@article{kumar_altererythrobacter_2008, title = {Altererythrobacter indicus sp. nov., isolated from wild rice (Porteresia coarctata Tateoka)}, author = {N Ramesh Kumar and Sudha Nair and Stefan Langer and Hans-Jürgen Busse and Peter Kämpfer}, journal = {International journal of systematic and evolutionary microbiology}, month = {April}, note = {PMID: 18398179}, pages = {839-44}, volume = {58}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/27a01718baddcee38150b6d0b3e102c50/recymikrobio}, abstract = {A Gram-negative, rod-shaped, non-spore-forming organism, strain MSSRF26(T), was isolated from mangrove-associated wild rice in India. On the basis of 16S rRNA gene sequence similarities, strain MSSRF26(T) was shown to belong to the Alphaproteobacteria, most closely related to Altererythrobacter luteolus and Altererythrobacter epoxidivorans (96.1 and 95.9 \% similarity to the respective type strains). Chemotaxonomic data [major ubiquinones Q-10 (91 \%) and Q-9 (9 \%); major polyamine spermidine, with putrescine, cadaverine and spermine detected only in trace amounts; major polar lipids phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and sphingoglycolipid; major fatty acid C(18 : 1)omega7c and C(14 : 0) 2-OH as hydroxylated fatty acid] supported the affiliation of MSSRF26(T) to the genus Altererythrobacter. Fatty acid data and physiological and biochemical tests allowed phenotypic differentiation of the isolate from described Altererythrobacter species. Strain MSSRF26(T) therefore represents a novel species, for which the name Altererythrobacter indicus sp. nov. is proposed, with the type strain MSSRF26(T) (=LMG 23789(T) =DSM 18604(T)).}, issn = {14665026}, keywords = {IFZ imported } } @article{kmpfer_pseudacidovorax_2008, title = {Pseudacidovorax intermedius gen. nov., sp. nov., a novel nitrogen-fixing betaproteobacterium isolated from soil}, author = {Peter Kämpfer and K Thummes and Horng-I Chu and Chen-Chung Tan and A B Arun and Wen-Ming Chen and Wei-An Lai and Fo-Ting Shen and P D Rekha and Chiu-Chung Young}, journal = {International journal of systematic and evolutionary microbiology}, month = {February}, note = {PMID: 18218955}, pages = {491-5}, volume = {58}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/276e1f65c417d52d7d01b71a9be0ee269/recymikrobio}, abstract = {A Gram-negative, short rod-shaped, nitrogen-fixing bacterium (CC-21(T)) was isolated from a soil sample collected from the regional agricultural research station in Kaohsiung County (Taiwan). Using 16S rRNA gene sequence analysis, it could be clearly demonstrated that this isolate was novel: it showed {\textless}97 \% similarity to species of the genera Acidovorax, Alicycliphilus, Giesbergeria, Simplicispira and Diaphorobacter. The organism used several organic acids, but only a few sugars as substrates. The fatty acid profile differed from those reported for members of the genera Acidovorax, Alicycliphilus, Giesbergeria, Simplicispira and Diaphorobacter. On the basis of 16S rRNA gene sequence analysis in combination with physiological data, strain CC-21(T) represents a novel species in a new genus, for which the name Pseudacidovorax intermedius gen. nov., sp. nov. is proposed; the type strain is CC-21(T) (=CCUG 54492(T)=CIP 109510(T)).}, issn = {14665026}, keywords = {16S Bacterial Bacterial_Typing_Techniques Cell_Wall Comamonadaceae DNA Fatty_Acids Genes IFZ Molecular_Sequence_Data Nitrogen_Fixation Phylogeny RNA Ribosomal Sequence_Analysis Soil_Microbiology Species_Specificity rRNA } } @article{young_chromobacterium_2008, title = {Chromobacterium aquaticum sp. nov., isolated from spring water samples}, author = {Chiu-Chung Young and A B Arun and Wei-An Lai and Wen-Ming Chen and Jiu-Hsing Chao and Fo-Ting Shen and P D Rekha and Peter Kämpfer}, journal = {International journal of systematic and evolutionary microbiology}, month = {April}, note = {PMID: 18398186}, pages = {877-80}, volume = {58}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/27a4c4e5d0ceca668e7b76b5657a3364f/recymikrobio}, abstract = {Strain CC-SEYA-1(T), a motile, Gram-negative, non-violet-pigmented bacterium, was isolated on nutrient agar from spring-water samples collected from Yang-Ming Mountain, Taipei County, Taiwan. 16S rRNA gene sequence studies showed that the strain clustered with Chromobacterium violaceum (96.8 \% similarity) and Chromobacterium subtsugae (96.5 \% similarity), followed by Aquitalea magnusonii (95.8 \% similarity). The fatty acid profile was slightly different from those reported for C. violaceum, C. subtsugae and A. magnusonii. The results of DNA-DNA hybridization, and physiological and biochemical tests allowed both genotypic and phenotypic differentiation of the isolate from the described Chromobacterium species. It is evident from the data obtained that the strain should be classified as a novel species in the genus Chromobacterium. The name proposed for this taxon is Chromobacterium aquaticum sp. nov.; the type strain is CC-SEYA-1(T) (=CCUG 55175(T)=BCRC 17769(T)).}, issn = {14665026}, keywords = {IFZ imported } } @article{herzog_chryseobacterium_2008, title = {Chryseobacterium ureilyticum sp. nov., Chryseobacterium gambrini sp. nov., Chryseobacterium pallidum sp. nov. and Chryseobacterium molle sp. nov., isolated from beer-bottling plants}, author = {Peter Herzog and Ilka Winkler and Dorothee Wolking and Peter Kämpfer and André Lipski}, journal = {International journal of systematic and evolutionary microbiology}, note = {PMID: 18175677}, pages = {26-33}, volume = {58}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/2149558e93eaf90e50c4549c1545de758/recymikrobio}, abstract = {Four Gram-negative, rod-shaped, non-spore-forming and non-motile bacterial strains were isolated from surfaces and biofilms associated with beer-bottling plants. Based on their 16S rRNA gene sequences these isolates were allocated to the genus Chryseobacterium. The sequence similarities of the isolates to the next most closely related type strains of this genus ranged from 96.4 to 98.3\%. The presence of menaquinone MK-6 and predominant fatty acids 15:0 iso, 17:1 iso cis9, 15:0 iso 2-OH and 17:0 iso 3-OH supported the affiliation of these strains to the genus. The results of DNA-DNA hybridization, biochemical tests and chemotaxonomic properties allowed genotypic and phenotypic differentiation of the strains from the next most closely related Chryseobacterium species with validly published names. Therefore, the isolates represent four novel species for which the names Chryseobacterium ureilyticum (type strain F-Fue-04IIIaaaa(T)=DSM 18017(T)=CCUG 52546(T)), Chryseobacterium gambrini (type strain 5-1St1a(T)=DSM 18014(T)=CCUG 52549(T)), Chryseobacterium pallidum (type strain 26-3St2b(T)=DSM 18015(T)=CCUG 52548(T)) and Chryseobacterium molle (type strain DW3(T)=DSM 18016(T)=CCUG 52547(T)) are proposed.}, issn = {14665026}, keywords = {16S Bacterial_Typing_Techniques Beer Biofilms Chryseobacterium DNA Fatty_Acids Genotype IFZ Industrial_Microbiology Molecular_Sequence_Data Nucleic_Acid_Hybridization Phenotype Phylogeny RNA Ribosomal Sequence_Analysis Species_Specificity Steel } } @article{scholz_brucella_2008, title = {Brucella microti sp. nov., isolated from the common vole Microtus arvalis}, author = {Holger C Scholz and Zdenek Hubalek and Ivo Sedlácek and Gilles Vergnaud and Herbert Tomaso and Sascha Al Dahouk and Falk Melzer and Peter Kämpfer and Heinrich Neubauer and Axel Cloeckaert and Marianne Maquart and Michel S Zygmunt and Adrian M Whatmore and Enevold Falsen and Peter Bahn and Cornelia Göllner and Martin Pfeffer and Birgit Huber and Hans-Jürgen Busse and Karsten Nöckler}, journal = {International journal of systematic and evolutionary microbiology}, month = {February}, note = {PMID: 18218934}, pages = {375-82}, volume = {58}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/23661356d26a6d4e299b61c94d4b6c65b/recymikrobio}, abstract = {Two Gram-negative, non-motile, non-spore-forming, coccoid bacteria (strains CCM 4915(T) and CCM 4916), isolated from clinical specimens of the common vole Microtus arvalis during an epizootic in the Czech Republic in 2001, were subjected to a polyphasic taxonomic study. On the basis of 16S rRNA (rrs) and recA gene sequence similarities, both isolates were allocated to the genus Brucella. Affiliation to Brucella was confirmed by DNA-DNA hybridization studies. Both strains reacted equally with Brucella M-monospecific antiserum and were lysed by the bacteriophages Tb, Wb, F1 and F25. Biochemical profiling revealed a high degree of enzyme activity and metabolic capabilities not observed in other Brucella species. The omp2a and omp2b genes of isolates CCM 4915(T) and CCM 4916 were indistinguishable. Whereas omp2a was identical to omp2a of brucellae from certain pinniped marine mammals, omp2b clustered with omp2b of terrestrial brucellae. Analysis of the bp26 gene downstream region identified strains CCM 4915(T) and CCM 4916 as Brucella of terrestrial origin. Both strains harboured five to six copies of the insertion element IS711, displaying a unique banding pattern as determined by Southern blotting. In comparative multilocus VNTR (variable-number tandem-repeat) analysis (MLVA) with 296 different genotypes, the two isolates grouped together, but formed a separate cluster within the genus Brucella. Multilocus sequence typing (MLST) analysis using nine different loci also placed the two isolates separately from other brucellae. In the IS711-based AMOS PCR, a 1900 bp fragment was generated with the Brucella ovis-specific primers, revealing that the insertion element had integrated between a putative membrane protein and cboL, encoding a methyltransferase, an integration site not observed in other brucellae. Isolates CCM 4915(T) and CCM 4916 could be clearly distinguished from all known Brucella species and their biovars by means of both their phenotypic and molecular properties, and therefore represent a novel species within the genus Brucella, for which the name Brucella microti sp. nov. with the type strain CCM 4915(T) (=BCCN 07-01(T)=CAPM 6434(T)) is proposed.}, issn = {14665026}, keywords = {16S Animals Arvicolinae Bacterial Bacterial_Outer_Membrane_Proteins Bacterial_Typing_Techniques Brucella Brucellosis DNA Genes Genotype IFZ Minisatellite_Repeats Molecular_Sequence_Data Nucleic_Acid_Hybridization Phenotype Phylogeny RNA Rec_A_Recombinases Ribosomal Rodent_Diseases Sequence_Analysis Species_Specificity rRNA } } @article{scholz_genetic_2008, title = {Genetic diversity and phylogenetic relationships of bacteria belonging to the Ochrobactrum-Brucella group by recA and 16S rRNA gene-based comparative sequence analysis}, author = {Holger C Scholz and Sascha Al Dahouk and Herbert Tomaso and Heinrich Neubauer and Angela Witte and Michael Schloter and Peter Kämpfer and Enevold Falsen and Martin Pfeffer and Marion Engel}, journal = {Systematic and applied microbiology}, month = {March}, note = {PMID: 18222618}, pages = {1-16}, volume = {31}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/21f0ba17ae5a8f2d61f11821025c74c09/recymikrobio}, abstract = {The genetic diversity and phylogenetic interrelationships among 106 Ochrobactrum strains (O. anthropi: 72, O. intermedium: 22, O. tritici: 5, O. oryzae: 2, O. grignonense: 2, O. gallinifaecis: 1, O. lupini: 2), the type strains of the eight Brucella species and other closely related taxa were studied by recA and rrs gene (16S rRNA) comparative sequence analysis. Both markers correctly delineated the various Ochrobactrum species; however, resolution at the subspecies level was considerably higher in the recA gene-based approach. Phylogenetic analyses using neighbor-joining, parsimony, and maximum likelihood algorithms generated trees with similar topologies but the overall branching order, and also the order of the subclades, were not stable in either assay, which could be explained by generally high recA and rrs sequence similarities. Ochrobactrum and Pseudochrobactrum formed separate clades distinct from other Alphaproteobacteria with Bartonella, Agrobacterium, and Rhizobium as the closest relatives. O. gallinifaecis was the most distinct member, when compared to the type species O. anthropi, with rrs and recA similarities of 96.2\% and 81.4\%. Brucella species were indistinguishable, exhibiting high rrs and recA gene similarities of 98.6\% and 85.5\% compared with Ochrobactrum intermedium. At the protein level, all RecA sequences among the various Ochrobactrum species and between Ochrobactrum and Brucella were highly similar with only a few amino acid substitutions. O. anthropi and O. tritici were indistinguishable by means of their RecA proteins. A set of initially biochemically classified strains did not cluster within their assigned species and they either grouped within other known species or grouped as potential novel Ochrobactrum species. In further investigations, these strains were reclassified and described as novel species. In summary, Ochrobactrum is a highly diverse genus comprising several novel species. We recommend recA- in addition to rrs gene-analysis for correct species allocation and subtyping of novel Ochrobactrum isolates.}, issn = {07232020}, keywords = {IFZ imported } } @article{kmpfer_reclassification_2008, title = {Reclassification of Pseudomonas mephitica Claydon and Hammer 1939 as a later heterotypic synonym of Janthinobacterium lividum (Eisenberg 1891) De Ley et al. 1978}, author = {Peter Kämpfer and Enevold Falsen and Hans-Jürgen Busse}, journal = {International journal of systematic and evolutionary microbiology}, note = {PMID: 18175698}, pages = {136-8}, volume = {58}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/21cdb5536f69cc573a585f7be391b6c81/recymikrobio}, abstract = {Pseudomonas mephitica CCUG 2513(T) has been reinvestigated to clarify its taxonomic position. 16S rRNA gene sequence comparisons demonstrated that this strain clusters phylogenetically closely with Janthinobacterium lividum (99.8\% sequence similarity to the type strain). Investigation of fatty acid patterns, polar lipid profiles, polyamine patterns and quinone systems supported this delineation. Substrate utilization profiles and biochemical characteristics displayed no differences from the type strain of J. lividum, CCUG 2344(T). Therefore, the reclassification of Pseudomonas mephitica as a later heterotypic synonym of Janthinobacterium lividum is proposed, based upon the estimated phylogenetic position derived from 16S rRNA gene sequence data and chemotaxonomic and biochemical data.}, issn = {14665026}, keywords = {16S Bacterial_Typing_Techniques DNA Fatty_Acids Genes IFZ Molecular_Sequence_Data Oxalobacteraceae Phenotype Phylogeny Pseudomonas RNA Ribosomal Sequence_Analysis rRNA } } @article{mazumdar_rapid_2007, title = {Rapid method for detection of Salmonella in milk by surface plasmon resonance (SPR)}, author = {Saikat Datta Mazumdar and Markus Hartmann and Peter Kämpfer and Michael Keusgen}, journal = {Biosensors \& bioelectronics}, month = {April}, note = {PMID: 17079127}, pages = {2040-6}, volume = {22}, year = {2007}, biburl = {http://www.bibsonomy.org/bibtex/2e95b85c9ac2438f96b644a1348939ddb/recymikrobio}, abstract = {The Plasmonic surface plasmon resonance (SPR) device was used to develop a rapid, simple and specific immunoassay for detection of Salmonella in milk. Rapid detection of Salmonella contamination is a major challenge for the food industry. Salmonella contamination is well known in all foods including pasteurised milk. The SPR assay was developed as a sandwich model using a polyclonal antibody against Salmonella as capture and detection antibody. Milk spiked with Salmonella typhimurium cells, killed by thimerosal (1\%, w/w) treatment was used. Using the Plasmonic SPR assay it was possible to detect S. typhimurium down to a concentration of 1.25 x 10(5) cells ml(-1) in both milk and buffer system. The results obtained are comparable with existing, approved rapid Salmonella detection techniques. No negative effects on the sensitivity of the assay are encountered due to the milk matrix. Hence, no sample preparation or clean-up steps are required. The sample volume requirement for the assay is only 10 microl. Using the assay S. typhimurium was detected in milk within 1h, whereas the cultural techniques require 3-4 days for presumptive positive isolates and further time for confirmation. The rapid tests require at least 24h for the results. The Plasmonic SPR device operates on the Kretschmann configuration and is a cuvette-based system with the advantage of having eight channels on one single SPR chip.}, issn = {09565663}, keywords = {Animals Food_Microbiology IFZ Milk Rabbits Salmonella_typhimurium Surface_Plasmon_Resonance } } @article{albrecht_recommendations_2008, title = {Recommendations for study design and sampling strategies for airborne microorganisms, MVOC and odours in the surrounding of composting facilities}, author = {Andreas Albrecht and Guido Fischer and Gefion Brunnemann-Stubbe and Udo Jäckel and Peter Kämpfer}, journal = {International journal of hygiene and environmental health}, month = {March}, note = {PMID: 17765659}, pages = {121-31}, volume = {211}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/2c0f9d07b5f5519370b23ddb366586b81/recymikrobio}, abstract = {Microorganisms and odour emissions from composting plants often lead to complaints by residents, especially by people living close to such plants. Both parameters were studied in a systematic approach under specific local meteorological conditions at nine different composting plants in Germany with emphasis on dispersal of microorganisms. Measurements were done at emission points and at sampling sites in the downwind and upwind directions of the facilities under 'normal case' (i.e. weather conditions typical for the location in combination with working activities at the plants) and 'real worst case' conditions (dispersal of bioaerosols into the surroundings expected to occur with high probability). Airborne microorganisms were sampled using filtration and impingement. Subsequent cultivation on four different culture media allowed quantification and identification of the culturable microflora. It turned out that a general assessment of emissions and dispersal of bioaerosols from composting plants is not possible because of the coherences of various factors influencing the dispersal. The site-specific meteorological situations must be considered carefully, whenever sampling locations are selected and need to be recorded in any sampling protocol. Air inversions in particular can lead to high concentrations of microorganisms ({\textgreater}10(4)-10(5)cfu m(-3) of thermophilic actinomycetes and thermotolerant fungi) in the surroundings of composting plants. Finally, it was shown that both thermotolerant fungi and thermophilic actinomycetes can serve as indicator organisms.}, issn = {14384639}, keywords = {IFZ imported } } @article{fischer_analysis_2008, title = {Analysis of airborne microorganisms, MVOC and odour in the surrounding of composting facilities and implications for future investigations}, author = {Guido Fischer and Andreas Albrecht and Udo Jäckel and Peter Kämpfer}, journal = {International journal of hygiene and environmental health}, month = {March}, note = {PMID: 17936684}, pages = {132-42}, volume = {211}, year = {2008}, biburl = {http://www.bibsonomy.org/bibtex/2a1b7c37c09fbba6fe669ced82cdbd5dc/recymikrobio}, abstract = {Emission and dispersal of microorganisms and odours from composting facilities were studied in a 3-year project at nine different composting facilities in Germany. Measurements were carried out under so-called 'normal-case', i.e. typical local climate conditions and working activities within the facilities, and 'real worst-case' conditions ('drainage flow' conditions) being characterized by the translocation of cold air mostly at night, and containing large amounts of bioaerosols. Highest concentrations of microorganisms were observed during turning of compost with a maximum of 2.4x10(6)cfu m(-3) for thermophilic actinomycetes. Other groups of microorganisms were detected in concentrations of about 10(5)cfu m(-3). During shredding of fresh organic material, the concentrations of all microorganisms reached 10(4)cfu m(-3). Here, odour concentrations turned out to be highest (up to 1,367 odour units (OU)m(-3)). At facilities equipped with a biofilter (odour reduction), a decrease in OU by a factor of 10 was observed. In the surrounding of the facilities, highest concentrations ranged between 10(1)-10(3)cfu m(-3) upwind and from 10(1)-10(4)cfu m(-3) downwind. The specific local meteorological situations must be considered carefully in advance and during sampling. Especially 'drainage flow' situations can lead to high microorganism concentrations ({\textgreater}10(4)-10(5)cfu m(-3) of thermophilic actinomycetes and thermophilic fungi) in the surroundings of composting facilities.}, issn = {14384639}, keywords = {IFZ imported } }