ABSTRACT
Weathering of mine tailings in Adak results in high As concentrations in surface and ground water, sediments, and soil. In spite of the oxic conditions, As-rich surface and ground water samples indicate As(III) species predominantly (up to 83%). Several microorganisms were isolated from the enrichment cultures that were involved in As cycling. Amongst them was Arsenicicoccus bolidensis - a novel gram-positive, facultatively anaerobic, coccus-shaped actinomycete, which actively reduced As(V) to As(III) in aqueous media. A. bolidensis reduced 0.06-0.20 mM day(-1) As(V). As(V) reduction displays a direct correlation between the initial As(V) concentration, growth rate, and biomass yield.
Subject(s)
Actinomycetales/metabolism , Arsenic/metabolism , Soil Pollutants/metabolism , Water Pollutants, Chemical/metabolism , Actinomycetales/genetics , Actinomycetales/growth & development , Arsenic/analysis , Base Sequence , Biodegradation, Environmental , Environmental Monitoring , Geologic Sediments/analysis , Mining , Molecular Sequence Data , Oxidation-Reduction , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Rivers/chemistry , Sequence Analysis, DNA , Soil Pollutants/analysis , Sulfides , Sweden , Water Pollutants, Chemical/analysisABSTRACT
Spatiotemporal particle patterning in evaporating droplets lacks a common design framework. Here, we demonstrate autonomous control of particle distribution in evaporating droplets through the imposition of a salt-induced self-generated electric field as a generalized patterning strategy. Through modeling, a new dimensionless number, termed "capillary-phoresis" (CP) number, arises, which determines the relative contributions of electrokinetic and convective transport to pattern formation, enabling one to accurately predict the mode of particle assembly by controlling the spontaneous electric field and surface potentials. Modulation of the CP number allows the particles to be focused in a specific region in space or distributed evenly. Moreover, starting with a mixture of two different particle types, their relative placement in the ensuing pattern can be controlled, allowing coassemblies of multiple, distinct particle populations. By this approach, hypermethylated DNA, prevalent in cancerous cells, can be qualitatively distinguished from normal DNA of comparable molecular weights. In other examples, we show uniform dispersion of several particle types (polymeric colloids, multiwalled carbon nanotubes, and molecular dyes) on different substrates (metallic Cu, metal oxide, and flexible polymer), as dictated by the CP number. Depending on the particle, the highly uniform distribution leads to surfaces with a lower sheet resistance, as well as superior dye-printed displays.
ABSTRACT
An obligatory anaerobic, Gram-positive, rod-shaped organism was isolated from faeces of a healthy human donor. It was characterized using biochemical, phenotypic and molecular taxonomic methods. The organism produced acetate, lactate, and ethanol as the major products of glucose fermentation. The G + C content was 53 mol%. Based on comparative 16S rRNA gene sequencing, the unidentified bacterium is a member of the Clostridium subphylum of the Gram-positive bacteria, and most closely related to species of the Clostridium coccoides cluster (rRNA cluster XIVa) [M.D. Collins et al., The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations, Int. J. Syst. Bacteriol. 44 (1994) 812-826]. Clostridium bolteae and Clostridium clostridioforme were identified as the most closely related described species. A 16S rRNA sequence divergence value of > 3% suggested that the isolate represents a new species. This was also supported by the gyrase-encoding gyrB gene sequences. Based on these findings, we propose the novel bacterium from human faeces to be classified as a new species, Clostridium asparagiforme. The type strain of C. asparagiforme is N6 (DSM 15981 and CCUG 48471).
Subject(s)
Clostridium/classification , Clostridium/isolation & purification , Feces/microbiology , Acetic Acid/metabolism , Anaerobiosis , Bacterial Proteins/genetics , Bacterial Typing Techniques , Base Composition , Clostridium/cytology , Clostridium/physiology , Clostridium Infections/microbiology , DNA Gyrase/genetics , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Ethanol/metabolism , Fatty Acids/analysis , Fatty Acids/isolation & purification , Genes, rRNA/genetics , Gentian Violet , Glucose/metabolism , Humans , Lactic Acid/metabolism , Microscopy, Electron, Scanning , Molecular Sequence Data , Phenazines , Phylogeny , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
Some cases of late-onset (regressive) autism may involve abnormal flora because oral vancomycin, which is poorly absorbed, may lead to significant improvement in these children. Fecal flora of children with regressive autism was compared with that of control children, and clostridial counts were higher. The number of clostridial species found in the stools of children with autism was greater than in the stools of control children. Children with autism had 9 species of Clostridium not found in controls, whereas controls yielded only 3 species not found in children with autism. In all, there were 25 different clostridial species found. In gastric and duodenal specimens, the most striking finding was total absence of non-spore-forming anaerobes and microaerophilic bacteria from control children and significant numbers of such bacteria from children with autism. These studies demonstrate significant alterations in the upper and lower intestinal flora of children with late-onset autism and may provide insights into the nature of this disorder.
Subject(s)
Autistic Disorder/microbiology , Clostridium/isolation & purification , Digestive System/microbiology , Age of Onset , Autistic Disorder/physiopathology , Child , Child, Preschool , Clostridium/classification , HumansABSTRACT
It has long been thought that the genera Mobiluncus and Falcivibrio contain the same organisms. Using a polyphasic approach, it was found that Mobiluncus curtisii and Mobiluncus mulieris were the same as Falcivibrio vaginalis and Falcivibrio grandis, respectively. As the genus name Mobiluncus takes precedence, it is proposed that F. vaginalis and F. grandis be transferred to the genus Mobiluncus. In agreement with previous studies, results from phenotypic tests did not support the separation of M. curtisii strains into its two subspecies, M. curtisii subsp. curtisii and M. curtisii subsp. holmesii. Phenotypic complexity within M. curtisii dictates that the species should be treated as a complex until more in-depth analyses of the species have been performed. Phylogenetic analyses, based on 16S rRNA gene sequences, demonstrated that the genus Mobiluncus was associated with Varibaculum cambriense and the two subspecies of Actinomyces neuii, and that A. neuii is only distantly related to Actinomyces sensu stricto.
Subject(s)
Bacteroides/classification , Mobiluncus/classification , Bacterial Proteins/metabolism , Bacteroides/genetics , Bacteroides/metabolism , Base Sequence , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Electrophoresis, Gel, Pulsed-Field , Electrophoresis, Polyacrylamide Gel , Mobiluncus/genetics , Mobiluncus/metabolism , Molecular Sequence Data , Phylogeny , Polymerase Chain Reaction , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 16S/genetics , Sequence AlignmentABSTRACT
Phenotypic and phylogenetic studies were performed on seven unidentified gram-negative, facultatively anaerobic, coccobacillus-shaped organisms isolated from human clinical specimens. Comparative 16S rRNA gene sequencing demonstrated that four of the strains corresponded to Dysgonomonas capnocytophagoides whereas the remaining three isolates represent a new sub-line within the genus Dysgonomonas, displaying greater than 5% sequence divergence with Dysgonomonas capnocytophagoides and Dysgonomonas gadei. The three novel isolates were readily distinguished from D.capnocytophagoides and D. gadei by biochemical tests. The DNA base composition of the novel species was consistent with its assignment to the genus Dysgonomonas. Based on phylogenetic and phenotypic evidence it is proposed that the unknown species, be classified as Dysgonomonas mossii sp. nov. The type strain of Dysgonomonas mossii is CCUG 43457T (= CIP 107079T).
Subject(s)
Gram-Negative Anaerobic Bacteria/classification , Gram-Negative Anaerobic Bacteria/isolation & purification , Base Sequence , DNA, Bacterial/genetics , Gram-Negative Anaerobic Bacteria/genetics , Gram-Negative Bacterial Infections/microbiology , Humans , Molecular Sequence Data , Phenotype , Phylogeny , RNA, Ribosomal, 16S/analysis , Sequence Analysis, DNAABSTRACT
Two strains of a previously undescribed Eubacterium-like bacterium were isolated from human faeces. The strains are Gram-variable, obligately anaerobic, catalase negative, asporogenous rod-shaped cells which produced acetate, butyrate and lactate as the end products of glucose metabolism. The two isolates displayed 99.9% 16S rRNA gene sequence similarity to each other and treeing analysis demonstrated the faecal isolates are far removed from Eubacterium sensu stricto and that they represent a new subline within the Clostridium coccoides group of organisms. Based on phenotypic and phylogenetic criteria, it is proposed that the two strains from faeces be classified as a new genus and species, Anaerostipes caccae. The type strain of Anaerostipes caccae is NCIMB 13811T (= DSM 14662T).
Subject(s)
Feces/microbiology , Gram-Positive Asporogenous Rods/isolation & purification , Acetates/metabolism , Base Sequence , Butyric Acid/metabolism , Gram-Positive Asporogenous Rods/enzymology , Gram-Positive Asporogenous Rods/genetics , Humans , Molecular Sequence Data , Phenotype , Phylogeny , RNA, Ribosomal, 16S/analysis , Species Specificity , Sucrose/metabolismABSTRACT
Phenorypic and phylogenetic studies were performed on four isolates of an unidentified gram-negative, microaerotolerant, non-spore-forming, rod-shaped bacterium isolated from the feces of children. The unknown organism was bile resistant and produced acetic acid as the major end product of metabolism of peptides and carbohydrates. It possessed a low DNA G + C content of 31 mol %. Comparative 16S rRNA gene sequencing demonstrated that the four isolates were phylogenetically identical (100% 16S rRNA sequence similarity) and represent a hitherto unknown sub-line within the genus Cetobacterium. The novel bacterium displayed approximately 5% sequence divergence with Cetobacterium ceti, and can be readily distinguished from the latter by physiological and biochemical criteria. Based on phylogenetic and phenotypic evidence, it is proposed that the unknown fecal bacterium be classified in the genus Cetobacterium, as Cetobacterium somerae sp. nov. The proposed type strain of Cetobacterium somerae is WAL 14325(T) (ATCC BAA-474(T) = CCUG 46254T).
Subject(s)
Autistic Disorder/microbiology , Feces/microbiology , Gram-Negative Aerobic Rods and Cocci/isolation & purification , Age of Onset , Autistic Disorder/drug therapy , Autistic Disorder/epidemiology , Bacterial Typing Techniques , Base Composition , Carbohydrate Metabolism , Child , Child, Preschool , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Fatty Acids/analysis , Gram-Negative Aerobic Rods and Cocci/classification , Gram-Negative Aerobic Rods and Cocci/genetics , Humans , Intestines/microbiology , Male , Molecular Sequence Data , Phenotype , Phylogeny , Ribotyping , Species Specificity , Vancomycin/therapeutic useABSTRACT
During studies on the bacteriology of appendicitis in children, we often isolated from inflamed and non-inflamed tissue samples, an unusual bile-resistant pigment-producing strictly anaerobic gram-negative rod. Phenotypically this organism resembles members of Bacteroides fragilis group of species, as it is resistant to bile and exhibits a special-potency-disk pattern (resistance to vancomycin, kanamycin and colistin) typical for the B. fragilis group. However, the production of brown pigment on media containing haemolysed blood and a cellular fatty acid composition dominated by iso-C15:0, suggests that the organism most closely resembles species of the genus Porphyromonas. However, the unidentified organism differs from porphyromonads by being bile-resistant and by not producing butyrate as a metabolic end-product. Comparative 16S ribosomal RNA gene sequencing studies show the unidentified organism represents a distinct sub-line, associated with but distinct from, the miss-classified species Bacteroides putredinis. The clustering of the unidentified bacterium with Bacteroides putredinis was statistically significant, but they displayed > 4% sequence divergence with each other. Chromosomal DNA-DNA pairing studies further confirmed the separateness of the unidentified bacterium and Bacteroides putredinis. Based on phenotypic and phylogenetic considerations, it is proposed that Bacteroides putredinis and the unidentified bacterium from human sources be classified in a new genus Alistipes, as Alistipes putredinis comb. nov. and Alistipes finegoldii sp. nov., respectively. The type strain of Alistipes finegoldii is CCUG 46020(T) (= AHN243(T)).
Subject(s)
Appendicitis/microbiology , Bacteroides/classification , Gram-Negative Bacteria/classification , Terminology as Topic , Bacterial Typing Techniques , Bacteroides/chemistry , Bacteroides/isolation & purification , Bile/microbiology , Child , DNA, Bacterial/genetics , Enterocolitis, Pseudomembranous/microbiology , Fatty Acids/analysis , Feces/microbiology , Humans , Lactose Intolerance/microbiology , Molecular Sequence Data , Nucleic Acid Hybridization , Pigments, Biological/analysis , Porphyromonas/chemistry , Ribotyping , Species SpecificityABSTRACT
Phenotypic and phylogenetic studies were performed on four unidentified Gram-positive staining, catalase-negative, alpha-hemolytic Streptococcus-like organisms recovered from the teeth of horses. SDS PAGE analysis of whole-cell proteins and comparative 16S rRNA gene sequencing demonstrated the four strains were highly related to each other but that they did not correspond to any recognised species of the genus Streptococcus. Phylogenetic analysis based on 16S rRNA gene sequences showed the unidentified organisms form a hitherto unknown sub-line within the Streptococcus genus, displaying a close affinity with Streptococcus mutans, Streptococcus ferus and related organisms. Sequence divergence values of > 5% with these and other reference streptococcal species however demonstrated the organisms from equine sources represent a novel species. Based on the phenotypic distinctiveness of the new bacterium and molecular chemical and molecular genetic evidence, it is proposed that the unknown species be classified as Streptococcus devriesei sp. nov. The type strain of Streptococcus devriesei is CCUG 47155T (= CIP 107809T).
Subject(s)
Dental Caries/veterinary , Horse Diseases/microbiology , Streptococcus/classification , Animals , Base Composition , Base Sequence , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , Dental Caries/microbiology , Horses , Molecular Sequence Data , Phylogeny , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Streptococcus/genetics , Streptococcus/isolation & purification , Streptococcus/metabolismABSTRACT
Seven obligately anaerobic, gram-positive, rod-shaped, spore-forming organisms isolated from human sources were characterized using phenotypic and molecular taxonomic methods. Comparative 16S rRNA gene sequencing showed that the strains were genetically highly related to each other (displaying >99% sequence similarity) and represent a previously unknown sub-line within the Clostridium coccoides rRNA group of organisms. Strains of the unidentified bacterium used carbohydrate as fermentable substrates, producing acetic acid and lactic acid as the major products of glucose metabolism. The closest described species to the novel bacterium corresponded to Clostridium clostridioforme, although a 16S rRNA sequence divergence of 3% demonstrated they represent different species. Genomic DNA-DNA pairing studies confirmed the separateness of the unknown species and Clostridium clostridioforme. Based on phenotypic and phylogenetic evidence, it is therefore proposed that the unknown bacterium, be classified as Clostridium bolteae sp. nov. The type strain of Clostridium bolteae is WAL 16351T (= ATCC(T) = BAA-613T, CCUG(T) = 46953T).
Subject(s)
Clostridium/classification , Clostridium/enzymology , Clostridium/genetics , Clostridium/isolation & purification , Culture Media , Esculin/metabolism , Feces/microbiology , Glucuronidase/biosynthesis , Humans , Microbial Sensitivity Tests , Phenotype , Phylogeny , RNA, Ribosomal, 16S/analysisABSTRACT
The 23S ribosomal RNA (rRNA) gene has been sequenced in strains of the fish pathogens Photobacterium damselae subsp. damselae (ATCC 33539) and subsp. piscicida (ATCC 29690), showing that 3 nucleotide positions are clearly different between subspecies. In addition, the 5S rRNA gene plus the intergenic spacer region between the 23S and 5S rRNA genes (ITS-2) were amplified, cloned and sequenced for the 2 reference strains as well as the field isolates RG91 (subsp. damselae) and DI21 (subsp. piscicida). A 100% similarity was found for the consensus 5S rRNA gene sequence in the 2 subspecies, although some microheterogeneity was detected as inter-cistronic variability within the same chromosome. Sequence analysis of the spacer region between the 23S and 5S rRNA genes revealed 2 conserved and 3 variable nucleotide sequence blocks, and 4 different modular organizations were found. The ITS-2 spacer region exhibited both inter-subspecies and intercistronic polymorphism, with a mosaic-like structure. The EMBL accession numbers for the 23S, 5S and ITS-2 sequences are: P. damselae subsp. piscicida 5S gene (AJ274379), P. damselae subsp. damselae 23S gene (Y18520), subsp. piscicida 23S gene (Y17901), P. damselae subsp. piscicida ITS-2 (AJ250695, AJ250696), P. damselae subsp. damselae ITS-2 (AJ250697, AJ250698).
Subject(s)
DNA, Ribosomal Spacer/genetics , Genetic Variation , Photobacterium/genetics , Phylogeny , Base Sequence , Cluster Analysis , DNA Primers , Molecular Sequence Data , Sequence Alignment , Sequence Analysis, DNA , Species SpecificityABSTRACT
Two strains of an unknown Gram-positive, catalase-negative, facultatively anaerobic, coccus-shaped bacterium, originating from a porpoise and a grey seal, were characterized using phenotypic, biochemical and molecular phylogenetic methods. Chemical studies revealed the presence of a cell-wall murein based on L-lysine (type L-lys-gly-D-Asp) and a DNA G+C content of 38 mol%. Comparative 16S rRNA gene sequencing showed that this unidentified coccus-shaped organism formed a hitherto unknown subline closely related to, albeit distinct from, a number of other catalase-negative genera which included Enterococcus, Melissococcus, Tetragenococcus and Vagococcus. Other known Gram-positive, catalase-negative taxa were more distantly related. Tree-branching considerations and sequence divergence values of >6% with recognized taxa were indicative of this novel bacterium representing a separate genus. Based on phenotypic and phylogenetic evidence, it is proposed that this unknown bacterium, recovered from a porpoise and a grey seal, be classified as a novel genus and species, Catellicoccus marimammalium gen. nov., sp. nov. The type strain is M35/04/3T (=CCUG 49459T=CIP 108575T).
Subject(s)
Catalase/metabolism , Gram-Positive Bacterial Infections/veterinary , Gram-Positive Cocci/classification , Porpoises/microbiology , Seals, Earless/microbiology , Anaerobiosis , Animals , Bacterial Typing Techniques , DNA, Bacterial/analysis , DNA, Ribosomal/analysis , Genes, rRNA , Gram-Positive Bacterial Infections/microbiology , Gram-Positive Cocci/genetics , Gram-Positive Cocci/isolation & purification , Gram-Positive Cocci/physiology , Molecular Sequence Data , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Species SpecificityABSTRACT
Phenotypic and phylogenetic studies were performed on three isolates of an unknown Gram-negative, facultatively anaerobic, non-motile, yellow-pigmented, rod-shaped organism isolated from raw sewage. 16S rRNA gene sequence analysis indicated that these strains were members of the Bergeyella-Chryseobacterium-Riemerella branch of the family Flavobacteriaceae. The unknown bacterium was readily distinguished from reference strains by 16S rRNA gene sequencing and biochemical tests. The organism contained menaquinone MK-6 as the predominant respiratory quinone and had a DNA G+C content of 31 mol%. A most probable number-PCR approach was developed to detect, and estimate the numbers of, this organism. Untreated wastewater from one plant yielded an estimated count of 1.4 x 10(5) cells ml(-1), and untreated wastewater from a second plant yielded an estimated count of 1.4 x 10(4) cells ml(-1). Signal was not detected from treated effluent or from human stool specimens. On the basis of the results of the study presented, it is proposed that the unknown bacterium be classified in a novel genus Cloacibacterium, as Cloacibacterium normanense gen. nov., sp. nov., which is also the type species. The type strain of Cloacibacterium normanense is strain NRS1(T) (=CCUG 46293(T) = CIP 108613(T) = ATCC BAA-825(T) = DSM 15886(T)).
Subject(s)
Flavobacteriaceae/classification , Waste Disposal, Fluid , Base Composition , DNA, Bacterial/chemistry , Flavobacteriaceae/genetics , Flavobacteriaceae/isolation & purification , Molecular Sequence Data , Phylogeny , RNA, Bacterial/genetics , RNA, Ribosomal, 16S/genetics , Sweden , Water MicrobiologyABSTRACT
We report a case of bacteremia in puppies caused by Streptococcus dysgalactiae subsp. dysgalactiae. Identification was achieved by phenotypic and molecular genetic methods. This is the first report of the recovery of S. dysgalactiae subsp. dysgalactiae from dogs.
Subject(s)
Bacteremia/veterinary , Dog Diseases/mortality , Streptococcal Infections/veterinary , Streptococcus/isolation & purification , Animals , Animals, Newborn , Bacteremia/microbiology , Bacteremia/mortality , Bacterial Typing Techniques , DNA, Bacterial/analysis , DNA, Ribosomal/analysis , Dog Diseases/microbiology , Dogs , Female , Nucleic Acid Hybridization , Phenotype , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Streptococcal Infections/microbiology , Streptococcal Infections/mortality , Streptococcus/classification , Streptococcus/geneticsABSTRACT
A novel Gram-positive, aerobic, catalase-negative, coccus-shaped organism originating from tobacco was characterized using phenotypic and molecular taxonomic methods. The organism contained a cell wall murein based on L-lysine (variation A4alpha, type L-lysine-L-glutamic acid), synthesized long-chain cellular fatty acids of the straight-chain saturated and monounsaturated types (with C(16:1)omega9, C(16:0) and C(18:1)omega9 predominating) and possessed a DNA G+C content of 46 mol%. Based on morphological, biochemical and chemical characteristics, the coccus-shaped organism did not conform to any presently recognized taxon. Comparative 16S rRNA gene sequencing studies confirmed the distinctiveness of the unknown coccus, with the bacterium displaying sequence divergence values of greater than 7% with other recognized Gram-positive taxa. Treeing analysis reinforced its distinctiveness, with the unidentified organism forming a relatively long subline branching at the periphery of an rRNA gene sequence cluster which encompasses the genera Alloiococcus, Allofustis, Alkalibacterium, Atopostipes, Dolosigranulum and Marinilactibacillus. Based on phenotypic and molecular phylogenetic evidence, it is proposed that the unknown organism from tobacco be classified as a new genus and species, Atopococcus tabaci gen. nov., sp. nov. The type strain of Atopococcus tabaci is CCUG 48253(T) (=CIP 108502(T)).
Subject(s)
Catalase/metabolism , Gram-Positive Cocci/classification , Nicotiana/microbiology , Bacterial Typing Techniques , DNA, Bacterial/analysis , DNA, Ribosomal/analysis , Genes, rRNA , Gram-Positive Cocci/chemistry , Gram-Positive Cocci/genetics , Gram-Positive Cocci/isolation & purification , Molecular Sequence Data , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNAABSTRACT
Phenotypically, Photobacterium damselae subsp. piscicida and P. damselae subsp. damselae are easily distinguished. However, their 16S rRNA gene sequences are identical, and attempts to discriminate these two subspecies by molecular tools are hampered by their high level of DNA-DNA similarity. The 16S-23S rRNA internal transcribed spacers (ITS) were sequenced in two strains of Photobacterium damselae subsp. piscicida and two strains of P. damselae subsp. damselae to determine the level of molecular diversity in this DNA region. A total of 17 different ITS variants, ranging from 803 to 296 bp were found, some of which were subspecies or strain specific. The largest ITS contained four tRNA genes (tDNAs) coding for tRNA(Glu(UUC)), tRNA(Lys(UUU)), tRNA(Val(UAC)), and tRNA(Ala(GGC)). Five amplicons contained tRNA(Glu(UUC)) combined with two additional tRNA genes, including tRNA(Lys(UUU)), tRNA(Val(UAC)), or tRNA(Ala(UGC)). Five amplicons contained tRNA(Ile(GAU)) and tRNA(Ala(UGC)). Two amplicons contained tRNA(Glu(UUC)) and tRNA(Ala(UGC)). Two different isoacceptor tRNA(Ala) genes (GGC and UGC anticodons) were found. The five smallest amplicons contained no tRNA genes. The tRNA-gene combinations tRNA(Glu(UUC))-tRNA(Val(UAC))-tRNA(Ala(UGC)) and tRNA(Glu(UUC))-tRNA(Ala(UGC)) have not been previously reported in bacterial ITS regions. The number of copies of the ribosomal operon (rrn) in the P. damselae chromosome ranged from at least 9 to 12. For ITS variants coexisting in two strains of different subspecies or in strains of the same subspecies, nucleotide substitution percentages ranged from 0 to 2%. The main source of variation between ITS variants was due to different combinations of DNA sequence blocks, constituting a mosaic-like structure.
Subject(s)
DNA, Ribosomal Spacer/analysis , Genetic Variation , Photobacterium/classification , RNA, Ribosomal, 16S/genetics , RNA, Ribosomal, 23S/genetics , Base Sequence , DNA, Bacterial/analysis , DNA, Ribosomal Spacer/genetics , Molecular Sequence Data , Photobacterium/genetics , RNA, Transfer/genetics , Sequence Alignment , Sequence Analysis, DNA , Species Specificity , rRNA OperonABSTRACT
A Gram-negative, aerobic to microaerophilic rod was isolated from 10 m depths of the hypersaline, heliothermal and meromictic Ekho Lake (East Antarctica). The strain was oxidase- and catalase-positive, metabolized a variety of carboxylic acids and sugars and produced lipase. Cells had an absolute requirement for artificial sea water, which could not be replaced by NaCl. A large in vivo absorption band at 870 nm indicated production of bacteriochlorophyll a. The predominant fatty acids of this organism were 16 : 0 and 18 : 1omega7c, with 3-OH 10 : 0, 16 : 1omega7c and 18 : 0 in lower amounts. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine. Ubiquinone 10 was produced. The DNA G+C content was 67 mol%. 16S rRNA gene sequence comparisons indicated that the isolate represents a member of the Roseobacter clade within the alpha-Proteobacteria. The organism showed no particular relationship to any members of this clade but clustered on the periphery of the genera Jannaschia, Octadecabacter and 'Marinosulfonomonas' and the species Ruegeria gelatinovorans. Distinct morphological, physiological and genotypic differences to these previously described taxa supported the description of a new genus and a novel species, for which the name Roseisalinus antarcticus gen. nov., sp. nov. is proposed. The type strain is EL-88T (=DSM 11466T=CECT 7023T).
Subject(s)
Bacteriochlorophyll A/biosynthesis , Fresh Water/microbiology , Rhodobacteraceae/classification , Aerobiosis , Antarctic Regions , Bacterial Typing Techniques , DNA, Ribosomal/analysis , Genes, rRNA , Genotype , Molecular Sequence Data , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Rhodobacteraceae/genetics , Rhodobacteraceae/isolation & purification , Rhodobacteraceae/metabolism , Sequence Analysis, DNA , Sodium ChlorideABSTRACT
Two strains of an unidentified, Gram-positive, catalase-negative, chain-forming, coccus-shaped organism recovered from seals were characterized using phenotypic and molecular taxonomic methods. Based on morphological and biochemical criteria the strains were tentatively identified as streptococci but they did not appear to correspond to any recognized species of the genus Streptococcus. Comparative 16S rRNA gene sequencing studies showed that the strains were closely related to each other and confirmed their placement in the genus Streptococcus. Sequence divergence values of >5 % with reference streptococcal species demonstrated the organisms from seals represent a novel species. SDS-PAGE analysis of whole-cell proteins confirmed that the two organisms were closely related to each other but were different from all currently defined streptococcal species. Based on biochemical criteria, molecular chemical and molecular genetic evidence, it is proposed that the unknown isolates from seals be assigned to a novel species of the genus Streptococcus, Streptococcus marimammalium sp. nov. The type strain is M54/01/1T (=CCUG 48494T=CIP 108309T).
Subject(s)
Phoca/microbiology , Seals, Earless/microbiology , Streptococcal Infections/veterinary , Streptococcus/classification , Streptococcus/isolation & purification , Animals , Bacterial Proteins/analysis , Bacterial Typing Techniques , DNA, Ribosomal/analysis , Electrophoresis, Polyacrylamide Gel , Genes, rRNA , Molecular Sequence Data , Phenotype , Phylogeny , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Streptococcal Infections/microbiology , Streptococcus/chemistry , Streptococcus/geneticsABSTRACT
A previously undescribed filamentous, beaded, Gram-positive, rod-shaped bacterium was isolated from pus of a human dental abscess. Based on its cellular morphology and the results of biochemical testing the organism was tentatively identified as a member of the genus Actinomyces, but it did not correspond to any currently recognized species of this genus. Comparative 16S rRNA gene sequencing studies showed the bacterium represents a distinct subline within the genus Actinomyces, clustering within a group of species that includes Actinomyces bovis, the type species of the genus. Sequence divergence values of >8 % with other recognized species within this phylogenetic group clearly demonstrated that the organism represents a hitherto unknown species. Based on biochemical and molecular phylogenetic evidence, it is proposed that the unidentified organism recovered from a dental abscess be classified as a novel species, Actinomyces dentalis sp. nov. The type strain is R18165T (=CCUG 48064T=CIP 108337T).