scholarly journals A phylogenetic comparison of the 16S rRNA sequence of the fish pathogen,Renibacterium salmoninarum, to Gram-positive bacteria

1991 ◽  
Vol 77 (2-3) ◽  
pp. 151-156 ◽  
Author(s):  
S.K. Gutenberger ◽  
S.J. Giovannoni ◽  
K.G. Field ◽  
J.L. Fryer ◽  
J.S. Rohovec
Keyword(s):  
16S Rrna ◽  
Fish Pathogen ◽  
Renibacterium Salmoninarum ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Gram Positive Bacteria ◽  
Phylogenetic Comparison

The “Nostocoida limicola” story: resolving the phylogeny of this morphotype responsible for bulking in activated sludge

2002 ◽  
Vol 46 (1-2) ◽  
pp. 105-110 ◽  
Author(s):  
R.J. Seviour ◽  
J.-R. Liu ◽  
E.M. Seviour ◽  
C.A. McKenzie ◽  
L.L. Blackall ◽  
...  
Keyword(s):  
16S Rrna ◽  
Activated Sludge ◽  
Pure Culture ◽  
Sequence Analyses ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Culture Studies ◽  
Gram Positive Bacteria ◽  
Morphological Variants

On the basis of 16S rRNA sequence analyses of several isolates of “Nostocoida limicola” from activated sludge plants in Australia and other countries, it is clear that “N. limicola” I, II and III are not three morphological variants of a single bacterium but at least three phylogenetically different bacteria. Data show that “N. limicola” I are members of at least two genera in the low mol% G+C Gram-positive bacteria, while some isolates of “N.limicola” II belong to the high mol% G+C Gram positive bacteria, and “N.limicola” III is a member of the Planctomycetales. Design and application of 16S rRNA targeted probes for each to biomass samples suggests that their phylogeny is more diverse than pure culture studies would suggest.

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.

Cleaning and Handling Implements as Potential Reservoirs for Bacterial Contamination of Some Ready-to-Eat Foods in Retail Delicatessen Environments

2007 ◽  
Vol 70 (12) ◽  
pp. 2878-2883 ◽  
Author(s):  
C. A. CHRISTISON ◽  
D. LINDSAY ◽  
A. von HOLY
Keyword(s):  
South Africa ◽  
Sequence Analysis ◽  
16S Rrna ◽  
Rrna Sequence ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Bacterial Populations ◽  
16S Rrna Sequence Analysis ◽  
And Staphylococcus Aureus ◽  
Disposable Plastic

This study assessed the association of bacteria with cleaning tools, such as floor mops (n = 25) and cleaning cloths (n = 39), and handling devices, such as disposable plastic gloves (n = 20), used during filled baguette and assorted salad preparation in four selected retail delicatessens in Johannesburg, South Africa. Samples of each cleaning or handling tool were prepared for aerobic (APC), coliform (CC), Escherichia coli (EC), Bacillus cereus (BCC), and Staphylococcus aureus (SAC) counts, as well as tested for the incidence of Listeria monocytogenes (LM) and Salmonella (SALM) by standard plating methods. Bacterial populations attached to the cleaning and handling tools were observed by scanning electron microscopy (SEM). Ten selected gram-positive isolates were further analyzed by 16S rRNA sequence analysis and compared with isolates from filled baguettes and assorted salads. The floor mops consistently yielded the highest APCs, CCs, and ECs (5.7, 4.1, and 3.0 log CFU/g, respectively), while gloves had the lowest corresponding counts (3.6, 2.0, and 1.0 log CFU/g, respectively). Low BCCs and SACs were recorded in this study (ca. 1.2 log CFU/g), while SALM and LM were each detected in five cleaning tool samples. SEM showed rods and cocci attached to handling and cleaning tools. Furthermore, results of 16S rRNA sequence analysis indicated that several gram-positive isolates were identified as S. aureus, Staphylococcus pasteuri, Staphylococcus sciuri, and Enterococcus faecalis. Genetically similar strains (100% similarity) were isolated from cleaning and handling tools and associated ready-to-eat (RTE) foods. Cleaning and handling tools may act as reservoirs of contamination for RTE foods during preparation in retail delicatessens in South Africa. The transfer of potential pathogens, such as S. aureus, to foods from cleaning and handling tools may hold food safety implications.

scholarly journals Bacterial Communities Associated with Flowering Plants of the Ni Hyperaccumulator Thlaspi goesingense

2004 ◽  
Vol 70 (5) ◽  
pp. 2667-2677 ◽  
Author(s):  
Rughia Idris ◽  
Radoslava Trifonova ◽  
Markus Puschenreiter ◽  
Walter W. Wenzel ◽  
Angela Sessitsch
Keyword(s):  
16S Rrna ◽  
Acc Deaminase ◽  
Rhizosphere Bacteria ◽  
Rrna Gene ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Plant Microbe Interaction ◽  
Gram Positive Bacteria ◽  
High Concentrations ◽  
Methylobacterium Mesophilicum

ABSTRACT Thlaspi goesingense is able to hyperaccumulate extremely high concentrations of Ni when grown in ultramafic soils. Recently it has been shown that rhizosphere bacteria may increase the heavy metal concentrations in hyperaccumulator plants significantly, whereas the role of endophytes has not been investigated yet. In this study the rhizosphere and shoot-associated (endophytic) bacteria colonizing T. goesingense were characterized in detail by using both cultivation and cultivation-independent techniques. Bacteria were identified by 16S rRNA sequence analysis, and isolates were further characterized regarding characteristics that may be relevant for a beneficial plant-microbe interaction—Ni tolerance, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and siderophore production. In the rhizosphere a high percentage of bacteria belonging to the Holophaga/Acidobacterium division and α-Proteobacteria were found. In addition, high-G+C gram-positive bacteria, Verrucomicrobia, and microbes of the Cytophaga/Flexibacter/Bacteroides division colonized the rhizosphere. The community structure of shoot-associated bacteria was highly different. The majority of clones affiliated with the Proteobacteria, but also bacteria belonging to the Cytophaga/Flexibacter/Bacteroides division, the Holophaga/Acidobacterium division, and the low-G+C gram-positive bacteria, were frequently found. A high number of highly related Sphingomonas 16S rRNA gene sequences were detected, which were also obtained by the cultivation of endophytes. Rhizosphere isolates belonged mainly to the genera Methylobacterium, Rhodococcus, and Okibacterium, whereas the majority of endophytes showed high levels of similarity to Methylobacterium mesophilicum. Additionally, Sphingomonas spp. were abundant. Isolates were resistant to Ni concentrations between 5 and 12 mM; however, endophytes generally tolerated higher Ni levels than rhizosphere bacteria. Almost all bacteria were able to produce siderophores. Various strains, particularly endophytes, were able to grow on ACC as the sole nitrogen source.

scholarly journals Screenning and determination of polyhydroxyalkanoate production by Bacillus sp. strains

2020 ◽  
Vol 3 (3) ◽  
pp. 165-172
Author(s):  
Da Nguyen Thi ◽  
Linh Nguyen Trong ◽  
Trang Nguyen Thu ◽  
Hai Tran Manh ◽  
Huyen La Thi ◽  
...  
Keyword(s):  
16S Rrna ◽  
Bacillus Megaterium ◽  
Basal Medium ◽  
Bacillus Sp ◽  
Reserve Material ◽  
Gram Positive ◽  
16S Rrna Sequence ◽  
Gram Positive Bacteria ◽  
Gene Coding

Polyhydroxyalkanoates (PHAs) are biodegradable polymers produced by microbes as reserve material when they were cultured in a limitation of nutrients and excess C source mediums. PHAs can be synthesized by various bacteria including gram positive and gram-negative bacteria. Among the PHA-producing gram-positive bacteria, Bacillus sp. produce and accumulate various monomer compositions of PHAs. In this study, about 83,3% of strains (05/06 strains) can accumulate PHAs production. Bacillus sp. DV01 accumulated a amount of PHA 23,9% of CWD after 96h when cultured in modified basal medium containing 1% (w/v) glucose. Bacillus sp.  DV01 was identified by sequecing the gene coding for 16S rRNA. BLAST results showed the obtained 16S rRNA sequence of this strain revealed 100% with the Bacillus megaterium and so-called Bacillus megaterium DV01.

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]).

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