bluuebunny/crossref_metadata_2025_split huggingface dataset:
Numerical classification and identification ofAcinetobactergenomic species
Authors: Kämpfer P. , Tjernberg Ingela , Ursing J. 
Published: March 2008

A total of 211Acinetobacterstrains (representing all currently recognized genomic species) were tested for 329 biochemical characters. Overall similarities of all strains were determined for 145 characters by numerical taxonomic techniques, the UPGMA algorithm and theSSMand theSJcoefficients as measures of similarity. Seven clusters (two or more strains) and three unclustered strains were recovered at a similarity level of 80.0% (SSM). At this level a complete correspondence between phenotypic cluster and genomic species was found only for genomic species 12 (Ac. radioresistens). At higher similarity levels (84.0% to 84.6% (SSM)), however, several subclusters were found, each representing a single genomic species. An exception were the strains belonging to the genetically closely related species of theAcinetobacter calcoaceticus‐baumanniicomplex. These were recovered scattered in several subclusters. The degree of genomic relatedness between some DNA groups correlated with phenotypic similarities, especially for DNA group 8 (Ac. lwoffii) and 15 of Tjernberg and Ursing, and for DNA group 4 (Ac. haemolyticus) and 6.For the majority of genomic species, two identification matrices were constructed consisting of 22 and 10 diagnostic characters, respectively. The correct identification rates for the matrices were 98.0% (22 tests) and 90.8% (10 tests) taking a Willcox probability >0.9. For unambiguous identification of some genomic species, however, additional methods (preferably DNA‐DNA hybridization or ribotyping) should be used.
Detection by in vitro amplification of the alpha‐toxin (phospholipase C) gene from Clostridium perfringens
Authors: Fach P. , Guillou J.P. 
Published: March 2008

A polymerase chain reaction (PCR) with thermostable DNA polymerase from Thermus aquaticus is described for the specific amplification of the phospholipase C (alpha‐toxin) gene of Clostridium perfringens. A set of primers selected for their high specificity could detect Cl. perfringens in stools with a detection limit of approximately 5 x 102 bacteria, after bi‐amplification. A modified PCR without thermal steps was performed to rapidly amplify, with a yield of 60%, the DNA template. With this PCR method Cl. perfringens alpha‐toxin gene could be detected within 2 h. The PCR method detected alpha‐toxin positive Cl. perfringens but did not react with phospholipase C‐producing Bacillus cereus, Pseudomonas aeruginosa, Cl. sordellii and Cl. bifermentans.The amplified PCR products were screened through ethidium bromide agarose gel electrophoresis or, in only 1 h, with the PhastSystem (Pharmacia). This PCR satisfies the criteria of specificity, sensitivity and rapidity required for a useful tool in epidemiology and for the diagnosis of the pathogen Cl. perfringens as it may be used directly on stool samples.
The production of antifungal volatiles by Bacillus subtilis
Authors: Fiddaman P.J. , Rossall S. 
Published: March 2008

A strain of Bacillus subtilis which produces an antibiotic metabolite was also found to produce a volatile compound(s) which was antifungal to Rhizoctonia solani and Pythium ultimum.Growth of the fungi was severely impaired in the presence of the volatiles and physiological abnormalities of the hyphae were observed, including hyphal distortion and vacuolation. A range of media were tested for volatile production and potato dextrose agar (PDA) was found to be the most active. Temperature had a considerable effect on antifungal volatile activity with the greatest inhibition occurring at 30°C. Addition of iron (III) chloride to Sabouraud's glucose agar (SGA) also enhanced the antifungal effect. The volatiles were found to be water soluble and remained active when trapped in SGA.
Time‐resolved fluoroimmunoassay as a method for detection of Erwinia chrysanthemi in potato peel extracts
Authors: van der Wolf J.M. 
Published: March 2008

J.M. VAN DER WOLF. 1993. Time‐resolved fluoroimmunoassay (TR‐FIA) was compared with double antibody sandwich (DAS)‐ELISA for detection of Erwinia chrysanthemi antigens in potato peel extracts. Pure cultures were used to optimize TR‐FIA with respect to the microplate washing procedure and dilution buffer compositions.The detection threshold level for spiked potato peel extracts with the optimized TR‐FIA format was 105 cells ml‐1 as for the detection level of DAS‐ELISA. The signal to background ratios at concentrations above 105 cells ml‐1 were higher with TR‐FIA than with DAS‐ELISA. The dynamic range of TR‐FIA was also superior to that of DAS‐ELISA.It can be concluded that TR‐FIA is an attractive alternative to DAS‐ELISA as a detection method for Erw. chrysanthemi, especially when quantification is required.
Comparison of Signal and Bactec NR‐660 blood culture systems
Authors: Stevens M. , Prentice M.B. , Swann R.A. , Mitchell C.J. , Donkin A. 
Published: March 2008

M. STEVENS, M.B. PRENTICE, R.A. SWANN, C.J. MITCHELL AND A. DONKIN. 1993. The Signal blood culture system was compared with the Bactec NR‐660. A total of 1617 blood culture sets yielded 143 (8.8%) significant isolates; 113 (79.0%) were from positive bottles in both the Bactec and Signal systems. Twelve organisms (8.4%) were detected and isolated from the Signal system only and another 18 (12.6%) from the Bactec system only. Of these 18, five were Signal‐positive but the organism was not recovered and four organisms were isolated from negative Signal bottles on terminal subculture. The time taken to detection for each system was similar; the Signal system detected 68% and the Bactec 63% of significant positives within 24 h. At 48 h Bactec detected 91% and the Signal 85%. A significantly‐reduced number of bottles which gave a positive signal but were negative by microscopical and cultural methods was found, compared with previous reports. The 1 h incubation period prior to the insertion of the Signal growth indicator device was considered to be the cause of this reduction in the proportion of false positives.Fifty‐five percent (42/77) of the Bactec false positives were due to delta growth value. This is when there is an increase in the growth index of ≥ 15 without the positive threshold level of 30 being attained. This occurred in the anaerobic bottle on day 2 with 42 bottles. Another 40% (31/77) of the false positives had a growth value between the positive threshold of 30 and a value of 35.Eighty (4.9%) of Bactec and 65 (4.0%) of Signal sets yielded clinically non‐significant isolates. Although the yield of significant isolates for the two systems was similar, Signal failed to detect a small number of medically important organisms without subculture.
The effect of electron beam irradiation and modified pH on the survival and recovery of Escherichia coli
Authors: Flelding L.M. , Cook P.E. , Grandison A.S. 
Published: March 2008

The severity of radiation processing can be reduced by combining irradiation with other treatments, such as low pH. An exponential phase culture of Escherichia coli was irradiated at doses of 0–2.4 kGy at pH values ranging between 7.0 and 4.0, in an enriched nutrient broth.At pH 4.3 and above there was no significant effect of lowering the pH prior to irradiation. At pH 4.13 and 4.0, a much higher level of cell death occurred compared with irradiation at pH 7.0. This synergistic effect was observed only when the pH was lowered before radiation processing.
Factors that interact with the antibacterial action of thyme essential oil and its active constituents
Authors: Juven B.J. , Kanner J. , Schved F. , Weisslowicz H. 
Published: March 2008

The viable counts of Salmonella typhimurium on nutrient agar (NA) decreased upon the addition of either the essential oil of thyme or its constituent thymol, especially under anaerobic conditions. Antagonistic effects of thymol against Staphylococcus aureus were also greater under anaerobic conditions. In contrast to the phenolic constituents of the oil, thymol and carvacrol, the chemically related terpenes p‐cymene and y‐terpinene had no antagonistic effects against Salm. typhimurium.The addition of Desferal to NA counteracted the antibacterial effects of both thyme oil and thymol. No support was obtained, however, for a possible role of iron in the oxygen‐related antibacterial action of the thyme oil and thymol or for the observed effect of Desferal. In the presence of thymol, the viable counts of Salm. typhimurium obtained on a minimal medium (MM) were lower than those obtained on NA. Addition of bovine serum albumin (BSA) neutralized the antibacterial action of thymol. It is suggested that the effects of BSA or Desferal are due to their ability to bind phenolic compounds through their amino and hydroxylamine groups, respectively, thus preventing complexation reactions between the oil phenolic constituents and bacterial membrane proteins. This hypothesis is supported by the marked decrease in the viable counts of Salm. typhimurium caused by either thyme oil or thymol when the pH of the medium was changed from 6.5 to 5.5 or the concentration of Tween 80 in the medium was reduced.
Growth rate and physiology of Yersinia enterocolitica; influence of temperature and presence of the virulence plasmid
Authors: Goverde Rosalina L. J. , Kusters J. G. , Huis in‘t Veld J. H. J. 
Published: March 2008

The effect of temperature on the growth rate, protein pattern and fatty acid composition of Yersinia enterocolitica strain W22703 pYV+, its plasmidless isogenic derivative W22703 pYV‐ and four recent field isolates was examined.The growth rate was clearly influenced by presence or absence of the virulence plasmid: pYV‐ strains grew consistently faster than pYV+ strains. This difference in growth rate was high at 30–35°C, moderate at 1–10°C and 25°C, but hardly significant at 15–20°C.Increasing the growth temperature above 25°C resulted in the induction of the 220 kDa virulence plasmid‐encoded Yop1 protein. In the 1–20°C range no obvious temperature‐ or plasmid‐related differences in protein patterns could be detected.The fatty acid composition showed a clear temperature‐dependent change: with all strains the degree of saturation was low at 1°C and gradually increased with raising temperatures. All strains had similar fatty acid patterns, except one of the field isolates which showed aberrant C16 : 1 and cyclic fatty acid contents in the 5–25°C and 15°C ranges respectively. With strain W22703, the presence or absence of the virulence plasmid did not significantly alter the fatty acid pattern.
Verification of ELISA results by immunomagnetic isolation of antigens from extracts and analysis with SDS‐PAGE and Western blotting, demonstrated for Erwinia spp. in potatoes
Authors: van der Wolf J.M. , van Beckhoven J.R.C.M. , de Vries Ph.M. , Vuurde J.W.L. van 
Published: March 2008

Isolation of antigens on immunomagnetic beads and subsequent analysis with SDS‐PAGE and Western blotting (immunomagnetic isolation‐Western blotting (IMI‐WB)) was used to verify positive ELISA results for Erwinia chrysanthemi and Erw. carotovora subsp. atroseptica in potato peel extracts. Direct analysis of highly contaminated extracts by Western blotting without previous immuno‐isolation resulted in background reactions, whereas immunomagnetic isolation resulted in distinct bands of specific antigens. Target cells as well as antigenic cell products were captured in IMI‐WB. Band patterns on IMI‐WB of cell‐free culture filtrates and cell suspensions were highly similar, but the removal of cells lowered the detection level by 10‐ to 100‐fold. Threshold levels of IMI‐WB were generally comparable with those of ELISA.No differences in threshold levels and band patterns were found between a direct format and an indirect format of immuno‐isolation.In IMI‐WB, blotting patterns differed between Erw. chrysanthemi and Erw. carotovora subsp. atroseptica. The patterns were identical for 15 Erw. chrysanthemi strains, isolated from potato peel extracts in The Netherlands. However, one of 15 strains of Erw. carotovora subsp. atroseptica from potato peel extracts in The Netherlands gave an aberrant pattern. Target bacteria could be easily distinguished from those of cross‐reacting strains on the basis of band patterns.Potato peel extracts naturally contaminated with Erw. chrysanthemi gave IMI‐WB patterns that were similar to pure cultures of the homologous strains.
Variations in concentrations of bacterial metabolites, enzyme activities, moisture, pH and bacterial composition between and within individuals in faeces of seven healthy adults
Authors: Ikeda N. , Saito Y. , Shimizu J. , Ochi A. , Mizutani J. , Watabe J. 
Published: March 2008

Variations between and within individuals, and correlations between concentrations of bacterial metabolites, including putrefactive products, ammonia and short chain fatty acids (SCFAs), enzyme activities, moisture and pH, as well as bacterial composition, were studied in faecal samples from seven healthy adults over a period of 7 months. Large variations, both between and within individuals, were observed in concentrations of putrefactive products. Although values for ammonia, SCFAs, enzyme activities, moisture and pH were generally variable, significant person‐to‐person differences were observed.While ranges of log viable counts of the predominant bacteria such as eubacteria, bifidobacteria and bacteroides in each subject remained between 0·2 and 1·3, those of enterobacteria, streptococci (including enterococci) and lecithinase‐negative clostridia varied between 0·4 and 3·0. Levels of bifidobacteria, enterobacteria, streptococci and total aerobic bacteria showed inter‐individual variations. Correlations were found among certain of the parameters: moisture correlated negatively with p‐cresol (r= ‐0·707), pH (r= ‐0–671) and β‐glucosidase activity (GS) (r= ‐0·608), and positively with acetic acid (r= 0·621), while negative correlations were observed in pH with acetic and butyric acids (r= ‐0·690 and ‐0·623, respectively).No significant correlations were found between bacterial compositions, and other faecal factors such as pH, moisture, metabolic enzyme activities and concentrations of putrefactive products.
Histamine production by wine lactic acid bacteria: isolation of a histamine‐producingstrain of Leuconostoc oenos
Authors: Lonvaud‐Funel Aline , Joyeux Annick 
Published: March 2008

Populations of Leuconostoc œnos were harvested from wines containing a relatively high concentration of biogenic amines. Cultivation of the biomass in synthetic media and wine showed that it consisted of histamine‐producing strains. Histamine levels after culture depended on the quantity of precursor available and on the presence of yeast lees, which certainly enriched the medium in histidine. Ethanol and pH, which control bacterial growth rate and total population, were also significant factors: pH and low ethanol concentration enhanced histamine production.Strain Leuc. œnos 9204 was isolated and studied since it retained its ability to produce histamine after several transfers. In synthetic medium this strain produced large amounts of histamine especially in the poorest nutritional conditions (no glucose, no L‐malic acid). These results clearly demonstrate that Leuc. œnos involvedin wine‐making might play a role in biogenic amine production. The vinification method might also influence the final amine concentration in wine.
Differential elimination of enteric bacteria by protists in a freshwater system
Authors: Iriberri J. , Azúa I. , Labirua‐Iturburu Ainhoa , Artolozaga Itxaso , Barcina Isabel 
Published: March 2008

J. IRIBERRI, I. AZÚA, A. LABIRUA‐ITURBURU, I. ARTOLOZAGA AND I. BARCINA. 1994. The short‐term (1 h) and long‐term (3 d) elimination of low and high densities of five enteric bacteria, Klebsiella pneumoniae, Aeromonas hydrophila, Escherichia coli, Enterococcus faecalis and Staphylococcus epidermidis, by flagellate and ciliate protists were measured in a freshwater system. In addition, the two processes, ingestion and digestion, which cause the disappearance of those enteric bacteria as time passes, were quantified.The results showed that the elimination of these enteric bacteria by protists depends on their initial density, which confirms that the lower the bacterial density the more difficult is their elimination. On the other hand, the short‐term and long‐term elimination rates of each enteric bacteria were different, and moreover, the order of priority for elimination in the two cases was not the same. Escherichia coli showed the highest elimination rate in short‐term experiments, while Aer. hydrophila disappeared at highest rates in long‐term experiments. This different order of priority in the elimination rates and the different digestion rates on the five enteric bacteria by phagotrophic protists indicated that the elimination in time is very much influenced by the digestive capacity on each enteric bacteria of those protists. Thus, the low digestion rates of Ent. faecalis and Staph. epidermidis by flagellates and ciliates as well as their low disappearance percentages in the long‐term experiments confirm that enteric Gram‐positive bacteria are eliminated from the aquatic systems at lower rates, because their digestion is difficult.
Comparative evaluation of plasmid profiling and ribotyping in the analysis of Lactobacillus plantarum strain heterogeneity in silage
Authors: Duffner Fiona , O'Connell M. 
Published: March 2008

F. DUFFNER AND M. O'CONNELL. 1995. Seventy‐two Lactobacillus plantarum isolates were recovered from six uninoculated grass silages for the purposes of firstly evaluating the usefulness of (1) restriction endonuclease digestion of total genomic DNA, (2) plasmid profiling and (3) ribotyping in Lact. plantarum strain differentiation and secondly, examining the strain heterogeneity in well preserved silage.The three methods for differentiation were applied to 72 of the isolates and allowed at least 32 different strains to be identified. Twenty‐five different plasmid profiles were detected (26 if the absence of plasmids is included as a profile). Ribotyping with Eco RI identified only 11 patterns among the silage isolates. A variety of restriction enzymes was screened to increase the sensitivity of ribotyping to detect strain differences and Bam HI was used successfully for this purpose, differentiating all of the strains tested.Two dominant strains (I and II) were identified in one particular silage, comprising 47% and 17% respectively of the isolates, while strains III and V comprised 37% and 25% of the Lact. plantarum population isolated from another of the silages.
Principles of separating micro‐organisms from suspensions using ultrasound
Authors: Miles C.A. , Morley M.J. , Hudson W.R. , Mackey B.M. 
Published: March 2008

C.A. MILES, M.J. MORLEY, W.R. HUDSON AND B.M. MACKEY. 1995. When particles in suspension are placed in a stationary ultrasonic field, they form bands of high concentration at half‐wavelength intervals. Several theoretical papers have recently contributed to an understanding of the process but, for particles as small as bacteria, there are substantial discrepancies between the different theories, and a lack of published observations.The threshold amplitudes required to band latex spheres (0.5‐5.0 μm diameter) were measured in the frequency range 1–3 MHz and used to establish conditions, reported here for the first time, suitable for banding and moving vegetative bacterial cells in pure culture. Ultrasonic means for separating and concentrating cream and bacteria at opposite ends of a tube containing a mixture of Escherichia coli and diluted milk are also described and the breakdown of theoretical equations at low particle size is discussed.
Influence of acidity and initial substrate temperature on germination of Rhizopus oligosporus sporangiospores during tempe manufacture
Authors: de Reu J.C. , Rombouts F.M. , Nout M.J.R. 
Published: March 2008

J.C. DE REU, F.M. ROMBOUTS AND M.J.R. NOUT. 1995. During the soaking of soya beans according to an accelerated acidification method organic acids were formed, resulting in a pH decrease from 6·0 to 3·9. After 24 h of fermentation at 30°C, lactic acid was the major organic acid (2·1% w/v soak water), while acetic acid (0·3% w/v soak water) and citric acid (0·5% w/v soak water) were also found. During cooking with fresh water (ratio raw beans: water, 1: 6·5) the concentrations of lactate/lactic acid and acetate/acetic acid in the beans were reduced by 45% and 51%, respectively.The effect of organic acids on the germination of Rhizopus olgosporus sporangiospores was studied in liquid media and on soya beans. Germination in aqueous suspensions was delayed by acetic acid: within 6 h no germination occurred at concentrations higher than 0·05% (w/v incubation medium), at pH 4·0. When soya beans were soaked in the presence of acetic acid, the inhibitory concentration depended on the pH after soaking. Lactic acid and citric acid enhanced germination in liquid medium, but not in tempe.Inoculation of soya beans with R. oligosporus at various temperatures followed by incubation at 30°C resulted in both increased and decreased periods for the lag phase of fungal growth. A maximum difference of 3 h lag phase was found between initial bean temperatures of 25 and 37°C.When pure cultures of homofermentative lactic acid bacteria were used in the initial soaking process, less lactic acid and acetic acid was formed during soaking than when the accelerated acidification method was used. This resulted in a reduction of the lag phase before growth of R. oligosporus by up to 4·7 h.
Microbiological profile in Serra ewes' cheese during ripening
Authors: Macedo A.C. , Malcata F.X. , Hogg T.A. 
Published: March 2008

The microflora of Serra cheese was monitored during a 35 d ripening period at three different periods within the ewe's lactation season. After 7 d ripening, the numbers of micro‐organisms reached their maximum, and lactic acid bacteria (LAB) and coliforms were the predominant groups. Pseudomonads were not detected after 1 week of ripening. At all stages of ripening, cheeses manufactured in spring exhibited the lowest numbers of LAB and yeasts, whereas cheeses manufactured in winter showed the lowest numbers of coliforms and staphylococci.Leuconostoc lactis was the most abundant LAB found in Serra cheese whereas Enterococcus faecium and Lactococcus lactis spp. lactis exhibited the highest decrease in percentage composition. Numbers of both Leuc. mesenteroides and Lactobacillus paracasei tended to increase throughout ripening. The most abundant coliform was Hafnia alvei. Klebsiella oxytoca was found in curd but declined in number during ripening. Staphylococcal flora of curd was mainly composed of Staphylococcus xylosus, Staph. aureus and Staph. epidermidis. Staphylococcus xylosus was the major species found at the end of ripening. Pseudomonas fluorescens, was the only Pseudomonas species isolated from the curd. Although a broad spectrum of yeasts were found in Serra cheese, Sporobolomyces roseus was the most abundant yeast isolated.