scholarly journals Antimicrobial Susceptibilities of Oral Isolates of Abiotrophia and Granulicatella According to the Consensus Guidelines for Fastidious Bacteria

Medicines ◽  
2018 ◽  
Vol 5 (4) ◽  
pp. 129 ◽  
Author(s):  
Taisei Kanamoto ◽  
Shigemi Terakubo ◽  
Hideki Nakashima
Keyword(s):  
Dna Hybridization ◽  
Vitamin B6 ◽  
Antimicrobial Agents ◽  
Oral Microbiota ◽  
Phenotypic Characteristics ◽  
Granulicatella Adiacens ◽  
Susceptibility Profiles ◽  
Susceptibility Rate ◽  
Type Strains ◽  
Culture Negative

Background: The genera Abiotrophia and Granulicatella, previously known as nutritionally variant streptococci (NVS), are fastidious bacteria requiring vitamin B6 analogs for growth. They are members of human normal oral microbiota, and are supposed to be one of the important pathogens for so-called “culture-negative” endocarditis. Methods: The type strains and oral isolates identified, by using both phenotypic profiles and the DNA–DNA hybridization method, were examined for susceptibilities to 15 antimicrobial agents including penicillin (benzylpenicillin, ampicillin, amoxicillin, and piperacillin), cephem (cefazolin, ceftazidime, ceftriaxone, and cefaclor), carbapenem (imipenem), aminoglycoside (gentamicin), macrolide (erythromycin), quinolone (ciprofloxacin), tetracycline (minocycline), glycopeptide (vancomycin), and trimethoprim-sulfamethoxazole complex. The minimum inhibitory concentration and susceptibility criterion were determined, according to the consensus guideline from the Clinical and Laboratory Standards Institute. Results: Isolates of Abiotrophia defectiva were susceptible to ampicillin, amoxicillin ceftriaxone, cefaclor, imipenem, ciprofloxacin, and vancomycin. Isolates of Granulicatella adiacens were mostly susceptible to benzylpenicillin, ampicillin, amoxicillin, cefazolin, ceftriaxone, imipenem, minocycline, and vancomycin. The susceptibility profile of Granulicatella elegans was similar to that of G. adiacens, and the susceptibility rate was higher than that of G. adiacens. Conclusions: Although Abiotrophia and Granulicatella strains are hardly distinguishable by their phenotypic characteristics, their susceptibility profiles to the antimicrobial agents were different among the species. Species-related differences in susceptibility of antibiotics should be considered in the clinical treatment for NVS related infections.

scholarly journals Flammeovirga kamogawensis sp. nov., isolated from coastal seawater in Japan

2007 ◽  
Vol 57 (6) ◽  
pp. 1327-1330 ◽  
Author(s):  
Shoichi Hosoya ◽  
Akira Yokota
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Rrna Gene ◽  
The Novel ◽  
Threshold Values ◽  
16S Rrna Gene Sequences ◽  
Phenotypic Characteristics ◽  
Coastal Seawater ◽  
Definition Of ◽  
Type Strains

Two strains of gliding, agarolytic bacteria, strains YS10T and YML5, were isolated from coastal seawater off Kamogawa, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that the novel isolates represent a separate lineage within the genus Flammeovirga. DNA–DNA hybridization values between these isolates and the type strains of species of the genus Flammeovirga were significantly lower than those accepted as threshold values for the phylogenetic definition of a species. Furthermore, some of the phenotypic characteristics indicate that the isolates differ from other Flammeovirga species. Based on these differences, it is suggested that the isolates represent a novel species, for which the name Flammeovirga kamogawensis sp. nov. is proposed. The type strain is YS10T (=IAM 15451T=NCIMB 14281T).

scholarly journals Demequina flava sp. nov. and Demequina sediminicola sp. nov., isolated from sea sediment

2013 ◽  
Vol 63 (Pt_1) ◽  
pp. 249-253 ◽  
Author(s):  
Moriyuki Hamada ◽  
Tomohiko Tamura ◽  
Hideki Yamamura ◽  
Ken-ichiro Suzuki ◽  
Masayuki Hayakawa
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Major Fatty Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Monophyletic Cluster ◽  
Link Type ◽  
Type Strains

Two novel Gram-stain-positive bacteria, designated HR08-7T and HR08-43T, were isolated from a sea sediment sample from Rishiri Island, Hokkaido, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons revealed that strains HR08-7T and HR08-43T and the members of the genus Demequina formed a monophyletic cluster with similarity range of 95.5–99.0 %. The peptidoglycan type of strains HR08-7T and HR08-43T was A4β. The predominant menaquinone of both strains was demethylmenaquinone DMK-9(H4) and the major fatty acid was anteiso-C15 : 0. The DNA G+C contents of strains HR08-7T and HR08-43T were 64.5 and 62.4 mol%, respectively. The results of phylogenetic analysis and DNA–DNA hybridization, along with differences of strains HR08-7T and HR08-43T from the recognized Demequina species in phenotypic characteristics, indicate that the two strains merit classification as representatives of two novel species of the genus Demequina , for which the names Demequina flava sp. nov. and Demequina sediminicola sp. nov. are proposed; the type strains are HR08-7T ( = NBRC 105854T = DSM 24865T) and HR08-43T ( = NBRC 105855T = DSM 24867T), respectively.

scholarly journals Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium from an Antarctic environment

2007 ◽  
Vol 57 (11) ◽  
pp. 2609-2612 ◽  
Author(s):  
Núria Bozal ◽  
M. Jesús Montes ◽  
Elena Mercadé
Keyword(s):  
Dna Hybridization ◽  
Cellular Fatty Acid ◽  
South Shetland Islands ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Shetland Islands ◽  
Gene Sequence Analysis ◽  
Psychrotolerant Bacterium ◽  
The Antarctic ◽  
Type Strains

Two Gram-negative, cold-adapted, aerobic bacteria, designated strains M8T and M6, were isolated from soil collected from the South Shetland Islands. The organisms were rod-shaped, catalase- and oxidase-positive and motile by means of polar flagella. These two psychrotolerant strains grew between −4 and 30 °C. 16S rRNA gene sequence analysis placed strains M8T and M6 within the genus Pseudomonas. DNA–DNA hybridization experiments between the Antarctic isolate M8T and type strains of phylogenetically related species, namely Pseudomonas peli and Pseudomonas anguilliseptica, revealed levels of relatedness of 33 and 37 %, respectively. Strain M6 showed 99 % DNA similarity to strain M8T. Several phenotypic characteristics, together with data on cellular fatty acid composition, served to differentiate strains M8T and M6 from related pseudomonads. On the basis of the polyphasic taxonomic evidence presented in this study, it can be concluded that strains M8T and M6 belong to the same genospecies, representing a novel species of the genus Pseudomonas, for which the name Pseudomonas guineae sp. nov. is proposed. The type strain is M8T (=LMG 24016T=CECT 7231T).

Agromyces iriomotensis sp. nov. and Agromyces subtropicus sp. nov., isolated from soil

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 833-838 ◽  
Author(s):  
Moriyuki Hamada ◽  
Chiyo Shibata ◽  
Yuumi Ishida ◽  
Tomohiko Tamura ◽  
Hideki Yamamura ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Sequence Comparisons ◽  
Content Type ◽  
Link Type ◽  
Type Strains

Three novel Gram-stain-positive bacteria, designated IY07-20T, IY07-56T and IY07-113, were isolated from soil samples from Iriomote Island, Okinawa, Japan, and their taxonomic positions were investigated by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequence comparisons showed that the three isolates were closely related to the members of the genus Agromyces , with similarity range of 95.6–98.7 %. The isolates contained l-2,4-diaminobutylic acid, d-alanine, d-glutamic acid and glycine in their peptidoglycans. The predominant menaquinone was MK-12 and the major fatty acids were anteiso-C15 : 0 and anteiso-C17 : 0. The DNA G+C contents were 70.9–72.9 mol%. The chemotaxonomic characteristics of the isolates matched those described for members of the genus Agromyces . The results of phylogenetic analysis and DNA–DNA hybridization, along with differences in phenotypic characteristics between strains IY07-20T, IY07-56T and IY07-113 and the species of the genus Agromyces with validly published names, indicate that the three isolates merit classification as representatives of two novel species of the genus Agromyces , for which the names Agromyces iriomotensis sp. nov. and Agromyces subtropica sp. nov. are proposed; the type strains are IY07-20T ( = NBRC 106452T = DSM 26155T) and IY07-56T ( = NBRC 106454T = DSM 26153T), respectively.

scholarly journals МОНГОЛ ОРНЫ ХӨРСНӨӨС ЯЛГАСАН АКТИНОМИЦЕТИЙН АНГИЛАЛЗҮЙН СУДАЛГААНЫ ДҮНГЭЭС

2016 ◽  
pp. 66-72
Author(s):  
Б Пагмадулам ◽  
Мониша Канна ◽  
Д Цэрэндулам ◽  
Ц Рэнцэнханд
Keyword(s):  
Phylogenetic Analysis ◽  
16S Rrna ◽  
Dna Hybridization ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Phenotypic Characteristics ◽  
Genus Streptomyces ◽  
Streptomyces Ghanaensis ◽  
Preliminary Study ◽  
Type Strains

Soil samples were collected from Khentii and Tuv provinces in Mongolia. Two strains (N11, N22) were selected for polyphasic approach which including morphological, physiological and phylogenetic analysis. Phylogenetic analysis revealed that the strain N22 has highest the 16S rRNA similarity of 99.39% with Streptomyces ghanaensis NBRC 15414(T). The 16S rRNA genes sequence of 1418 nucleotides was generated for N11 and compared to the validly described species of genus Streptomyces as closest neighbors. Phylogenetic analysis revealed that the strain N11 has highest the 16S rRNA similarity of 98.51% with Streptomyces yerevanensis NBRC 12517(T). Also some phenotypic characteristics were different from type strains. Preliminary study shows that strain N11 might be new actinomycete species. However, need to determine the genetic distance between two microorganisms by using DNA-DNA hybridization methods.

scholarly journals Streptomonospora halotolerans sp. nov., an actinomycete isolated from soil

2015 ◽  
Vol 65 (Pt_9) ◽  
pp. 3183-3189 ◽  
Author(s):  
Junwei Zhao ◽  
Lifeng Guo ◽  
Chongxi Liu ◽  
Pengyu Sun ◽  
Jiansong Li ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Dna Hybridization ◽  
Northern China ◽  
Diaminopimelic Acid ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Diamino Acid ◽  
Type Strains ◽  
The 16S Rrna Gene

A novel actinomycete, designated strain NEAU-Jh2-17T, was isolated from muddy soil collected from a riverbank in Jilin Province, northern China, and characterized using a polyphasic approach. The 16S rRNA gene sequence of strain NEAU-Jh2-17T showed highest similarity to those of Streptomonospora nanhaiensis 12A09T (99.26 %), Nocardiopsis rosea YIM 90094T (97.31 %), Streptomonospora halophila YIM 91355T (97.24 %) and Streptomonospora arabica S186T (97.02 %). Phylogenetic analysis based on 16S rRNA gene sequences demonstrated that strain NEAU-Jh2-17T fell within a cluster consisting of the type strains of species of the genus Streptomonospora and formed a stable clade with S. nanhaiensis 12A09T in trees generated with two algorithms. Key morphological and chemotaxonomic properties also confirmed the affiliation of strain NEAU-Jh2-17T to the genus Streptomonospora. The cell wall contained meso-diaminopimelic acid as the diagnostic diamino acid and whole-cell hydrolysates contained glucose, ribose and galactose. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), phosphatidylinositol (PI), phosphatidylinositol mannoside (PIM), two unknown phospholipids (PLs) and two unknown glycolipids (GLs). The predominant menaquinones were MK-10(H2), MK-10(H8), MK-10(H6) and MK-10(H4). Major fatty acids were C18 : 0 10-methyl, anteiso-C17 : 0, C16 : 0 10-methyl, iso-C15 : 0, C17 : 0 10-methyl and C18 : 0. The DNA G+C content was 71.82 mol%. However, a combination of DNA–DNA hybridization results and some phenotypic characteristics demonstrated that strain NEAU-Jh2-17T could be distinguished from its closely related relatives. Therefore, strain NEAU-Jh2-17T is considered to represent a novel species of the genus Streptomonospora, for which the name Streptomonospora halotolerans sp. nov. is proposed. The type strain is NEAU-Jh2-17T ( = CGMCC 4.7218T = JCM 30347T).

scholarly journals Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov., isolated from effective nodules of peanut

2015 ◽  
Vol 65 (Pt_12) ◽  
pp. 4655-4661 ◽  
Author(s):  
Yong Hua Li ◽  
Rui Wang ◽  
Xiao Xia Zhang ◽  
J. Peter. W. Young ◽  
En Tao Wang ◽  
...  
Keyword(s):  
Arachis Hypogaea ◽  
Dna Hybridization ◽  
Gene Sequence ◽  
Novel Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Lablab Purpureus ◽  
Phenotypic Characteristics ◽  
Slow Growing ◽  
Type Strains

Seven slow-growing rhizobia isolated from effective nodules of Arachis hypogaea were assigned to the genus Bradyrhizobium based on sharing 96.3–99.9 % 16S rRNA gene sequence similarity with the type strains of recognized Bradyrhizobium species. Multilocus sequence analysis of glnII, recA, gyrB and dnaK genes indicated that the seven strains belonged to two novel species represented by CCBAU 51649T and CCBAU 53363T. Strain CCBAU 51649T shared 94, 93.4, 92.3 and 94.9 % and CCBAU 53363T shared 91.4, 94.5, 94.6 and 97.7 % sequence similarity for the glnII, recA, gyrB and dnaK genes, respectively, with respect to the closest related species Bradyrhizobium manausense BR 3351T and Bradyrhizobium yuanmingense CCBAU 10071T. Summed feature 8 and C16 : 0 were the predominant fatty acid components for strains CCBAU 51649T and CCBAU 53363T. DNA–DNA hybridization and analysis of phenotypic characteristics also distinguished these strains from the closest related Bradyrhizobium species. The strains formed effective nodules on Arachis hypogaea, Lablab purpureus and Aeschynomene indica, and they had identical nodA genes to Bradyrhizobium sp. PI237 but were phylogenetically divergent from other available nodA genes at less than 66 % similarity. Based in these results, strains CCBAU 51649T ( = CGMCC 1.15034T = LMG 28620T) and CCBAU 53363T ( = CGMCC 1.15035T = LMG 28621T) are designated the type strains of two novel species, for which the names Bradyrhizobium guangdongense sp. nov. and Bradyrhizobium guangxiense sp. nov. are proposed, respectively.

scholarly journals Lysobacter concretionis sp. nov., isolated from anaerobic granules in an upflow anaerobic sludge blanket reactor

2005 ◽  
Vol 55 (3) ◽  
pp. 1155-1161 ◽  
Author(s):  
Hee-Sung Bae ◽  
Wan-Taek Im ◽  
Sung-Taik Lee
Keyword(s):  
Dna Hybridization ◽  
Sequence Similarity ◽  
Upflow Anaerobic Sludge Blanket ◽  
Anaerobic Sludge ◽  
Rrna Gene ◽  
Phenotypic Characteristics ◽  
Long Rod ◽  
Anaerobic Sludge Blanket ◽  
Gliding Movement ◽  
Type Strains

The taxonomic positions of Lysobacter species with validly published names and a novel strain Ko07T, which was newly isolated from an upflow anaerobic sludge blanket reactor treating wastewater from a brewery, were (re)estimated on the basis of results obtained by using a polyphasic taxonomy approach. Phylogenetic inference based on 16S rRNA gene sequences showed that strain Ko07T and all Lysobacter species with validly published names clustered together in a phylogenetic branch within the class ‘Gammaproteobacteria’. The sequence similarity of strain Ko07T to the type strains of established Lysobacter species was in the range 94·9–96·7 %. Ubiquinone Q-8 and branched fatty acids, C11 : 0 iso, C15 : 0 iso, C16 : 0 iso, iso C17 : 1 ω9c and C11 : 0 iso 3OH, predominantly appeared in strain Ko07T as well as in all type strains of the recognized Lysobacter species. The DNA–DNA hybridization values of strain Ko07T with those of recognized Lysobacter species were estimated to be 2–20 %. Despite sharing common taxonomic features in important phenotypic characteristics, such as gliding movement, long-rod shape and proteolytic activity, strain Ko07T could be distinguished from the Lysobacter species with validly published names by its low DNA–DNA hybridization value, a comparatively low DNA G+C content (63·8 mol%), substrate utilization and some physiochemical characteristics. On the basis of the results obtained in this study, it is proposed that strain Ko07T should be classified as representing a novel member of the genus Lysobacter, for which the name Lysobacter concretionis sp. nov. is proposed. The type strain is Ko07T (=KCTC 12205T=DSM 16239T).

Actinoalloteichus nanshanensis sp. nov., isolated from the rhizosphere of a fig tree (Ficus religiosa)

2011 ◽  
Vol 61 (5) ◽  
pp. 1165-1169 ◽  
Author(s):  
Wensheng Xiang ◽  
Chongxi Liu ◽  
Xiangjing Wang ◽  
Jing Du ◽  
Lijun Xi ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Type Strain ◽  
Novel Species ◽  
Rrna Gene ◽  
Malt Extract ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Ficus Religiosa ◽  
Fig Tree ◽  
Type Strains

A Gram-positive, aerobic actinomycete, designated strain NEAU 119T, was isolated from the rhizosphere of a fig tree and was characterized using a polyphasic approach. The isolate formed branching, non-fragmenting vegetative hyphae and produced black pigment on yeast extract/malt extract (ISP medium 2). The G+C content of the DNA was 76.6 mol%. The organism had chemotaxonomic characteristics typical of the genus Actinoalloteichus and was closely related to the type strains of Actinoalloteichus cyanogriseus, Actinoalloteichus spitiensis and Actinoalloteichus hymeniacidonis, currently the only three recognized species of the genus Actinoalloteichus, sharing 16S rRNA gene similarities of 96.4, 96.6 and 98.1 %, respectively. However, the results of DNA–DNA hybridization studies demonstrated that the novel strain showed only 46.8 % relatedness with the type strain of A. hymeniacidonis. In addition, a set of phenotypic characteristics also readily distinguished strain NEAU 119T from the type strains of recognized species of the genus Actinoalloteichus. According to the above data, it is proposed that strain NEAU 119T represents a novel species, Actinoalloteichus nanshanensis sp. nov. The type strain of Actinoalloteichus nanshanensis is NEAU 119T ( = CGMCC 4.5714T = NBRC 106685T).

scholarly journals Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods

2015 ◽  
Vol 65 (Pt_8) ◽  
pp. 2485-2490 ◽  
Author(s):  
Mika Miyashita ◽  
Pattaraporn Yukphan ◽  
Winai Chaipitakchonlatarn ◽  
Taweesak Malimas ◽  
Masako Sugimoto ◽  
...  
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Fermented Food ◽  
Rrna Gene ◽  
Fermented Foods ◽  
The Novel ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
Traditional Fermented Foods

Three Lactobacillus-like strains, NB53T, NB446T and NB702, were isolated from traditional fermented food in Thailand. Comparative 16S rRNA gene sequence analysis indicated that these strains belong to the Lactobacillus plantarum group. Phylogenetic analysis based on the dnaK, rpoA, pheS and recA gene sequences indicated that these three strains were distantly related to known species present in the L. plantarum group. DNA–DNA hybridization with closely related strains demonstrated that these strains represented two novel species; the novel strains could be differentiated based on chemotaxonomic and phenotypic characteristics. Therefore, two novel species of the genus Lactobacillus, Lactobacillus plajomi sp. nov. (NB53T) and Lactobacillus modestisalitolerans sp. nov. (NB446T and NB702), are proposed with the type strains NB53T ( = NBRC 107333T = BCC 38054T) and NB446T ( = NBRC 107235T = BCC 38191T), respectively.

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