A crypticBacillus isolate exhibited narrow 16S rRNA gene sequence divergence withBacillus thuringiensis and showed low maintenance requirements in hyper-osmotic complex substrate cultivations

2005 ◽  
Vol 91 (7) ◽  
pp. 838-847 ◽  
Author(s):  
Ramaiah Sachidanandham ◽  
Yousif Al-Shayji ◽  
Nader Al-Awadhi ◽  
Karina Yew-Hoong Gin
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Maintenance Requirements

Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family ‘Oxalobacteraceae’ isolated from China

2005 ◽  
Vol 55 (3) ◽  
pp. 1149-1153 ◽  
Author(s):  
Ping Xu ◽  
Wen-Jun Li ◽  
Shu-Kun Tang ◽  
Yu-Qin Zhang ◽  
Guo-Zhong Chen ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Growth Temperature ◽  
Gene Sequence ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Optimum Growth Temperature ◽  
The Family

A taxonomic study was performed on strain YIM 31775T, which was isolated from a soil sample collected from Yunnan Province, China. The isolate was chemo-organotrophic, aerobic and Gram-negative. Cells were short rods and motile, with one or more polar flagella. Growth temperature and pH ranged from 4 to 55 °C and 6·5 to 12·0, respectively; the optimum growth temperature and pH were 28–37 °C and 7·0–9·0, respectively. Q-8 was the predominant respiratory lipoquinone. The major fatty acids were C16 : 1 ω7c (42·4 %) and C16 : 0 (28·1 %). The DNA G+C content was 62·4±0·3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 31775T should be placed within the family ‘Oxalobacteraceae’, in which it formed a distinct lineage. Based on the high 16S rRNA gene sequence divergence and phenotypic characteristics, it is proposed that strain YIM 31775T should be classified as representing a novel member of the family ‘Oxalobacteraceae’, for which the name Naxibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain is YIM 31775T (=CCTCC AA 204003T=KCTC 12194T).

scholarly journals Flindersiella endophytica gen. nov., sp. nov., an endophytic actinobacterium isolated from the root of Grey Box, an endemic eucalyptus tree

2011 ◽  
Vol 61 (9) ◽  
pp. 2135-2140 ◽  
Author(s):  
Onuma Kaewkla ◽  
Christopher M. M. Franco
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Divergence ◽  
Gene Signature ◽  
Diaminopimelic Acid ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Endophytic Actinobacterium

A novel endophytic actinobacterium, designated strain EUM 378T, was isolated from the surface-sterilized root tissue of Eucalyptus microcarpa, a eucalyptus tree known as Grey Box. Phylogenetic evaluation based on 16S rRNA gene sequence analysis, including alignment with taxon-specific 16S rRNA gene signature nucleotides, placed this isolate as a member of the family Nocardioidaceae. Strain EUM 378T showed >5.5 % 16S rRNA gene sequence divergence from other members of this family and was related most closely to Actinopolymorpha alba YIM 48868T (94.2 %) and Actinopolymorpha singaporensis IM 7744T (94.4 %). This Gram-positive, aerobic actinobacterium has well-developed substrate mycelia that fragment into small rods. Chemotaxonomic data revealed that the cell wall contains ll-diaminopimelic acid, ribose, glucose and rhamnose. MK-10(H6) is the predominant menaquinone. Chemotaxonomic and phylogenetic evidence confirmed that strain EUM 378T represents a novel species of a new genus, for which the name Flindersiella endophytica gen. nov., sp. nov. is proposed. The type strain is EUM 378T ( = DSM 45355T = ACM 5289T).

scholarly journals Streptococcus porci sp. nov., isolated from swine sources

2010 ◽  
Vol 60 (1) ◽  
pp. 104-108 ◽  
Author(s):  
A. I. Vela ◽  
M. Perez ◽  
L. Zamora ◽  
L. Palacios ◽  
L. Domínguez ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Taxonomic Analysis ◽  
Gene Sequence Analysis

Two unidentified Gram-positive, catalase-negative, coccus-shaped organisms were recovered from pigs and subjected to a polyphasic taxonomic analysis. Based on cellular morphology and biochemical criteria, the isolates were tentatively assigned to the genus Streptococcus, although the organisms did not appear to correspond to any recognized species. Comparative 16S rRNA gene sequence studies confirmed this identification and showed that the nearest phylogenetic relatives of the unknown cocci were Streptococcus plurextorum 1956-02T and Streptococcus suis NCTC 10234T (97.9 and 96.0 % 16S rRNA gene sequence similarity, respectively). The new isolates were related most closely to S. suis CIP 103217T based on rpoB gene sequence analysis (<8 % sequence divergence). DNA–DNA pairing studies showed that one of the unidentified strains (2923-03T) displayed DNA relatedness values of 26.6 and 27.2 % with S. plurextorum CECT 7308T and S. suis NCTC 10234T, respectively. On the basis of phenotypic and phylogenetic evidence, it is proposed that the unknown isolates from pigs be classified in the genus Streptococcus as members of Streptococcus porci sp. nov., with the type strain 2923-03T (=CECT 7374T =CCUG 55896T).

scholarly journals Sinococcus qinghaiensis gen. nov., sp. nov., a novel member of the order Bacillales from a saline soil in China

2006 ◽  
Vol 56 (6) ◽  
pp. 1189-1192 ◽  
Author(s):  
Wen-Jun Li ◽  
Yu-Qin Zhang ◽  
Peter Schumann ◽  
Xin-Peng Tian ◽  
Yue-Qin Zhang ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
North West ◽  
Novel Genus And Species

A Gram-positive, non-spore-forming isolate, designated YIM 70212T, was isolated from a hypersaline soil sample collected from Qinghai, north-west China. Cells of the isolate were orange-pigmented, motile cocci with multiple flagella. A polyphasic taxonomic investigation was carried out on the isolate. The organism grew at 10–45 °C and pH 7.5–11.0, with optimum growth at 28 °C and pH 8.0–9.5. Strain YIM 70212T grew optimally in the presence of 10 % NaCl, KCl or MgCl2.6H2O and growth was observed in 1–25 % NaCl, KCl or MgCl2.6H2O. The peptidoglycan type was A1γ. Ribose and minor amounts of galactose were detected as the whole-cell sugars. MK-5 was the only menaquinone. The major cellular fatty acids were ai-C15 : 0 (52.4 %) and ai-C17 : 0 (26.5 %). The DNA G+C content was 47.0 mol%. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain YIM 70212T formed a distinct lineage within the order Bacillales and was most closely related to members of the genus Marinococcus, showing 16S rRNA gene sequence similarity levels of 91.0–91.4 %. Based on the high 16S rRNA gene sequence divergence and differences in phenotypic characteristics, it is proposed that the unknown strain be classified in a novel genus and species with the name Sinococcus qinghaiensis gen. nov., sp. nov.; the type strain of Sinococcus qinghaiensis is YIM 70212T (=KCTC 3943T=DSM 17008T).

scholarly journals Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., isolated from human faeces

2005 ◽  
Vol 55 (5) ◽  
pp. 2143-2147 ◽  
Author(s):  
Maki Kitahara ◽  
Mitsuo Sakamoto ◽  
Masako Ike ◽  
Shinji Sakata ◽  
Yoshimi Benno
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Divergence ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Human Faeces ◽  
Type Strains ◽  
Sequence Similarities

Nine strains of Gram-negative, anaerobic rod were isolated from human faeces. Based on phylogenetic analysis and specific phenotypic characteristics, these strains were included within the Bacteroides cluster and were divided into two clusters. Strains from the two clusters showed 16S rRNA gene sequence similarities of 90·4 and 92·7 % to the nearest recognized species, Bacteroides vulgatus. The strains also formed two clusters exhibiting a 16S rRNA gene sequence divergence of approximately 6 %. DNA–DNA hybridization studies confirmed that the two novel strain clusters were distinct from each other. Based on the phenotypic and phylogenetic findings, two novel species, Bacteroides plebeius sp. nov. and Bacteroides coprocola sp. nov., are proposed, each representing one of the two strain clusters. The DNA G+C content of the type strains were 43·9 mol% for B. plebeius (M12T=JCM 12973T=DSM 17135T) and 42·4 mol% for B. coprocola (M16T=JCM 12979T=DSM 17136T).

scholarly journals Streptomonospora litoralis sp. nov., a halophilic thiopeptides producer isolated from sand collected at Cuxhaven beach

2021 ◽  
Author(s):  
Shadi Khodamoradi ◽  
Richard L. Hahnke ◽  
Yvonne Mast ◽  
Peter Schumann ◽  
Peter Kämpfer ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Bioinformatic Analysis ◽  
Biosynthetic Gene Cluster ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Polar Lipid Profile

AbstractStrain M2T was isolated from the beach of Cuxhaven, Wadden Sea, Germany, in course of a program to attain new producers of bioactive natural products. Strain M2T produces litoralimycin and sulfomycin-type thiopeptides. Bioinformatic analysis revealed a potential biosynthetic gene cluster encoding for the M2T thiopeptides. The strain is Gram-stain-positive, rod shaped, non-motile, spore forming, showing a yellow colony color and forms extensively branched substrate mycelium and aerial hyphae. Inferred from the 16S rRNA gene phylogeny strain M2T affiliates with the genus Streptomonospora. It shows 96.6% 16S rRNA gene sequence similarity to the type species Streptomonospora salina DSM 44593 T and forms a distinct branch with Streptomonospora sediminis DSM 45723 T with 97.0% 16S rRNA gene sequence similarity. Genome-based phylogenetic analysis revealed that M2T is closely related to Streptomonospora alba YIM 90003 T with a digital DNA-DNA hybridisation (dDDH) value of 26.6%. The predominant menaquinones of M2T are MK-10(H6), MK-10(H8), and MK-11(H6) (> 10%). Major cellular fatty acids are iso-C16:0, anteiso C17:0 and C18:0 10-methyl. The polar lipid profile consisted of diphosphatidylglycerol phosphatidyl glycerol, phosphatidylinositol, phosphatidylcholine, phosphatidylethanolamine, three glycolipids, two unknown phospholipids, and two unknown lipids. The genome size of type strain M2T is 5,878,427 bp with 72.1 mol % G + C content. Based on the results obtained from phylogenetic and chemotaxonomic studies, strain M2T (= DSM 106425 T = NCCB 100650 T) is considered to represent a novel species within the genus Streptomonospora for which the name Streptomonospora litoralis sp. nov. is proposed.

scholarly journals Faecalicoccus acidiformans gen. nov., sp. nov., isolated from the chicken caecum, and reclassification of Streptococcus pleomorphus (Barnes et al. 1977), Eubacterium biforme (Eggerth 1935) and Eubacterium cylindroides (Cato et al. 1974) as Faecalicoccus pleomorphus comb. nov., Holdemanella biformis gen. nov., comb. nov. and Faecalitalea cylindroides gen. nov., comb. nov., respectively, within the family Erysipelotrichaceae

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3877-3884 ◽  
Author(s):  
Celine De Maesschalck ◽  
Filip Van Immerseel ◽  
Venessa Eeckhaut ◽  
Siegrid De Baere ◽  
Margo Cnockaert ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Content Type ◽  
Link Type

Strains LMG 27428T and LMG 27427 were isolated from the caecal content of a chicken and produced butyric, lactic and formic acids as major metabolic end products. The genomic DNA G+C contents of strains LMG 27428T and LMG 27427 were 40.4 and 38.8 mol%. On the basis of 16S rRNA gene sequence similarity, both strains were most closely related to the generically misclassified Streptococcus pleomorphus ATCC 29734T. Strain LMG 27428T could be distinguished from S. pleomorphus ATCC 29734T based on production of more lactic acid and less formic acid in M2GSC medium, a higher DNA G+C content and the absence of activities of acid phosphatase and leucine, arginine, leucyl glycine, pyroglutamic acid, glycine and histidine arylamidases, while strain LMG 27428 was biochemically indistinguishable from S. pleomorphus ATCC 29734T. The novel genus Faecalicoccus gen. nov. within the family Erysipelotrichaceae is proposed to accommodate strains LMG 27428T and LMG 27427. Strain LMG 27428T ( = DSM 26963T) is the type strain of Faecalicoccus acidiformans sp. nov., and strain LMG 27427 ( = DSM 26962) is a strain of Faecalicoccus pleomorphus comb. nov. (type strain LMG 17756T = ATCC 29734T = DSM 20574T). Furthermore, the nearest phylogenetic neighbours of the genus Faecalicoccus are the generically misclassified Eubacterium cylindroides DSM 3983T (94.4 % 16S rRNA gene sequence similarity to strain LMG 27428T) and Eubacterium biforme DSM 3989T (92.7 % 16S rRNA gene sequence similarity to strain LMG 27428T). We present genotypic and phenotypic data that allow the differentiation of each of these taxa and propose to reclassify these generically misnamed species of the genus Eubacterium formally as Faecalitalea cylindroides gen. nov., comb. nov. and Holdemanella biformis gen. nov., comb. nov., respectively. The type strain of Faecalitalea cylindroides is DSM 3983T = ATCC 27803T = JCM 10261T and that of Holdemanella biformis is DSM 3989T = ATCC 27806T = CCUG 28091T.

scholarly journals 16S rRNA Gene Sequence Analysis ofPhotobacterium damselae and Nested PCR Method for Rapid Detection of the Causative Agent of Fish Pasteurellosis

1999 ◽  
Vol 65 (7) ◽  
pp. 2942-2946 ◽  
Author(s):  
Carlos R. Osorio ◽  
Matthew D. Collins ◽  
Alicia E. Toranzo ◽  
Juan L. Barja ◽  
Jesús L. Romalde
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Causative Agent ◽  
Nested Pcr ◽  
Gene Sequence ◽  
16S Rrna Gene Sequence ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Photobacterium Damselae

ABSTRACT The causative agent of fish pasteurellosis, the organism formerly known as Pasteurella piscicida, has been reclassified asPhotobacterium damselae subsp. piscicida on the basis of 16S rRNA gene sequence comparisons and chromosomal DNA-DNA hybridization data; thus, this organism belongs to the same species asPhotobacterium damselae subsp. damselae(formerly Vibrio damselae). Since reassignment of P. damselae subsp. piscicida was based on only two strains, one objective of the present work was to confirm the taxonomic position of this fish pathogen by sequencing the 16S rRNA genes of 26 strains having different geographic and host origins. In addition, a nested PCR protocol for detection of P. damselae based on 16S rRNA was developed. This PCR protocol was validated by testing 35 target and 24 nontarget pure cultures, and the detection limits obtained ranged from 1 pg to 10 fg of DNA (200 to 20 cells). A similar level of sensitivity was observed when the PCR protocol was applied to fish tissues spiked with bacteria. The PCR approach described in this paper allows detection of the pathogen in mixed plate cultures obtained from asymptomatic fish suspected to be carriers of P. damselae subsp. piscicida, in which growth of this bacterium cannot be visualized. Our results indicate that the selective primers which we designed represent a powerful tool for sensitive and specific detection of fish pasteurellosis.

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