Search results for "16S ribosomal RNA"
showing 10 items of 165 documents
Vibrio renipiscarius sp. nov., isolated from cultured gilthead sea bream (Sparus aurata)
2015
Two strains of Gram-negative, facultatively anaerobic, slightly halophilic bacteria, isolated from healthy gilthead sea bream (Sparus aurata) cultured in Spanish Mediterranean fish farms, were different from their closest relatives,Vibrio scophthalmiandV. ichthyoenteri, by phenotypic, phylogenetic and genomic standards. The strains were negative for decarboxylase tests and lacked extracellular hydrolytic activities, but were able to fermentd-mannitol, sucrose, cellobiose andd-gluconate, among other carbohydrates. The major cellular fatty acids were C16:1and C16:0, in agreement with other species of the genusVibrio. Their 16S rRNA gene sequences were 98.4 and 97.2 % similar to those of the t…
Reinekea blandensis sp. nov., a marine, genome-sequenced gammaproteobacterium
2007
6 pages, 2 figures, 2 tables
Euzebyella saccharophila gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae.
2010
Strain 7SM30T , an aerobic marine, Gram-negative, heterotrophic and yellow- to orange-pigmented bacterium isolated from seawater from Castellón, Spain, was characterized using a polyphasic approach. Analysis of the 16S rRNA gene sequence showed that the isolate represented a novel lineage within the family Flavobacteriaceae. The most closely related genera were Pseudozobellia, Zobellia and Kriegella. Cells of strain 7SM30T were non-motile rods that required sea salts for growth, used a wide variety of carbohydrates as sole carbon and energy sources and, unlike species of the genera Pseudozobellia and Zobellia, did not possess flexirubin-type pigment or hydrolyse agar. Strain 7SM30T containe…
Multilocus Sequence Analysis of the redefined clade Scophthalmi in the genus Vibrio.
2015
A Multilocus Sequence Analysis (MLSA) was performed on members of the Scophthalmi clade in the genus Vibrio, including type and reference strains of the species V. scophthalmi, V. ichthyoenteri, and 39 strains phenotypically identified as Vibrio ichthyoenteri-like, with the aim of better defining boundaries between these two closely related, fish-associated species. The type strain of V. ponticus, recently added to the clade Scophthalmi, was also included. The study was based on partial sequences of the protein-coding housekeeping genes rpoD, mreB, recA, ftsZ, and gyrB, and the 16S rRNA. While the 16S rRNA gene-based trees were unable to pull apart members of V. scophthalmi or V. ichthyoent…
Multilocus sequence analysis of the central clade of the genus Vibrio by using the 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR genes.
2009
The central clade of the genus Vibrio, also called the Vibrio core group, comprises six species that are tightly related (DNA–DNA reassociation values are very close to 70 % for most species pairs). Identification of novel strains to the species level within this group is troublesome and results are quite often dependent on the methodology employed. Therefore, this group represents an excellent framework to test the robustness of multilocus sequence analysis (MLSA) not only for inferring phylogeny but also as an identification tool without the need for DNA–DNA hybridization assays. The genes selected, 16S rRNA, recA, pyrH, rpoD, gyrB, rctB and toxR, were amplified by direct PCR from 44 Vibr…
Identification and typing of food-borne Staphylococcus aureus by PCR-based techniques.
2005
Abstract The possibility of using PCR for rapid identification of food-borne Staphylococcus aureus isolates was evaluated as an alternative to the API-Staph system. A total of 158 strains, 15 S. aureus , 12 other staphylococcal species, and 131 isolates recovered from 164 food samples were studied. They were phenotypically characterized by API-Staph profiles and tested for PCR amplification with specific primers directed to thermonuclease ( nuc ) and enterotoxin ( sea to see ) genes. Disagreement between the PCR results and API-Staph identification was further assessed by the analysis of randomly amplified polymorphic DNA (RAPD) profiles obtained with three universal primers (M13, T3, and T…
In vitro and in vivo sulfate reduction in the gut contents of the termite Mastotermes darwiniensis and the rose-chafer Pachnoda marginata.
2005
Sulfate-reducing bacteria (SRB) from termites have been assigned to the genus Desulfovibrio. Desulfovibrio intestinalis lives in the gut of the Australian termite Mastotermes darwiniensis. For the first time we were able to enrich and identify a sulfate-reducing bacterium from the gut of the rose-chafer Pachnoda marginata, which showed the highest 16S rDNA sequence identity (93%) to Desulfovibrio intestinalis and Desulfovibrio strain STL1. Compared to Mastotermes darwiniensis (1x10(7) cells of SRB per ml gut contents), sulfate-reducing bacteria occurred in higher numbers in the gut contents of Pachnoda marginata reaching cell titers of up to 2x10(8) cells per ml gut contents. In vitro sulfa…
Tropicibacter multivorans sp. nov., an aerobic alphaproteobacterium isolated from surface seawater.
2011
Strain MD5T, an aerobic marine alphaproteobacterium, was isolated from Mediterranean seawater at Malvarrosa beach, Valencia, Spain. The strain was characterized in a polyphasic study and was placed phylogenetically within the Roseobacter clade in the family Rhodobacteraceae . Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MD5T is related to Tropicibacter naphthalenivorans C02T, Phaeobacter inhibens T5T, P. gallaeciensis BS107T and P. daeponensis TF-218T, with 96.9, 96.2, 96.1 and 96.1 % sequence similarity, respectively. Phylogenetic analyses also showed that strain MD5T forms a stable clade only with T. naphthalenivorans C02T. Strain MD5T requires Na+ plus a diva…
Functional and genomic diversity of methylotrophic Rhodocyclaceae: description of Methyloversatilis discipulorum sp. nov.
2015
Three strains of methylotrophic Rhodocyclaceae (FAM1T, RZ18-153 and RZ94) isolated from Lake Washington sediment samples were characterized. Based on phylogenetic analysis of 16S rRNA gene sequences the strains should be assigned to the genus Methyloversatilis. Similarly to other members of the family, the strains show broad metabolic capabilities and are able to utilize a number of organic acids, alcohols and aromatic compounds in addition to methanol and methylamine. The main fatty acids were 16:1ω7c (49–59 %) and 16:0 (32–29 %). Genomes of all isolates were sequenced, assembled and annotated in collaboration with the DOE Joint Genome Institute (JGI). Genome comparison revealed that the s…
Pseudomonas lini sp. nov., a novel species from bulk and rhizospheric soils.
2002
The taxonomic position of eight fluorescent Pseudomonas strains isolated from bulk and rhizospheric soils, and from water was examined. These eight strains clustered in one phenon together with Pseudomomas mandelii (CFBP 4844T), but could still be differentiated from this type strain by four phenotypic features. The eight stains exhibited internal DNA-DNA hybridization values ranging from 60 to 100%, with deltaTm below 5 degrees C (3.9 and 4.3 degrees C) for the lowest values (60 and 66%). The percentages of hybridization with type or reference strains of other Pseudomonas species tested ranged from 12 to 60% (deltaTm = 5.5 degrees C), indicating that the eight isolates studied constituted …