scholarly journals Staphylococcal Species Detected in Free-Living Trouts of East Slovakian Water Sources and their Relation to Antimicrobials

2013 ◽  
Vol 57 (2) ◽  
pp. 167-171 ◽  
Author(s):  
Andrea Lauková ◽  
Anna Kandričáková ◽  
Viola Strompfová ◽  
Jean-Paul Chacornac ◽  
Sabine Léroy ◽  
...  
Keyword(s):  
Superoxide Dismutase ◽  
16S Rrna ◽  
Water Sources ◽  
Oligonucleotide Array ◽  
Coagulase Negative Staphylococci ◽  
Free Living ◽  
Colony Forming Units ◽  
Species Specific ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Abstract The aim of the study was to isolate and identify staphylococci from the intestinal samples of 24 trouts from East Slovakian waters. Moreover, their relation to antimicrobials was tested. The count of staphylococci in the trouts reached in average 4.0 x 101 colony forming units per gram. Twenty-two strains were identified by validated species-specific oligonucleotide array targeting the manganese-dependent superoxide dismutase-sodA gene. The identified strains were allotted to five species (Staphylococcus warneri, S. haemolyticus, S. epidermidis, S. hominis, S. pasteuri) clustered to three groups according to 16S rRNA sequences (S. epidermidis group, S. haemolyticus group, S. warneri group). These species belong to coagulase-negative staphylococci. All strains were sensitive to eight antibiotics out of 14 tested; the majority of strains were also sensitive to the remaining six antibiotics with the inhibitory zones from 13 to 41 mm. The strains were also sensitive at least to three enterocins of nine tested. Strains SW24/2, SHo 19/2, SHo20/1, SP19/1 were sensitive to eight of nine enterocins. All strains were sensitive to Ent A, P=EK13, and Ent EM41 with activity 100-6400 AU/mL. Strains SHo19/2 and SP19/1 were sensitive to Ent 2019 with activity up to 25600 AU/mL.

Oligonucleotide probes based on 16S rRNA sequences for the identification of four Azospirillum species

1995 ◽  
Vol 41 (12) ◽  
pp. 1081-1087 ◽  
Author(s):  
Md Mahbubul Kabir ◽  
Denis Faure ◽  
Jacqueline Haurat ◽  
Philippe Normand ◽  
René Bally ◽  
...  
Keyword(s):  
16S Rrna ◽  
Oligonucleotide Probe ◽  
Oligonucleotide Probes ◽  
Probe Sequence ◽  
Bacterial Isolation ◽  
Nontarget Organisms ◽  
Isolation Techniques ◽  
Species Specific ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Partial sequences of the 16S rRNA molecules of nine strains belonging to four Azospirillum species were used to design species-specific oligonucleotide probes. Azospirillum strains sequences were analyzed and three homologous fragments containing 16 nucleotides were determined. These three probes were found to be characteristic of A. lipoferum (Al), A. irakense (Ai), and A. brasilense/amazonense species (Aba) and of few nontarget organisms. The specificity of these three probes was tested both against sequences in the GenBank data base and in numerous colony hybridization experiments. As a few non-target organisms hyridized with the different Azospirillum probes, the use of these probes in bulk soil hybridization is not permitted. However, their use together with specific isolation techniques is validated.Key words: Azospirillum, bacterial isolation, hybridization, oligonucleotide probe, sequence analysis, 16S rRNA.

scholarly journals Evolutionary Relationships among Primary Endosymbionts of the Mealybug Subfamily Phenacoccinae (Hemiptera: Coccoidea: Pseudococcidae)

2010 ◽  
Vol 76 (22) ◽  
pp. 7521-7525 ◽  
Author(s):  
Matthew E. Gruwell ◽  
Nate B. Hardy ◽  
Penny J. Gullan ◽  
Katharina Dittmar
Keyword(s):  
16S Rrna ◽  
Nucleotide Substitution ◽  
Phylogenetic Analyses ◽  
Sister Group ◽  
Buchnera Aphidicola ◽  
Free Living ◽  
Bacterial Endosymbionts ◽  
Rrna Sequences ◽  
Living Bacteria ◽  
16S Rrna Sequences

ABSTRACT Mealybugs (Coccoidea: Pseudococcidae) are sap-sucking plant parasites that harbor bacterial endosymbionts within specialized organs. Previous studies have identified two subfamilies, Pseudococcinae and Phenacoccinae, within mealybugs and determined the primary endosymbionts (P-endosymbionts) of the Pseudococcinae to be Betaproteobacteria (“Candidatus Tremblaya princeps”) containing Gammaproteobacteria secondary symbionts. Here, the P-endosymbionts of phenacoccine mealybugs are characterized based on 16S rRNA from the bacteria of 20 species of phenacoccine mealybugs and four outgroup Puto species (Coccoidea: Putoidae) and aligned to more than 100 published 16S rRNA sequences from symbiotic and free-living bacteria. Phylogenetic analyses recovered three separate lineages of bacteria from the Phenacoccinae, and these are considered to be the P-endosymbionts of their respective mealybug hosts, with those from (i) the mealybug genus Rastrococcus belonging to the Bacteroidetes, (ii) the subterranean mealybugs, tribe Rhizoecini, also within Bacteroidetes, in a clade sister to cockroach endosymbionts (Blattabacterium), and (iii) the remaining Phenacoccinae within the Betaproteobacteria, forming a well-supported sister group to “Candidatus Tremblaya princeps.” Names are proposed for two strongly supported lineages: “Candidatus Brownia rhizoecola” for P-endosymbionts of Rhizoecini and “Candidatus Tremblaya phenacola” for P-endosymbionts of Phenacoccinae excluding Rastrococcus and Rhizoecini. Rates of nucleotide substitution among lineages of Tremblaya were inferred to be significantly faster than those of free-living Betaproteobacteria. Analyses also recovered a clade of Gammaproteobacteria, sister to the P-endosymbiont lineage of aphids (“Candidatus Buchnera aphidicola”), containing the endosymbionts of Putoidae, the secondary endosymbionts of pseudococcine mealybugs, and the endosymbionts of several other insect groups.

scholarly journals Correction to: Bacterial community assemblages in classroom floor dust of 50 public schools in a large city: characterization using 16S rRNA sequences and associations with environmental factors

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Ju-Hyeong Park ◽  
Angela R. Lemons ◽  
Jerry Roseman ◽  
Brett J. Green ◽  
Jean M. Cox-Ganser
Keyword(s):  
Public Schools ◽  
Environmental Factors ◽  
Bacterial Community ◽  
16S Rrna ◽  
Large City ◽  
Floor Dust ◽  
Community Assemblages ◽  
Rrna Sequences ◽  
16S Rrna Sequences

An amendment to this paper has been published and can be accessed via the original article.

scholarly journals 16S rRNA sequences reveal uncultured inhabitants of a well-studied thermal community

1990 ◽  
Vol 75 (2-3) ◽  
pp. 105-115 ◽  
Author(s):  
David M. Ward ◽  
Roland Weller ◽  
Mary M. Bateson
Keyword(s):  
16S Rrna ◽  
Rrna Sequences ◽  
16S Rrna Sequences

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.

scholarly journals Occurrence of diazotrophic bacteria in Araucaria angustifolia

2007 ◽  
Vol 64 (3) ◽  
pp. 303-304 ◽  
Author(s):  
Rafaela de Fátima Neroni ◽  
Elke Jurandy Bran Nogueira Cardoso
Keyword(s):  
16S Rrna ◽  
Acetylene Reduction ◽  
Araucaria Angustifolia ◽  
Diazotrophic Bacteria ◽  
Araucaria Forest ◽  
Solid Media ◽  
Reduction Assay ◽  
Semi Solid ◽  
Rrna Sequences ◽  
16S Rrna Sequences

Araucaria angustifolia is an environmentally threatened tree and the whole biota of the Araucaria Forest should be investigated with the aim of its preservation. Diazotrophic bacteria are extremely important for the maintenance of ecosystems, but they have never been studied in Araucaria Forests. In this study, diazotrophic bacteria were isolated from Araucaria roots and soil, when grown in semi-specific, semi-solid media. The diazotrophic character of some recovered isolates could be confirmed using the acetylene reduction assay. According to their 16S rRNA sequences, most of these isolates belong to the genus Burkholderia.

scholarly journals Identification of Streptococci to Species Level by Sequencing the Gene Encoding the Manganese-Dependent Superoxide Dismutase

1998 ◽  
Vol 36 (1) ◽  
pp. 41-47 ◽  
Author(s):  
Claire Poyart ◽  
Gilles Quesne ◽  
Stephane Coulon ◽  
Patrick Berche ◽  
Patrick Trieu-Cuot
Keyword(s):  
Superoxide Dismutase ◽  
Pcr Assay ◽  
Degenerate Primers ◽  
Gene Encoding ◽  
Genes Encoding ◽  
Type Strains ◽  
Internal Fragment ◽  
Rrna Sequences ◽  
16S Rrna Sequences

We have used a PCR assay based on the use of degenerate primers in order to characterize an internal fragment (sodAint ) representing approximately 85% of the genes encoding the manganese-dependent superoxide dismutase in various streptococcal type strains (S. acidominimus,S. agalactiae, S. alactolyticus, S. anginosus, S. bovis, S. constellatus,S. canis, S. cricetus, S. downei,S. dysgalactiae, S. equi subsp.equi, S. equi subsp. zooepidemicus,S. equinus, S. gordonii, S. iniae,S. intermedius, S. mitis, S. mutans, S. oralis, S. parasanguis,S. pneumoniae, S. porcinus, S. pyogenes, S. salivarius, S. sanguis,S. sobrinus, S. suis, S. thermophilus, and S. vestibularis). Phylogenetic analysis of these sodAint fragments yields an evolutionary tree having a topology similar to that of the tree constructed with the 16S rRNA sequences. We have shown that clinical isolates could be identified by determining the positions of theirsodAint fragments on the phylogenetic tree of the sodAint fragments of the type species. We propose this method for the characterization of strains that cannot be assigned to a species on the basis of their conventional phenotypic reactions.

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