Determination of the nucleotide composition of a deoxyribonucleic acid by high-performance liquid chromatography of its enzymatic hydrlysate: a review

Quantification of phosphorus in DNA using capillary electrophoresis hyphenated with inductively coupled plasma mass spectrometry

We have analyzed phosphorus in an enzymatically digested DNA molecule using capillary electrophoresis (CE) hyphenated with inductively coupled plasma mass spectrometry (ICP-MS). The DNA concentration was quantified by the phosphorus value obtained in the CE-ICP-MS analysis. The CE-ICP-MS measurement, for which the interface device AIF-01 equipped three layered nebulizer was adopted, was achieved with limited μL/min nebulizing without loss of sample in the vaporizing chamber. The samples of nucleotides and free phosphate were separated well in the CE-ICP-MS measurement, and the calibration curve (0.1-10μg/mL) of the phosphorus showed a linear (R(2)=0.999) increase in intensity. After digestion of the 100-bp double-strand DNA sample to deoxyribonucleotide-5'-monophosphates (dNMPs) by phosphodiesterase-I, phosphorus was detected by CE-ICP-MS without further purification steps. In this study, we applied two calculation schemes of DNA analysis using a dNMP concentration obtained from CE-ICP-MS. Comparative CE-ICP-MS analysis with DNA digested to dNMPs showed that the assay gave an equal value obtained from the total DNA quantification using fluorescence detection. The detection limits of the DNA sample obtained from these species and phosphorus in nucleotides using CE-ICP-MS were 3.1-26ng/mL. These LOD values were equal to the conventional fluorescence determination of DNA.

Bacillus herbersteinensis sp. nov

Two bacterial strains, designated D-1,5a(T) and D-1,5b, were isolated from a medieval wall painting in the chapel of Castle Herberstein, Styria (Austria). The Gram-positive, heterotrophic, aerobic, spore-forming rods showed nearly identical whole-cell protein patterns, identical genomic fingerprints and identical physiological profiles, demonstrating their relationship at the species level. Both strains contained meso-diaminopimelic acid in their peptidoglycan, possessed a quinone system comprising menaquinone MK-7 and had fatty acid profiles in which C(15:0) iso and C(15:0) anteiso were predominant. The 16S rRNA gene sequence of D-1,5a(T) showed the highest similarity (99.5%) to the sequence of Bacillus sp. LMG 20243, and Bacillus flexus IFO 15715(T) was the next most closely related established species (96.5%). Other type strains, such as Bacillus fastidiosus DSM 91(T), Bacillus indicus SD/3(T), Bacillus cibi JG-30(T), Bacillus megaterium IAM 13418(T), Bacillus cohnii DSM 6308(T), Bacillus bataviensis LMG 21833(T) and Bacillus soli LMG 21838(T), shared 96.0-96.1% 16S rRNA gene sequence similarity with D-1,5a(T). The combination of physiological and chemotaxonomic traits distinguishes the two strains from those species sharing the highest sequence similarities (96.0-96.5%). On the basis of these characteristics and the phylogenetic position of strain D-1,5a(T) (=DSM 16534(T)=CCM 7228(T)), this strain is assigned as the type strain of a novel species of the genus Bacillus, for which the name Bacillus herbersteinensis sp. nov. is proposed.

Silanimonas lenta gen. nov., sp. nov., a slightly thermophilic and alkaliphilic gammaproteobacterium isolated from a hot spring

A moderately thermophilic aerobic bacterium, strain 25-4T, was isolated from a hot spring at Baekdoo Mountain in Korea. The cells were Gram-negative, motile rods each having a polar flagellum. Analysis of the 16S rRNA gene sequence indicated that the strain represented a new lineage within the family ‘Xanthomonadaceae’ of the ‘Gammaproteobacteria’, being most closely related to the genera Thermomonas, Xanthomonas, Luteimonas, Pseudoxanthomonas, Stenotrophomonas and Xylella and having 16S rRNA gene sequence similarities to the most related species of the genera of between 92·9 and 94·4 %. The strain contained Q-8 as the major isoprenoid quinone and had a fatty acid profile with predominant iso-branched fatty acids. Growth occurred at pH 6·0–10, with an optimum at pH 9·0, and at 25–53 °C, with an optimum at 47 °C. The G+C content of the genomic DNA was 50·7 mol%. On the basis of phylogenetic analyses and its phenotypic characteristics, strain 25-4T belongs to a new genus, Silanimonas gen. nov., within the ‘Gammaproteobacteria’. The sole species of this genus is Silanimonas lenta sp. nov. (type strain, 25-4T=DSM 16282T=KCTC 12236T).

Sphingomonas aurantiaca sp. nov., Sphingomonas aerolata sp. nov. and Sphingomonas faeni sp. nov., air- and dustborne and Antarctic, orange-pigmented, psychrotolerant bacteria, and emended description of the genus Sphingomonas

Seven psychrotolerant, Gram-negative bacterial strains, five dust- and airborne isolates (MA101b(T), MA306a, MA405/90, MA-olki(T) and NW12(T)) and two from the Antarctic (Ant 20 and M3C203B-B), were subjected to a polyphasic characterization to determine their taxonomic position. High 16S rDNA sequences similarities (99.3-100.0 %) demonstrated that they were closely related to each other. Phylogenetic evaluation of their 16S rDNA sequences revealed that they are members of the genus Sphingomonas sensu stricto, encompassing a separate branch within this genus. They shared 94.4-96.6 % 16S rDNA sequence similarity with species of this genus. All Sphingomonas-specific signature nucleotides were also detected. The presence of the major ubiquinone Q-10, sym-homospermidine as the predominant polyamine, Sphingomonadaceae-specific sphingoglycolipid in the polar lipid patterns and a fatty acid profile containing C(14 : 0) 2-OH and lacking 3-OH fatty acids were in agreement with identification of these strains as members of the genus Sphingomonas sensu stricto. Results from DNA-DNA hybridizations and comparison of protein patterns indicated that the seven strains are members of three distinct species. One species is represented by strains MA101b(T), MA306a and MA405/90, the second by strains NW12(T), Ant 20 and M3C203B-B and the third by one strain, MA-olki(T). Their distinction at the species level was also supported by results of biochemical characterization and partly supported by riboprints and genomic fingerprints. On the basis of these results, three novel species of the genus Sphingomonas are proposed: Sphingomonas aurantiaca sp. nov., consisting of strains MA101b(T) (=DSM 14748(T)=LMG 21377(T)), MA306a and MA405/90 (=DSM 14749=LMG 21378), Sphingomonas faeni sp. nov. MA-olki(T) (=DSM 14747(T)=LMG 21379(T)) and Sphingomonas aerolata sp. nov., represented by strains NW12(T) (=DSM 14746(T)=LMG 21376(T)), Ant 20 (=ICMP 13599) and M3C203B-B (=SMCC M3C203B-B).

Screening and identification of a novel lipase from Burkholderia sp. YY62 which hydrolyzes t-butyl esters effectively

Fatty acid esters composed of sterically hindered alcohol are very poor substrates for known lipases. In order to obtain a novel lipase, t-butyl octanoate (TBO) was selected as a model substrate to screen for bacteria-producing lipase(s) which can preferentially hydrolyze bulky esters. Of 279 strains isolated from 350 soil samples based on the ability to grow with TBO as a sole carbon source, one strain (YY62) was chosen for its strong TBO-hydrolyzing activity. Strain YY62 is a Gram-negative motile rod and was identified as Burkholderia sp. from the taxonomic characters and phylogenetic analysis of 16S rDNA nucleotide sequences. Using the activity ratio between TBO and p-nitrophenyl acetate as a measure for preference to bulky esters, we confirmed that the lipase of strain YY62 was 100-fold superior to commercial lipases in terms of TBO-hydrolyzing activity.

Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics

Most of the bacterial species are still unknown. Consequently, our knowledge about bacterial ecology is poor and expectations about specialized species with novel enzymatic functions or new products are high. Thus, bacterial identification is a growing field of interest within microbiology. In this review, suitability of developments for identification based on miniaturized biochemical and physiological investigations of bacteria are evaluated. Special emphasis is given to chemotaxonomic methods such as analysis of quinone system, fatty acid profiles, polar lipid patterns, polyamine patterns, whole cell sugars, peptidoglycan diaminoacids, as well as analytical fingerprinting methods and cellular protein patterning. 16S rDNA sequencing introduced to investigate the phylogenetic relationships of bacteria, nucleic acids hybridization techniques and G + C content determination are discussed as well as restriction fragment length polymorphism (RFLP), macrorestriction analysis and random amplified polymorphic DNA (RAPD). The importance of the different approaches in classification and identification of bacteria according to phylogenetic relationships are demonstrated on selected examples.

Some taxonomical characteristics of encapsulated Lactobacillus sp. KPB-167B isolated from kefir grains and characterization of its extracellular polysaccharide

A capsular polysaccharide-producing strain KPB-167B isolated from kefir grains was identified as a homofermentative Lactobacillus. The carbohydrate fermentation pattern and DNA base composition of the strain were different from those of other capsular Lactobacillus species previously isolated from kefir grains. The polysaccharide produced by Lactobacillus sp. KPB-167B was found similar to kefiran by 13C-NMR and methylation analysis. Lactobacillus sp. KPB-167B could grow and produce capsular polysaccharide in MRSL medium with better yield than L. kefiranofaciens, which suggested that it is suitable for kefiran production.

Serological studies of Porphyromonas (Bacteroides) gingivalis and correlation with enzyme activity

Porphyromonas gingivalis from the human oral cavity was serologically characterized using absorbed and unabsorbed rabbit antisera. The reference strains were ATCC 33277, W50, W83, 381 and hara 1. The 432 isolates were from periodontal pockets of 63 patients with adult periodontitis. Using sonicated antigens, four serotypes were identified by immunodiffusion tests and immunoelectrophoresis. Each patient harbored only one serotype of P. gingivalis, and serotypes I and IV predominated. The incidence of serotype I was four times higher than that of serotype II, and approximately seven times higher than that of serotype III. The collagenolytic and some proteolytic enzymes of representatives of each serotype were assessed. Although all strains produced these enzymes to some degree, some differences in their levels were observed. Serotype II strains were more collagenolytic than serotypes I or III, and serotype III exhibited lower activities of N-CBz-glycyl-glycyl-arginyl peptidase than other serotypes. Antibiotic sensitivity was also compared with antimicrobial disks, and serotype IV strains exhibited high sensitivity to the four antibiotics used.

Black-pigmented, asaccharolytic Bacteroides species resembling Porphyromonas gingivalis (Bacteroides gingivalis) from beagle dogs

Black-pigmented, asaccharolytic Bacteroides strains, which positively reacted with anti-Bacteroides gingivalis (now reclassified as Porphyromonas gingivalis) serum, were isolated from beagle dogs, and their characteristics were studied and compared with those of P. gingivalis. The strains from dogs were different from P. gingivalis in their catalase activity, nutritional requirements and oxygen tolerance, and double-immunodiffusion tests showed serological dissimilarity between the strains from dogs and P. gingivalis. However, the strains from dogs had guanine-plus-cytosine contents of 49.0 to 49.3 mol %, which were very similar to P. gingivalis, and they showed strong DNA-DNA hybridization with P. gingivalis. These results indicated that beagle dogs had Porphyromonas species analogous to P. gingivalis in their oral cavities.

Legionella gratiana sp. nov. isolated from French spa water

During an epidemiologic survey, an unidentified strain of Legionella was isolated from water of a thermal spa in France. The strain (Lyon 8420412) had the cultural and biochemical characteristics typical of the genus Legionella. In direct immunofluorescence tests, the strain reacted weakly with fluorescein-conjugated antisera prepared against L. bozemanii serogroups 1 and 2, L. longbeachae serogroups 1 and 2 and L. anisa, and failed to react with sera prepared against 36 other species or serogroups. A fluorescein-conjugated antiserum prepared against strain Lyon 8420412 reacted strongly with the homologous strain and only weakly with the above-mentioned species. The cell-wall fatty acid profile, with a predominance of hexadecenoic (16:1) and hexadecanoic (16:0) acids, ubiquinone Q10 as the major quinone and a characteristic protein electrophoresis profile suggested that the isolate was different from other Legionella species. In DNA-DNA hybridization experiments, the strain was distinct from all named Legionella species, and from all unnamed species currently under study at the Centers for Disease Control. The name Legionella gratiana is proposed for the new species (type strain Lyon 8420412; CDC 1242). A serologic survey of antibodies reacting against L. gratiana indicated that personnel or patients at the spa therapy centre where the organism was isolated had higher antibody titres than a control population.

Determination of G + C content of DNA using high-performance liquid chromatography for the identification of staphylococci and micrococci

The guanine-plus-cytosine (G + C) content of different species of Staphylococcus and Micrococcus was determined by high-performance liquid chromatography. Purified bacterial DNA was hydrolysed by nuclease P1. The nucleotides were separated by chromatography and quantified by measurement of the optical density at 260 nm. The G + C content of staphylococci ranged from 31.5 to 37.9 moles %, and that of micrococci from 68.7 to 75.2. Most of our results were comparable to those obtained with the thermal method.