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PubMed2002

Microbiology of acute otitis externa.

OBJECTIVE: To isolate and characterize bacteria and fungi from acute otitis externa (AOE) and to obtain susceptibility profiles on each bacterial isolate. STUDY DESIGN: Prospective core series. METHODS: Specimens were collected from the external canals of subjects with clinically diagnosed acute otitis externa. Species-level identification for each bacterial isolate recovered was obtained by combining phenotypic and genotypic data. End point mean inhibitory concentration (MIC) testing was performed using National Committee for Clinical Laboratory Standards (NCCLS) recommended methods. RESULTS: In Alcon-sponsored clinical studies conducted in 1998 to 2000, microbiology specimens were collected from 2039 subjects (2240 diseased ears) by 101 investigators throughout the United States. A total of 2838 bacteria, 32 yeast, and 17 molds were recovered from 2048 ears clinically diagnosed as acute otitis externa. Of the 202 bacterial species recovered, the species most frequently isolated was Pseudomonas aeruginosa (38%). The next 10 species most frequently isolated were: Staphylococcus epidermidis, 9.1%; Staphylococcus aureus, 7.8%; Microbacterium otitidis, 6.6%; Microbacterium alconae, 2.9%; Staphylococcus caprae, 2.6%; Staphylococcus auricularis, 2.0%; Enterococcus faecalis, 1.9%; Enterobacter cloacae, 1.6%; Staphylococcus capitis subsp. Ureolyticus,1.4%; and Staphylococcus haemolyticus, 1.3%. Susceptibility profiles of S. epidermidis isolates revealed the greatest frequency of high-level resistance to selected antibiotics (>/=8 microg/mL): 23%, neomycin-resistant; 11%, oxacillin-resistant; and 12%, ofloxacin-resistant. Susceptibility profiles of S. aureus isolates revealed a lower frequency of high-level resistance: 6.3%, neomycin-resistant; 2.7%, oxacillin-resistant; and 4.5%, ofloxacin-resistant. P. aeruginosa with high-level resistance to quinolones (>/=128 mcg/mL for ofloxacin) was recovered from only 1 subject. Likewise, resistance of P. aeruginosa to aminoglycosides was rare. Twenty isolates had neomycin MICs >/=64 mcg/mL and 10 isolates had gentamicin MICs >/=16 mcg/mL. The coryneform isolates identified as Microbacterium otitidis had an intrinsic lack of susceptibility to quinolones (ofloxacin MICs >/=16 mcg/mL) and aminoglycosides (tobramycin MICs >/=32 mcg/mL and gentamicin MICs >/=8 mcg/mL). CONCLUSIONS: Bacterial infections of the external ear canal are most often caused by P. aeruginosa. However, there are a great number of other gram-positive and gram-negative bacterial species that are recovered from patients with acute otitis externa. Because of this diverse etiology, the best topical therapeutic choice for topical therapy is for the most potent, broad-spectrum (especially anti-P. aeruginosa) antibiotic available.

Acute Disease↗
PubMed2000

Testing drug response in the presence of genetic information: sampling issues for clinical trials.

Progress towards construction of a dense map of di-allelic markers across the human genome has generated considerable enthusiasm for pharmacogenomic applications. To date, however, nearly all of the effort on single nucleotide polymorphism (SNP) projects has been focused on marker identification and screening, not on how the SNP genotype data actually can be used in clinical trials to advance medical practice. Here, we explore how different properties of SNPs impact the size, scope and design of clinical trials using a simple trial design. We evaluate the clinical trial sampling requirements under different allele frequencies, gene action, gene effect size and number of markers in a genome screen. Power and sample size calculations suggest that allele frequency and type of gene action can have a dramatic impact on trial sample sizes, in that under some conditions the required sample sizes are too large to be applicable in a costly clinical trial setting. In other situations, however, pharmacogenomic clinical trials can yield significant sampling/cost savings over traditional trials. These properties are discussed with regard to the general usage of genetic information in clinical trial settings.

Clinical Trials as Topic↗
PubMed2002

Fine mapping of polymorphic alcohol-related quantitative trait loci candidate genes using interval-specific congenic recombinant mice.

BACKGROUND: The inbred long-sleep (ILS) and inbred short-sleep (ISS) strains of mice are widely studied as a model of initial sensitivity to alcohol. Recently, a large comparative DNA sequencing study of candidate genes located within the four Lore quantitative trait loci (QTLs) associated with the ethanol-induced loss of righting reflex in ILS and ISS mice has identified eight genes that contain coding region differences corresponding to amino acid changes. Here, recently developed interval-specific congenic recombinant mice (ISCRs) have been used to map these genes in relationship to newly narrowed QTL regions. METHODS: Regions of candidate genes containing DNA differences corresponding to previously identified amino acid changes between ISS and ILS mice were amplified from either genomic DNA or complementary DNA from ISCR mice using polymerase chain reaction. The products were purified and directly sequenced to determine the genotypes for each polymorphism. On the basis of these genotypic data, each candidate gene was determined to be located either within or outside of recently narrowed Lore QTL intervals. RESULTS: Of these eight candidates with protein-coding differences, five are now excluded from their respective Lore intervals. The other three (Znf142, Ptprn, and Znf133) have been localized to the narrowed QTL intervals. CONCLUSIONS: These three central nervous system genes (Znf142, Ptprn, and Znf133) represent promising candidates for involvement in the differential sensitivity to alcohol exhibited between ILS and ISS mice. This study also demonstrates how the combination of high-throughput comparative gene sequencing and concomitant genetic fine mapping of QTL regions with ISCRs can be an effective tool for accelerating the process of moving from QTL to gene.

Alcoholism↗
PubMed2003

Linkage analysis of candidate loci for end-stage renal disease due to diabetic nephropathy.

Diabetic nephropathy (DN), a major cause of ESRD, is undoubtedly multifactorial and is caused by environmental and genetic factors. To identify a genetic basis for DN susceptibility, we are collecting multiplex DN families in the Caucasian (CA) and African-American (AA) populations for whole genome scanning and candidate gene analysis. A candidate gene search of diabetic sibs discordantly affected, concordantly affected and concordantly unaffected for DN was performed with microsatellite markers in genomic regions suspected to harbor nephropathy susceptibility loci. Regions examined were at human chromosome 10p,10q (orthologous to the rat renal susceptibility Rf-1 locus), and at NPHS1 (nephrin), CD2AP, Wilms tumor (WT1), and NPHS2 (podocin) loci. Linkage analyses were conducted using model-free methods (SIBPAL, S.A.G.E.) for AA, CA, and the combined sample. Allele frequencies and the identity by descent sharing were estimated separately for AA and CA, and race was included as a covariate in the final linkage analysis. To date, we have collected 212 sib pairs from 46 CA and 50 AA families. The average age of diabetes onset was 46.8 yr versus 36.2 yr for CA and 39.5 yr versus 40.2 yr for AA, in males versus females respectively. Genotyping data were available for 106 sib pairs (43 CA, 63 AA) from 27 CA (44% male probands) and 38 AA families (43% male probands). Average AA and CA sibship size was 2.73. Singlepoint and multipoint linkage analyses indicate that marker D10S1654 on chromosome 10p is potentially linked to DN (CA only multipoint P = 4 x 10(-3)). Interestingly, the majority of the linkage evidence derives from the CA sib pairs. We are now adding sib pairs and increasing marker density on chromosome 10. We have excluded linkage with candidate regions for nephrin, CD2AP, WT1, and podocin in this sample. In conjunction with previous reports, our data support evidence for a DN susceptibility locus on chromosome 10.

Aged↗
PubMed2026

A systematic review and network meta-analysis of single nucleotide polymorphisms associated with oral submucous fibrosis risk.

BACKGROUND: Oral submucous fibrosis (OSF) is a chronic and insidious oral disease characterized by hyalinization of the subepithelial connective tissue and progressive fibrosis of the oral submucosa. It is a precancerous condition of oral squamous cell carcinoma. Studies have demonstrated that single nucleotide polymorphisms (SNPs) are closely associated with susceptibility to OSF. This study aims to comprehensively evaluate the association between SNPs and OSF risk and to rank the strength of the association between different genetic models and OSF susceptibility. METHODS: Literature related to OSF was comprehensively searched from PubMed, Web of Science, Embase, Cochrane Library, CNKI, and Wangfang databases up to July 2025. Full-text case-control studies with patients diagnosed with OSF were included. Quality assessment was performed to evaluate the risk of bias. RevMan 5.4, GeMTC 0.14.3, and STATA 17.0 were used for the pairwise and Bayesian network meta-analysis. RESULTS: A total of 24 studies with 2545 cases and 3772 controls, covering 13 SNPs in 11 genes, were included in our meta-analysis. We found that CYP1A1 rs4646903:T>C, CYP1A1 rs1048943:A>G, GSTT1 null genotype, GSTM1 null genotype, and XRCC3 rs861539:C>T were associated with an increased risk of OSF, while MMP2 rs243865:C>T and MMP3 rs3025058: 5A>6A were associated with a decreased risk of OSF. Further Bayesian network meta-analysis indicated the top 5 genetic models with the highest association with OSF risk in network group 1 were the dominant model, homozygous model, allelic model, and recessive model of CYP1A1 rs1048943:A>G (ranked 1-4), and the heterozygous/dominant model of CYP1A1 rs4646903:T>C (both ranked 5). While the allelic models of XRCC3 rs861539:C>T and MMP3 rs3025058: 5A>6A ranked first for predicting OSF in group 2 and group 3, respectively. CONCLUSION: Some specific SNPs are significantly related to the risk of OSF. Among them, the dominant model of CYP1A1 rs1048943:A>G may be the most strongly associated genetic model with OSF risk. Future large-sample, well-designed studies with detailed genotype data are needed to validate the roles of these SNPs in OSF risk.

Humans↗
PubMed1999

Streptococcus waius sp. nov., a thermophilic Streptococcus from a biofilm.

Thermophilic streptococci were isolated from biofilms on stainless steel samples exposed to pasteurized skimmed milk and from dairy products from a dairy manufacturing plant. The phenotypic characters of these isolates were distinct from those of other thermophilic streptococci of dairy origin (Streptococcus thermophilus and Streptococcus bovis). Genotypic data [restriction endonuclease analysis, ribotyping, random amplified polymorphic DNA (RAPD) profiles, DNA-DNA hybridization and G + C contents] support the classification of these isolates as a new species. The sequence of the 16S rRNA was compared with that of 29 species of streptococci and shown to be significantly different. The sequence of the 16S-23S rRNA intergenic spacer region also differed from published sequences of closely related species. A fluorescent in situ hybridization probe prepared to a specific part of the 16S rRNA gene sequence was able to distinguish the unknown isolates from reference isolates of S. thermophilus and S. bovis. It is proposed that these thermophilic streptococcal isolates from a dairy environment be classified in the genus Streptococcus as a new species, Streptococcus waius (from waiu, the New Zealand Maori word for milk). The type strain is 3/1T (= NZRCC 20100T).

Animals↗
PubMed2001

Genotypic and chemotaxonomic evidence for the reclassification of Pseudomonas woodsii (Smith 1911) Stevens 1925 as Burkholderia andropogonis (Smith 1911) Gillis et al. 1995.

It was reported before that [Pseudomonas] woodsii and Burkholderia andropogonis are phenotypically indistinguishable and probably represent the same taxon, for which the name B. andropogonis has been proposed. In the present study, it was found that [P.] woodsii and B. andropogonis strains were indistinguishable by whole-cell protein electrophoresis and have a highly similar cellular fatty acid composition. A high DNA-DNA binding value of 95% was found between the type strains of both species. In addition, the 16S rDNA sequence of [P.] woodsii strain LMG 2362T was very similar to that of B. andropogonis LMG 2129T (99.0%). The chemotaxonomic and genotypic data confirm that [P.] woodsii and B. andropogonis represent the same species, for which it is proposed to retain the name B. andropogonis.

Bacterial Proteins↗
PubMed2002

Thermobifida cellulolytica sp. nov., a novel lignocellulose-decomposing actinomycete.

Four actinomycete strains, isolated from the overheated region of manure compost, were assigned to the genus Thermobifida on the basis of morphological, physiological and biochemical characteristics. All strains produced single, ovoid, heat-sensitive spores on dichotomically branched aerial hyphae. On the basis of chemotaxonomic traits, these isolates showed strong affinity towards members of the genus Thermobifida. Cell-wall analysis revealed the presence of meso-diaminopimelic acid, but no other characteristic amino acids or sugars in the murein (cell wall type III). According to polar lipid analysis, all strains showed PL II-type phospholipid composition; phosphatidylethanolamine and glycolipid were detected together with some unidentified phospholipids. The isoprenoid quinone composition of the new isolates differed slightly from that of the other two Thermobifida species described thus far. The partial 16S rDNA sequence similarity of the four strains reached 99.8-100%, whereas a nearly complete 16S rDNA sequence of TB100T, the representative strain of this collection, showed only 97.4 and 97.8% similarity to the corresponding rDNA sequences of the type strains of Thermobifida fusca and Thermobifida alba, respectively. These four isolates constituted a homogeneous group with levels of DNA-DNA homology ranging from 94.6 to 99.1%. The DNA-DNA relative homology values of strain TB100T to Thermobifida fusca ATCC 27730T and Thermobifida alba DSM 43795T were 48.1 and 57%, respectively. On the basis of phenotypic, chemotaxonomic and genotypic data, the strains are assigned to a new species within the genus Thermobifida under the name Thermobifida cellulolytica sp. nov. The type strain is TB100T (= DSM 44535T = NCAIM B01997T).

Actinomycetales↗
PubMed2002

Carnobacterium viridans sp. nov., an alkaliphilic, facultative anaerobe isolated from refrigerated, vacuum-packed bologna sausage.

A facultatively anaerobic, non-spore-forming, psychrophilic, gram-positive, non-aciduric but alkaliphilic, rod-shaped bacterium (MPL-11T) was found to be responsible for green discoloration of refrigerated vacuum-packaged bologna upon opening of the package. Although Aerococcus viridans, which had been implicated earlier in causing the same problem, was also found, this is the first report of discoloration caused by an organism shown to be a species of Carnobacterium. Bacterial discoloration was caused by H2O2 production upon exposure of the meat to air. Strain MPL-11T is catalase- and oxidase-negative. It is not motile and does not reduce nitrate to nitrite or produce ammonia from arginine. It does not grow in acetate-containing broth or agar (Rogosa) or produce H2S. The peptidoglycan is of the meso-diaminopimelic acid type and it produces predominantly L(+)-lactic acid from glucose. It grows from at least 2 to 30 degrees C over a pH range from 5.5 to 9.1. Ribotyping suggested that strain MPL-11T could be a species of either Lactobacillus or Carnobacterium, but analysis using DNA sequences from the 16S rRNA gene showed conclusively that the organism belonged to the genus Carnobacterium. Since acid is not produced from amygdalin, inulin, mannitol, methyl alpha-D-glucoside or D-xylose, the organism differs from the seven described species of Carnobacterium. In addition, strain MPL-11T is the first member of the genus found that does not produce acid from ribose. It is capable of acid production/growth on galactose, glucose, fructose, mannose, N-acetylglucosamine, aesculin, cellobiose, maltose, lactose, sucrose, trehalose and tagatose. Although extremely salt tolerant, it does not grow in > or = 4% NaCl. On the basis of phenotypic and genotypic data, it is concluded that this isolate represents a separate, novel species. Accordingly, the name Carnobacterium viridans sp. nov. is proposed. The type strain is strain MPL-11T (= ATCC BAA-336T = DSM 14451T).

DNA, Bacterial↗
PubMed2003

Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov.

Genotypic fingerprinting to analyse the bacterial flora of an industrial sourdough revealed a coherent group of strains which could not be associated with a valid species. Comparative 16S rDNA sequence analysis showed that these strains formed a homogeneous cluster distinct from their closest relatives, Lactobacillus farciminis, Lactobacillus alimentarius and Lactobacillus kimchii. To characterize them further, physiological (sugar fermentation, formation of DL-lactate, hydrolysis of arginine, growth temperature, CO2 production) and chemotaxonomic properties have been determined. The DNA G +C content was 37.5 0.2 mol%. The peptidoglycan was of the lysine-D-iso-asparagine (L-Lys-D-Asp) type. The strains were homofermentative, Gram-positive, catalase-negative, non-spore-forming, non-motile rods. They were found as a major stable component of a rye flour sourdough fermentation. Physiological, biochemical as well as genotypic data suggested them to be a new species of the genus Lactobacillus. This was confirmed by DNA-DNA hybridization of genomic DNA, and the name Lactobacillus mindensis is proposed. The type strain of this species is DSM 14500T (=LMG 21508T).

Base Composition↗
PubMed2003

Marinobacter lipolyticus sp. nov., a novel moderate halophile with lipolytic activity.

In the course of a screening programme in hypersaline habitats of southern Spain to isolate halophilic bacteria that are able to produce different extracellular enzymes, a novel, moderately halophilic bacterium (strain SM19(T)) that displays lipolytic activity has been isolated and characterized. Strain SM19(T) is a Gram-negative rod that grows optimally in culture media that contain 7.5 % NaCl. The DNA G+C content was 57.0 mol%. According to phenotypic and genotypic data, this strain was assigned to the genus MARINOBACTER: However, 16S rDNA sequence similarity between strain SM19(T) and species of the genus Marinobacter was <96.7 %; this value is sufficiently low to propose its designation as a novel species. In addition, DNA-DNA hybridization with reference strains of close phylogenetic relatives was between 11 and 19 %. On the basis of these data, the inclusion of strain SM19(T) in the genus Marinobacter as a novel species is proposed, with the name Marinobacter lipolyticus sp. nov. The type strain of the novel species is SM19(T) (=DSM 15157(T)=NCIMB 13907(T)=CIP 107627(T)=CCM 7048(T)).

Alteromonadaceae↗
PubMed2003

Herbaspirillum lusitanum sp. nov., a novel nitrogen-fixing bacterium associated with root nodules of Phaseolus vulgaris.

Several bacterial strains were isolated from root nodules of Phaseolus vulgaris plants grown in a soil from Portugal. The strains were Gram-negative, aerobic, curved rod-shaped and motile. The isolates were catalase- and oxidase-positive. The TP-RAPD (two-primer randomly amplified polymorphic DNA) patterns of all strains were identical, suggesting that they belong to the same species. The complete 16S rDNA sequence of a representative strain was obtained and phylogenetic analysis based on the neighbour-joining method indicated that this bacterium belongs to the beta-Proteobacteria and that the closest related genus is Herbaspirillum. The DNA G+C content ranged from 57.9 to 61.9 mol%. Growth was observed with many different carbohydrates and organic acids including caprate, malate, citrate and phenylacetate. No growth was observed with maltose, meso-inositol, meso-erythritol or adipate as sole carbon source. According to the phenotypic and genotypic data obtained in this work, the bacterium represents a novel species of the genus Herbaspirillum, and the name Herbaspirillum lusitanum sp. nov. is proposed. The type strain is P6-12(T) (=LMG 21710(T)=CECT 5661(T)).

Geography↗
PubMed2005

Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta.

A Gram-positive, endospore-forming, xylanase-producing bacterium isolated from a rice field was studied taxonomically. The strain grows at 10-40 degrees C and in the presence of lysozyme or 5 % (w/v) NaCl. Chemotaxonomic analysis revealed that MK-7 was the predominant menaquinone of the isolated strain, while the major fatty acid was anteiso-C(15 : 0). Comparison of 16S rRNA gene sequences showed that strain BP-23(T) fell within the radiation of the cluster comprising Paenibacillus species. The highest 16S rRNA gene sequence similarities were found with Paenibacillus illinoisensis (97.4 %), Paenibacillus pabuli (97.1 %) and Paenibacillus amylolyticus (96.9 %). The DNA-DNA relatedness of strain BP-23(T) with respect to these three species was very low (32.7, 31.6 and 23.0 %, respectively). On the basis of phenotypic and genotypic data, strain BP-23(T) should be placed in the genus Paenibacillus and designated a novel species, for which the name Paenibacillus barcinonensis sp. nov. is proposed. The type strain is BP-23(T) (=CECT 7022(T)=DSM 15478(T)).

DNA, Bacterial↗
PubMed2006

Nesiotobacter exalbescens gen. nov., sp. nov., a moderately thermophilic alphaproteobacterium from an Hawaiian hypersaline lake.

A Gram-negative bacterium, designated LA33B(T), was isolated from water collected from a hypersaline lake on uninhabited Laysan Atoll in the Northwestern Hawaiian Islands. Cells of strain LA33B(T) are motile, straight rods that grow between 4 and 45 degrees C and in media containing 1-17.5% (w/v) NaCl. The strain oxidizes carbohydrates, nucleosides, amino acids and organic acids presented as sole carbon sources and constitutive lipolytic and proteolytic enzymes are expressed. Over 75% of the fatty acid pool is cis-11-octadecenoic acid (18:1omega7c). Comparative sequence analysis of the 16S rRNA gene indicates that the strain forms a new lineage in the alpha-2 subclass of the Proteobacteria, with the closest recognized strains being Stappia aggregata NCIMB 2208T and Roseibium denhamense JCM 10543T, with which it shares 94-95% sequence similarity. Strain LA33B(T) differs phenotypically from extant Stappia and Roseibium species, however, in that it is a moderate thermophile, it requires NaCl and tolerates higher NaCl concentrations and it does not express beta-galactosidase or oxidize glycerol. On the basis of genotypic data and phenotypic characteristics, we propose that strain LA33B(T) does not belong to the genera Stappia or Roseibium and that it represents the type species of a new genus, Nesiotobacter. Strain LA33B(T) (= ATCC BAA-994T = CIP 108449T) is proposed as the type strain of the type species of this genus, with the name Nesiotobacter exalbescens gen. nov., sp. nov.

Alphaproteobacteria↗
PubMed2005

Sphingomonas yunnanensis sp. nov., a novel gram-negative bacterium from a contaminated plate.

A Gram-negative bacterium, YIM 003T, which was isolated from a contaminated plate in the laboratory, was subjected to a polyphasic taxonomic study. The organism had short-rod-shaped, motile cells, formed yellow-pigmented colonies on ISP2 medium and its optimum growth pH was 7.0-7.5. The major respiratory lipoquinone was ubiquinone Q-10. The phosphate-containing lipids detected in strain YIM 003T were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid and one unidentified phospholipid. The major fatty acids were C(18 : 1)omega7c (59.8 %), C(16 : 0) (9.9 %), ai-C(17 : 0) (5.3 %), i-C(17 : 0) (4.4 %) and C(14 : 0) 2-OH (15.8 %). The G+C content of the genomic DNA was 67.5 mol%. Strain YIM 003T exhibited levels of 16S rRNA gene sequence similarity of 98.2 % to Sphingomonas phyllosphaerae FA2T and 98.0 % to Sphingomonas adhaesiva DSM 7418T but showed less than 97.0 % similarity with respect to other species with validly published names. The DNA-DNA relatedness values of the isolate with S. phyllosphaerae FA2T and S. adhaesiva DSM 7418T were 59 and 26 %, respectively. The phenotypic characteristics and genotypic data indicate that strain YIM 003T should be distinguished from S. phyllosphaerae FA2T and S. adhaesiva DSM 7418T. Therefore, on the basis of the polyphasic taxonomic data presented, a novel species of the genus Sphingomonas, Sphingomonas yunnanensis sp. nov., is proposed, with the type strain YIM 003T (=CCTCC AB 204064T=KCTC 12346T).

Bacterial Typing Techniques↗
PubMed2006

Amycolatopsis taiwanensis sp. nov., from soil.

An actinomycete strain (0345M-7(T)) was isolated from a soil sample from Yilan county, Taiwan. The isolate displayed substrate mycelia, upon which were borne short spore chains. The spore chains were composed of non-motile, smooth-surfaced, oval spores. Strain 0345M-7(T) had meso-diaminopimelic acid in its peptidoglycan. Whole-cell sugars were galactose, glucose, arabinose and ribose. The only phospholipid found was phosphatidylethanolamine. The predominant menaquinone was MK-9(H(4)). Mycolic acids were not detected. Major cellular fatty acids were iso-C(16 : 0) (38.1 %) and C(17 : 1) (25.4 %). The DNA G+C content of strain 0345M-7(T) was 68.9 mol%. On the basis of phenotypic and genotypic data, it is proposed that strain 0345M-7(T) (=BCRC 16802(T)=KCTC 19116(T)) should be classified as the type strain of a novel species of the genus Amycolatopsis, Amycolatopsis taiwanensis sp. nov.

Actinobacteria↗
PubMed2006

Devosia soli sp. nov., isolated from greenhouse soil in Korea.

A Gram-negative, obligately aerobic, rod-shaped bacterium was isolated from greenhouse soil used to cultivate lettuce. The strain, GH2-10T, was characterized on the basis of phenotypic and genotypic data. 16S rRNA gene sequence analysis revealed that the isolate belonged to the genus Devosia, with highest sequence similarity (98.5%) to Devosia riboflavina IFO 13584T. Sequence similarities with other strains tested were below 97.0%. Strain GH2-10T had Q-10 as the predominant ubiquinone and C18:1omega7c and C16:0 as the major fatty acids. The G+C content of the genomic DNA was 59.5 mol%. The results of DNA-DNA hybridization experiments (47% relatedness between D. riboflavina DSM 7230T and strain GH2-10T) and physiological and biochemical tests suggested that strain GH2-10T represents a novel species of the genus Devosia, for which the name Devosia soli sp. nov. is proposed. The type strain is GH2-10T (=KACC 11509T=DSM 17780T).

Bacterial Typing Techniques↗
PubMed2006

Microbacterium deminutum sp. nov., Microbacterium pumilum sp. nov. and Microbacterium aoyamense sp. nov.

Three novel bacterial strains were isolated from a soil sample collected in Japan by culture on a GPM agar plate supplemented with superoxide dismutase and catalase. The strains were Gram-positive, catalase-positive, non-motile bacteria with L-ornithine as a diagnostic diamino acid of the peptidoglycan. The acyl type of the peptidoglycan was N-glycolyl. The major menaquinones were MK-12, 13 and 14. Mycolic acids were not detected. G+C contents of the DNA were in the range 69-71 mol%. Comparative 16S rRNA gene sequence analysis revealed that the isolates belonged to the genus Microbacterium and were closely related to Microbacterium terregens, Microbacterium aurum, Microbacterium koreense, Microbacterium schleiferi and Microbacterium lacticum. However, M. aurum, M. koreense and M. lacticum clearly differed from the isolated strains based on the presence of L-lysine as the cell-wall diamino acid and various other chemotaxonomic characteristics. Levels of DNA-DNA relatedness showed that the isolated strains represented three separate genomic species. Based on both phenotypic and genotypic data, the following novel species of the genus Microbacterium are proposed: Microbacterium deminutum sp. nov. (type strain KV-483(T)=NRRL B-24453(T)=NBRC 101278(T)), Microbacterium pumilum sp. nov. (type strain KV-488(T)=NRRL B-24452(T)=NBRC 101279(T)) and Microbacterium aoyamense sp. nov. (type strain KV-492(T)=NRRL B-24451(T)=NBRC 101280(T)).

Actinomycetales↗