Monitoring ofBacillus thermodenitrificansOHT-1 in compost by whole cell hybridization

2002 ◽  
Vol 48 (9) ◽  
pp. 848-852 ◽  
Author(s):  
Masahiro Hatsu ◽  
Junji Ohta ◽  
Kazuhiro Takamizawa
Keyword(s):  
16S Rrna ◽  
Liquid Culture ◽  
Oligonucleotide Probe ◽  
Thermophilic Bacteria ◽  
Fluorescein Isothiocyanate ◽  
Rrna Sequence ◽  
Cell Hybridization ◽  
16S Rrna Sequence ◽  
Whole Cell ◽  
Growth Experiments

Thermophilic aerobic composting is a widely practiced method for the disposal of exhaust materials. We isolated a thermophilic bacteria strain from a compost sample under aerobic conditions at 60°C. On the basis of its 16S rRNA sequence and physiological characteristics, this strain was identified as Bacillus thermodenitrificans OHT-1. An 18-subunit oligonucleotide probe for 16S rRNA, labeled with fluorescein isothiocyanate, was developed for the detection of B. thermodenitrificans. Spores and vegetative cells of B. thermodenitrificans OHT-1 were detected in liquid culture and laboratory compost by whole cell hybridization using this oligonucleotide probe. The results obtained by whole cell hybridization were evaluated in growth experiments of B. thermodenitrificans OHT-1 in laboratory compost and were used to enumerate spores and vegetative cells.Key words: compost, Bacillus thermodenitrificans, 16S rRNA, whole cell hybridization.

scholarly journals Fluorescent Whole-Cell Hybridization with 16S rRNA-Targeted Oligonucleotide Probes To Identify Brucellaspp. by Flow Cytometry

2000 ◽  
Vol 38 (7) ◽  
pp. 2768-2771 ◽  
Author(s):  
Luis Fernández-Lago ◽  
F. Javier Vallejo ◽  
Ignacio Trujillano ◽  
Nieves Vizcaíno
Keyword(s):  
Flow Cytometry ◽  
16S Rrna ◽  
Clinical Isolates ◽  
Hybridization Assay ◽  
Hybridization Technique ◽  
Oligonucleotide Probes ◽  
Cell Hybridization ◽  
16S Rrna Sequence ◽  
Whole Cell ◽  
Detection And Identification

A whole-cell hybridization assay with fluorescent oligonucleotide probes derived from the 16S rRNA sequence of Brucella abortus in combination with flow cytometry has been developed. With the three fluorescent probes selected, a positive signal was observed with all the representative strains of the species and biovars of Brucella and with a total of nine differentBrucella clinical isolates. Using the B9 probe in the hybridization assay, it was possible to discriminate betweenBrucella suis biovars 2, 3, 4, and 5 and almost all the other Brucella spp. On the basis of differences in fluorescence intensities, no discrimination was established betweenBrucella spp. and other phylogenetically related microorganisms. No positive fluorescence signals were detected with any of the bacteria showing serological cross-reactions withBrucella spp. and with a total of 17 clinical isolates not belonging to the genus Brucella. These results suggest that the 16S rRNA whole-cell hybridization technique could be a valuable diagnostic tool for the detection and identification ofBrucella spp.

scholarly journals In Situ Detection of an Uncultured Predominant Bacillus in Dutch Grassland Soils

1998 ◽  
Vol 64 (11) ◽  
pp. 4588-4590 ◽  
Author(s):  
Andreas Felske ◽  
Antoon D. L. Akkermans ◽  
Willem M. De Vos
Keyword(s):  
In Situ Hybridization ◽  
16S Rrna ◽  
Cell Type ◽  
Grassland Soils ◽  
Rrna Sequence ◽  
16S Rrna Sequence ◽  
Whole Cell ◽  
Shaped Cell ◽  
In Situ Detection

ABSTRACT Uncultured predominant Bacillus ribotype DA001 in Dutch Drentse A grassland soils, as revealed by its 16S rRNA sequence, was detected in soil by fluorescent whole-cell in situ hybridization. A prominent rod-shaped cell type was identified in bacterial suspensions prepared from soil by a multiple 16S rRNA probing approach.

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

scholarly journals Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons

2004 ◽  
Vol 186 (9) ◽  
pp. 2629-2635 ◽  
Author(s):  
Silvia G. Acinas ◽  
Luisa A. Marcelino ◽  
Vanja Klepac-Ceraj ◽  
Martin F. Polz
Keyword(s):  
16S Rrna ◽  
Thermophilic Bacteria ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Bacterial Genomes ◽  
16S Rrna Sequence ◽  
Thermoanaerobacter Tengcongensis ◽  
Copy Numbers ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT The level of sequence heterogeneity among rrn operons within genomes determines the accuracy of diversity estimation by 16S rRNA-based methods. Furthermore, the occurrence of widespread horizontal gene transfer (HGT) between distantly related rrn operons casts doubt on reconstructions of phylogenetic relationships. For this study, patterns of distribution of rrn copy numbers, interoperonic divergence, and redundancy of 16S rRNA sequences were evaluated. Bacterial genomes display up to 15 operons and operon numbers up to 7 are commonly found, but ∼40% of the organisms analyzed have either one or two operons. Among the Archaea, a single operon appears to dominate and the highest number of operons is five. About 40% of sequences among 380 operons in 76 bacterial genomes with multiple operons were identical to at least one other 16S rRNA sequence in the same genome, and in 38% of the genomes all 16S rRNAs were invariant. For Archaea, the number of identical operons was only 25%, but only five genomes with 21 operons are currently available. These considerations suggest an upper bound of roughly threefold overestimation of bacterial diversity resulting from cloning and sequencing of 16S rRNA genes from the environment; however, the inclusion of genomes with a single rrn operon may lower this correction factor to ∼2.5. Divergence among operons appears to be small overall for both Bacteria and Archaea, with the vast majority of 16S rRNA sequences showing <1% nucleotide differences. Only five genomes with operons with a higher level of nucleotide divergence were detected, and Thermoanaerobacter tengcongensis exhibited the highest level of divergence (11.6%) noted to date. Overall, four of the five extreme cases of operon differences occurred among thermophilic bacteria, suggesting a much higher incidence of HGT in these bacteria than in other groups.

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.

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