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P De Vos

Publications and source records attributed to P De Vos.

At least 19 recordsLinked to original sources
PubMed2006

Validation of the correct start codon of norX/nxrX and universality of the norAXB/nxrAXB gene cluster in nitrobacter species.

The complete norX/nxrX sequence of five Nitrobacter strains was determined showing that the norAXB/nxrAXB gene cluster is present in all hitherto described Nitrobacter species. Evidence is provided that the previously published sequence of norX in N. hamburgensis X14(T) contains an invalid base "insertion," which resulted in a frameshift and a misidentified start codon.

Codon, Initiator↗
PubMed2005

Brevibacillus levickii sp. nov. and Aneurinibacillus terranovensis sp. nov., two novel thermoacidophiles isolated from geothermal soils of northern Victoria Land, Antarctica.

Thirteen strains of endospore-forming bacteria were isolated from geothermal soils at Cryptogam Ridge, the north-west slope of Mt Melbourne, and at the vents and summit of Mt Rittmann in northern Victoria Land, Antarctica. 16S rRNA gene sequencing, SDS-PAGE and routine phenotypic characterization tests indicated that the seven isolates from the north-west slope of Mt Melbourne represent a novel species of Brevibacillus and that the six isolates from Cryptogam Ridge and the vents and summit of Mt Rittmann represent a novel species of Aneurinibacillus. Brevibacillus strains were not isolated from the sites at Mt Rittmann or Cryptogam Ridge and Aneurinibacillus strains were not isolated from the north-west slope of Mt Melbourne. Preliminary metabolic studies revealed that L-glutamic acid, although not essential for growth, was utilized by both species. The Brevibacillus species possessed an uptake system specific for L-glutamic acid, whereas the Aneurinibacillus species possessed a more general uptake system capable of transporting other related amino acids. Both species utilized a K(+) antiport system and similar energy systems for the uptake of l-glutamic acid. The rate of uptake by the Brevibacillus species type strain was 20-fold greater than that shown by the Aneurinibacillus species type strain. The names Brevibacillus levickii sp. nov. and Aneurinibacillus terranovensis sp. nov. are proposed for the novel taxa; the type strains are Logan B-1657(T) (= LMG 22481(T) = CIP 108307(T)) and Logan B-1599(T) (LMG 22483(T) = CIP 108308(T)), respectively.

Amino Acid Transport Systems↗
PubMed2005

Failure of the ammonia oxidation process in two pharmaceutical wastewater treatment plants is linked to shifts in the bacterial communities.

AIMS: To investigate whether two different wastewater treatment plants (WWTPs) -- treating the same pharmaceutical influent -- select for a different bacterial and/or ammonia oxidizing bacterial (AOB) community. METHODS AND RESULTS: Molecular fingerprinting demonstrated that each WWTP had its own total bacterial and AOB community structure, but Nitrosomonas eutropha and N. europea were dominant in both WWTP A and B. The DNA and RNA analysis of the AOB communities revealed different patterns; so the most abundant species may not necessarily be the most active ones. Nitritation failures, monitored by chemical parameter analysis, were reflected as AOB community shifts and visualized by denaturing gradient gel electrophoresis (DGGE)-based moving window analysis. CONCLUSIONS: This research demonstrated the link between functional performance (nitritation parameters) and the presence and activity of a specific microbial ecology (AOB). Clustering and moving window analysis based on DGGE showed to be valuable to monitor community shifts in both WWTPs. SIGNIFICANCE AND IMPACT OF THE STUDY: This study of specific community shifts together with functional parameter analysis has potential as a tool for relating functional instability (such as operational failures) to specific-bacterial community shifts.

Ammonia↗
PubMed2005

Pseudomonads associated with midrib rot and soft rot of butterhead lettuce and endive.

During the past ten years, bacterial soft rot and midrib rot of glasshouse-grown butterhead lettuce (Lactuca sativa L. var. capitata) and field-grown endive (Cichorium endivia L.) has become increasingly common in the region of Flanders, Belgium. Severe losses and reduced market quality caused by bacterial rot represent an important economical threat for the production sector. Symptoms of midrib rot are a brownish rot along the midrib of one or more inner leaves, often accompanied by soft rot of the leaf blade. Twenty-five symptomatic lettuce and endive samples were collected from commercial growers at different locations in Flanders. Isolations of dominant bacterial colony types on dilution plates from macerated diseased tissue extracts yielded 282 isolates. All isolates were characterized by colony morphology and fluorescence on pseudomonas agar F medium, oxidase reaction, and soft rot ability on detached chicory leaves. Whole-cell fatty acid methyl esters profile analyses identified the majority of isolates (85%) as belonging to the Gammaproteobacteria, which included members of the family Enterobacteriaceae (14%) and of the genera Pseudomonas (73%), Stenotrophomonas (9%), and Acinetobacter (3%). Predominant bacteria were a diverse group of fluorescent Pseudomonas species. They were further differentiated based on the non-host hypersensitive reaction on tobacco and the ability to rot potato slices into 4 phenotypic groups: HR-/P- (57 isolates), HR-/P+ (54 isolates), HR+/P (16 isolates) and HR+/P+ (35 isolates). Artificial inoculation of suspensions of HR-, pectolytic fluorescent pseudomonads in the leaf midrib of lettuce plants produced various symptoms of soft rot, but they did not readily cause symptoms upon spray inoculation. Fluorescent pseudomonads with phenotype HR+ were consistently isolated from typical dark midrib rot symptoms, and selected isolates reproduced the typical midrib rot symptoms when spray-inoculated onto healthy lettuce plants.

Cichorium intybus↗
PubMed2004

Effect of culture conditions on the achievable taxonomic resolution of Raman spectroscopy disclosed by three Bacillus species.

Confocal micro-Raman spectroscopy requires a minimum of sample handling and no reagents and allows fast identification of microorganisms. Since it reflects the overall molecular composition of the cells, it provides much more information than classical, microbial analyses. However, since the molecular makeup of a cell depends on culture conditions, it can be argued that this will affect the reproducibility and discrimination ability of Raman spectroscopy. We used Bacillus cereus, Bacillus pumilus, and Bacillus licheniformis, which are known to be clearly distinct from each other and each displaying important phenotypic heterogeneity, in a wide variety of culture conditions to analyze this. It is illustrated that the influence of culture conditions on the identification accuracy and taxonomic resolution of Raman spectroscopy is important though the effect on the final identification is limited within the set of stains studied. Furthermore, some conditions even allow for better discrimination than others. From a practical point of view, it is especially important that differences in culturing time (and culturing temperature) can be accommodated.

Bacillus↗
PubMed2004

Isolation and biodiversity of hitherto undescribed soil bacteria related to Bacillus niacini.

The hitherto largely not described phylogenetic neighborhood of Bacillus niacini has been explored by a comprehensive cultivation experiment and genomic variety studies. Previous culture-independent studies demonstrated that approximately 15% of all Bacillus 16S rDNA directly extracted from soils worldwide was affiliated to B. niacini. Seven different media were inoculated with soil suspensions in serial dilutions and incubated at different temperatures. Then, bacterial colonies were picked and analyzed by sequencing. A mineral medium with acetate as carbon source yielded a B. niacini rate of >3% of all picked colonies. Other media were less efficient but also successful. Applying this culturing approach, we succeeded in obtaining 64 isolates from different Dutch soils. The isolates turned out to be diverse, although closely related to B. niacini as revealed by 16S rDNA sequencing. Close matches with environmental clones were also found, thus demonstrating much more diversity beyond previously known 16S rDNA sequences. The rep-PCR fingerprinting method revealed a high genomic variety, redundancy could not be observed among our isolates. Hence, the hitherto neglected B. niacini lineage, apparently among the most abundant soil Bacillus, was accessible to our cultivation approach.

Bacillus↗
PubMed2004

Screening of bacterial contamination during gelatine production by means of denaturing gradient gel electrophoresis, focussed on Bacillus and related endospore-forming genera.

AIMS: To screen for bacterial contamination during gelatine production by means of denaturing gradient gel electrophoresis (DGGE). As members of Bacillus and related genera were found to persist in the final product, this study focussed on these taxa. METHODS AND RESULTS: Template DNA was extracted from gelatine samples at five crucial points of a gelatine production process. A primer specific for Bacillus and related genera was designed and used in a selective PCR, followed by a nested DGGE-PCR targeting the V9 region of the 16S rDNA. DGGE analysis of the resulting amplicons, and sequence analysis of selected bands, showed high sequence similarities of these bands with Bacillus fumarioli, B. licheniformis, B. coagulans and Clostridium perfringens. When the selective PCR was omitted, primarily Lactobacillus bands were retrieved. CONCLUSIONS: PCR-DGGE analysis of gelatine extracts can be used for tracing and screening of bacterial contamination during gelatine production. A selective PCR, nested with DGGE-PCR, gave much more accurate information about endospore-forming contaminants than did the direct DGGE procedure alone. SIGNIFICANCE AND IMPACT OF THE STUDY: Use of this nested DGGE-PCR protocol may provide important information about possible hazards to the final microbiological quality and/or safety of gelatine, so allowing production parameters and/or remediation procedures may be adjusted on-line.

Bacillus↗
PubMed2004

Design of a 5' exonuclease-based real-time PCR assay for simultaneous detection of Bacillus licheniformis, members of the 'B. cereus group' and B. fumarioli in gelatine.

AIMS: The design of a fast, sensitive and specific detection method for Bacillus licheniformis, members of the 'B. cereus group' and B. fumarioli in gelatine. METHODS AND RESULTS: Specific Taqman probes were designed and tested in a real-time PCR setting. A specific fluorescent signal could be obtained for all gelatine isolates attributed to these species in one single real-time PCR reaction. After sample preparation, a gelatine sample spiked with 1 CFU provided enough template DNA for a significant signal. CONCLUSION: The potential of a real-time PCR assay for simultaneous detection of B. licheniformis, members of the 'B. cereus group' and B. fumarioli in gelatine is demonstrated. SIGNIFICANCE AND IMPACT OF THE STUDY: Implementation of the assay in gelatine producing plants may shorten delivery terms and inform on hazards to public health and suitable remediation procedures.

Bacillus↗
PubMed2004

Isolation, characterization, and identification of bacterial contaminants in semifinal gelatin extracts.

Bacterial contamination of gelatin is of great concern. Indeed, this animal colloid has many industrial applications, mainly in food and pharmaceutical products. In a previous study (E. De Clerck and P. De Vos, Syst. Appl. Microbiol. 25:611-618), contamination of a gelatin production process with a variety of gram-positive and gram-negative bacteria was demonstrated. In this study, bacterial contamination of semifinal gelatin extracts from several production plants was examined. Since these extracts are subjected to harsh conditions during production and a final ultrahigh-temperature treatment, the bacterial load at this stage is expected to be greatly reduced. In total, 1,129 isolates were obtained from a total of 73 gelatin batches originating from six different production plants. Each of these batches was suspected of having bacterial contamination based on quality control testing at the production plant from which it originated. For characterization and identification of the 1,129 bacterial isolates, repetitive-element PCR was used to obtain manageable groups. Representative strains were identified by means of 16S rRNA gene sequencing, species-specific gyrB PCR, and gyrA and rpoB sequencing and were tested for gelatinase activity. The majority of isolates belonged to members of Bacillus or related endospore-forming genera. Representative strains were identified as Bacillus cereus, Bacillus coagulans, Bacillus fumarioli, Bacillus amyloliquefaciens, Bacillus licheniformis, Bacillus pumilus, Bacillus sonorensis, Bacillus subtilis, Bacillus gelatini, Bacillus thermoamylovorans, Anoxybacillus contaminans, Anoxybacillus flavithermus, Brevibacillus agri, Brevibacillus borstelensis, and Geobacillus stearothermophilus. The majority of these species include strains exhibiting gelatinase activity. Moreover, some of these species have known pathogenic properties. These findings are of great concern with regard to the safety and quality of gelatin and its applications.

Animals↗
PubMed2003

Properties of Bacillus thuringiensis isolated from bank voles.

AIMS: To assess the properties of B. thuringiensis naturally occurring in the intestines of bank voles. METHODS AND RESULTS: Seventeen Bacillus thuringiensis strains, exhibiting typical growth on selective medium for the B. cereus group and characterized by the ability to produce parasporal crystals, were isolated from bank voles trapped in the Łomza Landscape Park of the Narew River Valley (north-east Poland). All isolates were characterized by pulsed field gel electrophoresis (PFGE) of chromosomal DNA and SDS polyacrylamide gel electrophoresis (SDS-PAGE) of whole-cell proteins. Six pulsotypes were found with PFGE typing, using SmaI or NotI as restriction enzymes. Significant differences in chromosome size, ranging from 2.4 to 4.2 Mb for the B. thuringiensis strains studied, were noted. Strain heterogeneity in pulsotypes was also reflected by the similarity of whole-cell protein profiles of the strains. Environmental isolates and reference strains grouped at 71% similarity according to SDS-PAGE data and at 84% on the basis of biochemical tests. CONCLUSIONS: B. thuringiensis from intestines of bank voles demonstrated an important level of heterogeneity. The comparison of PFGE profiles and SDS-PAGE of whole-cell protein patterns may be useful to evaluate the relationship between B. thuringiensis isolates. SIGNIFICANCE AND IMPACT OF THE STUDY: The results presented in this paper may help to explain the diversity of B. thuringiensis.

Animals↗
PubMed2002

Polymerase chain reaction identification of Bacillus sporothermodurans from dairy sources.

AIMS: A new polymerase chain reaction (PCR) method for the identification of Bacillus sporothermodurans strains from sterilized or ultrahigh temperature-treated milk and milk products and from other non-milk sources and environments, including the dairy farm. METHODS AND RESULTS: Two strains from raw milk and feed concentrate could be allocated to B. sporothermodurans based on 16S rDNA sequencing and DNA-DNA hybridization results. Two specific PCR primers were derived from the 16S rRNA gene of B. sporothermodurans. CONCLUSIONS: The PCR identification method was validated using a collection of B. sporothermodurans strains from different sources and on a large collection of dairy and non-dairy Bacillus spp. and other relevant taxa. SIGNIFICANCE AND IMPACT OF THE STUDY: This PCR method was used as a screening method for strains with very heat-resistant endospores, isolated at the dairy farm level after heat treatment for 30 min at 100 degrees C. Seventeen strains isolated at the dairy farm were identified as B. sporothermodurans. They originated mainly from feed concentrate and also from soy, pulp and silage. The PCR identification method described here can, therefore, contribute to a better understanding of the route by which B. sporothermodurans contaminates raw and/or heat-treated milk.

Animal Feed↗
PubMed2002

Polyphasic identification of Bacillus and Brevibacillus strains from clinical, dairy and industrial specimens and proposal of Brevibacillus invocatus sp. nov..

Thirty-three clinical, dairy and industrial isolates of aerobic endospore-forming bacteria which were unreactive in routine identification tests were characterized genotypically by using amplified rDNA restriction analysis (ARDRA), 16S rDNA sequencing and DNA-DNA reassociation, and phenotypically by using fatty acid methyl ester (FAME) analysis, SDS-PAGE of whole-cell proteins, API Biotype 100 assimilation tests and 16 other routine phenotypic tests. Three isolates were identified as strains of Bacillus badius, 12 as Brevibacillus agri, including 3 strains associated with an outbreak of waterborne illness, 4 as Brevibacillus centrosporus and 2 as Brevibacillus parabrevis; 12 strains contaminating an antibiotic production plant were recognized as members of a new species, for which the name Brevibacillus invocatus is proposed, with the type strain LMG 18962T (= B2156T = CIP 106911T = NCIMB 13772T).

Bacillus↗
PubMed2002

Enterovibrio norvegicus gen. nov., sp. nov., isolated from the gut of turbot (Scophthalmus maximus) larvae: a new member of the family Vibrionaceae.

Twenty-two isolates originating from the gut of healthy cultured turbot larvae in Norway were investigated using a polyphasic approach. Amplified fragment length polymorphism fingerprinting analysis showed that the isolates have typical patterns and form two main groups. Phylogenetic analysis revealed that the isolates belong to the gamma-Proteobacteria, with Vibrio hollisae as their closest neighbour. DNA-DNA hybridization, chemotaxonomic and phenotypic analyses further proved that these isolates represent a tight novel taxon that differs from currently described species in the family Vibrionaceae. It is proposed that these novel isolates be accommodated in a new genus, Enterovibrio gen. nov., with Enterovibrio norvegicus sp. nov. as the type species. Isolates were motile by a polar flagellum, positive for oxidase, catalase, arginine dihydrolase and beta-galactosidase, but negative for the Voges-Proskauer reaction. They produced indole, did not reduce nitrate and were resistant to the vibriostatic agent O/129. The DNA G+C content of E. norvegicus was 47.1-47.9 mol%. The type strain is E. norvegicus LMG 19839(T) (= CAIM 430(T)).

Animals↗
PubMed2001

Entrapment of dispersed pancreatic islet cells in CultiSpher-S macroporous gelatin microcarriers: Preparation, in vitro characterization, and microencapsulation.

Immunoprotection of pancreatic islets for successful allo- or xenotransplantation without chronic immunosuppression is an attractive, but still elusive, approach for curing type 1 diabetes. It was recently shown that, even in the absence of fibrotic overgrowth, other factors, mainly insufficient nutrition to the core of the islets, represent a major barrier for long-term survival of intraperitoneal microencapsulated islet grafts. The use of dispersed cells might contribute to solve this problem due to the conceivably easier nutritional support to the cells. In the present study, purified bovine islets, prepared by collagenase digestion and density gradient purification, and dispersed bovine islet cells, obtained by trypsin and DNAsi (viability > 90%), were entrapped into either 2% (w/v) sodium alginate (commonly used for encapsulation purposes) or (dispersed islet cells only) macroporous gelatin microcarriers (CulthiSpher-S, commonly used for the production of biologicals by animal cells). Insulin release studies in response to glucose were performed within 1 week and after 1 month from preparation of the varying systems and showed no capability of dispersed bovine islet cells within sodium alginate microcapsules to sense glucose concentration changes. On the contrary, bovine islet cells entrapped in CulthiSpher-S microcarriers showed maintained capacity of increasing insulin secretion upon enhanced glucose concentration challenge. In this case, insulin release was approximately 60% of that from intact bovine islets within sodium alginate microcapsules. MTT and hematoxylineosin staining of islet cell-containing microcarriers showed the presence of viable and metabolically active cells throughout the study period. This encouraging functional data prompted us to test whether the microcarriers could be immunoisolated for potential use in transplantation. The microcarriers were embedded within 3% sodium alginate, which was then covered with a poly-L-lysine layer and a final outer alginate layer. Maintained insulin secretion function of this system was observed, which raises the possibility of using microencapsulated CulthiSpher-S microcarriers, containing dispersed pancreatic islet cells, in experimental transplantation studies.

Animals↗
PubMed2001

Attenuation of atherogenesis by systemic and local adenovirus-mediated gene transfer of interleukin-10 in LDLr-/- mice.

In view of its multifaceted anti-inflammatory properties, interleukin-10 (IL-10) has been deemed to be potentially anti-atherogenic. We have evaluated the capacity of adenoviral gene transfer of IL-10 for the modulation of de novo atherosclerotic lesion formation by systemic and by local overexpression. Atherogenesis was initiated in the carotid arteries of low-density lipoprotein receptor deficient mice by perivascular placement of silastic collars. One week after collar placement, mice were injected intravenously with 1 x 109 plaque-forming units (pfu's) of IL-10 (AdV.IL-10) or control adenovirus (AdV.empty). Administration of AdV.IL-10 resulted in extended systemic expression of IL-10 (peak serum level 3.0 +/- 1.1 ng/ml) and a reduction in atherosclerotic lumen stenosis by 62.2% (P<0.02). This finding was accompanied by monocyte deactivation and lowering of serum cholesterol levels (maximum decrease 44%). In a second experiment, collared arteries were transfected locally by transluminal instillation of adenovirus (titer 1.5x1010 pfu/ml). Systemic parameters remained unchanged following local transfection, but the degree of stenosis was, nonetheless, decreased by 44.9% (P<0.05). We conclude that a marked inhibition of atherogenesis can be achieved by systemic overexpression of AdV.IL-10, owing to its metabolic and immunomodulatory effects. Local IL-10 transfer is virtually equipotent, however, and it may represent a valuable addition to the armory of anti-atherosclerotic therapies.

Adenoviridae↗
PubMed2001

C-peptide responses after meal challenge in mice transplanted with microencapsulated rat islets.

AIMS/HYPOTHESIS: This study aimed to assess a response of microencapsulated rat islets to a meal challenge after being transplanted intraperitoneally into diabetic mice. METHODS: Microencapsulated rat islets or control naked syngeneic mouse islets were transplanted intraperitoneally into mice with streptozotocin-induced diabetes. Meal challenges were done 3, 6 and 9 weeks after transplantation. Glucose-induced insulin secretion from microencapsulated islets before and after transplantation was assessed in vitro. RESULTS: Within the first week, all animals transplanted with either microencapsulated rat islets or with syngeneic murine islets became normoglycaemic (< 11 mmol/l). At 4 and 6 weeks, body weight was less than normal in the non-diabetic control mice. Mice with the encapsulated rat islets had lower fasting glucose concentrations and more rapid glucose clearance after a meal challenge than the control mice. The group of mice with transplanted syngeneic islets had similar glucose profiles to control mice, except for slightly accelerated glucose clearance. The C peptide responses of mice with either microencapsulated or naked islets were clearly lower than the controls. An increase of C peptide appeared as early as 20 min in the plasma of the group with encapsulated islets, but this was considerably slower than in the other two groups. Microencapsulated rat islets retrieved 9 weeks after transplantation did not lose their ability to respond to glucose, but their output was less than half of the pretransplant control islets. CONCLUSION/INTERPRETATION: The delivery of C peptide and presumably the accompanying insulin are delayed by restrictions of the capsules and the peritoneal location. However, this delay in reaching peripheral target organs does not prevent microencapsulated grafts from efficiently clearing glucose after a meal.

Alginates↗
PubMed2001

Occurrence of Bacillus sporothermodurans and other aerobic spore-forming species in feed concentrate for dairy cattle.

AIMS: To determine the aerobic spore composition and presence of Bacillus sporothermodurans spores in feed concentrate for dairy cattle. METHODS AND RESULTS: Six feed concentrate samples from five different farms were analysed. High levels of spores (up to 10(6) spores g(-1)) were found. Identification of 100 selected isolates was obtained by a combination of fatty acid methyl esters analysis, amplified ribosomal DNA restriction analysis and 16S rDNA sequencing. Ninety-seven isolates could be identified to the species level or assigned to a phylogenetic species group. Most of the isolates obtained after a heat treatment of 10 min at 80 degrees C were identified as members of the B. subtilis group (32 isolates), B. pumilus (25 isolates), B. clausii (eight isolates) and B. licheniformis (eight isolates). The isolates with very heat-resistant spores, obtained after a heat treatment of 30 min at 100 degrees C, were identified as members of the B. subtilis group (five isolates), B. sporothermodurans (three isolates), B. amyloliquefaciens (one isolate), B. oleronius (one isolate) and B. pallidus (one isolate). Bacillus cereus was present in each feed concentrate sample and was isolated using a selective mannitol egg yolk polymyxin agar medium. CONCLUSIONS: Feed concentrate for dairy cattle contains known as well as as yet unknown species of Bacillus and related genera with properties relevant to the dairy sector. SIGNIFICANCE AND IMPACT OF THE STUDY: The results formulate the hypothesis that feed concentrate can be a contamination source of spores, including those of B. sporothermodurans, for raw milk at the farm level.

Animal Feed↗