A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: a means to access and use genes from uncultured microorganisms

To examine as randomly as possible the role of the beta-ketoacyl and acyl carrier protein (ACP) components of bacterial type II polyketide synthases (PKSs), homologs of the chain-length-factor (CLF) genes were cloned from the environmental community of microorganisms. With PCR primers derived from conserved regions of known ketosynthase (KSalpha) and ACP genes specifying the formation of 16- to 24-carbon polyketides, two CLF (KSbeta) genes were cloned from unclassified streptomycetes isolated from the soil, and two were cloned from soil DNA without the prior isolation of the parent microorganism. The sequence and deduced product of each gene were distinct from those of known KSbeta genes and, by phylogenetic analysis, belonged to antibiotic-producing PKS gene clusters. Hybrid PKS gene cassettes were constructed with each novel KSbeta gene substituted for the actI-ORF2 or tcmL KSbeta subunit genes, along with the respective actI-ORF1 or tcmK KSalpha, tcmM ACP, and tcmN cyclase genes, and were found to produce an octaketide or decaketide product characteristic of the ones known to be made by the heterologous KSalpha gene partner. Since substantially less than 1% of the microorganisms present in soil are thought to be cultivatable by standard methods, this work demonstrates a potential way to gain access to a more extensive range of microbial molecular diversity and to biosynthetic pathways whose products can be tested for biological applications.     

Pathogenic organisms in milk and milk products: the situation in France and in Europe

Milk and dairy products harbour a natural microbial flora and/or other micro-organisms, which vary within the wide range of products available on the French market. The origin of contamination by pathogenic bacteria varies with the type of product and the mode of production and processing. Contamination of milk and dairy products by pathogenic micro-organisms can be of endogenous origin, following excretion from the udder of an infected animal. Contamination may also be of exogenous origin, through direct contact with infected herds or through the environment (e.g. water, personnel). Treatment and processing of milk can inhibit or encourage the multiplication of micro-organisms. The authors describe the relevant aspects of bacterial physiology and ecology, the occurrence of bacteria in dairy products, and the public health significance for each of the principal micro-organisms found in such products. Bacteria most frequently involved are mycobacteria, Brucella sp., Listeria monocytogenes, Staphylococcus aureus and enterobacteria (including toxigenic Escherichia coli and Salmonella). At present, systems of testing and surveillance are required for the control of pathogenic bacteria in milk and dairy products, as specified by regulations currently being developed for all countries in the European Union. Preventive measures should take into account the well-established facts concerning the potential microbiological impact of pathogenic bacteria on milk and dairy products. There should be increased recourse to risk analysis methods to assess the threat to the consumer with regard to the presence of pathogenic bacteria in food.     

Ratios of carbon isotopes in microbial lipids as an indicator of substrate usage

The occurrence and abundance of microbial fatty acids have been used for the identification of microorganisms in microbial communities. However, these fatty acids can also be used as indicators of substrate usage. For this, a systematic investigation of the discrimination of the stable carbon isotopes by different microorganisms is necessary. We grew 11 strains representing major bacterial and fungal species with four different isotopically defined carbon sources and determined the isotope ratios of fatty acids of different lipid fractions. A comparison of the differences of delta13C values of palmitic acid (C16:0) with the delta13C values of the substrates revealed that the isotope ratio is independent of the growth stage and that most microorganisms showed enrichment of C16:0 with 13C when growing on glycerol. With the exception of Burkholderia gladioli, all microorganism showed depletion of 13C in C16:0 while incorporating the carbons of glucose, and most of them were enriched with 13C from mannose, with the exception of Pseudomonas fluorescens and the Zygomycotina. Usually, the glycolipid fractions are depleted in 13C compared to the phospholipid fractions. The delta13C pattern was not uniform within the different fatty acids of a given microbial species. Generally, tetradecanoic acid (C14:0) was depleted of 13C compared to palmitic acid (C16:0) while octadecanoic acid (C18:0) was enriched. These results are important for the calibration of a new method in which delta13C values of fatty acids from the environment delineate the use of bacterial substrates in an ecosystem.     

固定化微生物对石油污染土壤修复条件优化研究

探讨固定化微生物降解石油污染土壤最佳理化条件,为修复石油污染土壤提供理论依据。从几种农业废弃物中选出固定化微生物的最优载体,并以吉林前郭油田原油为降解对象,考察固定化微生物投入量、原油初始浓度、表面活性剂投加量、孔隙率、含水率、pH及营养成分含量对原油降解率的影响。秸秆为固定化微生物最佳载体。取1 500g土样进行单因素试验,投入60g原油,最优化的降解条件是添加固定化微生物50g/L,最佳环境因素是:孔隙率45%、含水率20%、pH=8,营养成分C/N=9。固定化微生物降解能力远超过游离菌降解石油污染土壤的能力,调节到最佳的土壤环境,投入一定量的固定化微生物,能够大幅提高石油污染土壤降解率。     

Results of AutoPap system-assisted and manual cytologic screening. A comparison

Previous studies have shown enteral nutritional solutions (ENS) contaminated with large numbers of microorganisms from the environment or gastrointestinal (GI) tract of patients have caused respiratory infections, acute and chronic enteritis, and septicemia. The introduction of "closed" enteral feeding systems has been used to prevent contaminating organisms from entering enteral feeding systems in large numbers. However, there is some discussion as to whether this has been an effective measure in reducing ENS-related infections because there is anecdotal evidence to suggest that disease processes resulting from enteral feeding are still commonplace in the hospital and home. This is because there is very little information about the growth of microorganisms in ENS and whether growth in ENS may affect the virulence and pathogenicity of microorganisms. This study shows that Escherichia coli and Pseudomonas aeruginosa may grow at 25 degrees C from either high or low initial numbers to up to 9.2 log colony-forming units per mL in a range of milk-based ENS. However, these organisms did not grow in the fruit-based ENS. The effect on the lipopolysaccharide (LPS) of culturing E. coli and P. aeruginosa in milk-based ENS as opposed to standard laboratory media was examined using polyacrylamide gel electrophoresis. We found that there were significant qualitative changes in the phenotype of O-polysaccharide side chains of the LPS from these organisms. O-polysaccharide is known to mediate in the complement, antibiotic and bile resistance, and affect adherence. Therefore, changes in the virulence and pathogenicity of these microorganisms when cultured in ENS may be indicated. Thus, the study provides further evidence for reevaluating the microbiologic and immunologic effects of enteral feeding, especially on the microbial flora of the GI tract.     

废弃铬渣厂土壤理化性质对微生物多样性的影响

以废弃铬渣厂及其周边表层土壤为研究对象,采集5个区域土壤样品,运用高通量测序技术,揭示了表层土壤微生物多样性及其环境主要影响因素之间的关系。结果表明,有机质（SOM）、总磷（TP）、速效磷（AP）、速效氮（AN）和铵态氮（NH4+-N）含量均在下游最高、车间最低。门水平上,Actinobacteria、Proteobacteria、Acidobacteria和Chloroflexi为优势菌种;纲水平上,Alphaproteobacteria、Actinobacteria、Vicinamibacteria、Gemmaproteobacteria和Chloroflexi为优势菌种。总体来看,在重金属与土壤环境因子共同作用下,微生物丰度更倾向于受土壤环境因子的影响,其中TP、硝态氮（NO3+-N）和大多数重金属元素是微生物变化的主要影响因素;Actinobacteria与大多数重金属具有趋同性,对重金属耐受能力最强;金属元素Pb对细菌的生长繁衍存在一定的选择性,即金属元素的不同对土壤细菌类群的影响有差异。综上,废弃厂区修复治理过程中应考虑营养元素的投入与优势菌种的选择。本文研究加深了对重金属污染土壤微生物的变化及其驱动因子的了解,为废弃铬渣厂受污染的土壤修复提供理论依据。     

Zymomonas mobilis--science and industrial application

Zymomonas mobilis is undoubtedly one of the most unique bacterium within the microbial world. Known since 1912 under the names Termobacterium mobilis, Pseudomonas linderi, and Zymomonas mobilis, reviews on its uniqueness have been published in 1977 and 1988. The bacterium Zymomonas mobilis not only exhibits an extraordinarily uniqueness in its biochemistry, but also in its growth behavior, energy production, and response to culture conditions, as well as cultivation techniques used. This uniqueness caused great interest in the scientific, biotechnological, and industrial worlds. Its ability to couple and uncouple energy production in favor of product formation, to respond to physical and chemical environment manipulation, as well as its restricted product formation, makes it an ideal microorganism for microbial process development. This review explores the advances made since 1987, together with new developments in the pure scientific and applied commercial areas.     

Model to Quantify Removal and Inactivation of Microorganisms Occluded in Effluent Wastewater Particles Using Filtration and Disinfection Systems

A model is presented to quantify microbial occlusion in effluent particles and improve understanding of the removal and inactivation of occluded microorganisms in filtration and disinfection systems. Microbial occlusion in particles is described in the model as a function of the particle size distribution, the microbial density (N1), which is the average quantity of target microorganisms within the subset of particles that contain microorganisms, and the frequency of association (N2), which is the ratio of particles that contain at least one target microorganism. To demonstrate the model, undisinfected secondary effluent samples were collected from an extended aeration treatment facility and analyzed to determine values for the model variables, N1 and N2 for heterotrophic bacteria and aerobic endospores and N2 for total coliform bacteria. Heterotrophic bacteria were present in most effluent particles (73–100%) at high densities (7–93 per particle), whereas aerobic endospores and total coliform bacteria were only present in a small percentage of effluent particles (0.1–6%) and the density of aerobic endospores in effluent particles was not appreciably higher than one per particle.     

Microbial degradation of xenobiotics in the environment

Biodegradation of naturally occurring organic compounds follows their synthesis. In contrast, man-made compounds, also known as xenobiotics, are often refractory to degradation. The main reason is that they cannot be recognized by naturally present organisms and therefore do not enter common metabolic pathways. The physical and chemical characteristics of the compounds, as well as environmental factors, may influence their biodegradability. Some compounds may be transformed only in the presence of another compound which appears as a carbon and energy source. Very often compounds are degraded sequentially through the activity of a series of different organisms. The main degraders in nature are microorganisms, mostly bacteria and some fungi. These organisms, due to their rapid rates of multiplication and great metabolic potential, are able to adapt to new substrates. Selection of degradative potent microorganisms and their successive adaptation to a naturally persistent compound might be a powerful means for environmental detoxification. Although numerous laboratory experiments have given positive results, very few are applicable on a large scale. It is necessary to select microorganisms or microbial communities capable of controlled degradation of persistent organic chemicals without their transformation to other, more hazardous compounds. Better understanding of metabolic pathways for the biodegradation of specific organic compounds as well as more thorough knowledge of degrading microorganisms will make purposeful application of biodegradation possible.     

Computer simulation of alternative sampling strategies to estimate risk of infection from Cryptosporidium

Microbial growth, sensory and chemical changes and composition of gas atmosphere were studied in vacuum packed (VP) and modified atmosphere packed (MAP) cod fillets stored at 0 degree C. Contrary to previous studies, coccobacilli and pleomorphic Gram-negative microorganisms (2-4 by 2-5 microns) and not Shewanella putrefaciens were found most likely to be the main spoilage organisms. These microorganisms, which may be Photobacterium phosphoreum, can explain the short shelf-life extension of VP and MAP fish products compared to meat products. It is suggested that they may inhibit the typical H2S-producing fish spoilage bacteria, S. putrefaciens, as the maximum concentration of H2S-producing bacteria found in MAP fish products is very low. Compared to VP, a shelf-life extension of 6-7 days was obtained with 48% CO2 in MAP. However, with pure CO2 the shelf life was only extended by 2-3 days. Poor texture and high drip loss indicated that the shelf life of these fillets was limited by chemical reactions and not only by microbial activity.     

Low-dose clozapine in acute and continuation treatment of severe borderline personality disorder

High-dose chemotherapy using autologous bone marrow or mobilized blood as the source of stem cells for haematologic rescue, is being widely used for a variety of haematological malignancies and solid tumours. To collect sufficient numbers of haematopoietic stem cells for successful engraftment, standard apheresis procedures are performed. Newer techniques and refinements of the procedure allow using only 1 to 2 apheresis products (AP) for autografting. Bacterial contamination of the AP, although very rare, sometimes occurs and may lead to generalized infection in the recipient. The apheresis must be repeated, sometimes even including time-consuming and costly mobilization. At our institution, the patients' blood stem cells are usually mobilized with chemotherapy followed by daily s.c. haematopoietic growth factor injections or with growth factor alone. An apheresis machine is used for collection through a central venous line and the AP is routinely checked for bacterial contamination. Results are only available after the product has been processed and cryopreserved. In the last 5 years, we observed bacterial contamination in four of our AP. Therefore, we investigated the possibility of in vitro antibiotic decontamination. Using standard antibiograms, we determined the sensitivities of the contaminating bacteria. By incubating the products with the specific antibiotics at bactericidal concentrations, we were able to sterilize the probes from the contaminating bacteria. In the concurrently performed controls without the active substance, bacteria were still detectable. We conclude that in selected cases, in vitro decontamination using pretested antibiotics, may be a feasible, cost-effective, and easy alternative to performing additional apheresis procedures.     

基于Lotka-Volterra的生物浸铀微生物生长动力学模型研究

前人研究表明,生物浸铀过程中浸矿和辅助浸矿微生物两者间存在协同作用,两者相互促进提高生物浸铀效率。浸矿和辅助浸矿微生物是如何相互促进,使彼此更好地得到生长,两者相互促进生长动力学模型是什么?Lotka-Volterra模型被广泛应用在两种间相互作用下生物数量增长模型研究中,对于生物浸铀中浸矿和辅助浸矿微生物生长动力学模型研究具有借鉴意义。由Lotka-Volterra模型得出了浸矿和辅助浸矿微生物独立共生和竞争共生方程,根据浸矿和辅助浸矿微生物协同特性建立了其生长动力学模型,由模型再推导出浸矿和辅助浸矿微生物协同作用稳定态点,该稳定态点与试验结果相差较小,说明生物浸铀浸矿和辅助浸矿微生物生长动力学模型拟合效果较好。将Lotka-Volterra模型应用到生物浸铀中,具有新颖性,提供了新的研究视角,对完善生物浸铀中微生物协同问题、提高生物浸铀效率具有重要的理论与实际意义。     

Development of a novel, rapid processing protocol for polymerase chain reaction-based detection of bacterial infections in synovial fluids

We describe the development of a molecular detection system designed for use with synovial fluid (SF)-based infections. The methodology employs a lysis/extraction procedure that effectively disrupts microorganisms allowing for release of the microbial DNA and its amplification by polymerase chain reaction (PCR). We tested the effectiveness of adding a mixed-bed, ion-exchange resin to the extract to remove PCR inhibitory components present in the SF. After centrifugation to separate the resin, DNA contained in the supernatant is subjected to PCR using oligonucleotide primers designed for broad-spectrum microorganism detection. Amplification products are analyzed by agarose gel electrophoresis and/or DNA hybridization methodology. We report here the detection sensitivity and specificity of the protocol using SF inoculated with Escherichia coli and Staphyloccocus aureus. We have applied this new methodology to clinical SF specimens with results superior to standard laboratory culturing assays.     

腐蚀微生物种类及腐蚀机理研究进展

目前微生物腐蚀（MIC）在工业环境中已成为普遍存在的严重问题,其是造成腐蚀损坏、设备故障和经济损失的主要原因之一.虽然部分经典的腐蚀理论能够解释一些微生物腐蚀的现象,但这些机理的片面性也逐渐暴露出来.随着对腐蚀菌种类的研究越来越多,人们对微生物腐蚀机理的认识也更加全面深入.本文重点介绍了易导致腐蚀的微生物种类及特征,如硫酸盐还原菌、硝酸盐还原菌和铁氧化菌等,并总结了微生物腐蚀机理中基于生物能学和生物电化学的最新研究进展,包括微生物胞外电子传递过程、代谢产物腐蚀和浓差电池作用等理论,为工业中厌氧及好氧条件下微生物腐蚀的诊断、预测及防治提供了理论指导.     

Food-packaging interactions influencing quality and safety

Interactions between foods and packaging can be detrimental to quality and/or safety. Changes in product flavour due to aroma sorption and the transfer of undesirable flavours from packaging to foods are important mechanisms of deterioration when foods are packaged in polymer-based materials. Careful consideration must be given to those factors affecting such interactions when selecting packaging materials in order to maximize product quality, safety, and shelf-life while minimizing undesirable changes. Product considerations include sensitivity to flavour and related deteriorations, colour changes, vitamin loss, microbial activity, and amount of flavour available. Storage considerations include temperature, time, and processing method. Polymer considerations include type of polymer and processing method, volume or mass of polymer to product ratio, and whether the interaction is Fickian or non-Fickian. Methodology to determine the extent of such interactions must be developed. Direct interactions between food and packaging are not necessarily detrimental. The same principles governing undesirable interactions can be used to affect desirable outcomes. Examples include films which directly intercept or absorb oxygen, inhibit microorganisms, remove undesirable flavours by sorption, or indicate safety and product shelf-life.     

Sequential enrichment of microbial populations exhibiting enhanced biodegradation of crude oil

The distribution of oil-degrading bacteria in the coastal water and sediments of Hokkaido, Japan, was surveyed. The potential of mixed microbial populations to degrade weathered crude oil was not confined to any ecological components (water or sediment) nor to the sampling stations. One microbial culture that was stable during repeated subculturing degraded 45% of the saturates and 20% of the aromatics present in crude oil in 10 days during the initial screening. The residual hydrocarbons in this culture were extracted by chloroform and dispersed in a fresh seawater-based medium and subsequently inoculated with microorganisms from the first culture. After full growth of the second culture, the residual hydrocarbons were again extracted and dispersed in a fresh medium in which microorganisms from the second culture had been inoculated. This sequential process was carried out six times to enrich those microorganisms that grew on the recalcitrant components of crude oil. After repeated exposure of the residual crude oil to the enriched microorganisms, about 80% of the initially added crude oil was degraded. The cultures obtained after each enrichment cycle were kept, and the degradation of fresh crude oil by the enriched microorganisms was examined. The degradative activity of the enriched cultures increased as the number of enrichment cycles increased. A microbial population that had been selected six times on the residual crude oil could degrade 70% of the saturates and 30% of the aromatics of crude oil. Thus, growth of a microbial population on residual crude oil improved its ability to biodegrade crude oil.     

Special considerations concerning regulatory requirements and drug development for peptides and biotech products in the EU

The marketing authorization for a new medicinal product is based on the scientific assessment of its quality, safety and efficacy. The marketing authorization application (MAA) which covers all the relevant documentation can be filed in the EU via different application procedures. For peptides and biological products special issues have to be taken into consideration during drug development. Due to special production procedures and the complexity of the active substance itself, peptides and biotech products are subject to specific regulatory requirements. This leads to the necessity to discuss the development program of a new peptide or biotech product with the health authorities on a case by case basis. This article will focus on the special regulatory requirements for peptides and biotech products including the registration procedures as well as technical, preclinical and clinical issues.     

Disposition and metabolism of the new hypocholesterolemic compound S-8921 in rats and dogs

Antimicrobial agents are appropriate treatment for acute, severe, persistent, or progressive infectious diseases. The efficacy of treatment depends on the accuracy of the diagnosis of infection and the appropriateness of the antimicrobial agent for the causative microorganism. In this symposium, the antimicrobial agents reviewed correspond with the bacterial, fungal, viral, mycobacterial, parasitic, chlamydial, and other microorganisms that cause disease in humans. Usually, the etiologic possibilities can be limited on the basis of the history and physical examination, laboratory tests, or results of treatment trials. Many of the same findings, however, can result from noninfectious, other inflammatory, or unknown mechanisms. Manifestations such as fever and organ dysfunction are nonspecific and often not caused by an infectious process. Even when infection is clinically apparent, the causative microorganism may not be identified, and empiric treatment with broad-spectrum agents is appropriate in many cases of serious disease.     

Essential histidyl residues at the active site(s) of sucrose-phosphate synthase from Prosopis juliflora

Antimicrobial resistance in nosocomial isolates is of increasing concern to the clinician, particularly in intensive care units. With more expensive drugs and prolonged periods of hospitalization required, resistance can result in increased healthcare costs. For the patient, infection with multiply resistant strains of bacteria is associated with high mortality rates. This review focuses on the prevalence of nosocomial infections throughout Europe, with particular emphasis on the prevalence of resistance to common antimicrobial agents. The beta-lactams are the most frequently prescribed antimicrobials, and the growing importance of extended spectrum beta-lactamases and the hyperproduction of chromosomal beta-lactamase by stably derepressed mutants in the development of microbial resistance are discussed. Given that the most common reason for modification of an initial empiric antibiotic treatment is the isolation of microorganisms not susceptible to the initial choice of treatment, the results from two European multicenter trials comparing the efficacy of the carbapenems, meropenem, and imipenem/cilastatin, for the treatment of serious nosocomial infections, are appraised. In light of these results, it can be concluded that the carbapenems are effective as initial empiric monotherapy for nosocomial infections because of their broad spectrum of efficacy and stability to beta-lactamases.     

生物浸出技术在铜工业中的应用

一般所说的生物冶金是指铜、镍、锌等硫化矿的生物提取方法，即在相关微生物存在时，由于微生物的催化氧化作用，应用浸矿微生物存在的酸性溶液使硫化矿物氧化分解浸出金属，溶液中的有价金属离子则通过萃取一电积、或其它湿法冶金方法制备高纯金属。目前生物冶金技术已广泛应用，并在铜的提取上实现了工业应用。本文系统地介绍了国内外生物技术在铜工业中的发展概况，总结了浸矿微生物的种类，探讨了微生物冶金过程中的直接作用和间接作用。指出了生物冶金技术的发展方向。