scholarly journals Rhodovulum marinum sp. nov., a novel phototrophic purple non-sulfur alphaproteobacterium from marine tides of Visakhapatnam, India

2006 ◽  
Vol 56 (7) ◽  
pp. 1651-1656 ◽  
Author(s):  
T. N. R. Srinivas ◽  
P. Anil Kumar ◽  
Ch. Sasikala ◽  
Ch. V. Ramana ◽  
J. Süling ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Eastern Coast ◽  
Rrna Gene ◽  
Rhodovulum Sulfidophilum ◽  
Gene Sequence Analysis ◽  
Intracytoplasmic Membranes ◽  
Seawater Samples ◽  
The 16S Rrna Gene

A yellowish-brown bacterium was isolated from enrichment cultures inoculated with seawater samples from the eastern coast of India (Visakhapatnam) under photoheterotrophic conditions. Enrichment and isolation in a medium containing 2 % NaCl (w/v) yielded strain JA128T, which has ovoid to rod-shaped cells, also forms chains and is non-motile. Phylogenetic analysis on the basis of 16S rRNA gene sequences showed that strain JA128T clusters with the Alphaproteobacteria and the sequence similarity with its closest relatives, Rhodovulum iodosum and Rhodovulum sulfidophilum, was 95 %. Strain JA128T contained vesicular intracytoplasmic membranes, bacteriochlorophyll a and carotenoids of the spheroidene series. Strain JA128T was mesophilic, slightly acidophilic, slightly halophilic and grew photoheterotrophically with a number of organic compounds as carbon source and electron donor. It was unable to grow photoautotrophically, chemoautotrophically or by fermentative modes. It did not utilize sulfide, thiosulfate or hydrogen as electron donors. Thiamine was required as a growth factor. Based on the 16S rRNA gene sequence analysis, morphological and physiological characteristics, strain JA128T was significantly different from other species of the genus Rhodovulum and was recognized as a novel species for which the name Rhodovulum marinum sp. nov. is proposed. The type strain is JA128T (=ATCC BAA 1215T=CCUG 52183T=JCM 13300T).

scholarly journals hsp60 and 16S rRNA gene sequence relationships among species of the genus Bacteroides with the finding that Bacteroides suis and Bacteroides tectus are heterotypic synonyms of Bacteroides pyogenes

2010 ◽  
Vol 60 (12) ◽  
pp. 2984-2990 ◽  
Author(s):  
Mitsuo Sakamoto ◽  
Natsuko Suzuki ◽  
Yoshimi Benno
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Single Species ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Type Strains ◽  
The 16S Rrna Gene

hsp60 gene sequences were determined for members of the genus Bacteroides and sequence similarities were compared with those obtained for the 16S rRNA gene. Among the 29 Bacteroides type strains, the mean sequence similarity of the hsp60 gene (84.5 %) was significantly less than that of the 16S rRNA gene (90.7 %), indicating a high discriminatory power of the hsp60 gene. Species of the genus Bacteroides were differentiated well by hsp60 gene sequence analysis, except for Bacteroides pyogenes JCM 6294T, Bacteroides suis JCM 6292T and Bacteroides tectus JCM 10003T. The hsp60 gene sequence analysis and the levels of DNA–DNA relatedness observed demonstrated that these three type strains are a single species. Consequently, B. suis and B. tectus are heterotypic synonyms of B. pyogenes. This study suggests that the hsp60 gene is an alternative phylogenetic marker for the classification of species of the genus Bacteroides.

scholarly journals Phyllobacterium loti sp. nov. isolated from nodules of Lotus corniculatus

2014 ◽  
Vol 64 (Pt_3) ◽  
pp. 781-786 ◽  
Author(s):  
Maximo Sánchez ◽  
Martha-Helena Ramírez-Bahena ◽  
Alvaro Peix ◽  
María J. Lorite ◽  
Juan Sanjuán ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Sequence Similarity ◽  
Carbon Sources ◽  
Lotus Corniculatus ◽  
Culture Conditions ◽  
Rrna Gene ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Strain S658T was isolated from a Lotus corniculatus nodule in a soil sample obtained in Uruguay. Phylogenetic analysis of the 16S rRNA gene and atpD gene showed that this strain clustered within the genus Phyllobacterium . The closest related species was, in both cases, Phyllobacterium trifolii PETP02T with 99.8 % sequence similarity in the 16S rRNA gene and 96.1 % in the atpD gene. The 16S rRNA gene contains an insert at the beginning of the sequence that has no similarities with other inserts present in the same gene in described rhizobial species. Ubiquinone Q-10 was the only quinone detected. Strain S658T differed from its closest relatives through its growth in diverse culture conditions and in the assimilation of several carbon sources. It was not able to reproduce nodules in Lotus corniculatus. The results of DNA–DNA hybridization, phenotypic tests and fatty acid analyses confirmed that this strain should be classified as a representative of a novel species of the genus Phyllobacterium , for which the name Phyllobacterium loti sp. nov. is proposed. The type strain is S658T( = LMG 27289T = CECT 8230T).

scholarly journals Lactobacillus hammesii sp. nov., isolated from French sourdough

2005 ◽  
Vol 55 (2) ◽  
pp. 763-767 ◽  
Author(s):  
Rosica Valcheva ◽  
Maher Korakli ◽  
Bernard Onno ◽  
Hervé Prévost ◽  
Iskra Ivanova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Fragment Length Polymorphism ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
Different Strains

Twenty morphologically different strains were chosen from French wheat sourdough isolates. Cells were Gram-positive, non-spore-forming, non-motile rods. The isolates were identified using amplified-fragment length polymorphism, randomly amplified polymorphic DNA and 16S rRNA gene sequence analysis. All isolates were members of the genus Lactobacillus. They were identified as representing Lactobacillus plantarum, Lactobacillus paralimentarius, Lactobacillus sanfranciscensis, Lactobacillus spicheri and Lactobacillus sakei. However, two isolates (LP38T and LP39) could be clearly discriminated from recognized Lactobacillus species on the basis of genotyping methods. 16S rRNA gene sequence similarity and DNA–DNA relatedness data indicate that the two strains belong to a novel Lactobacillus species, for which the name Lactobacillus hammesii is proposed. The type strain is LP38T (=DSM 16381T=CIP 108387T=TMW 1.1236T).

scholarly journals Nocardia shimofusensis sp. nov., isolated from soil, and Nocardia higoensis sp. nov., isolated from a patient with lung nocardiosis in Japan

2004 ◽  
Vol 54 (6) ◽  
pp. 1927-1931 ◽  
Author(s):  
Akiko Kageyama ◽  
Katsukiyo Yazawa ◽  
Akira Mukai ◽  
Mari Kinoshita ◽  
Nobukatsu Takata ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Novel Species ◽  
Sequence Similarity ◽  
Taxonomic Status ◽  
Rrna Gene ◽  
Gene Sequence Analysis ◽  
Morphological Criteria ◽  
Respective Type ◽  
Type Strains

Three actinomycete strains isolated from soils and one strain isolated from a patient with lung nocardiosis in 1999 and 2001 in Japan have been provisionally assigned to the genus Nocardia on the basis of morphological criteria. These isolates were further investigated to determine their specific taxonomic status. Detailed chemotaxonomic characterization and 16S rRNA gene sequence analysis of these isolates confirmed that they belong to the genus Nocardia. The 16S rRNA gene sequences of the four strains were most similar to that of Nocardia farcinica. However, the sequence similarity values between these four strains and N. farcinica were <98·9 %. These four strains were susceptible to 5-fluorouracil, and they have the ability to decompose urea, which is a very characteristic trait. Furthermore, DNA–DNA relatedness data revealed that IFM 10311T, IFM 10312 and IFM 10313 comprise a single novel species of Nocardia, that IFM 10084T represents another novel species of Nocardia and that these two novel species could be distinguished from N. farcinica. The names Nocardia shimofusensis sp. nov. and Nocardia higoensis sp. nov. are proposed, with IFM 10311T (=NBRC 100134T=JCM 12122T=DSM 44733T) and IFM 10084T (=NBRC 100133T=JCM 12121T=DSM 44732T) as the respective type strains.

scholarly journals Description of Herbiconiux flava sp. nov. and emended description of the genus Herbiconiux

2012 ◽  
Vol 62 (Pt_4) ◽  
pp. 795-799 ◽  
Author(s):  
Moriyuki Hamada ◽  
Chiaki Komukai ◽  
Tomohiko Tamura ◽  
Lyudmila I. Evtushenko ◽  
Natalia G. Vinokurova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Differences ◽  
Gene Sequence Analysis ◽  
Lipid Pattern

A non-motile and non-endospore-forming rod, strain NBRC 16403T, was isolated from the phyllosphere of a sedge (Carex sp.). 16S rRNA gene sequence analysis indicated that strain NBRC 16403T was closely related to Herbiconiux solani DSM 19813T (98.6 % 16S rRNA gene sequence similarity), Herbiconiux ginsengi wged11T (97.8 %) and Herbiconiux moechotypicola RB-62T (97.8 %). The peptidoglycan (B2γ type) contained d- and l-2,4-diaminobutyric acids, d-alanine, glycine and threo-3-hydroxyglutamic acid, which replaced glutamic acid almost completely. The predominant menaquinones were MK-10 and MK-11. The polar lipid pattern comprised diphosphatidylglycerol, phosphatidylglycerol, three glycolipids and minor amounts of other polar lipids. The major fatty acids were anteiso-C15 : 0, iso-C16 : 0 and anteiso-C17 : 0; no cyclohexyl-C17 : 0 was detected. The DNA G+C content was 71.0 mol%. The results of phylogenetic and DNA–DNA relatedness studies, along with phenotypic differences between strain NBRC 16403T and recognized members of the genus Herbiconiux, indicated that the isolate should be assigned to a novel species of the genus Herbiconiux, for which the name Herbiconiux flava sp. nov. is proposed. The type strain is NBRC 16403T ( = VKM Ac-2058T).

Genome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Priya Lakra ◽  
Helianthous Verma ◽  
Chandni Talwar ◽  
Durgesh Narain Singh ◽  
Nirjara Singhvi ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Sequence Similarity ◽  
Rrna Gene ◽  
Species Delineation ◽  
16S Rrna Gene Analysis ◽  
Content Type ◽  
Link Type ◽  
The 16S Rrna Gene

Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensi s DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA–DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species. Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans .

Calditerricola satsumensis gen. nov., sp. nov. and Calditerricola yamamurae sp. nov., extreme thermophiles isolated from a high-temperature compost

2011 ◽  
Vol 61 (3) ◽  
pp. 631-636 ◽  
Author(s):  
Toshiyuki Moriya ◽  
Tomohisa Hikota ◽  
Isao Yumoto ◽  
Takashi Ito ◽  
Yusuke Terui ◽  
...  
Keyword(s):  
High Temperature ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Sequence Similarity ◽  
Synthetic Medium ◽  
Rrna Gene ◽  
Isoleucine Leucine ◽  
Micro Organisms ◽  
The 16S Rrna Gene

Two novel thermophilic micro-organisms, designated YMO81T and YMO722T, were isolated from a high-temperature compost (internal temperature >95 °C). The isolates were able to grow at 80 °C in a nutrient broth and in a synthetic medium. Cells were aerobic, Gram-negative rods (0.3×4.0 μm). Spore formation was not observed. Strain YMO81T grew at 83 °C and pH 6.9–8.9 and grew optimally at 78 °C and pH 7.5 with 2 % NaCl. For growth in a synthetic minimal medium at 70 °C, the vitamins biotin, folic acid and thiamine and the amino acids glutamine and methionine were essential for growth of both strains; at 80 °C, strain YMO81T also required histidine, isoleucine, leucine, lysine, phenylalanine, serine, tryptophan and valine. Cellular fatty acids of the isolates comprised mainly iso-C17 : 0 and anteiso-C17 : 0. The DNA G+C contents of strains YMO81T and YMO722T were 70 and 64 mol%, respectively. When the 16S rRNA gene sequences of the isolates were compared with those of other bacteria, highest similarity was observed with Planifilum yunnanense LA5T (90 % 16S rRNA gene sequence similarity). DNA–DNA relatedness between strain YMO722T and strain YMO81T was 55 %. N 4-Aminopropylspermine was identified as a major polyamine, which suggested that the isolates were distinct from other related taxa. On the basis of phylogenetic, phenotypic and chemotaxonomic analyses, we propose a new genus, Calditerricola gen. nov., and two novel species, the type species Calditerricola satsumensis sp. nov., with type strain YMO81T (=ATCC BAA-1462T =JCM 14719T =DSM 45223T), and Calditerricola yamamurae sp. nov., with type strain YMO722T (=ATCC BAA-1461T =JCM 14720T =DSM 45224T).

scholarly journals Soehngenia longivitae sp. nov., a Fermenting Bacterium Isolated from a Petroleum Reservoir in Azerbaijan, and Emended Description of the Genus Soehngenia

2020 ◽  
Vol 8 (12) ◽  
pp. 1967
Author(s):  
Tamara N. Nazina ◽  
Salimat K. Bidzhieva ◽  
Denis S. Grouzdev ◽  
Diyana S. Sokolova ◽  
Tatyana P. Tourova ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
High Throughput Sequencing ◽  
Biochemical Characterization ◽  
Sequence Similarity ◽  
Phylogenomic Analysis ◽  
Rrna Gene ◽  
Petroleum Reservoir ◽  
Ph Range ◽  
The 16S Rrna Gene

A methanogenic enrichment growing on a medium with methanol was obtained from a petroleum reservoir (Republic of Azerbaijan) and stored for 33 years without transfers to fresh medium. High-throughput sequencing of the V4 region of the 16S rRNA gene revealed members of the genera Desulfovibrio, Soehngenia, Thermovirga, Petrimonas, Methanosarcina, and Methanomethylovorans. A novel gram-positive, rod-shaped, anaerobic fermentative bacterium, strain 1933PT, was isolated from this enrichment and characterized. The strain grew at 13–55 °C (optimum 35 °C), with 0–3.0% (w/v) NaCl (optimum 0–2.0%) and in the pH range of 6.7–8.0 (optimum pH 7.0). The 16S rRNA gene sequence similarity, the average nucleotide identity (ANI) and in silico DNA–DNA hybridization (dDDH) values between strain 1933PT and the type strain of the most closely related species Soehngenia saccharolytica DSM 12858T were 98.5%, 70.5%, and 22.6%, respectively, and were below the threshold accepted for species demarcation. Genome-based phylogenomic analysis and physiological and biochemical characterization of the strain 1933PT (VKM B-3382T = KCTC 15984T) confirmed its affiliation to a novel species of the genus Soehngenia, for which the name Soehngenia longivitae sp. nov. is proposed. Genome analysis suggests that the new strain has potential in the degradation of proteinaceous components.

scholarly journals Pseudosphingobacterium domesticum gen. nov., sp. nov., isolated from home-made compost

2007 ◽  
Vol 57 (7) ◽  
pp. 1535-1538 ◽  
Author(s):  
Ivone Vaz-Moreira ◽  
M. Fernanda Nobre ◽  
Olga C. Nunes ◽  
Célia M. Manaia
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Gene Sequence Analysis ◽  
The Family

A bacterial strain, DC-186T, isolated from home-made compost, was characterized for its phenotypic and phylogenetic properties. The isolate was a Gram-negative rod that was able to grow at 15–36 °C and pH 5.5–8.0. Strain DC-186T was positive in tests for catalase, oxidase and β-galactosidase activities and aesculin hydrolysis. The predominant fatty acids were the summed feature C16 : 1/iso-C15 : 0 2-OH (42 %) and iso-C15 : 0 (26 %), the major respiratory quinone was menaquinone-7 and the genomic DNA G+C content was 42 mol%. 16S rRNA gene sequence analysis and phenetic characterization indicated that this organism belongs to the phylum Bacteroidetes and revealed its affiliation to the family Sphingobacteriaceae. Of recognized taxa, strain DC-186T was most closely related to Sphingobacterium daejeonense (90 % sequence similarity) based on 16S rRNA gene sequence analysis. The low 16S rRNA gene sequence similarity with other recognized taxa and the identification of distinctive phenetic features for this isolate support the definition of a new genus within the family Sphingobacteriaceae. The name Pseudosphingobacterium domesticum gen. nov., sp. nov. is proposed, with strain DC-186T (=CCUG 54353T=LMG 23837T) as the type strain.

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