Search results for "sequence analysis"
showing 10 items of 1349 documents
Novosphingobium lentum sp. nov., a psychrotolerant bacterium from a polychlorophenol bioremediation process
2005
A polychlorophenol-degrading strain, designated MT1T, and three MT1-like strains, MT101, MT103 and MT104, were isolated from a cold (4–8 °C) fluidized-bed process treating chlorophenol-contaminated groundwater in southern Finland. The organisms were Gram-negative, rod-shaped, catalase-positive, non-spore-forming and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the strains belonged to the α-4 subclass of the Proteobacteria and were members of the genus Novosphingobium. The highest 16S rRNA gene sequence similarity observed for these strains was 96·5 % with the type strains of Novosphingobium hassiacum, Novosphingobium aromaticivorans and Novosphingobium s…
Neptuniibacter caesariensis gen. nov., sp. nov., a novel marine genome-sequenced gammaproteobacterium.
2007
7 pages, 1 figure, 1 table
Rapid differentiation and in situ detection of 16 sourdough lactobacillus species by multiplex PCR.
2005
ABSTRACT A two-step multiplex PCR-based method was designed for the rapid detection of 16 species of lactobacilli known to be commonly present in sourdough. The first step of multiplex PCR was developed with a mixture of group-specific primers, while the second step included three multiplex PCR assays with a mixture of species-specific primers. Primers were derived from sequences that specify the 16S rRNA, the 16S-23S rRNA intergenic spacer region, and part of the 23S rRNA gene. The primer pairs designed were shown to exclusively amplify the targeted rrn operon fragment of the corresponding species. Due to the reliability of simultaneously identifying Lactobacillus plantarum , Lactobacillus…
A chromosome map of the Flavescence dorée phytoplasma
2008
International audience; The Flavescence dorée phytoplasma (FD-P), a non-cultivable, plant-pathogenic bacterium of the class Mollicutes, is the causal agent of a quarantine disease affecting vineyards of southern Europe, mainly in southern France and northern Italy. To investigate FD-P diversity and phytoplasma genetic determinants governing the FD-P life cycle, a genome project has been initiated. A physical map of the chromosome of FD-P strain FD92, purified from infected broad beans, was constructed by performing restriction digests of the chromosome and resolving the fragments by PFGE. Single and double digestions of the chromosome with the enzymes SalI, BssHII, MluI and EagI were perfor…
Engineering of a bacterial tyrosinase for improved catalytic efficiency towards D-tyrosine using random and site directed mutagenesis approaches
2013
The tyrosinase gene from Ralstonia solanacearum (GenBank NP518458) was subjected to random mutagenesis resulting in tyrosinase variants (RVC10 and RV145) with up to 3.2-fold improvement in kcat, 5.2-fold lower Km and 16-fold improvement in catalytic efficiency for D-tyrosine. Based on RVC10 and RV145 mutated sequences, single mutation variants were generated with all variants showing increased kcat for D-tyrosine compared to the wild type (WT). All single mutation variants based on RV145 had a higher kcat and Km value compared to the RV145 and thus the combination of four mutations in RV145 was antagonistic for turnover, but synergistic for affinity of the enzyme for D-tyrosine. Single muta…
Description of Tropicibacter mediterraneus sp. nov. and Tropicibacter litoreus sp. nov.
2013
Four strains (M15∅_3, M17(T), M49 and R37(T)) were isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. Together with an older preserved isolate (strain 2OM6) from cultured oysters at Vinaroz, Castellón, Spain, the strains were thoroughly characterized in a polyphasic study and were placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae. Highest 16S rRNA sequence similarities of the five strains to the types of any established species corresponded to Tropicibacter multivorans (95.8-96.4%), Phaeobacter inhibens (95.9-96.3%) and Phaeobacter gallaeciensis (95.9-96.2%). On the other hand, whole genome (ANI) and protein fingerprinting (MALDI-TOF…
Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen
2010
Abstract Background Helicobacter mustelae causes gastritis, ulcers and gastric cancer in ferrets and other mustelids. H. mustelae remains the only helicobacter other than H. pylori that causes gastric ulceration and cancer in its natural host. To improve understanding of H. mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the H. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome. Results The H. mustelae genome lacks orthologs of major H. pylori virulence factors including CagA, VacA, BabA, SabA and OipA. However, it encodes ten autotransporter surface proteins, seven of which were detec…
Phylogenetic analysis of the genera Proteus, Morganella and Providencia by comparison of rpoB sequences of type and clinical strains suggests the cla…
2010
Phylogenetic analysis of partial rpoB gene sequences of type and clinical strains belonging to different 16S rRNA gene-fingerprinting ribogroups within 11 species of enterobacteria of the genera Proteus, Morganella and Providencia was performed and allowed the definition of rpoB clades, supported by high bootstrap values and confirmed by ≥2.5 % nucleotide divergence. None of the resulting clades included strains belonging to different species and the majority of the species were confirmed as discrete and homogeneous. However, more than one distinct rpoB clade could be defined among strains belonging to the species Proteus vulgaris (two clades), Providencia alcalifaciens (two clades) and Pro…
Molecular analysis of the dominant lactic acid bacteria of chickpea liquid starters and doughs and propagation of chickpea sourdoughs with selected W…
2020
Abstract Fermented chickpea liquid is used as a leavening agent in chickpea bread production. In the present study, traditional chickpea liquid starter and dough samples were collected from bakeries in Turkey and microbiologically investigated. Culture-independent analysis for microbiota diversity, performed by MiSeq Illumina, identified Clostridium perfringens as major group in all samples, while Weissella spp. Dominated LAB community. A culture-dependent methodology was applied and 141 isolates were confirmed to be members of the LAB group based on 16s rRNA gene sequence analysis. In particular, 11 different LAB species were identified confirming the high frequency of isolation of weissel…
Identification of Beijerinckia fluminensis strains CIP 106281T and UQM 1685T as Rhizobium radiobacter strains, and proposal of Beijerinckia doeberein…
2009
During the course of a research project with free-living, nitrogen-fixing bacteria, we determined the 16S rRNA gene sequence of Beijerinckia fluminensis strains UQM 1685T and CIP 106281T and discovered that they were only 90.6–91.2 % similar to the sequences of strains of other Beijerinckia species and subspecies. Moreover, the highest similarity to these sequences (99.7 %) corresponded to strains of Rhizobium radiobacter (including Agrobacterium tumefaciens). Other diagnostic features confirmed that the two strains have the same origin but do not descend from the nomenclatural type. At the same time, B. fluminensis LMG 2819 was characterized and it was found that its properties also do not…