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Individual Strains (individual + strain)
Selected AbstractsDevelopment of a molecular method for the typing of Brettanomyces bruxellensis (Dekkera bruxellensis) at the strain levelJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2007C. Miot-Sertier Abstract Aims:, In recent years, Brettanomyces/Dekkera bruxellensis has caused increasingly severe quality problems in the wine industry. A typing method at the strain level is needed for a better knowledge of the dispersion and the dynamics of these yeasts from grape to wine. Methods and Results:, Three molecular tools, namely random-amplified polymorphic DNA, PCR fingerprinting with microsatellite oligonucleotide primers and SAU-PCR, were explored for their relevance to typing strains of Brettanomyces bruxellensis. The results indicated that discrimination of each individual strain was not possible with a single PCR typing technique. We described a typing method for B. bruxellensis based on restriction enzyme analysis and pulse field gel electrophoresis (REA-PFGE). Results showed that electrophoretic profiles were reproducible and specific for each strain under study. Conclusions:, Consequently, REA-PFGE should be considered for the discrimination of B. bruxellensis strains. This technique allowed a fine discrimination of B. bruxellensis, as strains were identified by a particular profile. Significance and Impact of the Study:, This study constitutes a prerequisite for accurate and appropriate investigations on the diversity of strains throughout the winemaking and ageing process. Such studies will probably give clearer and more up-to-date information on the origin of the presence of Brettanomyces in wine after vinification when they are latent spoilage agents. [source] Changes in the community structure and activity of betaproteobacterial ammonia-oxidizing sediment bacteria along a freshwater,marine gradientENVIRONMENTAL MICROBIOLOGY, Issue 4 2006Thomas E. Freitag Summary To determine whether the distribution of estuarine ammonia-oxidizing bacteria (AOB) was influenced by salinity, the community structure of betaproteobacterial ammonia oxidizers (AOB) was characterized along a salinity gradient in sediments of the Ythan estuary, on the east coast of Scotland, UK, by denaturant gradient gel electrophoresis (DGGE), cloning and sequencing of 16S rRNA gene fragments. Ammonia-oxidizing bacteria communities at sampling sites with strongest marine influence were dominated by Nitrosospira cluster 1-like sequences and those with strongest freshwater influence were dominated by Nitrosomonas oligotropha- like sequences. Nitrosomonas sp. Nm143 was the prevailing sequence type in communities at intermediate brackish sites. Diversity indices of AOB communities were similar at marine- and freshwater-influenced sites and did not indicate lower species diversity at intermediate brackish sites. The presence of sequences highly similar to the halophilic Nitrosomonas marina and the freshwater strain Nitrosomonas oligotropha at identical sampling sites indicates that AOB communities in the estuary are adapted to a range of salinities, while individual strains may be active at different salinities. Ammonia-oxidizing bacteria communities that were dominated by Nitrosospira cluster 1 sequence types, for which no cultured representative exists, were subjected to stable isotope probing (SIP) with 13C-HCO3,, to label the nucleic acids of active autotrophic nitrifiers. Analysis of 13C-associated 16S rRNA gene fragments, following CsCl density centrifugation, by cloning and DGGE indicated sequences highly similar to the AOB Nitrosomonas sp. Nm143 and Nitrosomonas cryotolerans and to the nitrite oxidizer Nitrospira marina. No sequence with similarity to the Nitrosospira cluster 1 clade was recovered during SIP analysis. The potential role of Nitrosospira cluster 1 in autotrophic ammonia oxidation therefore remains uncertain. [source] Development of an ex vivo model for the study of microbial infection in human teethINTERNATIONAL ENDODONTIC JOURNAL, Issue 5 2007B. Patel Aims, (1) To infect human teeth artificially to mimic root canal and dentine infection, using the Constant Depth Film Fermenter (CDFF); (2) To verify the similarity of the infections to those found, in vivo, using culture and microscopy (SEM, LM and TEM). Methodology, Human teeth [n = 38 and n = 28, for phases I (preliminary) and II (definitive), respectively] were infected within the CDFF for a period of 28 days and at pre-selected time points were removed, externally decontaminated using validated protocols and subjected to either culture-dependent or microscopy protocols. The condition of the teeth was varied in phase I to establish the feasibility of the approach and identify optimal conditions. This informed the selection of optimal conditions for definitive test in phase II. For culture-dependent analysis in this phase, a dentine filing sample was obtained from the apical 5 mm of the root canal and cultured anaerobically to allow isolation of individual strains. Bacterial DNA was extracted from purified isolates, the 16S rRNA genes amplified by PCR and the amplicons sequenced for identity using sequence databases. Teeth assigned for microscopy were post-fixed in 3% gluteraldehyde after removal from the CDFF and then subjected to appropriate protocols prior to microscopic evaluation of the infection. Results, All three microscopy techniques and culture-dependent analysis confirmed infection of the human teeth using the CDFF, with root canal infections visually resembling closely those seen in vivo. Furthermore, partial 16S rRNA gene sequencing of DNA from cultured isolates confirmed a selective number of 7,9 genera/species in the apical portion of two teeth each at 7 and 28 days; these taxa are also commonly recovered from teeth with apical periodontitis, in vivo. There were no objective measures other than speciation and topographical evaluation to compare the artificial and real (in vivo) infections. Conclusions, The proposed ex vivo model has the potential for development into an investigative tool for studying the dynamics of bacterial ecology in infected root canals, both before and after treatment. Its advantage is the ability to control both the abiotic and biotic factors. There is a need for the development of objective measures to compare artificial and real bacterial biofilms. [source] Factors affecting the attachment of micro-organisms isolated from ultrafiltration and reverse osmosis membranes in dairy processing plantsJOURNAL OF APPLIED MICROBIOLOGY, Issue 2 2009X. Tang Abstract Aims:, To identify the types of micro-organisms involved in the formation of biofilms on dairy ultrafiltration and reverse osmosis membranes and investigate factors affecting the attachment of those isolates. Methods and Results:, Micro-organisms isolated from industrial membranes following standard cleaning were identified using the API culture identification system. Thirteen different isolates representing eight genera were isolated and their ability to attach to surfaces was compared using a microtitre plate assay. Three Klebsiella strains attached best, while mixed strains of Pseudomonas and Klebsiella attached better than individual strains. Whey enhanced the attachment of the isolates. The micro-organisms were characterized according to cell surface hydrophobicity using the microbial adhesion to hydrocarbon (MATH) test, and cell surface charge by measuring the zeta potential. These cell surface characteristics did not show a clear relationship with the attachment of our strains. Conclusions:, A variety of different micro-organisms is associated with dairy ultrafiltration and reverse osmosis membranes after cleaning, suggesting several possible sources of contamination. The cleaning of these membranes may be inadequate. The attachment of the different isolates is highly variable and enhanced in the presence of whey. Significance and Impact of the Study:, Knowledge of persistent microflora colonizing dairy membrane systems will help develop strategies to mitigate biofilm development in this environment, improving hygiene in membrane processing plants. [source] Plant growth promotion and biological control of Pythium aphanidermatum, a pathogen of cucumber, by endophytic actinomycetesJOURNAL OF APPLIED MICROBIOLOGY, Issue 1 2009K.A. El-Tarabily Abstract Aims:, To evaluate the potential of Actinoplanes campanulatus, Micromonospora chalcea and Streptomyces spiralis endophytic in cucumber roots, to promote plant growth and to protect seedlings and mature plants of cucumber from diseases caused by Pythium aphanidermatum, under greenhouse conditions. Methods and Results:, Three endophytic isolates, out of 29, were selected through tests aimed at understanding their mechanisms of action as biocontrol agents and plant growth promoters. When applied individually or in combination, they significantly promoted plant growth and reduced damping-off and crown and root rot of cucumber. The combination of the three isolates resulted in significantly better suppression of diseases and plant growth promotion, than where the plants were exposed to individual strains. Conclusions:, The three selected actinomycete isolates colonized cucumber roots endophytically for 8 weeks, promoted plant growth and suppressed pathogenic activities of P. aphanidermatum on seedling and mature cucumber plants. Significance and Impact of the Study:, The results clearly show that the endophytic, glucanase-producing actinomycetes used, especially as a combined treatment, could replace metalaxyl, which is the currently recommended fungicide for Pythium diseases in the United Arab Emirates. These endophytic isolates also have the potential to perform as plant growth promoters, which is a useful attribute for crop production in nutrient impoverished soils. [source] Amplified fragment length polymorphism (AFLP) and biochemical typing of Photobacterium damselae subsp. damselaeJOURNAL OF APPLIED MICROBIOLOGY, Issue 4 2002S. Botella Aims: The aim of the present study was to characterize subspecifically Photobacterium damselae subsp. damselae strains isolated from cultured Sparus aurata and Dicentrarchus labrax by means of phenotypic and molecular typing techniques (amplified fragment length polymorphism, AFLP). Methods and Results: Seventy-one strains of P. damselae subsp. damselae were isolated from 38 cultured fishes at different fish farms located on the Mediterranean coast near Valencia, Spain. Most fish studied were asymptomatic and some were recovered during infectious outbreaks. Phenotypic characterization revealed a considerable degree of variability within the subspecies, including some characters, such as production of urease, which are used to differentiate P. damselae subsp. damselae from P. damselae subsp. piscicida. Genetic characterization was conducted on a selection of 33 strains, including two reference strains. Dice coefficient (Sd) and the unweighted pair group method with average linkage (UPGMA) were used for numerical analysis of banding patterns. AFLP type was defined on the basis of 100% similarity in the dendrogram obtained, yielding 24 distinct AFLP profiles. At 70% similarity, 13 clusters were defined, thus confirming the great variability observed for the phenotypic traits. Conclusions: The AFLP variability shown by the isolates was high enough to discriminate between different strains which colonize the same fish. However, closely related AFLP types were usually derived from strains isolated at the same fish farm, indicating an epidemiological relationship. Significance and Impact of the Study: This study has confirmed that the AFLP technique allows discrimination of individual strains within P. damselae subsp. damselae for epidemiological studies, and that this subspecies exhibits greater variability than that described for subspecies piscicida. [source] The influence of extracellular H2O2 production on decolorization ability in fungiJOURNAL OF BASIC MICROBIOLOGY, Issue 6 2006Ivana Eichlerová Dr. A set of 50 randomly chosen fungal strains belonging to different basidiomycete species was tested for H2O2 and ligninolytic enzyme production and for decolorization of synthetic dyes Orange G and Remazol Brilliant Blue R. The decolorization capacity of individual strains was influenced by the level of H2O2 and laccase activity. The strains producing H2O2 at a concentration of 1.0,1.5 µM exhibited the most efficient decolorization; higher or lower H2O2 concentration reduced this ability. None of the strains without a detectable laccase activity was able to decolorize the tested dyes. (© 2006 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] VARIATION OF LAG TIME AND SPECIFIC GROWTH RATE AMONG 11 STRAINS OF SALMONELLA INOCULATED ONTO STERILE GROUND CHICKEN BREAST BURGERS AND INCUBATED AT 25C,JOURNAL OF FOOD SAFETY, Issue 4 2000THOMAS P. OSCAR ABSTRACT One strain of 11 serotypes or 11 strains of Salmonella, which were isolated from the ceca of broilers, were surveyed for their growth kinetics on sterile ground chicken breast burgers incubated at 25C to determine the variation of lag time and specific growth rate. Growth curves, four per strain, were fit to a two-phase linear model to determine lag time (h) and specific growth rate (log10/h). Repeatability of growth kinetics measurements for individual strains had a mean coefficient of variation of 11.7% for lag time (range: 5.8 to 17.3%) and a mean coefficient of variation of 6.7% for specific growth rate (range: 2.7 to 13.3%). Lag time among strains ranged from 2.2 to 3.1 h with a mean of 2.8 h for all strains, whereas specific growth rate among strains ranged from 0.3 to 0.38 log10 per h with a mean of 0.35 log10per h for all strains. One-way analysis of variance indicated that lag time (P =0.029) and specific growth rate (P =0.025) differed slightly among strains. S. Haardt had a shorter (P < 0.05) lag time than S. Agona and S. Brandenburg, whereas the specific growth rate of S. Enteritidis was less than (P < 0.05) the specific growth rates of S. Typhimurium and S. Brandenburg. All other strains had similar lag times and specific growth rates. The coefficient of variation among strains was 9.4% for lag time and 5.7% for specific growth rate. These results indicate that there were only minor differences in the lag times and specific growth rates among the strains of Salmonella surveyed. Thus, the growth kinetic values obtained with one strain of Salmonella may be useful for predicting the growth of other strains of Salmonella for which data do not currently exist. [source] In vitro fermentability of human milk oligosaccharides by several strains of bifidobacteriaMOLECULAR NUTRITION & FOOD RESEARCH (FORMERLY NAHRUNG/FOOD), Issue 11 2007Robert E. Ward Abstract This study was conducted to investigate the catabolism and fermentation of human milk oligosaccharides (HMO) by individual strains of bifidobacteria. Oligosaccharides were isolated from a pooled sample of human milk using solid-phase extraction, and then added to a growth medium as the sole source of fermentable carbohydrate. Of five strains of bifidobacteria tested (Bifidobacterium longum biovar infantis, Bifidobacterium bifidum, Bifidobacterium longum biovar longum, Bifidobacterium breve, and Bifidobacterium adolescentis), B. longum bv. infantis grew better, achieving triple the cell density then the other strains. B. bifidum did not reach a high cell density, yet generated free sialic acid, fucose and N-acetylglucosamine in the media, suggesting some capacity for HMO degradation. Thin layer chromatography profiles of spent fermentation broth suggests substantial degradation of oligosaccharides by B. longum bv. infantis, moderate degradation by B. bifidum and little degradation by other strains. While all strains were able to individually ferment two monosaccharide constituents of HMO, glucose and galactose, only B. longum bv. infantis and B. breve were able to ferment glucosamine, fucose and sialic acid. These results suggest that as a potential prebiotic, HMO may selectively promote the growth of certain bifidobacteria strains, and their catabolism may result in free monosaccharides in the colonic lumen. [source] Classical sheep transmissible spongiform encephalopathies: pathogenesis, pathological phenotypes and clinical diseaseNEUROPATHOLOGY & APPLIED NEUROBIOLOGY, Issue 4 2007M. Jeffrey Scrapie is a prion disease or transmissible spongiform encephalopathy (TSE) of sheep, goats and moufflon. As with its human counterparts, pathology consists of vacuolation, gliosis and accumulations of abnormal forms of a host prion protein (PrPd) in the brain of affected individuals. Immunohistochemical methods can be used to identify both the intracellular truncation sites of PrPd in different cell types (PrPd epitope mapping) and the different morphological patterns of accumulation (PrPd profiling). Differences in the inferred truncation sites of PrPd are found for different strains of sheep TSEs and for different infected cell types within individual strains. Immunochemical methods of characterizing strains broadly correspond to PrPd mapping discriminatory results, but distinct PrPd profiles, which provide strain- and source-specific information on both the cell types which sustain infection (cellular tropisms) and the cellular processing of PrPd, have no immunoblotting counterparts. The cause of neurological dysfunction in human is commonly considered to be neuronal loss secondary to a direct or indirect effect of the accumulation of PrPd. However, in sheep scrapie there is no significant neuronal loss, and relationships between different magnitudes, topographical and cytological forms of PrPd accumulation and clinical signs are not evident. PrPd accumulation also occurs in lymphoid tissues, for which there is indirect evidence of a pathological effect, in the peripheral nervous system and in other tissues. It is generally assumed that neuroinvasion results from infection of the enteric nervous system neurones subsequent to amplification of infectivity in lymphoid tissues and later spread via sympathetic and parasympathetic pathways. The evidence for this is, however, circumstantial. Accumulation of PrPd and presence of infectivity in tissues other than the nervous and lymphoreticular systems gives insights on the ways of transmission of infection and on food safety. [source] Rhizobacteria-mediated resistance against the blackeye cowpea mosaic strain of bean common mosaic virus in cowpea (Vigna unguiculata)PEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 10 2009Arakere Chunchegowda Udaya Shankar Abstract BACKGROUND: The present study investigated the effect of seven Bacillus -species plant-growth-promoting rhizobacteria (PGPR) seed treatments on the induction of disease resistance in cowpea against mosaic disease caused by the blackeye cowpea mosaic strain of bean common mosaic virus (BCMV). RESULTS: Initially, although all PGPR strains recorded significant enhancement of seed germination and seedling vigour, GBO3 and T4 strains were very promising. In general, all strains gave reduced BCMV incidence compared with the non-bacterised control, both under screen-house and under field conditions. Cowpea seeds treated with Bacillus pumilus (T4) and Bacillus subtilis (GBO3) strains offered protection of 42 and 41% against BCMV under screen-house conditions. Under field conditions, strain GBO3 offered 34% protection against BCMV. The protection offered by PGPR strains against BCMV was evaluated by indirect enzyme-linked immunosorbent assay (ELISA), with lowest immunoreactive values recorded in cowpea seeds treated with strains GBO3 and T4 in comparison with the non-bacterised control. In addition, it was observed that strain combination worked better in inducing resistance than individual strains. Cowpea seeds treated with a combination of strains GBO3 + T4 registered the highest protection against BCMV. CONCLUSION: PGPR strains were effective in protecting cowpea plants against BCMV under both screen-house and field conditions by inducing resistance against the virus. Thus, it is proposed that PGPR strains, particularly GBO3, could be potential inducers against BCMV and growth enhancers in cowpea. Copyright © 2009 Society of Chemical Industry [source] Recent developments in the molecular discrimination of formae speciales of Fusarium oxysporumPEST MANAGEMENT SCIENCE (FORMERLY: PESTICIDE SCIENCE), Issue 8 2008Bart Lievens Abstract Rapid and reliable detection and identification of potential plant pathogens is required for taking appropriate and timely disease management measures. For many microbial species of which all strains generally are plant pathogens on a known host range, this has become quite straightforward. However, for some fungal species this is quite a challenge. One of these is Fusarium oxysporum Schlechtend:Fr., which, as a species, has a very broad host range, while individual strains are usually highly host-specific. Moreover, many strains of this fungus are non-pathogenic soil inhabitants. Thus, with regard to effective disease management, identification below the species level is highly desirable. So far, the genetic basis of host specificity in F. oxysporum is poorly understood. Furthermore, strains that infect a particular plant species are not necessarily more closely related to each other than to strains that infect other hosts. Despite these difficulties, recently an increasing number of studies have reported the successful development of molecular markers to discriminate F. oxysporum strains below the species level. Copyright © 2008 Society of Chemical Industry [source] | ||||||||||||||||