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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
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*
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
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
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*
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
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*
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
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*
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
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*
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*
Fulltext Clinical and bacteriological profile of diabetic foot infections in a tertiary care

Goh TC, Bajuri MY, C Nadarajah S, Abdul Rashid AH, Baharuddin S, Zamri KS

J Foot Ankle Res, 2020 Jun 16;13(1):36.
PMID: 32546270 DOI: 10.1186/s13047-020-00406-y

BACKGROUND: Diabetic foot infection is a worldwide health problem is commonly encountered in daily practice. This study was conducted to identify the microbiological profile and antibiotic sensitivity patterns of causative agents identified from diabetic foot infections (DFIs). In addition, the assessment included probable risk factors contributing to infection of ulcers that harbour multidrug-resistant organisms (MDROs) and their outcomes.
METHODS: We carried out a prospective analysis based on the DFI samples collected from 2016 till 2018. Specimens were cultured with optimal techniques in addition to antibiotic susceptibility based on recommendations from The Clinical and Laboratory Standards Institute (CLSI). A total of 1040 pathogens were isolated with an average of 1.9 pathogens per lesion in 550 patients who were identified with having DFIs during this interval.
RESULTS: A higher percentage of Gram-negative pathogens (54%) were identified as compared with Gram-positive pathogens (33%) or anaerobes (12%). A total of 85% of the patients were found to have polymicrobial infections. Pseudomonas aeruginosa (19%), Staphylococcus aureus (11%) and Bacteroides species (8%) appeared to be the predominant organisms isolated. In the management of Gram-positive bacteria, the most efficacious treatment was seen with the use of Vancomycin, while Imipenem and Amikacin proved to be effective in the treatment of Gram-negative bacteria.
CONCLUSION: DFI's are common among Malaysians with diabetes, with a majority of cases displaying polymicrobial aetiology with multi-drug resistant isolates. The data obtained from this study will be valuable in aiding future empirical treatment guidelines in the treatment of DFIs. This study investigated the microbiology of DFIs and their resistance to antibiotics in patients with DFIs that were managed at a Tertiary Care Centre in Malaysia.

Matched MeSH terms: Gram-Negative Bacteria/isolation & purification; Gram-Positive Bacteria/isolation & purification
Investigation of physico-chemical properties and microbial community during poultry manure co-composting process

Farah Nadia O, Xiang LY, Lie LY, Chairil Anuar D, Mohd Afandi MP, Azhari Baharuddin S

J Environ Sci (China), 2015 Feb 1;28:81-94.
PMID: 25662242 DOI: 10.1016/j.jes.2014.07.023

Co-composting of poultry manure and rubber wood sawdust was performed with the ratio of 2:1 (V/V) for a period of 60 days. An investigation was carried out to study the extracellular enzymatic activities and structural degradation utilizing Fourier transform infrared spectroscopy (FT-IR), thermogravimetry and differential thermal analysis (TG/DTA) and scanning electron microscopy (SEM). The microbial succession was also determined by using denaturing gel gradient electrophoresis (DGGE). The compost was able to reach its highest temperature of 71°C at day 3 and stabilized between 30 and 40°C for 8 weeks. CMCase, FPase and β-glucosidase acted synergistically in order to degrade the cellulosic substrate. The xylanase activities increased gradually during the composting and reached the peak value of 11.637 U/g on day 35, followed by a sharp decline. Both LiP and MnP activities reached their peak values on day 35 with 0.431 and 0.132 U/g respectively. The FT-IR spectra revealed an increase in aromaticity and a decrease in aliphatic compounds such as carbohydrates as decomposition proceeded. TGA/DTG data exhibited significant changes in weight loss in compost samples, indicating degradation of organic matter. SEM micrographs showed higher amounts of parenchyma exposed on the surface of rubber wood sawdust at day 60, showing significant degradation. DGGE and 16S rDNA analyses showed that Burkholderia sp., Pandoraea sp., and Pseudomonas sp. were present throughout the composting process. Ornithinibacillus sp. and Castellaniella ginsengisoli were only found in the initial stage of the composting, while different strains of Burkholderia sp. also occurred in the later stage of composting.

Matched MeSH terms: Bacteria/isolation & purification*
Fulltext Phylogenetic relationship of phosphate solubilizing bacteria according to 16S rRNA genes

Javadi Nobandegani MB, Saud HM, Yun WM

Biomed Res Int, 2015;2015:201379.
PMID: 25632387 DOI: 10.1155/2015/201379

Phosphate solubilizing bacteria (PSB) can convert insoluble form of phosphorous to an available form. Applications of PSB as inoculants increase the phosphorus uptake by plant in the field. In this study, isolation and precise identification of PSB were carried out in Malaysian (Serdang) oil palm field (University Putra Malaysia). Identification and phylogenetic analysis of 8 better isolates were carried out by 16S rRNA gene sequencing in which as a result five isolates belong to the Beta subdivision of Proteobacteria, one isolate was related to the Gama subdivision of Proteobacteria, and two isolates were related to the Firmicutes. Bacterial isolates of 6upmr, 2upmr, 19upmnr, 10upmr, and 24upmr were identified as Alcaligenes faecalis. Also, bacterial isolates of 20upmnr and 17upmnr were identified as Bacillus cereus and Vagococcus carniphilus, respectively, and bacterial isolates of 31upmr were identified as Serratia plymuthica. Molecular identification and characterization of oil palm strains as the specific phosphate solubilizer can reduce the time and cost of producing effective inoculate (biofertilizer) in an oil palm field.

Matched MeSH terms: Bacteria/isolation & purification
Pyrosequencing analysis of microbial community and food-borne bacteria on restaurant cutting boards collected in Seri Kembangan, Malaysia, and their correlation with grades of food premises

Abdul-Mutalib NA, Amin Nordin S, Osman M, Ishida N, Tashiro K, Sakai K, et al.

Int J Food Microbiol, 2015 May 4;200:57-65.
PMID: 25679309 DOI: 10.1016/j.ijfoodmicro.2015.01.022

This study adopts the pyrosequencing technique to identify bacteria present on 26 kitchen cutting boards collected from different grades of food premises around Seri Kembangan, a city in Malaysia. Pyrosequencing generated 452,401 of total reads of OTUs with an average of 1.4×10(7) bacterial cells/cm(2). Proteobacteria, Firmicutes and Bacteroides were identified as the most abundant phyla in the samples. Taxonomic richness was generally high with >1000 operational taxonomic units (OTUs) observed across all samples. The highest appearance frequencies (100%) were OTUs closely related to Enterobacter sp., Enterobacter aerogenes, Pseudomonas sp. and Pseudomonas putida. Several OTUs were identified most closely related to known food-borne pathogens, including Bacillus cereus, Cronobacter sakazaki, Cronobacter turisensis, Escherichia coli, E. coli O157:H7, Hafnia alvei, Kurthia gibsonii, Salmonella bongori, Salmonella enterica, Salmonella paratyphi, Salmonella tyhpi, Salmonella typhimurium and Yersinia enterocolitica ranging from 0.005% to 0.68% relative abundance. The condition and grade of the food premises on a three point cleanliness scale did not correlate with the bacterial abundance and type. Regardless of the status and grades, all food premises have the same likelihood to introduce food-borne bacteria from cutting boards to their foods and must always prioritize the correct food handling procedure in order to avoid unwanted outbreak of food-borne illnesses.

Matched MeSH terms: Bacteria/isolation & purification*
Optimizing supercritical carbon dioxide in the inactivation of bacteria in clinical solid waste by using response surface methodology

Hossain MS, Nik Ab Rahman NN, Balakrishnan V, Alkarkhi AF, Ahmad Rajion Z, Ab Kadir MO

Waste Manag, 2015 Apr;38:462-73.
PMID: 25636860 DOI: 10.1016/j.wasman.2015.01.003

Clinical solid waste (CSW) poses a challenge to health care facilities because of the presence of pathogenic microorganisms, leading to concerns in the effective sterilization of the CSW for safe handling and elimination of infectious disease transmission. In the present study, supercritical carbon dioxide (SC-CO2) was applied to inactivate gram-positive Staphylococcus aureus, Enterococcus faecalis, Bacillus subtilis, and gram-negative Escherichia coli in CSW. The effects of SC-CO2 sterilization parameters such as pressure, temperature, and time were investigated and optimized by response surface methodology (RSM). Results showed that the data were adequately fitted into the second-order polynomial model. The linear quadratic terms and interaction between pressure and temperature had significant effects on the inactivation of S. aureus, E. coli, E. faecalis, and B. subtilis in CSW. Optimum conditions for the complete inactivation of bacteria within the experimental range of the studied variables were 20 MPa, 60 °C, and 60 min. The SC-CO2-treated bacterial cells, observed under a scanning electron microscope, showed morphological changes, including cell breakage and dislodged cell walls, which could have caused the inactivation. This espouses the inference that SC-CO2 exerts strong inactivating effects on the bacteria present in CSW, and has the potential to be used in CSW management for the safe handling and recycling-reuse of CSW materials.

Matched MeSH terms: Bacteria/isolation & purification
Detection of multiple potentially pathogenic bacteria in Matang mangrove estuaries, Malaysia

Ghaderpour A, Mohd Nasori KN, Chew LL, Chong VC, Thong KL, Chai LC

Mar Pollut Bull, 2014 Jun 15;83(1):324-30.
PMID: 24820641 DOI: 10.1016/j.marpolbul.2014.04.029

The deltaic estuarine system of the Matang Mangrove Forest Reserve of Malaysia is a site where several human settlements and brackish water aquaculture have been established. Here, we evaluated the level of fecal indicator bacteria (FIB) and the presence of potentially pathogenic bacteria in the surface water and sediments. Higher levels of FIB were detected at downstream sampling sites from the fishing village, indicating it as a possible source of anthropogenic pollution to the estuary. Enterococci levels in the estuarine sediments were higher than in the surface water, while total coliforms and E. coli in the estuarine sediments were not detected in all samples. Also, various types of potentially pathogenic bacteria, including Klebsiella pneumoniae, Serratia marcescens and Enterobacter cloacae were isolated. The results indicate that the Matang estuarine system is contaminated with various types of potential human bacterial pathogens which might pose a health risk to the public.

Matched MeSH terms: Bacteria/isolation & purification
Bacterial detection: from microscope to smartphone

Gopinath SC, Tang TH, Chen Y, Citartan M, Lakshmipriya T

Biosens Bioelectron, 2014 Oct 15;60:332-42.
PMID: 24836016 DOI: 10.1016/j.bios.2014.04.014

The ubiquitous nature of bacteria enables them to survive in a wide variety of environments. Hence, the rise of various pathogenic species that are harmful to human health raises the need for the development of accurate sensing systems. Sensing systems are necessary for diagnosis and epidemiological control of pathogenic organism, especially in the food-borne pathogen and sanitary water treatment facility' bacterial populations. Bacterial sensing for the purpose of diagnosis can function in three ways: bacterial morphological visualization, specific detection of bacterial component and whole cell detection. This paper provides an overview of the currently available bacterial detection systems that ranges from microscopic observation to state-of-the-art smartphone-based detection.

Matched MeSH terms: Bacteria/isolation & purification*
Fulltext Microbial and heavy metal contamination in commonly consumed traditional Chinese herbal medicines

Ting A, Chow Y, Tan W

J Tradit Chin Med, 2013 Feb;33(1):119-24.
PMID: 23596824

The increasing popularity and widespread use of traditional Chinese herbs as alternative medicine have sparked an interest in understanding their biosafety, especially in decoctions that are consumed. This study aimed to assess the level of microbial and heavy metal contamination in commonly consumed herbal medicine in Malaysia and the effects of boiling on these contamination levels.

Matched MeSH terms: Bacteria/isolation & purification*

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