Displaying publications 21 - 40 of 915 in total

  1. Carrión O, Gibson L, Elias DMO, McNamara NP, van Alen TA, Op den Camp HJM, et al.
    Microbiome, 2020 06 03;8(1):81.
    PMID: 32493439 DOI: 10.1186/s40168-020-00860-7
    BACKGROUND: Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees.

    RESULTS: DNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome-assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere.

    CONCLUSION: This study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas. Video abstract.

    Matched MeSH terms: Bacteria/classification; Bacteria/metabolism
  2. Rahman RNZRA, Latip W, Adlan NA, Sabri S, Ali MSM
    Arch Microbiol, 2022 Nov 12;204(12):701.
    PMID: 36370212 DOI: 10.1007/s00203-022-03316-8
    Waxy crude oil is a problem to the oil and gas industry because wax deposition in pipelines reduces the quality of the crude oil. Currently, the industry uses chemicals to solve the problem but it is not environmentally friendly. As an alternative, the biodegradation approach is one of the options. Previously eleven thermophilic bacteria were isolated and exhibited high ability to degrade hydrocarbon up to 70% of waxy crude oil. However, despite the successful study on these single bacteria strains, it is believed that biodegradation of paraffin wax requires more than a single species. Five consortia were developed based on the biodegradation efficiency of 11 bacterial strains. Consortium 3 showed the highest biodegradation (77.77%) with more long-chain alkane degraded throughout the incubation compared to other consortia. Enhancement of hydrocarbon degradation was observed for all consortia especially in long chain alkane (C18-C40). Consortium 3 exhibited higher alkane monooxygenase, alcohol dehydrogenase, lipase, and esterase activities. Moreover, the dominant bacteria in the consortia were determined by denaturing gradient gel electrophoresis (DGGE), which showed the domination of genera Geobacillus, Parageobacillus, and Anoxybacillus. It can be concluded that the bacterial consortia showed higher biodegradation and improved degrading more long-chain hydrocarbon compared to a single isolate.
    Matched MeSH terms: Bacteria/genetics; Bacteria/metabolism
  3. Izzati Mohamad N, Tan WS, Chang CY, Keng Tee K, Yin WF, Chan KG
    Genome Announc, 2015;3(1).
    PMID: 25700398 DOI: 10.1128/genomeA.00022-15
    Pantoea stewartii strain M073a is a Gram-negative bacterium isolated from a tropical waterfall. This strain exhibits quorum-sensing activity. Here, the assembly and annotation of its genome are presented.
    Matched MeSH terms: Gram-Negative Bacteria
  4. Chan KG, Yin WF, Lim YL
    Genome Announc, 2014;2(2).
    PMID: 24699957 DOI: 10.1128/genomeA.00246-14
    Here, we report the complete genome sequence of Pseudomonas aeruginosa strain YL84, which was isolated from compost. This strain was found to be a chitinase-producing quorum-sensing bacterium.
    Matched MeSH terms: Bacteria
  5. Gan HY, Gan HM, Savka MA, Triassi AJ, Wheatley MS, Smart LB, et al.
    Genome Announc, 2014;2(3).
    PMID: 24812212 DOI: 10.1128/genomeA.00288-14
    Shrub willow, Salix spp. and hybrids, is an important bioenergy crop. Here we report the whole-genome sequences and annotation of 13 endophytic bacteria from stem tissues of Salix purpurea grown in nature and from commercial cultivars and Salix viminalis × Salix miyabeana grown in bioenergy fields in Geneva, New York.
    Matched MeSH terms: Bacteria
  6. Chan XY, Hong KW, Yin WF, Chan KG
    Sci Rep, 2016 Jan 28;6:20016.
    PMID: 26817720 DOI: 10.1038/srep20016
    Tropical carnivorous plant, Nepenthes, locally known as "monkey cup", utilises its pitcher as a passive trap to capture insects. It then secretes enzymes into the pitcher fluid to digest the insects for nutrients acquisition. However, little is known about the microbiota and their activity in its pitcher fluid. Eighteen bacteria phyla were detected from the metagenome study in the Nepenthes pitcher fluid. Proteobacteria, Bacteroidetes and Actinobacteria are the dominant phyla in the Nepenthes pitcher fluid. We also performed culturomics approach by isolating 18 bacteria from the Nepenthes pitcher fluid. Most of the bacterial isolates possess chitinolytic, proteolytic, amylolytic, and cellulolytic and xylanolytic activities. Fifteen putative chitinase genes were identified from the whole genome analysis on the genomes of the 18 bacteria isolated from Nepenthes pitcher fluid and expressed for chitinase assay. Of these, six clones possessed chitinase activity. In conclusion, our metagenome result shows that the Nepenthes pitcher fluid contains vast bacterial diversity and the culturomic studies confirmed the presence of biocatalytic bacteria within the Nepenthes pitcher juice which may act in symbiosis for the turn over of insects trapped in the Nepenthes pitcher fluid.
    Matched MeSH terms: Bacteria/classification; Bacteria/genetics; Bacteria/metabolism; Genome, Bacterial
  7. Yong D, Ee R, Lim YL, Chang CY, Yin WF, Chan KG
    Genome Announc, 2015;3(3).
    PMID: 25953192 DOI: 10.1128/genomeA.00409-15
    Lysinibacillus fusiformis strain RB21 is a quorum-quenching bacterium that is able to degrade quorum-sensing signaling molecules. Here, we present the first complete genome sequence of L. fusiformis strain RB21. The finished genome is 4.8 Mbp in size, and the quorum-quenching gene was identified.
    Matched MeSH terms: Bacteria
  8. Mohd Nadzir M, Nurhayati RW, Idris FN, Nguyen MH
    Polymers (Basel), 2021 Feb 10;13(4).
    PMID: 33578978 DOI: 10.3390/polym13040530
    Bacterial exopolysaccharides (EPSs) are an essential group of compounds secreted by bacteria. These versatile EPSs are utilized individually or in combination with different materials for a broad range of biomedical field functions. The various applications can be explained by the vast number of derivatives with useful properties that can be controlled. This review offers insight on the current research trend of nine commonly used EPSs, their biosynthesis pathways, their characteristics, and the biomedical applications of these relevant bioproducts.
    Matched MeSH terms: Bacteria
  9. Kim M, Singh D, Lai-Hoe A, Go R, Abdul Rahim R, Ainuddin AN, et al.
    Microb Ecol, 2012 Apr;63(3):674-81.
    PMID: 21990015 DOI: 10.1007/s00248-011-9953-1
    Recent work has suggested that in temperate and subtropical trees, leaf surface bacterial communities are distinctive to each individual tree species and dominated by Alpha- and Gammaproteobacteria. In order to understand how general this pattern is, we studied the phyllosphere bacterial community on leaves of six species of tropical trees at a rainforest arboretum in Malaysia. This represents the first detailed study of 'true' tropical lowland tree phyllosphere communities. Leaf surface DNA was extracted and pyrosequenced targeting the V1-V3 region of 16S rRNA gene. As was previously found in temperate and subtropical trees, each tree species had a distinctive bacterial community on its leaves, clustering separately from other tree species in an ordination analysis. Bacterial communities in the phyllosphere were unique to plant leaves in that very few operational taxonomic units (0.5%) co-occurred in the surrounding soil environment. A novel and distinctive aspect of tropical phyllosphere communities is that Acidobacteria were one of the most abundant phyla across all samples (on average, 17%), a pattern not previously recognized. Sequences belonging to Acidobacteria were classified into subgroups 1-6 among known 24 subdivisions, and subgroup 1 (84%) was the most abundant group, followed by subgroup 3 (15%). The high abundance of Acidobacteria on leaves of tropical trees indicates that there is a strong relationship between host plants and Acidobacteria in tropical rain forest, which needs to be investigated further. The similarity of phyllosphere bacterial communities amongst the tree species sampled shows a significant tendency to follow host plant phylogeny, with more similar communities on more closely related hosts.
    Matched MeSH terms: Bacteria/classification; Bacteria/genetics; Bacteria/isolation & purification*
  10. Tin HS, Palaniveloo K, Anilik J, Vickneswaran M, Tashiro Y, Vairappan CS, et al.
    Microb Ecol, 2018 Feb;75(2):459-467.
    PMID: 28779295 DOI: 10.1007/s00248-017-1043-6
    Decline in forest productivity due to forest conversion is defining the Bornean landscape. Responses of bacterial communities due to land-use changes are vital and could define our understanding of ecosystem functions. This study reports the changes in bacterial community structure in organic soil (0-5 cm; O-Horizon) and organic-mineral soil (5-15 cm; A-Horizon) across Maliau Basin Conservation Area old growth forest (MBOG), Fragment E logged forest (FELF) located in Kalabakan Forest Reserve to Benta Wawasan oil palm plantation (BWOP) using two-step PCR amplicon analysis of bacteria DNA on Illumina Miseq next generation sequencing. A total of 30 soil samples yielded 893,752-OTU reads at ≥97% similarity from 5,446,512 good quality sequences. Soil from BWOP plantation showed highest unshared OTUs for organic (49.2%) and organic-mineral (50.9%) soil. MBOG soil showed a drop in unshared OTUs between organic (48.6%) and organic-mineral (33.9%). At phylum level, Proteobacteria dominated MBOG but shifted to Actinobacteria in logged and plantation soil. Present findings also indicated that only FELF exhibited change in bacterial communities along the soil depth, moving from the organic to the organic-mineral layer. Both layers of BWOP plantation soils deviated from other forests' soil in β-diversity analysis. To our knowledge, this is the first report on transitions of bacterial community structures with different soil horizons in the tropical rainforest including Borneo, Sabah. Borneo tropical soils form a large reservoir for soil bacteria and future exploration is needed for fully understanding the diversity structure and their bacterial functional properties.
    Matched MeSH terms: Bacteria/classification; Bacteria/genetics; Bacteria/isolation & purification*
  11. Liew KJ, Teo SC, Shamsir MS, Goh KM
    Microbiol Resour Announc, 2019 Nov 14;8(46).
    PMID: 31727717 DOI: 10.1128/MRA.01238-19
    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.
    Matched MeSH terms: Bacteria
  12. Lim YL, Ee R, Yong D, Tee KK, Yin WF, Chan KG
    J Biotechnol, 2015 Nov 20;214:83-4.
    PMID: 26393955 DOI: 10.1016/j.jbiotec.2015.09.018
    Pandoraea pnomenusa RB-38 is a bacterium isolated from a former sanitary landfill site. Here, we present the complete genome of P. pnomenusa RB38 in which an oxalate utilization pathway was identified. The genome analysis suggested the potential of this strain as an effective biocontrol agent against oxalate-producing phytopathogens.
    Matched MeSH terms: Bacteria
  13. Chukwuma OB, Rafatullah M, Tajarudin HA, Ismail N
    PMID: 34204975 DOI: 10.3390/ijerph18116001
    Discovering novel bacterial strains might be the link to unlocking the value in lignocellulosic bio-refinery as we strive to find alternative and cleaner sources of energy. Bacteria display promise in lignocellulolytic breakdown because of their innate ability to adapt and grow under both optimum and extreme conditions. This versatility of bacterial strains is being harnessed, with qualities like adapting to various temperature, aero tolerance, and nutrient availability driving the use of bacteria in bio-refinery studies. Their flexible nature holds exciting promise in biotechnology, but despite recent pointers to a greener edge in the pretreatment of lignocellulose biomass and lignocellulose-driven bioconversion to value-added products, the cost of adoption and subsequent scaling up industrially still pose challenges to their adoption. However, recent studies have seen the use of co-culture, co-digestion, and bioengineering to overcome identified setbacks to using bacterial strains to breakdown lignocellulose into its major polymers and then to useful products ranging from ethanol, enzymes, biodiesel, bioflocculants, and many others. In this review, research on bacteria involved in lignocellulose breakdown is reviewed and summarized to provide background for further research. Future perspectives are explored as bacteria have a role to play in the adoption of greener energy alternatives using lignocellulosic biomass.
    Matched MeSH terms: Bacteria
  14. Sam KK, Lau NS, Furusawa G, Amirul AA
    Genome Announc, 2017 Oct 19;5(42).
    PMID: 29051257 DOI: 10.1128/genomeA.01147-17
    Hahella sp. strain CCB-MM4 is a halophilic bacterium isolated from estuarine mangrove sediment. The genome sequence of Hahella sp. CCB-MM4 provides insights into exopolysaccharide biosynthesis and the lifestyle of the bacterium thriving in a saline mangrove environment.
    Matched MeSH terms: Bacteria; Gammaproteobacteria
  15. Firdose A, Chong NHH, Ramli R, Aqma WS
    Lett Appl Microbiol, 2023 Feb 16;76(2).
    PMID: 36702549 DOI: 10.1093/lambio/ovad013
    The aim of this study was to test the antimicrobial, antiadhesive, and antibiofilm activities of a rhamnolipid extracted from Pseudomonas aeruginosa UKMP14T previously isolated from oil-contaminated soil in Malaysia against ESKAPE (i.e. multidrug resistant) pathogens. Zones of inhibition in an agar well diffusion assay were observed at 50 µg mL-1 concentrations of rhamnolipid for all the ESKAPE bacteria. The MIC and MBC values ranged between 7.81-62.5 µg mL-1 and 31.25-1000 µg mL-1, respectively. Percent killing was recorded to be >90% except for Klebsiella pneumoniae (86.84%). Furthermore, antiadhesion studies showed that there was 76% hindrance in attachment of Enterococcus faecium and 91% in Acinetobacter baumannii at 4 × MIC. The highest inhibition in adhesion was found at 4 × MIC, which was 46% for Ac. baumannii and 62% for Enterococcus faecium. Finally, the antibiofilm capability of the rhamnolipid was determined, which ranged between 25%-76% in Ac. baumannii and 35%-88% in Enterococcus faecium. To the best of our knowledge, this is the first study to include research on antimicrobial, antiadhesive and antibiofilm activities of rhamnolipid from the local isolate Ps. aeruginosa UKMP14T against ESKAPE bacteria. Obtained results suggest that this rhamnolipid can be exploited commercially for the production of novel antibiotics.
    Matched MeSH terms: Bacteria
  16. Farouk AE, Benafri A
    Saudi Med J, 2007 Sep;28(9):1422-4.
    PMID: 17768473
    Objective: To evaluate methanolic, ethanolic, acetone and aqueous extracts from different parts of Eurycoma longifolia (E. longifolia) (leave, stem, and root) for antibacterial activity against Gram-positive and Gram-negative bacteria and to utilize the leaves and stem parts rather than the root, which is already used for male sexual enhancement in Malaysia.

    Methods: The study took place in the Laboratory of Molecular Biology of Biotechnology Engineering Department, Malaysia between January 2005 and June 2006. Methanolic, ethanolic, acetone and aqueous extracts of leaves, stems and roots of E. longifolia were investigated for their antibacterial properties using Agar-well diffusion method.

    Results: The alcoholic and acetone extracts of the leaves and stem extracts were active on both Gram-positive and Gram-negative bacteria except against 2 strains of Gram-negative bacteria (Escherichia coli and Salmonella typhi). The root extracts had no antibacterial activity against Gram-positive and Gram-negative bacteria tested. Aqueous leaves extract showed antibacterial activity against Staphylococcus aureus and Serratia marscesens.

    Conclusion: The alcoholic and acetone extracts from leaves and stems of E. longifolia contain potent antibacterial agent(s). This plant can serve as a potential source of antibacterial compounds.
    Matched MeSH terms: Gram-Negative Bacteria/drug effects*; Gram-Negative Bacteria/growth & development; Gram-Positive Bacteria/drug effects*; Gram-Positive Bacteria/growth & development
  17. Zarkasi KZ, Taylor RS, Abell GC, Tamplin ML, Glencross BD, Bowman JP
    Microb Ecol, 2016 Apr;71(3):589-603.
    PMID: 26780099 DOI: 10.1007/s00248-015-0728-y
    To better understand salmon GI tract microbial community dynamics in relation to diet, a feeding trial was performed utilising diets with different proportions of fish meal, protein, lipid and energy levels. Salmon gut dysfunction has been associated with the occurrence of casts, or an empty hind gut. A categorical scoring system describing expressed digesta consistency was evaluated in relation to GI tract community structure. Faster growing fish generally had lower faecal scores while the diet cohorts showed minor differences in faecal score though the overall lowest scores were observed with a low protein, low energy diet. The GI tract bacterial communities were highly dynamic over time with the low protein, low energy diet associated with the most divergent community structure. This included transiently increased abundance of anaerobic (Bacteroidia and Clostridia) during January and February, and facultatively anaerobic (lactic acid bacteria) taxa from February onwards. The digesta had enriched populations of these groups in relation to faecal cast samples. The majority of samples (60-86 %) across all diet cohorts were eventually dominated by the genus Aliivibrio. The results suggest that an interaction between time of sampling and diet is most strongly related to community structure. Digesta categorization revealed microbes involved with metabolism of diet components change progressively over time and could be a useful system to assess feeding responses.
    Matched MeSH terms: Bacteria/classification; Bacteria/genetics; Bacteria/isolation & purification; Bacteria/metabolism*
  18. Chung WY, Zhu Y, Mahamad Maifiah MH, Shivashekaregowda NKH, Wong EH, Abdul Rahim N
    J Antibiot (Tokyo), 2021 02;74(2):95-104.
    PMID: 32901119 DOI: 10.1038/s41429-020-00366-2
    Antimicrobial resistance (AMR) threatens the effective prevention and treatment of a wide range of infections. Governments around the world are beginning to devote effort for innovative treatment development to treat these resistant bacteria. Systems biology methods have been applied extensively to provide valuable insights into metabolic processes at system level. Genome-scale metabolic models serve as platforms for constraint-based computational techniques which aid in novel drug discovery. Tools for automated reconstruction of metabolic models have been developed to support system level metabolic analysis. We discuss features of such software platforms for potential users to best fit their purpose of research. In this work, we focus to review the development of genome-scale metabolic models of Gram-negative pathogens and also metabolic network approach for identification of antimicrobial drugs targets.
    Matched MeSH terms: Anti-Bacterial Agents/pharmacology*; Bacteria/drug effects; Gram-Negative Bacteria/drug effects*; Gram-Negative Bacteria/genetics*; Gram-Negative Bacterial Infections/microbiology*
  19. Lee HY, Loong SK, Ya'cob Z, Low VL, Teoh BT, Ahmad-Nasrah SN, et al.
    Acta Trop, 2021 Jul;219:105923.
    PMID: 33878305 DOI: 10.1016/j.actatropica.2021.105923
    Although the microbiome of blood-feeding insects serves an integral role in host physiology, both beneficial and pathogenic, little is known of the microbial community of black flies. An investigation, therefore, was undertaken to identify culturable bacteria from one of Malaysia's most common black flies, Simulium tani Takaoka and Davies, using 16S rDNA sequencing, and then evaluate the isolates for antibiotic resistance and virulence genes. A total of 20 isolates representing 11 bacterial species in four genera were found. Five isolates showed β-hemolysis on Columbia agar, and virulence genes were found in three of these isolates. Some degree of resistance to six of the 12 tested antibiotics was found among the isolates. The baseline data from this study suggest rich opportunities for comparative studies exploring the diversity and roles of the microbiome of S. tani and other Southeast Asian black flies.
    Matched MeSH terms: Bacteria/drug effects; Bacteria/genetics; Bacteria/growth & development*; Bacteria/isolation & purification*; Drug Resistance, Bacterial
  20. Kardi SN, Ibrahim N, Rashid NA, Darzi GN
    Environ Sci Pollut Res Int, 2016 Feb;23(4):3358-64.
    PMID: 26490910 DOI: 10.1007/s11356-015-5538-8
    Microbial fuel cells (MFCs) represent one of the most attractive and eco-friendly technologies that convert chemical bond energy derived from organic matter into electrical power by microbial catabolic activity. This paper presents the use of a H-type MFC involving a novel NAR-2 bacterial consortium consisting of Citrobacter sp. A1, Enterobacter sp. L17 and Enterococcus sp. C1 to produce electricity whilst simultaneously decolourising acid red 27 (AR27) as a model dye, which is also known as amaranth. In this setup, the dye AR27 is mixed with modified P5 medium (2.5 g/L glucose and 5.0 g/L nutrient broth) in the anode compartment, whilst phosphate buffer solution (PBS) pH 7 serves as a catholyte in the cathode compartment. After several electrochemical analyses, the open circuit voltage (OCV) for 0.3 g/L AR27 with 24-h retention time at 30 °C was recorded as 0.950 V, whereas (93%) decolourisation was achieved in 220-min operation. The maximum power density was reached after 48 h of operation with an external load of 300 Ω. Scanning electron microscopy (SEM) analysis revealed the surface morphology of the anode and the bacterial adhesion onto the electrode surface. The results of this study indicate that the decolourisation of AR27 dye and electrical power generation was successfully achieved in a MFC operated by a bacterial consortium. The consortium of bacteria was able to utilise AR27 in a short retention time as an electron acceptor and to shuttle the electrons to the anode surface for bioelectricity generation.
    Matched MeSH terms: Bacteria/genetics; Bacteria/isolation & purification; Bacteria/metabolism*; Bacteria/chemistry; Bacterial Adhesion
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