Identification of Sphingomonas paucimobolis from a case of soft tissue injury, based on the phenotypic characteristics and 16S rRNA gene sequence

2015 ◽  
Vol 26 (2) ◽  
pp. 70-73
Author(s):  
Yu Song ◽  
Shu-qing Ma ◽  
Yan-ni Bi ◽  
Ming-yi Wang
Keyword(s):  
Soft Tissue ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Tissue Injury ◽  
Soft Tissue Injury ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics

Bacteroides chinchillae sp. nov. and Bacteroides rodentium sp. nov., isolated from chinchilla (Chinchilla lanigera) faeces

2011 ◽  
Vol 61 (4) ◽  
pp. 877-881 ◽  
Author(s):  
Maki Kitahara ◽  
Sayaka Tsuchida ◽  
Koh Kawasumi ◽  
Hiromi Amao ◽  
Mitsuo Sakamoto ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Strain ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Distinct Line

Gram-negative anaerobic rods were isolated from chinchilla (Chinchilla lanigera) faeces and three strains, ST170T, ST180 and ST28T, were investigated taxonomically. On the basis of phylogenetic analyses and specific phenotypic characteristics, the three strains belonged to the genus Bacteroides. Phylogenetic analysis of their 16S rRNA gene sequences revealed that strains ST170T and ST180 formed a single cluster and a distinct line of descent. Strain ST170T exhibited 99.7 % 16S rRNA gene sequence similarity with strain ST180 and 95.1, 94.6 and 94.4 % 16S rRNA gene sequence similarity with Bacteroides massiliensis JCM 13223T, Bacteroides dorei JCM 13471T and Bacteroides vulgatus JCM 5826T, respectively. Strain ST28T also formed a distinct line of descent and exhibited the highest 16S rRNA gene sequence similarity with Bacteroides uniformis JCM 5828T (98.1 %). Low DNA–DNA relatedness (1 %) between strain ST28T and B. uniformis JCM 5828T clearly indicated that they belonged to different species. Analysis of hsp60 sequences also supported these relationships. The DNA G+C contents of strains ST170T and ST28T were 45.2 and 41.0 mol%, respectively. On the basis of phenotypic characteristics and phylogenetic data, two novel species, Bacteroides chinchillae sp. nov. (type strain ST170T  = JCM 16497T  = CCUG 59335T) and Bacteroides rodentium sp. nov. (type strain ST28T  = JCM 16496T  = CCUG 59334T), are proposed.

scholarly journals Novel methylotrophic isolates from lake sediment, description of Methylotenera versatilis sp. nov. and emended description of the genus Methylotenera

2012 ◽  
Vol 62 (1) ◽  
pp. 106-111 ◽  
Author(s):  
Marina G. Kalyuzhnaya ◽  
David A. C. Beck ◽  
Alexey Vorobev ◽  
Nicole Smalley ◽  
Dennis D. Kunkel ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
Limited Range ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Emended Description

Phylogenetic positions, and genotypic and phenotypic characteristics of three novel methylotrophic isolates, strains 301T, 30S and SIP3-4, from sediment of Lake Washington, Seattle, USA, are described. The strains were restricted facultative methylotrophs capable of growth on single carbon compounds (methylamine and methanol) in addition to a limited range of multicarbon compounds. All strains used the N-methylglutamate pathway for methylamine oxidation. Strain SIP3-4 possessed the canonical (MxaFI) methanol dehydrogenase, but strains 301T and 30S did not. All three strains used the ribulose monophosphate pathway for C1 assimilation. The major fatty acids in the three strains were C16 : 0 and C16 : 1ω7c. The DNA G+C contents of strains 301T and SIP3-4 were 42.6 and 54.6 mol%, respectively. Based on 16S rRNA gene sequence phylogeny and the relevant phenotypic characteristics, strain SIP3-4 was assigned to the previously defined species Methylovorus glucosotrophus. Strains 301T and 30S were closely related to each other (100 % 16S rRNA gene sequence similarity) and shared 96.6 % 16S rRNA gene sequence similarity with a previously described isolate, Methylotenera mobilis JLW8T. Based on significant genomic and phenotypic divergence with the latter, strains 301T and 30S represent a novel species within the genus Methylotenera, for which the name Methylotenera versatilis sp. nov. is proposed; the type strain is 301T ( = VKM B-2679T = JCM 17579T). An emended description of the genus Methylotenera is provided.

Yaniella fodinae sp. nov., isolated from a coal mine

2011 ◽  
Vol 61 (3) ◽  
pp. 535-539 ◽  
Author(s):  
Soniya Dhanjal ◽  
Arunachalam Ruckmani ◽  
Swaranjit Singh Cameotra ◽  
Rüdiger Pukall ◽  
Hans-Peter Klenk ◽  
...  
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Coal Mine ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Phenotypic Characteristics ◽  
Gene Sequence Analysis

An orange bacterial strain, designated G5T, was isolated during the study of the bacterial diversity of a coal mine. The cell wall of strain G5T contained peptidoglycan type A4α (l-Lys–Gly–l-Glu) and the sugars xylose and mannose. The major menaquinones were MK-8 (45.0 %) and MK-9 (34.0 %) and minor amounts of MK-7 and MK-8(H2) were also found. The major fatty acids were anteiso-C15 : 0 (44.9 %) and iso-C15 : 0 (44.2 %). The main cellular polar lipids were diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. 16S rRNA gene sequence analysis showed that strain G5T was closely related to Yaniella halotolerans YIM 70085T and Yaniella flava YIM 70178T (both 96.7 % 16S rRNA gene sequence similarity). The genomic DNA G+C content of strain G5T was 61.6 mol%. These data and other phenotypic characteristics clearly indicated that strain G5T represents a novel species of the genus Yaniella, for which the name Yaniella fodinae sp. nov. is proposed. The type strain is G5T (=MTCC 9846T=DSM 22966T).

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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