Displaying publications 101 - 120 of 158 in total

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  1. Ceftazidime/metronidazole versus netilmicin/metronidazole in the treatment of perforated appendicitis in children
    Kooi GH, Pit S
    Clin Ther, 1990 Jan-Feb;12(1):54-60.
    PMID: 2183940
    One hundred children with peritonitis resulting from a perforated appendix were treated with ceftazidime or netilmicin. Metronidazole was added to both groups to treat the anaerobic organisms commonly associated with the infecting aerobic organisms in peritonitis. Escherichia coli was the most common aerobe found in peritoneal pus. Wound infection occurred in nine patients of the netilmicin group and in none treated with ceftazidime (P less than 0.01). No bacterial resistance was evident in the ceftazidime group, but gram-positive streptococci found in eight patients were resistant to netilmicin. Thus it is recommended that an antibiotic of the penicillin group be added if netilmicin is used to treat peritonitis. The results indicate that ceftazidime was more effective than netilmicin in the treatment of children with peritonitis resulting from a perforated appendix.
    Matched MeSH terms: Bacteria/isolation & purification
  2. Fulltext Microbial diversity of thermophiles with biomass deconstruction potential in a foliage-rich hot spring
    Lee LS, Goh KM, Chan CS, Annie Tan GY, Yin WF, Chong CS, et al.
    Microbiologyopen, 2018 12;7(6):e00615.
    PMID: 29602271 DOI: 10.1002/mbo3.615
    The ability of thermophilic microorganisms and their enzymes to decompose biomass have attracted attention due to their quick reaction time, thermostability, and decreased risk of contamination. Exploitation of efficient thermostable glycoside hydrolases (GHs) could accelerate the industrialization of biofuels and biochemicals. However, the full spectrum of thermophiles and their enzymes that are important for biomass degradation at high temperatures have not yet been thoroughly studied. We examined a Malaysian Y-shaped Sungai Klah hot spring located within a wooded area. The fallen foliage that formed a thick layer of biomass bed under the heated water of the Y-shaped Sungai Klah hot spring was an ideal environment for the discovery and analysis of microbial biomass decay communities. We sequenced the hypervariable regions of bacterial and archaeal 16S rRNA genes using total community DNA extracted from the hot spring. Data suggested that 25 phyla, 58 classes, 110 orders, 171 families, and 328 genera inhabited this hot spring. Among the detected genera, members of Acidimicrobium, Aeropyrum, Caldilinea, Caldisphaera, Chloracidobacterium, Chloroflexus, Desulfurobacterium, Fervidobacterium, Geobacillus, Meiothermus, Melioribacter, Methanothermococcus, Methanotorris, Roseiflexus, Thermoanaerobacter, Thermoanaerobacterium, Thermoanaerobaculum, and Thermosipho were the main thermophiles containing various GHs that play an important role in cellulose and hemicellulose breakdown. Collectively, the results suggest that the microbial community in this hot spring represents a good source for isolating efficient biomass degrading thermophiles and thermozymes.
    Matched MeSH terms: Bacteria/isolation & purification*
  3. Fulltext Host-specific microbial communities in three sympatric North Sea sponges
    Naim MA, Morillo JA, Sørensen SJ, Waleed AA, Smidt H, Sipkema D
    FEMS Microbiol Ecol, 2014 Nov;90(2):390-403.
    PMID: 25088929 DOI: 10.1111/1574-6941.12400
    The establishment of next-generation technology sequencing has deepened our knowledge of marine sponge-associated microbiota with the identification of at least 32 phyla of Bacteria and Archaea from a large number of sponge species. In this study, we assessed the diversity of the microbial communities hosted by three sympatric sponges living in a semi-enclosed North Sea environment using pyrosequencing of bacterial and archaeal 16S ribosomal RNA gene fragments. The three sponges harbor species-specific communities each dominated by a different class of Proteobacteria. An α-proteobacterial Rhodobacter-like phylotype was confirmed as the predominant symbiont of Halichondria panicea. The microbial communities of Haliclona xena and H. oculata are described for the first time in this study and are dominated by Gammaproteobacteria and Betaproteobacteria, respectively. Several common phylotypes belonging to Chlamydiae, TM6, Actinobacteria, and Betaproteobacteria were detected in all sponge samples. A number of phylotypes of the phylum Chlamydiae were present at an unprecedentedly high relative abundance of up to 14.4 ± 1.4% of the total reads, which suggests an important ecological role in North Sea sponges. These Chlamydiae-affiliated operational taxonomic units may represent novel lineages at least at the genus level as they are only 86-92% similar to known sequences.
    Matched MeSH terms: Bacteria/isolation & purification*
  4. Fulltext The effects of daily fasting hours on shaping gut microbiota in mice
    Li L, Su Y, Li F, Wang Y, Ma Z, Li Z, et al.
    BMC Microbiol, 2020 03 24;20(1):65.
    PMID: 32209070 DOI: 10.1186/s12866-020-01754-2
    BACKGROUND: It has recently been reported that intermittent fasting shapes the gut microbiota to benefit health, but this effect may be influenced to the exact fasting protocols. The purpose of this study was to assess the effects of different daily fasting hours on shaping the gut microbiota in mice. Healthy C57BL/6 J male mice were subjected to 12, 16 or 20 h fasting per day for 1 month, and then fed ad libitum for an extended month. Gut microbiota was analyzed by 16S rRNA gene-based sequencing and food intake was recorded as well.

    RESULTS: We found that cumulative food intake was not changed in the group with 12 h daily fasting, but significantly decreased in the 16 and 20 h fasting groups. The composition of gut microbiota was altered by all these types of intermittent fasting. At genus level, 16 h fasting led to increased level of Akkermansia and decreased level of Alistipes, but these effects disappeared after the cessation of fasting. No taxonomic differences were identified in the other two groups.

    CONCLUSIONS: These data indicated that intermittent fasting shapes gut microbiota in healthy mice, and the length of daily fasting interval may influence the outcome of intermittent fasting.

    Matched MeSH terms: Bacteria/isolation & purification
  5. Diversity and Coding Potential of the Microbiota in the Photic and Aphotic Zones of Tropical Man-Made Lake with Intensive Aquaculture Activities: a Case Study on Temengor Lake, Malaysia
    Lau NS, Zarkasi KZ, Md Sah ASR, Shu-Chien AC
    Microb Ecol, 2019 Jul;78(1):20-32.
    PMID: 30397794 DOI: 10.1007/s00248-018-1283-0
    Although freshwater biomes cover less than 1% of the Earth's surface, they have disproportionate ecological significances. Attempts to study the taxonomy and function of freshwater microbiota are currently limited to samples collected from temperate lakes. In this study, we investigated samples from the photic and aphotic of an aquaculture site (disturbed) of Temengor Lake, a tropical lake in comparison with the undisturbed site of the lake using 16S rRNA amplicon and shotgun metagenomic approaches. Vertical changes in bacterial community composition and function of the Temengor Lake metagenomes were observed. The photic water layer of Temengor Lake was dominated by typical freshwater assemblages consisting of Proteobacteria, Actinobacteria, Bacteroidetes, Verrucomicrobia, and Cyanobacteria lineages. On the other hand, the aphotic water featured in addition to Proteobacteria, Bacteroidetes, Verrucomicrobia, and two more abundant bacterial phyla that are typically ubiquitous in anoxic habitats (Chloroflexi and Firmicutes). The aphotic zone of Temengor Lake exhibited genetic potential for nitrogen and sulfur metabolisms for which terminal electron acceptors other than oxygen are used in the reactions. The aphotic water of the disturbed site also showed an overrepresentation of genes associated with the metabolism of carbohydrates, likely driven by the enrichment of nutrient resulting from aquaculture activities at the site. The results presented in this study can serve as a basis for understanding the structure and functional capacity of the microbial communities in the photic and aphotic zones/water layers of tropical man-made lakes.
    Matched MeSH terms: Bacteria/isolation & purification*
  6. Distinct bacterial communities dominate tropical and temperate zone leaf litter
    Kim M, Kim WS, Tripathi BM, Adams J
    Microb Ecol, 2014 May;67(4):837-48.
    PMID: 24549745 DOI: 10.1007/s00248-014-0380-y
    Little is known of the bacterial community of tropical rainforest leaf litter and how it might differ from temperate forest leaf litter and from the soils underneath. We sampled leaf litter in a similarly advanced stage of decay, and for comparison, we also sampled the surface layer of soil, at three tropical forest sites in Malaysia and four temperate forest sites in South Korea. Illumina sequencing targeting partial bacterial 16S ribosomal ribonucleic acid (rRNA) gene revealed that the bacterial community composition of both temperate and tropical litter is quite distinct from the soils underneath. Litter in both temperate and tropical forest was dominated by Proteobacteria and Actinobacteria, while soil is dominated by Acidobacteria and, to a lesser extent, Proteobacteria. However, bacterial communities of temperate and tropical litter clustered separately from one another on an ordination. The soil bacterial community structures were also distinctive to each climatic zone, suggesting that there must be a climate-specific biogeographical pattern in bacterial community composition. The differences were also found in the level of diversity. The temperate litter has a higher operational taxonomic unit (OTU) diversity than the tropical litter, paralleling the trend in soil diversity. Overall, it is striking that the difference in community composition between the leaf litter and the soil a few centimeters underneath is about the same as that between leaf litter in tropical and temperate climates, thousands of kilometers apart. However, one substantial difference was that the leaf litter of two tropical forest sites, Meranti and Forest Research Institute Malaysia (FRIM), was overwhelmingly dominated by the single genus Burkholderia, at 37 and 23 % of reads, respectively. The 454 sequencing result showed that most Burkholderia species in tropical leaf litter belong to nonpathogenic "plant beneficial" lineages. The differences from the temperate zone in the bacterial community of tropical forest litter may be partly a product of its differing chemistry, although the unvarying climate might also play a role, as might interactions with other organisms such as fungi. The single genus Burkholderia may be seen as potentially playing a major role in decomposition and nutrient cycling in tropical forests, but apparently not in temperate forests.
    Matched MeSH terms: Bacteria/isolation & purification*
  7. Rainforest Conversion to Rubber Plantation May Not Result in Lower Soil Diversity of Bacteria, Fungi, and Nematodes
    Kerfahi D, Tripathi BM, Dong K, Go R, Adams JM
    Microb Ecol, 2016 08;72(2):359-71.
    PMID: 27221090 DOI: 10.1007/s00248-016-0790-0
    Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function.
    Matched MeSH terms: Bacteria/isolation & purification
  8. Microbial dynamics, metabolomic profiles, and the correlation between them during fermentation of serofluid dish
    Wei J, Ren W, Wang L, Liu M, Tian X, Ding G, et al.
    J Sci Food Agric, 2020 Dec;100(15):5627-5636.
    PMID: 32712996 DOI: 10.1002/jsfa.10690
    BACKGROUND: Serofluid dish, a traditional Chinese fermented food, possesses unique flavors and health beneficial effects. These properties are likely due to the sophisticated metabolic networks during fermentation, which are mainly driven by microbiota. However, the exact roles of metabolic pathways and the microbial community during this process remain equivocal.

    RESULTS: Here, we investigated the microbial dynamics by next-generation sequencing, and outlined a differential non-targeted metabolite profiling in the process of serofluid dish fermentation using the method of hydrophilic interaction liquid chromatography column with ultra-high-performance liquid chromatography-quadruple time-of-flight mass spectrometry. Lactobacillus was the leading genus of bacteria, while Pichia and Issatchenkia were the dominant fungi. They all accumulated during fermentation. In total, 218 differential metabolites were identified, of which organic acids, amino acids, sugar and sugar alcohols, fatty acids, and esters comprised the majority. The constructed metabolic network showed that tricarboxylic acid cycle, urea cycle, sugar metabolism, amino acids metabolism, choline metabolism, and flavonoid metabolism were regulated by the fermentation. Furthermore, correlation analysis revealed that the leading fungi, Pichia and Issatchenkia, were linked to organic acids, amino acid and sugar metabolism, flavonoids, and several other flavor and functional components. Antibacterial tests indicated the antibacterial effect of serofluid soup against Salmonella and Staphylococcus.

    CONCLUSION: This work provides new insights into the complex microbial and metabolic networks during serofluid dish fermentation, and a theoretical basis for the optimization of its industrial production. © 2020 Society of Chemical Industry.

    Matched MeSH terms: Bacteria/isolation & purification*
  9. Epidemiology and trends in the antibiotic susceptibilities of Gram-negative bacilli isolated from patients with intra-abdominal infections in the Asia-Pacific region, 2010-2013
    Chang YT, Coombs G, Ling T, Balaji V, Rodrigues C, Mikamo H, et al.
    Int J Antimicrob Agents, 2017 Jun;49(6):734-739.
    PMID: 28435019 DOI: 10.1016/j.ijantimicag.2017.01.030
    This study was conducted to investigate the epidemiology and antimicrobial susceptibility patterns of Gram-negative bacilli (GNB) isolated from intra-abdominal infections (IAIs) in the Asia-Pacific region (APR) from 2010-2013. A total of 17 350 isolates were collected from 54 centres in 13 countries in the APR. The three most commonly isolated GNB were Escherichia coli (46.1%), Klebsiella pneumoniae (19.3%) and Pseudomonas aeruginosa (9.8%). Overall, the rates of extended-spectrum β-lactamase (ESBL)-producing E. coli and K. pneumoniae were 38.2% and 24.3%, respectively, and they were highest in China (66.6% and 38.7%, respectively), Thailand (49.8% and 36.5%, respectively) and Vietnam (47.9% and 30.4%, respectively). During 2010-2013, the rates of ESBL-producing E. coli and K. pneumoniae isolates causing community-associated (CA) IAIs (collected <48 h after admission) were 26.0% and 13.5%, respectively, and those causing hospital-associated (HA) IAIs were 48.0% and 30.6%, respectively. Amikacin, ertapenem and imipenem were the most effective agents against ESBL-producing isolates. Piperacillin/tazobactam displayed good in vitro activity (91.4%) against CA ESBL-producing E. coli. For other commonly isolated Enterobacteriaceae, fluoroquinolones, cefepime and carbapenems exhibited better in vitro activities than third-generation cephalosporins. Amikacin possessed high in vitro activity against all GNB isolates (>80%) causing IAIs, except for Acinetobacter calcoaceticus-baumannii (ACB) complex (30.9% for HA-IAI isolates). All of the antimicrobial agents tested exhibited <45% in vitro activity against ACB complex. Antimicrobial resistance is a persistent threat in the APR and continuous monitoring of evolutionary trends in the susceptibility patterns of GNB causing IAIs in this region is mandatory.
    Matched MeSH terms: Gram-Negative Bacteria/isolation & purification
  10. Gut bacteria of Varanus salvator possess potential antitumour molecules
    Soopramanien M, Khan NA, Sagathevan K, Siddiqui R
    Int Microbiol, 2021 Jan;24(1):47-56.
    PMID: 32737845 DOI: 10.1007/s10123-020-00139-9
    Pollution, unhygienic conditions and organic waste are detrimental to human health. On the contrary, animals living in polluted environments, feeding on organic waste and exposed to noxious agents such as heavy metals must possess remarkable properties against contracting diseases. Species such as cockroaches and water monitor lizards thrive in unhygienic conditions and feed on decaying matter. Here, we investigated the antitumour properties of metabolites produced by gut bacteria isolated from Varanus salvator (Asian water monitor lizard). An adult water monitor lizard and a juvenile water monitor lizard were acquired, and dissected. Their aerobic gut bacteria were isolated and identificated through 16S rDNA sequencing. Next, bacterial conditioned media (CM) were prepared and utilised for subsequent assays. Growth inhibition, MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide cell viability assay, cytotoxicity and cell survival assays were accomplished against a panel of cancer cells as well as a normal cell line. Furthermore, liquid chromatography-mass spectrometry (LC-MS) was employed to identify potential antitumour molecules. A plethora of bacteria were isolated from the gut of juvenile and adult V. salvator respectively. Moreover, CM prepared from selected bacteria exhibited antitumour activity. Of note, LC-MS results indicated the presence of several molecules with reported antitumour activity, namely, 3-butylidene-7-hydroxyphthalide, C75, enigmol, estrone 16-oxime, proglumide and S-allyl-L-cysteine. Furthermore, 356 potentially novel molecules from juvenile V. salvator and 184 from adult V. salvator were depicted. Thus, the gut microbiota of V. salvator might be considered as a great niche of antitumour molecules; however, further in vitro and in vivo studies are needed to assess the antitumour properties of these molecules.
    Matched MeSH terms: Bacteria/isolation & purification
  11. Fulltext An eight-year review of blood culture and susceptibility among sepsis cases in an emergency department in Northeastern Malaysia
    Hashairi F, Hasan H, Azlan K, Deris ZZ
    Trop Biomed, 2011 Dec;28(3):599-605.
    PMID: 22433889 MyJurnal
    An understanding of common pathogens and their antibiotic sensitivity patterns is critical for proper management of sepsis in Emergency Department (ED). The goal of the study was to identify common organisms isolated from blood cultures of patients attended to ED and their antimicrobial susceptibility. Beginning from 2002, all cases of positive blood culture collected by the ED, Hospital Universiti Sains Malaysia (HUSM) were recorded and analysed. Over the period of eight years, we documented 995 cases of positive blood cultures. Of these samples, 549 (55.2%) were Gram-negative bacteria; 419 (42.1%) were Gram-positive bacteria; 10 (1.0%) were anaerobic organisms; 10 (1.0%) were fungus; and 7 (0.7%) cases were mixed organisms. Gram-negative bacteria were observed to develop more resistance to antimicrobial agents, especially those commonly used in an outpatient setting with less than 80% sensitivity to ampicillin, cotrimoxazole and ciprofloxacin. By contrast, there has been no marked change in the sensitivity trends of Gram-positive bacteria over the same period. In conclusion, ED physicians are more equipped to initiate empirical antimicrobial therapy especially when dealing with possibility of Gram-negative sepsis.
    Study site: Emergency department, Hospital Universiti Sains Malaysia (HUSM), Kelantan, Malaysia
    Matched MeSH terms: Bacteria/isolation & purification*
  12. Fulltext Prospective surveillance of nosocomial device-associated bacteremia in three adult intensive units in Malaysia
    Gopal Katherason S, Naing L, Jaalam K, Kamarul Iman Musa K, Nik Abdullah NM, Aiyar S, et al.
    Trop Biomed, 2010 Aug;27(2):308-16.
    PMID: 20962730 MyJurnal
    Nosocomial blood stream infection (or nosocomial bacteremia) is a common problem in hospitals worldwide, including Malaysia. A three-year prospective cohort study (October 2003-March 2007) of the incidences, risk factors, and patterns of the microorganisms causing bacteremia was conducted using a validated surveillance form in three intensive care units (ICUs) in Malaysia. Center for Disease Control criteria were used to diagnose bacteremia. Patients were monitored from admission until the end point of study, which was the first detection of bacteremia in the blood in each patient. The frequency of occurrence of bacteremia with clinical symptoms was 10.7% (n=23). Bacteremia was observed to occur within a mean length of stay of 10 days in ICU. The rate of device-related infection was 10.4% per device utilization days with a device utilization rate of 95.9%/1000 patient days. The total number of patient days was 2309 and the period of device utilization was 2211 days. The common bacteria detected were extended-spectrum beta-lactamases (ESBLs) Klebsiella pneumoniae (n=6); Pseudomonas aeruginosa (n=6); Acinetobacter species (n=5); Methicillin-resistant Staphylococcus aureus (MRSA)(n=3); and (non- ESBL) Klebsiella pneumoniae (n=2). Multivariable analysis using Cox Proportional Hazard Model showed that the predictors for developing bacteremia were cancer, MRSA carriage, duration of central venous catheter (CVC) infusion, frequency change of CVC, and the administration of hydrocortisone drugs. These results indicate that a combination of nursing and medical interventions as well as patients' severity of illness could lead to bacteremia in ICU. Strategic implementation of quality assurance measures in ICUs could help to control this problem.
    Matched MeSH terms: Bacteria/isolation & purification
  13. Antibiotic resistance and sensitivity pattern of Metallo-β-Lactamase Producing Gram-Negative Bacilli in ventilator-associated pneumonia in the intensive care unit of a public medical school hospital in Bangladesh
    Nusrat T, Akter N, Rahman NAA, Godman B, D Rozario DT, Haque M
    Hosp Pract (1995), 2020 Aug;48(3):128-136.
    PMID: 32271642 DOI: 10.1080/21548331.2020.1754687
    BACKGROUND: Ventilator-associated pneumonia (VAP) is the most common nosocomial infection in intensive care units (ICU), accounting for 25% of all ICU infections. Antimicrobial resistance is increasing and becoming a significant health problem worldwide, increasing hospital length of stay, mortality and costs. Identifying antibiotic resistance patterns in VAP is important as this can cause outbreaks in ICUs. To date, there have been limited studies assessing this in Bangladesh. Consequently, the primary objective of this research was to study the species of bacterial growth and to determine the antibiotic resistance patterns of Metallo-β-Lactamase (MBL) producing gram-negative bacilli among ICU patients with VAP in a public medical school hospital, Bangladesh. In addition, identify the factors associated with a positive culture to provide future guidance.

    METHOD: Cross-sectional study performed in the Chattogram Medical College Hospital, Bangladesh. Mueller Hinton agar plates were used for antibiotic sensitivity testing by the Kirby-Buer disc diffusion test.

    RESULTS: Among 105 clinically suspected VAP cases, qualitative cultures were positive in 95 (90%) of them. The most common bacteria identified were Acinetobacter spp. (43.2%), Klebsiella spp. (20%) and Pseudomonas spp. (18.9%). A positive culture was not associated with patients' age or gender. Among 41 isolated Acinetobacter spp., 38 (92.7%) were resistant to gentamicin followed by 36 (87.8%) to ceftriaxone. Among 24 isolated Klebsiella spp., 22 (83.3%) were resistant to ceftriaxone. Among 18 isolated Pseudomonas spp., 16 (88.8%) were resistant to ciprofloxacin, and 13 (72.2%) were resistant to ceftriaxone. Among nine isolated E.coli, all were resistant to ceftriaxone and ciprofloxacin. All four Proteus spp. (100%) isolated were resistant to ciprofloxacin. Additionally, phenotype MBL producing was 65.22% and genotype was 45.65% among imipenem resistant pathogens. Imipenem resistant pathogens were sensitive to amoxyclav, amikacin¸ azithromycin, ceftazidime, ceftriaxone, colistin and gentamycin.

    CONCLUSION: A positive culture was detected in 90% of VAP patients, but it was not associated with the patients' age and gender. The most common bacteria identified were Acinetobacter spp., Klebsiella spp. and Pseudomonas spp., where the majority of these were resistant to ceftriaxone. The results are being used to provide future guidance on the empiric management of VAP in this hospital.

    Matched MeSH terms: Gram-Negative Bacteria/isolation & purification*
  14. Fulltext AidP, a novel N-Acyl homoserine lactonase gene from Antarctic Planococcus sp
    See-Too WS, Ee R, Lim YL, Convey P, Pearce DA, Yin WF, et al.
    Sci Rep, 2017 02 22;7:42968.
    PMID: 28225085 DOI: 10.1038/srep42968
    Planococcus is a Gram-positive halotolerant bacterial genus in the phylum Firmicutes, commonly found in various habitats in Antarctica. Quorum quenching (QQ) is the disruption of bacterial cell-to-cell communication (known as quorum sensing), which has previously been described in mesophilic bacteria. This study demonstrated the QQ activity of a psychrotolerant strain, Planococcus versutus strain L10.15T, isolated from a soil sample obtained near an elephant seal wallow in Antarctica. Whole genome analysis of this bacterial strain revealed the presence of an N-acyl homoserine lactonase, an enzyme that hydrolyzes the ester bond of the homoserine lactone of N-acyl homoserine lactone (AHLs). Heterologous gene expression in E. coli confirmed its functions for hydrolysis of AHLs, and the gene was designated as aidP (autoinducer degrading gene from Planococcus sp.). The low temperature activity of this enzyme suggested that it is a novel and uncharacterized class of AHL lactonase. This study is the first report on QQ activity of bacteria isolated from the polar regions.
    Matched MeSH terms: Planococcus Bacteria/isolation & purification
  15. Level of chemical and microbiological contaminations in chili bo (paste)
    Zaini NA, Harith HH, Olusesan AT, Zulkifli AH, Bakar FA, Osman A, et al.
    J Food Prot, 2010 Mar;73(3):541-6.
    PMID: 20202342
    The objective of this study was to determine the level of preservatives and microbiological loads in various brands of commercially available chili bo (paste). Fifteen different brands of chili bo obtained from the local market and hypermarkets were analyzed for pH, moisture and benzoic acid content, microbiological loads (aerobic, anaerobic, aerobic spores, and fungi), and thermophilic microorganisms. Results showed that both moisture content and pH vary among samples. The concentrations of benzoic acid detected in chili bo were found to be in the range of 537 to 5,435 mg/kg. Nine of fifteen brands were found to exceed the maximum level permitted by the Malaysian Food Law in accordance with the Codex Alimentarius (1,000 mg/kg for benzoic acid). An apparent correlation between benzoic acid concentration and microbiological loads present in the chili bo was observed. The microbiological loads were found to be relatively low in the end products containing high amounts of benzoic acid. The heat-resistant (70 to 80 degrees C) microorganisms present in chili bo were identified as Ochrobacterum tritici, Stenotrophomonas rhizophila, Microbacterium maritypicum, Roseomonas spp., CDC group II-E subgroup A, Flavimonas oryzihabitans, and Pseudomonas aeruginosa, with M. maritypicum being the most frequently found (in 9 of 15 samples) microorganism. Most of these identified microorganisms were not known to cause foodborne illnesses.
    Matched MeSH terms: Bacteria/isolation & purification*
  16. Fulltext Dynamics of Microbial Populations Responsible for Biodegradation during the Full-Scale Treatment of Palm Oil Mill Effluent
    Mohd-Nor D, Ramli N, Sharuddin SS, Hassan MA, Mustapha NA, Ariffin H, et al.
    Microbes Environ, 2019 Jun 27;34(2):121-128.
    PMID: 30905894 DOI: 10.1264/jsme2.ME18104
    Despite efforts to address the composition of the microbial community during the anaerobic treatment of palm oil mill effluent (POME), its composition in relation to biodegradation in the full-scale treatment system has not yet been extensively examined. Therefore, a thorough analysis of bacterial and archaeal communities was performed in the present study using MiSeq sequencing at the different stages of the POME treatment, which comprised anaerobic as well as facultative anaerobic and aerobic processes, including the mixed raw effluent (MRE), mixing pond, holding tank, and final discharge phases. Based on the results obtained, the following biodegradation processes were suggested to occur at the different treatment stages: (1) Lactobacillaceae (35.9%) dominated the first stage, which contributed to high lactic acid production; (2) the higher population of Clostridiaceae in the mixing pond (47.7%) and Prevotellaceae in the holding tank (49.7%) promoted acetic acid production; (3) the aceticlastic methanogen Methanosaetaceae (0.6-0.8%) played a role in acetic acid degradation in the open digester and closed reactor for methane generation; (4) Syntrophomonas (21.5-29.2%) appeared to be involved in the degradation of fatty acids and acetic acid by syntrophic cooperation with the hydrogenotrophic methanogen, Methanobacteriaceae (0.6-1.3%); and (5) the phenols and alcohols detected in the early phases, but not in the final discharge phase, indicated the successful degradation of lignocellulosic materials. The present results contribute to a better understanding of the biodegradation mechanisms involved in the different stages of the full-scale treatment of POME.
    Matched MeSH terms: Bacteria/isolation & purification
  17. Fulltext Microbial Diversity in Decaying Oil Palm Empty Fruit Bunches (OPEFB) and Isolation of Lignin-degrading Bacteria from a Tropical Environment
    Tahir AA, Mohd Barnoh NF, Yusof N, Mohd Said NN, Utsumi M, Yen AM, et al.
    Microbes Environ, 2019 Jun 27;34(2):161-168.
    PMID: 31019143 DOI: 10.1264/jsme2.ME18117
    Oil palm empty fruit bunches (OPEFB) are the most abundant, inexpensive, and environmentally friendly lignocellulosic biomass in Malaysia. Investigations on the microbial diversity of decaying OPEFB may reveal microbes with complex enzymes that have the potential to enhance the conversion of lignocellulose into second-generation biofuels as well as the production of other value-added products. In the present study, fungal and bacterial diversities in decaying OPEFB were identified using Illumina MiSeq sequencing of the V3 region of the 16S rRNA gene and V4 region of the 18S rRNA gene. Fungal diversity in decaying OPEFB was dominated by the phylum Ascomycota (14.43%), while most of the bacterial sequences retrieved belonged to Proteobacteria (76.71%). Three bacterial strains isolated from decaying OPEFB, designated as S18, S20, and S36, appeared to grow with extracted OPEFB-lignin and Kraft lignin (KL) as the sole carbon source. 16S rRNA gene sequencing identified the 3 isolates as Paenibacillus sp.. The molecular weight distribution of KL before and after degradation showed significant depolymerization when treated with bacterial strains S18, S20, and S36. The presence of low-molecular-weight lignin-related compounds, such as vanillin and 2-methoxyphenol derivatives, which were detected by a GC-MS analysis, confirmed the KL-degrading activities of isolated Paenibacillus strains.
    Matched MeSH terms: Bacteria/isolation & purification*
  18. Fulltext Impact of logging and forest conversion to oil palm plantations on soil bacterial communities in Borneo
    Lee-Cruz L, Edwards DP, Tripathi BM, Adams JM
    Appl Environ Microbiol, 2013 Dec;79(23):7290-7.
    PMID: 24056463 DOI: 10.1128/AEM.02541-13
    Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.
    Matched MeSH terms: Bacteria/isolation & purification*
  19. Fulltext Helminth colonization is associated with increased diversity of the gut microbiota
    Lee SC, Tang MS, Lim YA, Choy SH, Kurtz ZD, Cox LM, et al.
    PLoS Negl Trop Dis, 2014 May;8(5):e2880.
    PMID: 24851867 DOI: 10.1371/journal.pntd.0002880
    Soil-transmitted helminths colonize more than 1.5 billion people worldwide, yet little is known about how they interact with bacterial communities in the gut microbiota. Differences in the gut microbiota between individuals living in developed and developing countries may be partly due to the presence of helminths, since they predominantly infect individuals from developing countries, such as the indigenous communities in Malaysia we examine in this work. We compared the composition and diversity of bacterial communities from the fecal microbiota of 51 people from two villages in Malaysia, of which 36 (70.6%) were infected by helminths. The 16S rRNA V4 region was sequenced at an average of nineteen thousand sequences per samples. Helminth-colonized individuals had greater species richness and number of observed OTUs with enrichment of Paraprevotellaceae, especially with Trichuris infection. We developed a new approach of combining centered log-ratio (clr) transformation for OTU relative abundances with sparse Partial Least Squares Discriminant Analysis (sPLS-DA) to enable more robust predictions of OTU interrelationships. These results suggest that helminths may have an impact on the diversity, bacterial community structure and function of the gut microbiota.
    Matched MeSH terms: Bacteria/isolation & purification
  20. Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia
    Sow SL, Khoo G, Chong LK, Smith TJ, Harrison PL, Ong HK
    World J Microbiol Biotechnol, 2014 Feb;30(2):757-66.
    PMID: 24078113
    Disused tin-mining ponds make up a significant amount of water bodies in Malaysia particularly at the Kinta Valley in the state of Perak where tin-mining activities were the most extensive, and these abundantly available water sources are widely used in the field of aquaculture and agriculture. However, the natural ecology and physicochemical conditions of these ponds, many of which have been altered due to secondary post-mining activities, remains to be explored. As ammonia-oxidizing bacteria (AOB) are directly related to the nutrient cycles of aquatic environments and are useful bioindicators of environmental variations, the focus of this study was to identify AOBs associated with disused tin-mining ponds that have a history of different secondary activities in comparison to ponds which were left untouched and remained as part of the landscape. The 16S rDNA gene was used to detect AOBs in the sediment and water sampled from the three types of disused mining ponds, namely ponds without secondary activity, ponds that were used for lotus cultivation and post-aquaculture ponds. When the varying pond types were compared with the sequence and phylogenetic analysis of the AOB clone libraries, both Nitrosomonas and Nitrosospira-like AOB were detected though Nitrosospira spp. was seen to be the most ubiquitous AOB as it was present in all ponds types. However, AOBs were not detected in the sediments of idle ponds. Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture indicated the highest richness of AOBs. Canonical correspondence analysis indicated that among the physicochemical properties of the pond sites, TAN and nitrite were shown to be the main factors that influenced the community structure of AOBs in these disused tin-mining ponds.
    Matched MeSH terms: Bacteria/isolation & purification
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