2517bp sequences of the 12S rRNA, tRNA(val), and 16S rRNA of mitochondrial DNA, and 2367bp sequences of the NCX1, POMC, and RAG1 of nuclear genes. In the mtDNA trees, Bornean L. kuhlii-like frogs formed a monophyletic group split into 18 species lineages including L. hikidai, with the deepest phylogenetic split separating L. cintalubang from the remaining species. Almost all of these lineages co-occur geographically, and two to three lineages were found syntopically in each locality. Co-occurrence of more than one lineage may be maintained by differential morphology and microhabitat selection. These syntopic lineages should be regarded as distinct species. Our results clearly indicate that taxonomic revision is urgent to clarify many evolutionary problems of Bornean L. kuhlii-like frogs.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics; RNA, Ribosomal, 16S/metabolism; RNA, Ribosomal, 16S/chemistry
  11. Universal mitochondrial 16s rRNA biomarker for mini-barcode to identify fish species in Malaysian fish products
    Hossain MAM, Uddin SMK, Chowdhury ZZ, Sultana S, Johan MR, Rohman A, et al.
    Food Addit Contam Part A Chem Anal Control Expo Risk Assess, 2019 Apr;36(4):493-506.
    PMID: 30865559 DOI: 10.1080/19440049.2019.1580389
    Mislabelling in fish products is a highly significant emerging issue in world fish trade in terms of health and economic concerns. DNA barcoding is an efficient sequencing-based tool for detecting fish species substitution but due to DNA degradation, it is in many cases difficult to amplify PCR products of the full-length barcode marker (~650 bp), especially in severely processed products. In the present study, a pair of universal primers targeting a 198 bp sequence of the mitochondrial 16s rRNA gene was designed for identification of fish species in the processed fish products commonly consumed in Malaysia. The specificity of the universal primers was tested by both in-silico studies using bioinformatics software and through cross-reaction assessment by practical PCR experiments against the DNA from 38 fish species and 22 other non-target species (animals and plants) and found to be specific for all the tested fish species. To eliminate the possibility of any false-negative detection, eukaryotic endogenous control was used during specificity evaluation. The developed primer set was validated with various heat-treated (boiled, autoclaved and microwaved) fish samples and was found to show high stability under all processing conditions. The newly developed marker successfully identified 92% of the tested commercial fish products with 96-100% sequence similarities. This study reveals a considerable degree of species mislabelling (20.8%); 5 out of 24 fish products were found to be mislabelled. The new marker developed in this work is a reliable tool to identify fish species even in highly processed products and might be useful in detecting fish species substitution thus protecting consumers' health and economic interests.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics*
  12. Fulltext Unexpectedly high levels of lineage diversity in Sundaland puddle frogs (Dicroglossidae: Occidozyga Kuhl and van Hasselt, 1822)
    Flury JM, Haas A, Brown RM, Das I, Pui YM, Boon-Hee K, et al.
    Mol Phylogenet Evol, 2021 10;163:107210.
    PMID: 34029720 DOI: 10.1016/j.ympev.2021.107210
    One of the most urgent contemporary tasks for taxonomists and evolutionary biologists is to estimate the number of species on earth. Recording alpha diversity is crucial for protecting biodiversity, especially in areas of elevated species richness, which coincide geographically with increased anthropogenic environmental pressures - the world's so-called biodiversity hotspots. Although the distribution of Puddle frogs of the genus Occidozyga in South and Southeast Asia includes five biodiversity hotspots, the available data on phylogeny, species diversity, and biogeography are surprisingly patchy. Samples analyzed in this study were collected throughout Southeast Asia, with a primary focus on Sundaland and the Philippines. A mitochondrial gene region comprising ~ 2000 bp of 12S and 16S rRNA with intervening tRNA Valine and three nuclear loci (BDNF, NTF3, POMC) were analyzed to obtain a robust, time-calibrated phylogenetic hypothesis. We found a surprisingly high level of genetic diversity within Occidozyga, based on uncorrected p-distance values corroborated by species delimitation analyses. This extensive genetic diversity revealed 29 evolutionary lineages, defined by the > 5% uncorrected p-distance criterion for the 16S rRNA gene, suggesting that species diversity in this clade of phenotypically homogeneous forms probably has been underestimated. The comparison with results of other anuran groups leads to the assumption that anuran species diversity could still be substantially underestimated in Southeast Asia in general. Many genetically divergent lineages of frogs are phenotypically similar, indicating a tendency towards extensive morphological conservatism. We present a biogeographic reconstruction of the colonization of Sundaland and nearby islands which, together with our temporal framework, suggests that lineage diversification centered on the landmasses of the northern Sunda Shelf. This remarkably genetically structured group of amphibians could represent an exceptional case for future studies of geographical structure and diversification in a widespread anuran clade spanning some of the most pronounced geographical barriers on the planet (e.g., Wallace's Line). Studies considering gene flow, morphology, ecological and bioacoustic data are needed to answer these questions and to test whether observed diversity of Puddle frog lineages warrants taxonomic recognition.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  13. Two Groups of Phytoplasmas from Japan Distinguished on the Basis of Amplification and Restriction Analysis of 16S rDNA
    Okuda S, Prince JP, Davis RE, Dally EL, Lee IM, Mogen B, et al.
    Plant Dis, 1997 Mar;81(3):301-305.
    PMID: 30861775 DOI: 10.1094/PDIS.1997.81.3.301
    Phytoplasmas (mycoplasmalike organisms, MLOs) associated with mitsuba (Japanese hone-wort) witches'-broom (JHW), garland chrysanthemum witches'-broom (GCW), eggplant dwarf (ED), tomato yellows (TY), marguerite yellows (MY), gentian witches'-broom (GW), and tsu-wabuki witches'-broom (TW) in Japan were investigated by polymerase chain reaction (PCR) amplification of DNA and restriction enzyme analysis of PCR products. The phytoplasmas could be separated into two groups, one containing strains JHW, GCW, ED, TY, and MY, and the other containing strains GW and TW, corresponding to two groups previously recognized on the basis of transmission by Macrosteles striifrons and Scleroracus flavopictus, respectively. The strains transmitted by M. striifrons were classified in 16S rRNA gene group 16SrI, which contains aster yellows and related phytoplasma strains. Strains GW and TW were classified in group 16SrIII, which contains phytoplasmas associated with peach X-disease, clover yellow edge, and related phytoplasmas. Digestion of amplified 16S rDNA with HpaII indicated that strains GW and TW were affiliated with subgroup 16SrIII-B, which contains clover yellow edge phytoplasma. All seven strains were distinguished from other phytoplasmas, including those associated with clover proliferation, ash yellows, elm yellows, and beet leafhopper-transmitted virescence in North America, and Malaysian periwinkle yellows and sweet potato witches'-broom in Asia.
    Matched MeSH terms: RNA, Ribosomal, 16S
  14. 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
  15. Fulltext Tsukamurella tyrosinosolvens intravascular catheter-related bacteremia in a haematology patient: a case report
    Karunakaran R, Halim HA, Ng KP, Hanifah YA, Chin E, Jaafar FL, et al.
    Eur Rev Med Pharmacol Sci, 2011 Nov;15(11):1343-6.
    PMID: 22195371
    Tsukamurella spp. are a rare but important cause of intravascular catheter-related bacteremia in immunocompromised patients. The organism is an aerobic, Gram-positive, weakly acid-fast bacillus that is difficult to differentiate using standard laboratory methods from other aerobic actinomycetales such as Nocardia spp., Rhododoccus spp., Gordonia spp., and the rapid growing Mycobacterium spp. We report a case of Tsukamurella tyrosinosolvens catheter-related bacteremia in a 51-year-old haematology patient who responded to treatment with imipenem and subsequent line removal. 16srRNA sequencing allowed for the prompt identification of this organism.
    Matched MeSH terms: RNA, Ribosomal, 16S/analysis
  16. Tropical soil bacterial communities in Malaysia: pH dominates in the equatorial tropics too
    Tripathi BM, Kim M, Singh D, Lee-Cruz L, Lai-Hoe A, Ainuddin AN, et al.
    Microb Ecol, 2012 Aug;64(2):474-84.
    PMID: 22395784 DOI: 10.1007/s00248-012-0028-8
    The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types--primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1-V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.
    Matched MeSH terms: RNA, Ribosomal, 16S
  17. Transcriptome analysis of methicillin-resistant Staphylococcus aureus in response to stigmasterol and lupeol
    Adnan SN, Ibrahim N, Yaacob WA
    J Glob Antimicrob Resist, 2017 03;8:48-54.
    PMID: 27992774 DOI: 10.1016/j.jgar.2016.10.006
    OBJECTIVES: Methicillin-resistant Staphylococcus aureus (MRSA) is an important pathogen with multiple antibiotic resistance that causes morbidity and mortality worldwide. Multidrug-resistant (MDR) MRSA with increased resistance to currently available antibiotics has challenged the world to develop new therapeutic agents. Stigmasterol and lupeol, from the plant Phyllanthus columnaris, exhibit antibacterial activities against MRSA. The aim of this study was to utilise next-generation sequencing (NGS) to provide further insight into the novel transcriptional response of MRSA exposed to stigmasterol and lupeol.

    METHODS: Time-kill analysis of one MRSA reference strain (ATCC 43300) and three clinical isolates (WM3, BM1 and KJ7) for both compounds was first performed to provide the bacteriostatic/bactericidal profile. Then, MRSA ATCC 43300 strain treated with both compounds was interrogated by NGS.

    RESULTS: Both stigmasterol and lupeol possessed bacteriostatic properties against all MRSA tested; however, lupeol exhibited both bacteriostatic and bactericidal properties within the same minimum inhibitory concentration and minimum bactericidal concentration values against BM1 (12.5mg/mL). Transcriptome profiling of MRSA ATCC 43300 revealed significant modulation of gene expression with multiple desirable targets by both compounds, which caused a reduction in the translation processes leading to inhibition of protein synthesis and prevention of bacterial growth.

    CONCLUSIONS: This study highlights the potential of both stigmasterol and lupeol as new promising anti-MRSA agents.

    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  18. Fulltext The upper respiratory tract microbiome of indigenous Orang Asli in north-eastern Peninsular Malaysia
    Cleary DW, Morris DE, Anderson RA, Jones J, Alattraqchi AG, A Rahman NI, et al.
    NPJ Biofilms Microbiomes, 2021 01 05;7(1):1.
    PMID: 33402693 DOI: 10.1038/s41522-020-00173-5
    Much microbiome research has focused on populations that are predominantly of European descent, and from narrow demographics that do not capture the socio-economic and lifestyle differences which impact human health. Here we examined the airway microbiomes of the Orang Asli, the indigenous peoples of Malaysia. A total of 130 participants were recruited from two sites in the north-eastern state of Terengganu in Peninsular Malaysia. Using 16S rRNA sequencing, the nasal microbiome was significantly more diverse in those aged 5-17 years compared to 50+ years (p = 0.023) and clustered by age (PERMANOVA analysis of the Bray-Curtis distance, p = 0.001). Hierarchical clustering of Bray-Curtis dissimilarity scores revealed six microbiome clusters. The largest cluster (n = 28; 35.4%) had a marked abundance of Corynebacterium. In the oral microbiomes Streptococcus, Neisseria and Haemophilus were dominant. Using conventional microbiology, high levels of Staphylococcus aureus carriage were observed, particularly in the 18-65 age group (n = 17/36; 47.2% 95% CI: 30.9-63.5). The highest carriage of pneumococci was in the <5 and 5 to 17 year olds, with 57.1% (4/7) and 49.2% (30/61), respectively. Sixteen pneumococcal serotypes were identified, the most common being the nonvaccine-type 23A (14.6%) and the vaccine-type 6B (9.8%). The prevalence of pneumococcal serotypes covered by pneumococcal conjugate vaccines support introduction into a Malaysian national immunisation schedule. In addition, the dominance of Corynebacterium in the airway microbiomes is intriguing given their role as a potentially protective commensal with respect to acute infection and respiratory health.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics
  19. The systematic status of Gonocephalus robinsonii Boulenger, 1908 (Squamata: Agamidae: Draconinae)
    Denzer W, Manthey U, Mahlow K, Böhme W
    Zootaxa, 2015;4039(1):129-44.
    PMID: 26624470 DOI: 10.11646/zootaxa.4039.1.5
    The generic assignment of the draconine lizard Gonocephalus robinsonii from the highlands of West-Malaysia has been uncertain since the original description. Here we present a study based on morphology, previously published karyotype data and molecular phylogenetics using 16S rRNA sequences to evaluate the systematic status of G. robinsonii. As a result we describe Malayodracon gen. nov. to accommodate the species.
    Matched MeSH terms: RNA, Ribosomal, 16S
  20. The mitochondrial 16 s rRNA reveals high anthropogenic influence on land snail diversity in a preliminary island survey
    Abu-Bakar SB, Razali NM, Naggs F, Wade C, Mohd-Nor SA, Aileen-Tan SH
    Mol Biol Rep, 2014 Mar;41(3):1799-805.
    PMID: 24443224 DOI: 10.1007/s11033-014-3029-5
    A total of 30 specimens belonging to five species, namely; Cryptozona siamensis, Sarika resplendens and Sarika sp. from the family Ariophantidae as well as Quantula striata and Quantula sp. from the family Dyakiidae were collected from the Langkawi Island in Northern Peninsular Malaysia. All specimens were identified through comparisons of shell morphology and amplification of a 500 bp segment of the 16S rRNA mtDNA gene. To assess phylogenetic insights, the sequences were aligned using ClustalW and phylogenetic trees were constructed. The analyses showed two major lineages in both Maximum Parsimony and Neighbour Joining phylogenetic trees. Each putative taxonomic group formed a monophyletic cluster. Our study revealed low species and intraspecies genetic diversities based on the 16S rRNA gene sequences. Thus, this study has provided an insight of land snail diversity in populations of an island highly influenced by anthropogenic activities through complementary use of shell morphological and molecular data.
    Matched MeSH terms: RNA, Ribosomal, 16S/genetics*
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