41 results on '"DE VOS, P."'
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2. Differentiation Between 2,3-Butanediol Producing Bacillus licheniformis and B. polymyxa Strains by Fermentation Product Profiles and Whole-Cell Protein Electrophoretic Patterns
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Raspoet, D., primary, Pot, B., additional, De Deyn, D., additional, De Vos, P., additional, Kersters, K., additional, and De Ley, J., additional
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- 1991
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3. Ethanol Production in Batch and Continuous Culture from Some Carbohydrates with Clostridium thermosaccharolyticum LMG 6564
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Vancanneyt, M., primary, De Vos, P., additional, Maras, M., additional, and De Ley, J., additional
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- 1990
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4. DNA Isolation Protocols Affect the Detection Limit of PCRApproaches of Bacteria in Samples from the HumanGastrointestinal Tract
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Zoetendal, Erwin G., Ben-Amor, Kaouther, Akkermans, Antoon D.L., Abee, Tjakko, and de Vos, Willem M.
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- 2001
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5. Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis Monitoring of Fecal Bifidobacterium Populations in a Prebiotic and Probiotic Feeding Trial
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Satokari, Reetta M., Vaughan, Elaine E., Akkermans, Antoon D.L., Saarela, Maria, and de Vos, Willem M.
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- 2001
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6. Bacterial Community Changes and Enrichment of Burkholderia-like Bacteria Induced by Chlorinated Benzoates in a Peat-Forest Soil-Microcosm
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Ramírez-Saad, Hugo C., Sessitsch, Angela, de Vos, Willem M., and Akkermans, Antoon D.L.
- Abstract
Bacterial community shifts in a peat-forest soil spiked with 3-chlorobenzoate (3CBA) or 2,5-dichlorobenzoate (2,5DCB) were monitored by PCR-amplification of the V6 to V8 regions of the 16S rRNA and rDNA, followed by separation of the amplicons by temperature gradient gel electrophoresis. 3CBA disappeared to non-detectable levels after 15 days by a biologically mediated process, while 2,5DCB remained at the initial concentration values. The experiments were conducted under microcosms systems. Addition of the chlorinated benzoates to the soil resulted in a rapid decrease of the microbial diversity, as judged by a time-dependent reduction in the number of amplicons detected by temperature gradient gel electrophoresis. Few amplicons specifically enriched in the spiked soils were cloned and characterised by sequence analysis. The identity of the cloned DNA and the corresponding soil amplicons was confirmed by hybridisation with a radioactively labelled V6-probe. Analysis of the 16S rDNA sequences indicated that Burkholderia-related bacteria dominated the enriched soil populations under 3CBA stress. In addition, enrichment cultures growing on 3CBA as sole C-source were obtained from the respective spiked soil, which were found to contain bacteria with identical 16S rDNA sequences as those induced by 3CBA stress in soil.
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- 2000
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7. The Role of Cold-Shock Proteins in Low-Temperature Adaptation of Food-Related Bacteria
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Wouters, Jeroen A., Rombouts, Frank M., Kuipers, Oscar P., de Vos, Willem M., and Abee, T.
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There is a considerable interest in the cold adaptation of food-related bacteria, including starter cultures for industrial food fermentations, food spoilage bacteria and food-borne pathogens. Mechanisms that permit low-temperature growth involve cellular modifications for maintaining membrane fluidity, the uptake or synthesis of compatible solutes, the maintenance of the structural integrity of macromolecules and macromolecule assemblies, such as ribosomes and other components that affect gene expression. A specific cold response that is shared by nearly all food-related bacteria is the induction of the synthesis so-called cold-shock proteins (CSPs), which are small (7 kDa) proteins that are involved in mRNA folding, protein synthesis and/or freeze protection. In addition, CSPs are able to bind RNA and it is believed that these proteins act as RNA chaperones, thereby reducing the increased secondary folding of RNA at low temperatures. In this review established and novel aspects concerning the structure, function and control of these CSPs are discussed. A model for bacterial cold adaptation, with a central role for ribosomal functioning, and possible mechanisms for low-temperature sensing are discussed.
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- 2000
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8. Amplified rDNA Restriction Analysis and Further Genotypic Characterisation of Metal-Resistant Soil Bacteria and Related Facultative Hydrogenotrophs
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Brim, Hassan, Heyndrickx, Marc, de Vos, Paul, Wilmotte, Annick, Springael, Dirk, Schlegel, Hans G., and Mergeay, Max
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The level of genotypic relationship between czc+soil bacteria mainly resistant to zinc (but also to various other metals), and related facultative hydrogenotrophs previously assigned to the genera Alcaligenes, Ralstonia, and Burkholderiawas evaluated using ARDRA (Amplified Ribosomal DNA Restriction Analysis). The analysis included 44 strains isolated from harsh industrial environments in sediments, soils and wastes with high content of heavy metals. These strains were selected by their ability to grow in the presence of high concentrations of multiple heavy metals and to hybridise with czcor nccprobes. The czcoperon confers resistance to cadmium, zinc and cobalt in strain Ralstonia eutrophaCH34. The nccoperon confers resistance to nickel, cobalt and cadmium in strain 31A known as Alcaligenes xylosoxidans.
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- 1999
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9. Biosafety Assessment of the Application of Genetically Modified Lactococcus lactisspp. in the Production of Fermented Milk Products
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Klijn, Nicolette, Weerkamp, Anton H., and De Vos, Willem M.
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The past decade has shown enormous progress in the understanding of microbial genetics and has resulted in the ability to genetically modify lactic acid bacteria for the production of fermented foods. However, before these genetically modified micro-organisms can be applied in the actual manufacture of fermented foods the biological safety aspects related to their use in fermentations, release into the environment and consumption by animals and humans need to be assessed. Because the direct application of genetically modified micro-organisms in food involves the intentional intake of usually high numbers of live microorganisms by the consumer, the biosafety assessment is especially complicated.
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- 1995
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10. Recent Changes in the Classification of the Pseudomonads: an Overview
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Kersters, Karel, Ludwig, Wolfgang, Vancanneyt, Marc, De Vos, Paul, Gillis, Monique, and Schleifer, Karl-Heinz
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- 1996
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11. Polyamine Distribution Among Authentic Pseudomonads and Azotobacteraceae
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Goris, Johan, Kersters, Karel, and De Vos, Paul
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Polyamine patterning of 176 bacterial strains, of which 158 either belong to the so-called PseudomonasrRNA group I (the authentic pseudomonads) or to the Azotobacteraceae(free-living nitrogen-fixers), indicate and confirm that both taxa are closely related. All strains show putrescine (PUT) and spermidine (SPD) in their pattern. The authentic pseudomonads could be split into a cadaverine lacking (CAD -) and a cadaverine containing (CAD +) group (including the type species Pseudomonas aeruginosa), while all (except Azomonas insignis) free-living nitrogen-fixers were CAD +. This observation also supports recent rRNA sequence data which show a phylogenetic closer relationship between Azotobacter vinelandiiand the Pseudomonas aeruginosarRNA sublineage than between Azotobacter vinelandiiand the Pseudomonas fluorescensrRNA sublineage.
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- 1998
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12. Isolation, characterization and identification of strictly anaerobic, thermophilic, ethanol producing bacteria from compost
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Vancanneyt, M., primary, De Vos, P., additional, Kersters, K., additional, and De Ley, J., additional
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- 1987
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13. Photoproduction of Molecular Hydrogen by Rhodobacter sulfidophilus
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Stevens, P., primary, Plovie, N., additional, De Vos, P., additional, and De Ley, J., additional
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- 1986
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14. An Alternative Parameter for Tm(e) in DNA:rRNA Hybridization Studies
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Van Landschoot, A., primary, De Vos, P., additional, and De Ley, J., additional
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- 1984
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15. Hydrogen gas production from continuous fermentation of glucose in a minimal medium with Clostridium butyricum LMG 1213t1
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Heyndrickx, M., primary, Vansteenbeeck, A., additional, De Vos, P., additional, and De Ley, J., additional
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- 1986
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16. Effect of various external factors on the fermentative production of hydrogen gas from glucose by Clostridium butyricum strains in batch culture
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Heyndrickx, M., primary, De Vos, P., additional, Hibau, B., additional, Stevens, P., additional, and De Ley, J., additional
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- 1987
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17. Photobacterium piscicola sp. nov., isolated from marine fish and spoiled packed cod.
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Figge MJ, Cleenwerck I, van Uijen A, De Vos P, Huys G, and Robertson L
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- Amplified Fragment Length Polymorphism Analysis, Animals, Aquatic Organisms microbiology, Bacterial Proteins genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Food Microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Photobacterium genetics, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Gadiformes microbiology, Photobacterium classification, Photobacterium isolation & purification
- Abstract
Five isolates from marine fish (W3(T), WM, W1S, S2 and S3) and three isolates misclassified as Photobacterium phosphoreum, originating from spoiled modified atmosphere packed stored cod (NCIMB 13482 and NCIMB 13483) and the intestine of skate (NCIMB 192), were subjected to a polyphasic taxonomic study. Phylogenetic analysis of 16S rRNA gene sequences showed that the isolates were members of the genus Photobacterium. Sequence analysis using the gapA, gyrB, pyrH, recA and rpoA loci showed that these isolates formed a distinct branch in the genus Photobacterium, and were most closely related to Photobacterium aquimaris, Photobacterium kishitanii, Photobacterium phosphoreum and Photobacterium iliopiscarium. The luxA gene was present in isolates W3(T), WM, W1S, S2 and S3 but not in NCIMB 13482, NCIMB 13483 and NCIMB 192. AFLP and (GTG)5-PCR fingerprinting indicated that the eight isolates represented at least five distinct genotypes. DNA-DNA hybridizations revealed 89% relatedness between isolate W3(T) and NCIMB 192, and values below 70% with the type strains of the phylogenetically closest species, P. iliopiscarium LMG 19543(T), P. kishitanii LMG 23890(T), P. aquimaris LMG 26951(T) and P. phosphoreum LMG4233(T). The strains of this new taxon could also be distinguished from the latter species by phenotypic characteristics. Therefore, we propose to classify this new taxon as Photobacterium piscicola sp. nov., with W3(T) (=NCCB 100098(T)=LMG 27681(T)) as the type strain., (Copyright © 2014 Elsevier GmbH. All rights reserved.)
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- 2014
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18. StrainInfo introduces electronic passports for microorganisms.
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Verslyppe B, De Smet W, De Baets B, De Vos P, and Dawyndt P
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- Classification methods, Computational Biology methods, Electronic Data Processing methods, Microbiological Techniques methods
- Abstract
Microbiology builds upon biological material deposited in biological resource centers (BRCs) as a reference framework for collaborative research. BRCs assign so-called strain numbers to label the deposited material and are responsible for long-term preservation and worldwide distribution of the material. Cultured microorganisms can be deposited into multiple BRCs and BRCs also mutually exchange their holdings. As a result, many different strain numbers can be attached to biological material that stems from the same isolate. In practice, this material is considered equivalent and used interchangeably. This implies that finding information on given biological material requires all equivalent strain numbers to be used when searching. StrainInfo introduces strain passports for microorganisms: a uniform overview of information known about a given microbial strain. It contains all known equivalent strain numbers and information on the exchange history, sequences and related literature of the strain. Each passport has an associated strain browser that gives direct access to the underlying BRC catalog entries on which the passport was based. Taxon, sequence and literature passports are implemented in a similar manner. In addition to web pages that serve human users, integrated information is also offered in machine readable formats useful for automated, large-scale analysis. StrainInfo is envisioned to be an open platform integrating microbial information. This platform can form the basis for new methods of microbiological research, leveraging the vast amount of electronic information available online. StrainInfo is available from http://www.StrainInfo.net., (Copyright © 2013 Elsevier GmbH. All rights reserved.)
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- 2014
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19. A generally applicable cryopreservation method for nitrite-oxidizing bacteria.
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Vekeman B, Hoefman S, De Vos P, Spieck E, and Heylen K
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- Bacteria metabolism, Cryoprotective Agents pharmacology, Oxidation-Reduction, Bacteria radiation effects, Cryopreservation methods, Microbial Viability radiation effects, Microbiological Techniques methods, Nitrites metabolism
- Abstract
Nitrite-oxidizing bacteria are key members of the global nitrogen cycle but their study is hampered by their limited availability in culture, mostly due to laborious cultivation procedures and the lack of stable preservation methods. In this study, it was demonstrated that long-term cryopreservation of nitrite-oxidizing bacteria assigned to the genera Nitrobacter, Nitrospina, Nitrococcus, Nitrotoga and Nitrospira was possible using a simple and rapid protocol. Their survival was tested with different cryoprotecting agents, DMSO and Hatefi, and in various carbon-rich preservation media, ten-fold diluted TSB, and ten-fold diluted TSB supplemented with 1% trehalose, and 1% sucrose. Optimal preservation conditions were strain-dependent and marine strains appeared to be more sensitive to freezing than non-marine strains. Nevertheless, a general cryopreservation protocol using 10% dimethyl sulfoxide with or without ten-fold diluted trypticase soy broth as a preservation medium allowed successful preservation of all tested strains., (Copyright © 2013 Elsevier GmbH. All rights reserved.)
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- 2013
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20. Filtering and ranking techniques for automated selection of high-quality 16S rRNA gene sequences.
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De Smet W, De Loof K, De Vos P, Dawyndt P, and De Baets B
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- Automation methods, Computational Biology methods, Genes, rRNA, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA methods
- Abstract
StrainInfo has augmented its type strain and species/subspecies passports with a recommendation for a high-quality 16S rRNA gene sequence available from the public sequence databases. These recommendations are generated by an automated pipeline that collects all candidate 16S rRNA gene sequences for a prokaryotic type strain, filters out low-quality sequences and retains a high-quality sequence from the remaining pool. Due to thorough automation, recommendations can be renewed daily using the latest updates of the public sequence databases and the latest species descriptions. We discuss the quality criteria constructed to filter and rank available 16S rRNA gene sequences, and show how a partially ordered set (poset) ranking algorithm can be applied to solve the multi-criteria ranking problem of selecting the best candidate sequence. The proof of concept of the recommender system is validated by comparing the results of automated selection with an expert selection made in the All-Species Living Tree Project. Based on these validation results, the pipeline may reliably be applied for non-type strains and developed further for the automated selection of housekeeping genes., (Copyright © 2013 Elsevier GmbH. All rights reserved.)
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- 2013
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21. Genetic diversity of non-pathogenic Clavibacter strains isolated from tomato seeds.
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Zaluga J, Van Vaerenbergh J, Stragier P, Maes M, and De Vos P
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- Actinomycetales genetics, Bacterial Proteins genetics, Cluster Analysis, DNA Gyrase genetics, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA-Binding Proteins genetics, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Sequence Analysis, DNA, Actinomycetales classification, Actinomycetales isolation & purification, Genetic Variation, Solanum lycopersicum microbiology, Seeds microbiology
- Abstract
Clavibacter michiganensis subsp. michiganensis (Cmm) is a seed-transmitted, quarantine pathogen which causes bacterial wilt and canker of tomato. Despite efforts to prevent seed contamination, new introductions are regularly detected, associated with new regions of tomato seed production. It seems as if the expanding diversity of Cmm also challenges the limited host range. Clavibacter-like isolates from tomato seed are phenotypically similar to Cmm in the common diagnostic semi-selective media and are identified as Cmm in the customary tests but are not pathogenic to tomato. In our first study four representatives formed a separate cluster in gyrB sequence analysis and in MALDI-TOF MS. Their presence on seed prevents clear judgment on the health status of tomato seeds. As their nature and function are unclear we aimed to investigate and compare them to Cmm. Twenty strains described as Clavibacter-like isolated from tomato seed and not pathogenic to tomato plantlets were selected. Leaf spots, wilting or cankers were not induced after local or systemic inoculation. Tomato stems were not colonized nor was there evidence of survival in tomato stems. Total DNA-DNA hybridization and sequence analysis of gyrB and dnaA proved that they belong to the Cm species but can be unambiguously separated from Cmm. Some of the genes encoding virulence determinants in Cmm strains were also detected in some of the non-pathogenic isolates. Moreover, Cmm strains formed a coherent group, while non-pathogenic Cm strains were heterogenic. The latter was confirmed by BOX-PCR. We speculate that tomato seeds likely represent a larger reservoir of unexplored Clavibacter diversity., (Copyright © 2013 Elsevier GmbH. All rights reserved.)
- Published
- 2013
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22. Pseudomonas asturiensis sp. nov., isolated from soybean and weeds.
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González AJ, Cleenwerck I, De Vos P, and Fernández-Sanz AM
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- Bacterial Typing Techniques, Cluster Analysis, DNA Gyrase genetics, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, DNA-Directed RNA Polymerases genetics, Fatty Acids analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas genetics, Pseudomonas physiology, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Sigma Factor genetics, Plant Weeds microbiology, Pseudomonas classification, Pseudomonas isolation & purification, Glycine max microbiology
- Abstract
Five strains of gram negative bacteria, isolated from soybean (LPPA 221(T), 222 and 223) and weeds (LPPA 816 and 1442), were analyzed by a polyphasic approach. The isolates showed variation in their phenotypic traits and were placed in the Pseudomonas fluorescens lineage, based on 16S rRNA gene sequence phylogeny, as a single but well separated cluster. MLSA analysis based on gyrB and rpoD sequences clustered the strains in a single branch in the Pseudomonas syringae group, and revealed P. viridiflava as closest relative. DNA-DNA hybridizations showed medium levels of DNA-DNA relatedness with the type strain of P. viridiflava (50%) and lower levels (<32%) with other type strains of the P. syringae group, supporting classification within a novel species of the genus Pseudomonas. The strains can be distinguished from species of the P. syringae group by the fatty acid C17:0 cyclo that is present in a low amount (2.5%) and from P. viridiflava by their inability to assimilate d-tartrate and d-sorbitol, and by the formation of red colonies on TTC medium. For this new species, the name Pseudomonas asturiensis sp. nov. is proposed. The type strain is LPPA 221(T) (=LMG 26898(T)=CECT 8095(T))., (Copyright © 2013 Elsevier GmbH. All rights reserved.)
- Published
- 2013
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23. Taxonomic evaluation of the genus Enterobacter based on multilocus sequence analysis (MLSA): proposal to reclassify E. nimipressuralis and E. amnigenus into Lelliottia gen. nov. as Lelliottia nimipressuralis comb. nov. and Lelliottia amnigena comb. nov., respectively, E. gergoviae and E. pyrinus into Pluralibacter gen. nov. as Pluralibacter gergoviae comb. nov. and Pluralibacter pyrinus comb. nov., respectively, E. cowanii, E. radicincitans, E. oryzae and E. arachidis into Kosakonia gen. nov. as Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov. and Kosakonia arachidis comb. nov., respectively, and E. turicensis, E. helveticus and E. pulveris into Cronobacter as Cronobacter zurichensis nom. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov., respectively, and emended description of the genera Enterobacter and Cronobacter.
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Brady C, Cleenwerck I, Venter S, Coutinho T, and De Vos P
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- Bacterial Proteins genetics, Bacterial Typing Techniques, Cluster Analysis, Cronobacter chemistry, Cronobacter physiology, Enterobacter chemistry, Enterobacter physiology, Fatty Acids analysis, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Homology, Cronobacter classification, Cronobacter genetics, DNA, Bacterial chemistry, DNA, Bacterial genetics, Enterobacter classification, Enterobacter genetics, Multilocus Sequence Typing
- Abstract
The taxonomy of Enterobacter has a complicated history, with several species transferred to and from this genus. Classification of strains is difficult owing to its polyphyletic nature, based on 16S rRNA gene sequences. It has been previously acknowledged that Enterobacter contains species which should be transferred to other genera. In an attempt to resolve the taxonomy of Enterobacter, MLSA based on partial sequencing of protein-encoding genes (gyrB, rpoB, infB and atpD) was performed on the type strains and reference strains of Enterobacter, Cronobacter and Serratia species, as well as members of the closely related genera Citrobacter, Klebsiella, Kluyvera, Leclercia, Mangrovibacter, Raoultella and Yokenella. Phylogenetic analyses of the concatenated nucleotide sequences revealed that Enterobacter can be divided into five strongly supported MLSA groups, suggesting that the species should be reclassified into five different genera. Further support for this was provided by a concatenated amino acid tree, phenotypic characteristics and fatty acid profiles, enabling differentiation of the MLSA groups. Three novel genera are proposed: Lelliottia gen. nov., Pluralibacter gen. nov. and Kosakonia gen. nov. and the following new combinations: Lelliottia nimipressuralis comb. nov., Lelliottia amnigena comb. nov., Pluralibacter gergoviae comb. nov., Pluralibacter pyrinus comb. nov., Kosakonia cowanii comb. nov., Kosakonia radicincitans comb. nov., Kosakonia oryzae comb. nov., Kosakonia arachidis comb. nov., Cronobacter helveticus comb. nov. and Cronobacter pulveris comb. nov. Additionally, the novel epithet Cronobacter zurichensis nom. nov. is proposed for the reclassification of Enterobacter turicensis into the genus Cronobacter, as Cronobacter turicensis (Iversen et al., 2008) is already in use., (Copyright © 2013 Elsevier GmbH. All rights reserved.)
- Published
- 2013
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24. Bioprospecting in potato fields in the Central Andean Highlands: screening of rhizobacteria for plant growth-promoting properties.
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Ghyselinck J, Velivelli SL, Heylen K, O'Herlihy E, Franco J, Rojas M, De Vos P, and Prestwich BD
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- Bacteria chemistry, Bacteria classification, Bolivia, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Molecular Sequence Data, Peru, Phytophthora infestans growth & development, RNA, Ribosomal, 16S genetics, Rhizoctonia growth & development, Sequence Analysis, DNA, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Antibiosis, Bacteria isolation & purification, Bacteria metabolism, Plant Growth Regulators metabolism, Soil Microbiology, Solanum tuberosum growth & development, Solanum tuberosum microbiology
- Abstract
The Central Andean Highlands are the center of origin of the potato plant (Solanum tuberosum). Ages of mutualism between potato plants and soil bacteria in this region support the hypothesis that Andean soils harbor interesting plant growth-promoting (PGP) bacteria. Therefore, the aim of this study was to isolate rhizobacteria from Andean ecosystems, and to identify those with PGP properties. A total of 585 bacterial isolates were obtained from eight potato fields in the Andes and they were screened for suppression of Phytophthora infestans and Rhizoctonia solani. Antagonistic mechanisms were determined and antagonistic isolates were further tested for phosphate solubilization, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and production of NH3- and indole-3-acetic acid (IAA). PGP was studied in healthy and R. solani diseased plantlets under growth room conditions. Performance was compared to the commercial strain B. subtilis FZB24(®) WG. Isolates were dereplicated with matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), and identified with 16S rRNA gene sequencing and multi locus sequence analysis (MLSA). A total of 10% of the isolates were effective antagonists, of which many were able to solubilize phosphate, and produce IAA, ACC deaminase, NH3 and hydrogen cyanide (HCN). During growth room experiments, 23 antagonistic isolates were associated with plant growth-promotion and/or disease suppression. Ten isolates had a statistically significant impact on test parameters compared to the uninoculated control. Three isolates significantly promoted plant growth in healthy plantlets compared to the commercial strain, and seven isolates outperformed the commercial strain in in vitro R. solani diseased plantlets., (Copyright © 2012 Elsevier GmbH. All rights reserved.)
- Published
- 2013
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25. Gluconacetobacter maltaceti sp. nov., a novel vinegar producing acetic acid bacterium.
- Author
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Slapšak N, Cleenwerck I, De Vos P, and Trček J
- Subjects
- Amplified Fragment Length Polymorphism Analysis, Bacterial Proteins genetics, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, DNA, Ribosomal Spacer chemistry, DNA, Ribosomal Spacer genetics, Gluconacetobacter genetics, Gluconacetobacter isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Acetic Acid metabolism, Gluconacetobacter classification, Gluconacetobacter metabolism
- Abstract
Comparison of HaeIII- and HpaII-restriction profiles of PCR-amplified 16S-23S rDNA ITS regions of Gluconacetobacter sp. LMG 1529(T) and SKU 1109 with restriction profiles of reference strains of acetic acid bacteria described by Trček and Teuber [34] revealed the same but unique restriction profiles for LMG 1529(T) and SKU 1109. Further analyses of nearly complete 16S rRNA gene sequences, nearly complete 16S-23S rDNA ITS sequences, as well as concatenated partial sequences of the housekeeping genes dnaK, groEL and rpoB, allocated both strains to a single phylogenetic cluster well separated from the other species of the genus Gluconacetobacter. DNA-DNA hybridizations confirmed their novel species identity by 73% DNA-DNA relatedness between both strains, and values below the species level (<70%) between SKU 1109 and the type strains of the closest phylogenetic neighbors. The classification of strains LMG 1529(T) and SKU 1109 into a single novel species was confirmed also by AFLP and (GTG)(5)-PCR DNA fingerprinting data, as well as by phenotypic data. Strains LMG 1529(T) and SKU 1109 can be differentiated from their closely related Gluconacetobacter species, Gluconacetobacter entanii and Gluconacetobacter hansenii, by their ability to form 2-keto-d-gluconic acid from d-glucose, their ability to use d-mannitol, d-gluconate and glycerol as carbon source and form acid from d-fructose, and their ability to grow without acetic acid. The major fatty acid of LMG 1529(T) and SKU 1109 is C(18:1ω7c) (60.2-64.8%). The DNA G+C content of LMG 1529(T) and SKU 1109 is 62.5 and 63.3mol% respectively. The name Gluconacetobacter maltaceti sp. nov. is proposed. The type strain is LMG 1529(T) (=NBRC 14815(T)=NCIMB 8752(T))., (Copyright © 2012 Elsevier GmbH. All rights reserved.)
- Published
- 2013
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26. Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names.
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Yarza P, Spröer C, Swiderski J, Mrotzek N, Spring S, Tindall BJ, Gronow S, Pukall R, Klenk HP, Lang E, Verbarg S, Crouch A, Lilburn T, Beck B, Unosson C, Cardew S, Moore ER, Gomila M, Nakagawa Y, Janssens D, De Vos P, Peiren J, Suttels T, Clermont D, Bizet C, Sakamoto M, Iida T, Kudo T, Kosako Y, Oshida Y, Ohkuma M, R Arahal D, Spieck E, Pommerening Roeser A, Figge M, Park D, Buchanan P, Cifuentes A, Munoz R, Euzéby JP, Schleifer KH, Ludwig W, Amann R, Glöckner FO, and Rosselló-Móra R
- Subjects
- Classification methods, DNA, Bacterial chemistry, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Bacteria classification, Bacteria genetics, DNA, Bacterial genetics, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA
- Abstract
High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues., (Copyright © 2013 Elsevier GmbH. All rights reserved.)
- Published
- 2013
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27. GyrB sequence analysis and MALDI-TOF MS as identification tools for plant pathogenic Clavibacter.
- Author
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Zaluga J, Heylen K, Van Hoorde K, Hoste B, Van Vaerenbergh J, Maes M, and De Vos P
- Subjects
- Base Sequence, DNA Gyrase chemistry, DNA, Bacterial chemistry, DNA, Bacterial genetics, Gene Amplification, Genes, Bacterial, Genetic Variation, Molecular Sequence Data, Plant Diseases microbiology, Sequence Analysis, DNA, DNA Gyrase genetics, Micrococcaceae enzymology, Micrococcaceae genetics, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization methods
- Abstract
The bacterial genus Clavibacter has only one species, Clavibacter michiganensis, containing five subspecies. All five are plant pathogens, among which three are recognized as quarantine pests (mentioned on the EPPO A2 list). Prevention of their introduction and epidemic outbreaks requires a reliable and accurate identification. Currently, identification of these bacteria is time consuming and often problematic, mainly because of cross-reactions with other plant-associated bacteria in immunological tests and false-negative results in PCR detection methods. Furthermore, distinguishing closely related subspecies is not straightforward. This study aimed at evaluating the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and a fragment of the gyrB sequence for the reliable and fast identification of the Clavibacter subspecies. Amplification and sequencing of gyrB using a single primer set had sufficient resolution and specificity to identify each subspecies based on both sequence similarities in cluster analyses and specific signatures within the sequences. All five subspecies also generated distinct and reproducible MALDI-TOF MS profiles, with unique and specific ion peaks for each subspecies, which could be used as biomarkers for identification. Results from both methods were in agreement and were able to distinguish the five Clavibacter subspecies from each other and from representatives of closely related Rathayibacter, Leifsonia or Curtobacterium species. Our study suggests that proteomic analysis using MALDI-TOF MS and gyrB sequence are powerful diagnostic tools for the accurate identification of Clavibacter plant pathogens., (Copyright © 2011 Elsevier GmbH. All rights reserved.)
- Published
- 2011
- Full Text
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28. Make Histri: reconstructing the exchange history of bacterial and archaeal type strains.
- Author
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Verslyppe B, De Smet W, De Baets B, De Vos P, and Dawyndt P
- Subjects
- Chryseobacterium, Software, Terminology as Topic, User-Computer Interface, Archaea classification, Bacteria classification, Databases, Factual
- Abstract
Each transfer of a microbial strain between a Biological Resource Center (BRC) and an individual researcher or another BRC imposes a risk of contamination or human error. Such artifacts jeopardize the quality of scientific results. In order to trace back possible scientific discrepancies that can be linked to failure of authenticity of the biological material involved, we launched the 'Make Histri' project that aims at reconstructing the exchange history ('Histri') of all bacterial and archaeal type strains as can be deduced from the information contained in BRC online catalogs. A Histri, visualized as a rooted tree, contains all known strain numbers attributed to the various cultures of a given strain, annotated with additional information about each transfer of microbial material., (Copyright © 2011 Elsevier GmbH. All rights reserved.)
- Published
- 2011
- Full Text
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29. Denitrification is a common feature among members of the genus Bacillus.
- Author
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Verbaendert I, Boon N, De Vos P, and Heylen K
- Subjects
- Bacillus genetics, Bacillus growth & development, Bacillus isolation & purification, Colony Count, Microbial, Culture Media, DNA, Bacterial genetics, Nitrogen metabolism, Nitrogen Oxides metabolism, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, RNA, Bacillus metabolism, Denitrification, Nitrates metabolism, Nitrites metabolism, Soil Microbiology
- Abstract
Although several Gram-positive denitrifiers have been characterized in the past, there is still uncertainty about the occurrence of the denitrification trait among these bacteria. In an isolation campaign on luvisol soil, Bacillus spp. were among the most abundant retrieved cultured denitrifiers next to members of Rhizobiaceae family and genus Cupriavidus. Subsequent screening of 180 representatives of the genus Bacillus (encompassing more than half of the current validly described species diversity in Bacillus) was performed and demonstrated the potential for dissimilatory reduction of nitrogen compounds in 45 of the 87 investigated species, with 19 species containing denitrifying members. The influence of several electron donors and acceptors was tested. The use of more than one electron acceptor, e.g. both nitrate and nitrite, was crucial to detect the denitrification potential of reference strains. Complex electron donors, most suitable for aerobic growth, were ideal for denitrification testing, while retrieval of denitrifiers from the environment was facilitated by the use of defined electron donors, due to less interference of other anaerobic growers. The outcome of the isolation campaign and screening of reference strain set suggest that bacilli may be potential contributors to denitrification in terrestrial and possibly other ecosystems., (Copyright © 2011 Elsevier GmbH. All rights reserved.)
- Published
- 2011
- Full Text
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30. Vibrio celticus sp. nov., a new Vibrio species belonging to the Splendidus clade with pathogenic potential for clams.
- Author
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Beaz-Hidalgo R, Diéguez AL, Cleenwerck I, Balboa S, Doce A, de Vos P, and Romalde JL
- Subjects
- Animals, Bacterial Proteins genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Spain, Vibrio genetics, Vibrio physiology, Bivalvia microbiology, Vibrio classification, Vibrio isolation & purification
- Abstract
A group of four motile facultative anaerobic marine isolates (Rd 8.15(T) [=CECT 7224(T), =LMG 23850(T)], Rd 16.13, Rd 6.8 [=LMG 25696] and Rd2L5) were obtained from cultured clams (Ruditapes philippinarum and Venerupis pullastra) in Galicia, north-western Spain. They formed a tight phylogenetic group based on sequences of the 16S rRNA gene and the four housekeeping genes rpoA (encoding the α-chain of RNA polymerase), rpoD (encoding the sigma factor of RNA polymerase), recA (encoding RecA protein), and atpA (encoding the α-subunit of bacterial ATP synthase). The phylogenies based on these sequences indicated that the four isolates represented a novel species in the genus Vibrio, and more precisely in the Splendidus clade. DNA-DNA hybridizations with the type strains of species showing more than 98.6% 16S rRNA gene sequence similarity, revealed a DNA-DNA relatedness below 70%. The isolates could be differentiated from the phylogenetically related Vibrio species on the basis of several phenotypic features. In addition, strain Rd 8.15(T) showed potential pathogenic activity for adult clams in virulence assays. The name Vibrio celticus sp. nov. is proposed for this new taxon, with the type strain being Rd 8.15(T) (=CECT 7224(T), =LMG 23850(T))., (Copyright © 2010 Elsevier GmbH. All rights reserved.)
- Published
- 2010
- Full Text
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31. Pseudomonas cichorii as the causal agent of midrib rot, an emerging disease of greenhouse-grown butterhead lettuce in Flanders.
- Author
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Cottyn B, Heylen K, Heyrman J, Vanhouteghem K, Pauwelyn E, Bleyaert P, Van Vaerenbergh J, Höfte M, De Vos P, and Maes M
- Subjects
- Bacterial Typing Techniques, Belgium, DNA, Bacterial isolation & purification, DNA, Ribosomal analysis, DNA-Directed RNA Polymerases genetics, Fatty Acids analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Polymerase Chain Reaction methods, Polysaccharide-Lyases metabolism, Pseudomonas genetics, Pseudomonas physiology, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Lactuca microbiology, Plant Diseases microbiology, Pseudomonas classification, Pseudomonas isolation & purification
- Abstract
Bacterial midrib rot of greenhouse-grown butterhead lettuce (Lactuca sativa L. var. capitata) is an emerging disease in Flanders (Belgium) and fluorescent pseudomonads are suspected to play an important role in the disease. Isolations from infected lettuces, collected from 14 commercial greenhouses in Flanders, yielded 149 isolates that were characterized polyphasically, which included morphological characteristics, pigmentation, pathogenicity tests by both injection and spraying of lettuce, LOPAT characteristics, FAME analysis, BOX-PCR fingerprinting, 16S rRNA and rpoB gene sequencing, as well as DNA-DNA hybridization. Ninety-eight isolates (66%) exhibited a fluorescent pigmentation and were associated with the genus Pseudomonas. Fifty-five of them induced an HR+ (hypersensitive reaction in tobacco leaves) response. The other 43 fluorescent isolates were most probably saprophytic bacteria and about half of them were able to cause rot on potato tuber slices. BOX-PCR genomic fingerprinting was used to assess the genetic diversity of the Pseudomonas midrib rot isolates. The delineated BOX-PCR patterns matched quite well with Pseudomonas morphotypes defined on the basis of colony appearance and variation in fluorescent pigmentation. 16S rRNA and rpoB gene sequence analyses allowed most of the fluorescent isolates to be allocated to Pseudomonas, and they belonged to either the Pseudomonas fluorescens group, Pseudomonas putida group, or the Pseudomonas cichorii/syringae group. In particular, the isolates allocated to this latter group constituted the vast majority of HR+ isolates and were identified as P. cichorii by DNA-DNA hybridization. They were demonstrated by spray-inoculation tests on greenhouse-grown lettuce to induce the midrib rot disease and could be re-isolated from lesions of inoculated plants. Four HR+ non-fluorescent isolates associated with one sample that showed an atypical midrib rot were identified as Dickeya sp.
- Published
- 2009
- Full Text
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32. Towards large-scale FAME-based bacterial species identification using machine learning techniques.
- Author
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Slabbinck B, De Baets B, Dawyndt P, and De Vos P
- Subjects
- Bacillus chemistry, Bacillus classification, Bacteria chemistry, Chromatography, Gas, Neural Networks, Computer, Pseudomonas chemistry, Pseudomonas classification, Species Specificity, Artificial Intelligence, Bacteria classification, Bacterial Typing Techniques methods, Fatty Acids analysis
- Abstract
In the last decade, bacterial taxonomy witnessed a huge expansion. The swift pace of bacterial species (re-)definitions has a serious impact on the accuracy and completeness of first-line identification methods. Consequently, back-end identification libraries need to be synchronized with the List of Prokaryotic names with Standing in Nomenclature. In this study, we focus on bacterial fatty acid methyl ester (FAME) profiling as a broadly used first-line identification method. From the BAME@LMG database, we have selected FAME profiles of individual strains belonging to the genera Bacillus, Paenibacillus and Pseudomonas. Only those profiles resulting from standard growth conditions have been retained. The corresponding data set covers 74, 44 and 95 validly published bacterial species, respectively, represented by 961, 378 and 1673 standard FAME profiles. Through the application of machine learning techniques in a supervised strategy, different computational models have been built for genus and species identification. Three techniques have been considered: artificial neural networks, random forests and support vector machines. Nearly perfect identification has been achieved at genus level. Notwithstanding the known limited discriminative power of FAME analysis for species identification, the computational models have resulted in good species identification results for the three genera. For Bacillus, Paenibacillus and Pseudomonas, random forests have resulted in sensitivity values, respectively, 0.847, 0.901 and 0.708. The random forests models outperform those of the other machine learning techniques. Moreover, our machine learning approach also outperformed the Sherlock MIS (MIDI Inc., Newark, DE, USA). These results show that machine learning proves very useful for FAME-based bacterial species identification. Besides good bacterial identification at species level, speed and ease of taxonomic synchronization are major advantages of this computational species identification strategy.
- Published
- 2009
- Full Text
- View/download PDF
33. Diversity of Vibrios associated with reared clams in Galicia (NW Spain).
- Author
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Beaz Hidalgo R, Cleenwerck I, Balboa S, De Wachter M, Thompson FL, Swings J, De Vos P, and Romalde JL
- Subjects
- Animals, Bacterial Proteins genetics, Bacterial Typing Techniques, DNA, Bacterial analysis, DNA, Bacterial isolation & purification, Genotype, Molecular Sequence Data, Phenotype, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 16S genetics, Rec A Recombinases genetics, Spain, Vibrio genetics, Vibrio isolation & purification, Aquaculture, Bivalvia microbiology, Genetic Variation, Sequence Analysis, DNA, Vibrio classification
- Abstract
The aim of the present study was to characterize and identify vibrios isolated from cultured clams in Galicia (NW Spain). A total of 759 isolates were obtained, phenotypically characterized, grouped and assigned to the genus Vibrio. Subsequently, the genomic diversity of 145 representative strains was analyzed by means of amplified fragment length polymorphism (AFLP), which revealed a high genetic diversity amongst these isolates. Only 57 out of 145 strains could be identified to the species level, and they were distributed in 13 AFLP clusters. V. cyclitrophicus, V. splendidus and V. alginolyticus were the most abundantly represented species. Eighty-eight isolates remained unidentified, 59 were distributed over 16 clusters, while 29 were unclustered. Sequencing of the 16S rRNA and two house-keeping genes (rpoA and recA) from representative strains belonging to eight unidentified clusters with the highest number of isolates confirmed their assignation to the Vibrionaceae family, and some of these probably represent new species within the genus. The present study confirmed that the phenotypic characterization of vibrios is not sufficient to identify them at the species level. A wide diversity of vibrios was found in cultured clams from all four geographic locations analyzed. In total, more than 12 Vibrio species and at least three potential new species in this genus were identified.
- Published
- 2008
- Full Text
- View/download PDF
34. Comparative analysis of the diversity of aerobic spore-forming bacteria in raw milk from organic and conventional dairy farms.
- Author
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Coorevits A, De Jonghe V, Vandroemme J, Reekmans R, Heyrman J, Messens W, De Vos P, and Heyndrickx M
- Subjects
- Animals, Bacteria, Aerobic genetics, Bacteria, Aerobic metabolism, DNA, Bacterial chemistry, DNA, Bacterial genetics, DNA, Ribosomal chemistry, DNA, Ribosomal genetics, Fatty Acids analysis, Genes, rRNA, Gram-Positive Endospore-Forming Bacteria genetics, Gram-Positive Endospore-Forming Bacteria metabolism, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction methods, RNA, Bacterial genetics, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Bacteria, Aerobic classification, Bacteria, Aerobic isolation & purification, Biodiversity, Food, Organic microbiology, Gram-Positive Endospore-Forming Bacteria classification, Gram-Positive Endospore-Forming Bacteria isolation & purification, Milk microbiology
- Abstract
Bacterial contamination of raw milk can originate from different sources: air, milking equipment, feed, soil, faeces and grass. It is hypothesized that differences in feeding and housing strategies of cows may influence the microbial quality of milk. This assumption was investigated through comparison of the aerobic spore-forming flora in milk from organic and conventional dairy farms. Laboratory pasteurized milk samples from five conventional and five organic dairy farms, sampled in late summer/autumn and in winter, were plated on a standard medium and two differential media, one screening for phospholipolytic and the other for proteolytic activity of bacteria. Almost 930 isolates were obtained of which 898 could be screened via fatty acid methyl ester analysis. Representative isolates were further analysed using 16S rRNA gene sequencing and (GTG)(5)-PCR. The majority of aerobic spore-formers in milk belonged to the genus Bacillus and showed at least 97% 16S rRNA gene sequence similarity with type strains of Bacillus licheniformis, Bacillus pumilus, Bacillus circulans, Bacillus subtilis and with type strains of species belonging to the Bacillus cereus group. About 7% of all isolates may belong to possibly new spore-forming taxa. Although the overall diversity of aerobic spore-forming bacteria in milk from organic vs. conventional dairy farms was highly similar, some differences between both were observed: (i) a relatively higher number of thermotolerant organisms in milk from conventional dairy farms compared to organic farms (41.2% vs. 25.9%), and (ii) a relatively higher number of B. cereus group organisms in milk from organic (81.3%) and Ureibacillus thermosphaericus in milk from conventional (85.7%) dairy farms. One of these differences, the higher occurrence of B. cereus group organisms in milk from organic dairy farms, may be linked to differences in housing strategy between the two types of dairy farming. However, no plausible clarification was found for the relatively higher number of thermotolerant organisms and the higher occurrence of U. thermosphaericus in milk from conventional dairy farms. Possibly this is due to differences in feeding strategy but no decisive indications were found to support this assumption.
- Published
- 2008
- Full Text
- View/download PDF
35. A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer.
- Author
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Martens M, Weidner S, Linke B, de Vos P, Gillis M, and Willems A
- Subjects
- Polymerase Chain Reaction, RNA, Ribosomal, 16S genetics, Rhizobiaceae genetics, Ribosomal Proteins metabolism, Oligonucleotide Array Sequence Analysis methods, RNA, Ribosomal, 16S analysis, Rhizobiaceae classification, Ribosomal Proteins genetics
- Abstract
To develop a reliable tool for the identification and classification of the different Ensifer species, without the need for sequencing, a prototype DNA microarray that targets the rpsA housekeeping gene was designed and tested. Internal segments of the rpsA gene from 34 reference strains, representing the different Ensifer species, were sequenced and the sequences were used to select 44 diagnostic oligonucleotides that served as probes for the identification microarray. Both, genomic DNA and specific rpsA PCR-products were tested as a target in hybridisation experiments. Experimental conditions were optimised and the diagnostic oligonucleotides were validated. Hybridisation results with the rpsA PCR-products showed reliable identification of the reference strains to species and genomovar level. Our data indicate that a microarray targeting housekeeping genes is a promising, accurate and relatively simple genotyping technique that would also be applicable for the identification and characterization of other bacterial groups of interest.
- Published
- 2007
- Full Text
- View/download PDF
36. The phylogeny of the genus Nitrobacter based on comparative rep-PCR, 16S rRNA and nitrite oxidoreductase gene sequence analysis.
- Author
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Vanparys B, Spieck E, Heylen K, Wittebolle L, Geets J, Boon N, and De Vos P
- Subjects
- Africa, Americas, Asia, Environmental Microbiology, Europe, Genes, Bacterial genetics, Genetic Variation, Nitrite Reductases metabolism, Nitrobacter classification, Oxidation-Reduction, Phylogeny, Species Specificity, Bacterial Proteins genetics, Nitrite Reductases genetics, Nitrobacter genetics, Polymerase Chain Reaction, RNA, Bacterial genetics, RNA, Ribosomal, 16S genetics, Sequence Analysis, Protein
- Abstract
Strains of Nitrobacter mediate the second step in the nitrification process by oxidizing nitrite to nitrate. The phylogenetic diversity of the genus is currently not well investigated. In this study, a rep-PCR profile and the nearly complete 16S rRNA gene sequence of 30 strains, comprising a wide physiological as well as ecological diversity and encompassing representatives of the four species, were determined. The sequence diversity of the 16S rRNA gene between different species was low, indicating the need for additional phylogenetic markers. Therefore, primers were developed for amplifying the complete nxrX gene and a 380bp fragment of the nxrB1 gene, which are both genes involved in the nitrite oxidation process. These genes confirmed the division into phylogenetic groups revealed by the 16S rRNA gene but showed a better discriminatory power. They can be a valuable additional tool for phylogenetic analysis within the genus Nitrobacter and can assist in the identification of new Nitrobacter isolates.
- Published
- 2007
- Full Text
- View/download PDF
37. Raman microspectroscopy as an identification tool within the phylogenetically homogeneous 'Bacillus subtilis' group.
- Author
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Hutsebaut D, Vandroemme J, Heyrman J, Dawyndt P, Vandenabeele P, Moens L, and de Vos P
- Subjects
- Bacillus subtilis growth & development, Species Specificity, Bacillus subtilis classification, Bacterial Typing Techniques, Spectrum Analysis, Raman methods
- Abstract
Vibrational methods have multiple advantages compared to more classic, chemotaxonomic and even molecular microbial tools for the identification of bacteria. Nevertheless, their definite breakthrough in diagnostic microbiology laboratories is determined by their identification potential. This paper reports on the profound evaluation of Raman spectroscopy to identify closely related species by means of 68 Bacillus strains that are assigned or closely related to the phylogenetically homogeneous 'Bacillus subtilis'-group (sensu stricto). These strains were chosen to represent biological variation within the selected species and to create a realistic view on the possibilities of this technique The evaluation resulted in 49/54 correct identifications at the species level for intern and 15/19 for extern testing. The correct identification of strains, which were not represented in the training set, supports the potential as an identification tool within the 'B. subtilis group'. Considering the vague borderline between the species studied, Raman spectroscopy can be regarded here as a promising application for identifications at the species level.
- Published
- 2006
- Full Text
- View/download PDF
38. Molecular characterisation of bacterial contamination in semi-final gelatine extracts, using denaturing gradient gel electrophoresis.
- Author
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de Clerck E, Devos J, and de Vos P
- Subjects
- Aerobiosis, Bacillus classification, Bacillus genetics, Bacillus isolation & purification, DNA Fingerprinting, DNA, Bacterial analysis, DNA, Bacterial chemistry, DNA, Bacterial isolation & purification, DNA, Ribosomal chemistry, DNA, Ribosomal isolation & purification, Drug Contamination, Electrophoresis, Polyacrylamide Gel, Food Microbiology, Gram-Positive Endospore-Forming Bacteria genetics, Molecular Sequence Data, Nucleic Acid Denaturation genetics, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Spores, Bacterial cytology, Temperature, Gelatin, Gram-Positive Endospore-Forming Bacteria classification, Gram-Positive Endospore-Forming Bacteria isolation & purification
- Abstract
Contamination of gelatine may affect the safety and/or quality of its applications. Characterisation of bacterial isolates from semi-final gelatine batches revealed thermotolerant, aerobic, endosporeforming contaminants. In this paper, bacterial contamination in gelatine batches is analysed without previous isolation, by means of denaturing gradient gel electrophoresis (DGGE) of PCR-amplified 16S rDNA sequences. V9 and V6-V8 regions of the 16S rDNA gene were found more suitable for this purpose than V1 or V3 regions. Bacillus fumarioli, Bacillus licheniformis, members of the 'Bacillus cereus group', Bacillus subtilis, Bacillus shackletonii, Brevibacillus borstelensis and Brevibacillus agri were detected.
- Published
- 2004
- Full Text
- View/download PDF
39. Study of the bacterial load in a gelatine production process focussed on Bacillus and related endosporeforming genera.
- Author
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De Clerck E and De Vos P
- Subjects
- Bacillus classification, Bacillus enzymology, Bacillus growth & development, Base Sequence, Colony Count, Microbial, Endospore-Forming Bacteria classification, Endospore-Forming Bacteria enzymology, Endospore-Forming Bacteria growth & development, Fatty Acids analysis, Gelatinases metabolism, Genetic Variation, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S, Spores, Bacterial growth & development, Spores, Bacterial isolation & purification, Bacillus isolation & purification, Endospore-Forming Bacteria isolation & purification, Food Microbiology, Gelatin, Industrial Microbiology
- Abstract
Gelatine is an animal protein with many industrial applications. Previous studies pointed out that endosporeforming bacteria, belonging to the genus Bacillus or related genera, might contaminate and survive the production process of gelatine, leading to products of low quality and safety. The aim of this study is to determine the bacterial diversity of contaminants isolated from a gelatine production chain with emphasis on aerobic endosporeforming bacteria. Contaminants were isolated from samples taken at five crucial points along two different production lines of a gelatine production process and from water supplies used for extraction and cooling. Gaschromatographic methyl ester analysis of fatty acids was performed to differentiate isolates at the genus level. Apart from members of the genus Bacillus or related endosporeforming genera, also members of Salmonella, Kluyvera, Staphylococcus, Burkholderia, Enterococcus, Pseudomonas, Yersinia, Streptococcus and Brevundimonas could be detected. Isolates identified as belonging to Bacillus and related endosporeforming genera were further characterised by gelatinase tests, rep-PCR and 16S rDNA sequencing. All these isolates showed the ability to liquefy gelatine. Endosporeforming isolates were assigned to Bacillus licheniformis, B. fumarioli, members of the B. cereus group, B. badius, B. coagulans, B. subtilis, Brevibacillus agri, Alicyclobacillus acidocaldarius and a yet undescribed Paenibacillus species.
- Published
- 2002
- Full Text
- View/download PDF
40. Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov., nodulate the roots of tropical legumes.
- Author
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Vandamme P, Goris J, Chen WM, de Vos P, and Willems A
- Subjects
- Base Sequence, Burkholderia cytology, Burkholderia genetics, Burkholderia isolation & purification, Fatty Acids analysis, Molecular Sequence Data, Phylogeny, Plant Roots metabolism, Plant Roots microbiology, RNA, Ribosomal, 16S, Soil Microbiology, Tropical Climate, Burkholderia classification, Fabaceae microbiology
- Abstract
The taxonomic status of five root nodule isolates from tropical legumes was determined using a polyphasic taxonomic approach. Two isolates were identified as B. caribensis, an organism originally isolated from soil in Martinique (the French West Indies). One isolate was identified as Burkholderia cepacia genomovar VI, a B. cepacia complex genomovar thus far only isolated from sputum of cystic fibrosis patients. The remaining two isolates were identified as novel Burkholderia species for which we propose the names Burkholderia tuberum sp. nov. and Burkholderia phymatum sp. nov. The type strains are LMG 21444T and LMG 21445T, respectively.
- Published
- 2002
- Full Text
- View/download PDF
41. Diversity of transconjugants that acquired plasmid pJP4 or pEMT1 after inoculation of a donor strain in the A- and B-horizon of an agricultural soil and description of Burkholderia hospita sp. nov. and Burkholderia terricola sp. nov.
- Author
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Goris J, Dejonghe W, Falsen E, De Clerck E, Geeraerts B, Willems A, Top EM, Vandamme P, and De Vos P
- Subjects
- 2,4-Dichlorophenoxyacetic Acid metabolism, Agriculture, Bacterial Proteins genetics, Betaproteobacteria classification, Biodegradation, Environmental, Culture Media, DNA, Bacterial analysis, DNA, Ribosomal analysis, Gene Transfer Techniques, Molecular Sequence Data, Nucleic Acid Hybridization, Plasmids genetics, RNA, Ribosomal, 16S genetics, Sequence Analysis, DNA, Soil Pollutants metabolism, Stenotrophomonas classification, Betaproteobacteria genetics, Burkholderia classification, Burkholderia genetics, Conjugation, Genetic, Soil Microbiology, Stenotrophomonas genetics
- Abstract
We examined the diversity of transconjugants that acquired the catabolic plasmids pJP4 or pEMT1, which encode degradation of 2,4-dichlorophenoxyacetic acid (2,4-D), in microcosms with agricultural soil inoculated with a donor strain (Dejonghe, W., Goris, J., El Fantroussi, S., Höfte, M., De Vos, P., Verstraete, W., and Top, E. M. Appl. Environ. Microbiol. 2000, p. 3297-3304). Using repetitive element PCR fingerprinting, eight different rep-clusters and six separate isolates could be discriminated among 95 transconjugants tested. Representative isolates were identified using 16S rDNA sequencing, cellular fatty acid analysis, whole-cell protein analysis and/or DNA-DNA hybridisations. Plasmids pJP4 and pEMT1 appeared to have a similar transfer and expression range, and were preferably acquired and expressed in soil by indigenous representatives of Ralstonia and Burkholderia. Two rep-clusters were shown to represent novel Burkholderia species, for which the names Burkholderia hospita sp. nov. and Burkholderia terricola sp. nov. are proposed. When easily degradable carbon sources were added together with the plasmid-bearing donor strain, also a significant proportion of Stenotrophomonas maltophilia isolates were found. The transconjugant collections isolated from A- (0-30 cm depth) and B-horizon (30-60 cm depth) soil were similar, except for B. terricola transconjugants, which were only isolated from the B-horizon.
- Published
- 2002
- Full Text
- View/download PDF
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