scholarly journals 16S rRNA Sequence-based Rapid and Sensitive Detection of Aquatic Bacteria by On-chip Hybridization Following Multiplex PCR

2008 ◽  
Vol 54 (1) ◽  
pp. 123-128 ◽  
Author(s):  
Tomoaki Ichijo ◽  
Nobuyasu Yamaguchi ◽  
Katsuji Tani ◽  
Masao Nasu
Keyword(s):  
16S Rrna ◽  
Multiplex Pcr ◽  
Sensitive Detection ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Aquatic Bacteria ◽  
On Chip

A new sand frog from Namaqualand, South Africa (Pyxicephalidae: Tomopterna)

Zootaxa ◽  
2019 ◽  
Vol 4609 (2) ◽  
pp. 225
Author(s):  
LYLE WILSON ◽  
ALAN CHANNING
Keyword(s):  
South Africa ◽  
New Species ◽  
16S Rrna ◽  
Advertisement Call ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Adult Morphology ◽  
Haplotype Networks ◽  
Tyr Gene

Tomopterna branchi sp. nov. is described from Namaqualand, South Africa. It differs from all other Tomopterna species by advertisement call, 16S rRNA sequence and consistent differences in adult morphology. The tadpole is similar to that of Tomopterna cryptotis. Haplotype networks of 16S and the nuclear tyr gene show that it is distinct from T. delalandii, with which it has been confused. A phylogeny of the genus, excluding the little-known T. monticola, shows that the new species is basal to a clade that includes T. delalandii and six other species. We extend the known range of T. damarensis to southern Namibia, and correct the identification of some GenBank material. 

scholarly journals Mycobacterium neoaurumBacteremia in a Hemodialysis Patient

2003 ◽  
Vol 14 (1) ◽  
pp. 45-48 ◽  
Author(s):  
Marissa L Becker ◽  
Amar A Suchak ◽  
Joyce N Wolfe ◽  
Ryan Zarychanski ◽  
Amin Kabani ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Hemodialysis Patient ◽  
Immunocompromised Host ◽  
Blood Cultures ◽  
Clinical Suspicion ◽  
Diabetic Woman ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
16S Rrna Sequence Analysis

Bacteremia due toMycobacterium neoaurum, a rapidly growing mycobacterium, is described in a diabetic woman on hemodialysis. This is the first reported case of M neoaurum bacteremia in Canada. The organism initially grew on standard BacT/Alert SA aerobic blood cultures, and was subsequently positively identified using 16S rRNA sequence analysis. The present case serves to reinforce the need for a high index of clinical suspicion of infections caused by unusual microorganisms in the context of an immunocompromised host.

scholarly journals Thermocrinis ruber gen. nov., sp. nov., a Pink-Filament-Forming Hyperthermophilic Bacterium Isolated from Yellowstone National Park

1998 ◽  
Vol 64 (10) ◽  
pp. 3576-3583 ◽  
Author(s):  
Robert Huber ◽  
Wolfgang Eder ◽  
Stefan Heldwein ◽  
Gerhard Wanner ◽  
Harald Huber ◽  
...  
Keyword(s):  
16S Rrna ◽  
Yellowstone National Park ◽  
National Park ◽  
Carbon Sources ◽  
Culture Conditions ◽  
The Novel ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Hyperthermophilic Bacterium ◽  
Outflow Channel

ABSTRACT A novel hyperthermophilic bacterium was isolated from pink filamentous streamers (pink filaments) occurring in the upper outflow channel (temperature, 82 to 88°C) of Octopus Spring in Yellowstone National Park, Wyo. The gram-negative cells grew at low salinity at temperatures up to 89°C in the neutral to alkaline pH range. Depending on the culture conditions, the organisms occurred as single motile rods, as aggregates, or as long filaments that formed streamer-like cell masses. The novel isolate grew chemolithoautotrophically with hydrogen, thiosulfate, and elemental sulfur as electron donors and oxygen as the electron acceptor. Alternatively, under aerobic conditions, formate and formamide served as sole energy and carbon sources. The novel isolate had a 16S rRNA sequence closely related to the 16S rRNA sequence obtained from uncultivated pink filaments. It represents a new genus in the orderAquificales, the type species of which we nameThermocrinis ruber (type strain, OC 1/4 [= DSM 12173]).

scholarly journals Phylogeny of the Defined Murine Microbiota: Altered Schaedler Flora

1999 ◽  
Vol 65 (8) ◽  
pp. 3287-3292 ◽  
Author(s):  
Floyd E. Dewhirst ◽  
Chih-Ching Chien ◽  
Bruce J. Paster ◽  
Rebecca L. Ericson ◽  
Roger P. Orcutt ◽  
...  
Keyword(s):  
16S Rrna ◽  
Single Species ◽  
Rapid Identification ◽  
Sequence Information ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
16S Rrna Analysis ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The “altered Schaedler flora” (ASF) was developed for colonizing germfree rodents with a standardized microbiota. The purpose of this study was to identify each of the eight ASF strains by 16S rRNA sequence analysis. Three strains were previously identified asLactobacillus acidophilus (strain ASF 360),Lactobacillus salivarius (strain ASF 361), andBacteroides distasonis (strain ASF 519) based on phenotypic criteria. 16S rRNA analysis indicated that each of the strains differed from its presumptive identity. The 16S rRNA sequence of strain ASF 361 is essentially identical to the 16S rRNA sequences of the type strains of Lactobacillus murinis and Lactobacillus animalis (both isolated from mice), and all of these strains probably belong to a single species. Strain ASF 360 is a novel lactobacillus that clusters with L. acidophilus andLactobacillus lactis. Strain ASF 519 falls into an unnamed genus containing [Bacteroides] distasonis, [Bacteroides] merdae, [Bacteroides] forsythus, and CDC group DF-3. This unnamed genus is in theCytophaga-Flavobacterium-Bacteroides phylum and is most closely related to the genus Porphyromonas. The spiral-shaped strain, strain ASF 457, is in the Flexistipesphylum and exhibits sequence identity with rodent isolates of Robertson. The remaining four ASF strains, which are extremely oxygen-sensitive fusiform bacteria, group phylogenetically with the low-G+C-content gram-positive bacteria (Firmicutes,Bacillus-Clostridium group). ASF 356, ASF 492, and ASF 502 fall into Clostridium cluster XIV of Collins et al. Morphologically, ASF 492 resembles members of this cluster,Roseburia cecicola, and Eubacterium plexicaudatum. The 16S rRNA sequence of ASF 492 is identical to that of E. plexicaudatum. Since the type strain and other viable original isolates of E. plexicaudatum have been lost, strain ASF 492 is a candidate for a neotype strain. Strain ASF 500 branches deeply in the low-G+C-content gram-positive phylogenetic tree but is not closely related to any organisms whose 16S rRNA sequences are currently in the GenBank database. The 16S rRNA sequence information determined in the present study should allow rapid identification of ASF strains and should permit detailed analysis of the interactions of ASF organisms during development of intestinal disease in mice that are coinfected with a variety of pathogenic microorganisms.

Aureivirga marina gen. nov., sp. nov., a marine bacterium isolated from the Mediterranean sponge Axinella verrucosa

2013 ◽  
Vol 63 (Pt_3) ◽  
pp. 1089-1095 ◽  
Author(s):  
Markus Haber ◽  
Sigal Shefer ◽  
Assunta Giordano ◽  
Pierangelo Orlando ◽  
Agata Gambacorta ◽  
...  
Keyword(s):  
16S Rrna ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Sea Salts ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Content Type ◽  
Link Type ◽  
The Family ◽  
The Mediterranean

Two bacterial strains, VI.14 and VIII.04T, were isolated from the Mediterranean sponge Axinella verrucosa collected off the Israeli coast near Sdot Yam. The non-motile, aerobic, Gram-negative isolates were oxidase-negative and catalase-positive, and formed golden-brown colonies on marine agar 2216. The pigment was neither diffusible nor flexirubin-like. Strain VIII.04T grew at 15–37 °C, at pH 6.0–9.0, in the presence of 20–50 g NaCl l−1 and 20–80 g sea salts l−1, The spectrum was narrower for strain VI.14, with growth at pH 7.0–8.0. and in the presence of 30–50 g NaCl l−1 and 30–70 g sea salts l−1. The predominant fatty acid (>50 %) in both strains was iso-C15 : 0, and the major respiratory quinone was MK-6. The DNA G+C content was 30.7 and 31.1 mol% for VIII.04T and VI.14, respectively. Results from 16S rRNA sequence similarity and phylogenetic analyses indicated that both strains are closely related to members of the family Flavobacteriaceae within the phylum Bacteroidetes , with as much as 91.7 % 16S rRNA sequence similarity. On the basis of data from the polyphasic analysis, we suggest that the strains represent a novel species in a new genus within the family Flavobacteriaceae , for which the name Aureivirga marina gen. nov., sp. nov. is proposed. Strain VIII.04T ( = ATCC BAA-2394T = LMG 26721T) is the type strain of Aureivirga marina.

The use of functional analysis of the ribosome as a tool to determine archaebacterial phylogeny

1989 ◽  
Vol 35 (1) ◽  
pp. 141-147 ◽  
Author(s):  
R. Amils ◽  
L. Ramírez ◽  
J. L. Sanz ◽  
I. Marín ◽  
A. G. Pisabarro ◽  
...  
Keyword(s):  
Functional Analysis ◽  
16S Rrna ◽  
Phylogenetic Tree ◽  
Functional Information ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Sequence Comparisons ◽  
Free System ◽  
Translation Apparatus ◽  
Evolutionary Clock

Forty different antibiotics with diverse kingdom and functional specificities were used to measure the functional characteristics of the archaebacterial translation apparatus. The resulting inhibitory curves, which are characteristic of the cell-free system analyzed, were transformed into quantitative values that were used to cluster the different archaebacteria analyzed. This cluster resembles the phylogenetic tree generated by 16S rRNA sequence comparisons. These results strongly suggest that functional analysis of an appropriate evolutionary clock, such as the ribosome, is of intrinsic phylogenetic value. More importantly, they indicate that the study of the nexus between genotypic and phenotypic (functional) information may shed considerable light on the evolution of the protein synthetic machinery.Key words: antibiotics, ribosomes, archaebacteria, phylogeny, functional analysis.

Mycobacterium marinum infections in humans and tracing of its possible environmental sources

2012 ◽  
Vol 58 (1) ◽  
pp. 39-44 ◽  
Author(s):  
Michal Slany ◽  
Petr Jezek ◽  
Vera Fiserova ◽  
Monika Bodnarova ◽  
Jiri Stork ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
16S Rrna ◽  
Correct Diagnosis ◽  
Low Frequency ◽  
Mycobacterium Marinum ◽  
Mycobacterium Fortuitum ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Mycobacterium Chelonae ◽  
16S Rrna Sequence Analysis

The low frequency of nontuberculous mycobacterial infections, nonspecific symptoms for individual mycobacteria, and the lack of specific identification methods could alter correct diagnosis. This study presents a combined microbiology and molecular-based approach for Mycobacterium marinum detection in four aquarists with cutaneous mycobacterial infection. Simultaneously, ecology screening for M. marinum presence in the aquarists’ fish tanks was performed. A total of 38 mycobacterial isolates originated from four human patients (n = 20), aquarium animals (n = 8), and an aquarium environment (n = 10). Isolate identification was carried out using 16S rRNA sequence analysis. A microbiology-based approach, followed by 16S rRNA sequence analysis, was successfully used for detection of M. marinum in all four patients. Animal and environmental samples were simultaneously examined, and a total of seven mycobacterial species were isolated: Mycobacterium chelonae , Mycobacterium fortuitum , Mycobacterium gordonae , Mycobacterium kansasii , Mycobacterium mantenii , Mycobacterium marinum , and Mycobacterium peregrinum . The presence of M. marinum was proven in the aquarium environments of two patients. Although M. marinum is described as being present in water, it was detected only in fish.

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