scholarly journals Prevalence of Corynebacterial 16S rRNA Sequences in Patients with Bacterial and “Nonbacterial” Prostatitis

1999 ◽  
Vol 37 (6) ◽  
pp. 1863-1870 ◽  
Author(s):  
Michael A. Tanner ◽  
Daniel Shoskes ◽  
Asha Shahed ◽  
Norman R. Pace
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Chronic Prostatitis ◽  
Bacterial Species ◽  
Rrna Genes ◽  
Prostatic Fluid ◽  
Identification Of Bacteria ◽  
Rrna Sequences ◽  
Prostate Fluid ◽  
16S Rrna Sequences

The etiology of chronic prostatitis syndromes in men is controversial, particularly when positive cultures for established uropathogens are lacking. Although identification of bacteria in prostatic fluid has relied on cultivation and microscopy, most microorganisms in the environment, including some human pathogens, are resistant to cultivation. We report here on an rRNA-based molecular phylogenetic approach to the identification of bacteria in prostate fluid from prostatitis patients. Positive bacterial signals were seen for 65% of patients with chronic prostatitis overall. Seven of 11 patients with bacterial signals but none of 6 patients without bacterial signals were cured with antibiotic-based therapy. Results indicate the occurrence in the prostate fluid of a wide spectrum of bacterial species representing several genera. Most rRNA genes were closely related to those of species belonging to the generaCorynebacterium, Staphylococcus,Peptostreptococcus, Streptococcus, andEscherichia. Unexpectedly, a wide diversity ofCorynebacterium species was found in high proportion compared to the proportions of other bacterial species found. A subset of these 16S rRNA sequences represent those of undescribed species on the basis of their positions in phylogenetic trees. These uncharacterized organisms were not detected in control samples, suggesting that the organisms have a role in the disease or are the consequence of the disease. These studies show that microorganisms associated with prostatitis generally occur as complex microbial communities that differ between patients. The results also indicate that microbial communities distinct from those associated with prostatitis may occur at low levels in normal prostatic fluid.

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 Relationships of Bradyrhizobia from the LegumesApios americana and Desmodium glutinosum

1999 ◽  
Vol 65 (11) ◽  
pp. 4914-4920 ◽  
Author(s):  
Matthew A. Parker
Keyword(s):  
16S Rrna ◽  
Root Nodule ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
23S Rrna ◽  
Enzyme Electrophoresis ◽  
Nodule Bacteria ◽  
Root Nodule Bacteria ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Multilocus enzyme electrophoresis, partial 23S rRNA sequences, and nearly full-length 16S rRNA sequences all indicated high genetic similarity among root-nodule bacteria associated with Apios americana, Desmodium glutinosum, andAmphicarpaea bracteata, three common herbaceous legumes whose native geographic ranges in eastern North America overlap extensively. A total of 19 distinct multilocus genotypes (electrophoretic types [ETs]) were found among the 35 A. americana and 33 D. glutinosum isolates analyzed. Twelve of these ETs (representing 78% of all isolates) were either identical to ETs previously observed in A. bracteatapopulations, or differed at only one locus. Within both 23S and 16S rRNA genes, several isolates from A. americana and D. glutinosum were either identical to A. bracteataisolates or showed only single nucleotide differences. Growth rates and nitrogenase activities of A. bracteata plants inoculated with isolates from D. glutinosum were equivalent to levels found with native A. bracteata bacterial isolates, but none of the three A. americana isolates tested had high symbiotic effectiveness on A. bracteata. Phylogenetic analysis of both 23S and 16S rRNA sequences indicated that bothA. americana and D. glutinosum harbored rare bacterial genotypes similar to Bradyrhizobium japonicumUSDA 110. However, the predominant root nodule bacteria on both legumes were closely related to Bradyrhizobium elkanii.

scholarly journals Soil Acidobacterial 16S rRNA Gene Sequences Reveal Subgroup Level Differences between Savanna-Like Cerrado and Atlantic Forest Brazilian Biomes

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Elisa C. P. Catão ◽  
Fabyano A. C. Lopes ◽  
Janaína F. Araújo ◽  
Alinne P. de Castro ◽  
Cristine C. Barreto ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Atlantic Forest ◽  
Phylogenetic Reconstruction ◽  
Soil Microbial Communities ◽  
Rrna Gene ◽  
Cerrado Vegetation ◽  
Starting Point ◽  
Rrna Sequences ◽  
16S Rrna Sequences

16S rRNA sequences from the phylum Acidobacteria have been commonly reported from soil microbial communities, including those from the Brazilian Savanna (Cerrado) and the Atlantic Forest biomes, two biomes that present contrasting characteristics of soil and vegetation. Using 16S rRNA sequences, the present work aimed to study acidobacterial diversity and distribution in soils of Cerrado savanna and two Atlantic forest sites. PCA and phylogenetic reconstruction showed that the acidobacterial communities found in “Mata de galeria” forest soil samples from the Cerrado biome have a tendency to separate from the other Cerrado vegetation microbial communities in the direction of those found in the Atlantic Forest, which is correlated with a high abundance of Acidobacteria subgroup 2 (GP2). Environmental conditions seem to promote a negative correlation between GP2 and subgroup 1 (GP1) abundance. Also GP2 is negatively correlated to pH, but positively correlated to high Al3+concentrations. The Cerrado soil showed the lowest Acidobacteria richness and diversity indexes of OTUs at the species and subgroups levels when compared to Atlantic Forest soils. These results suggest specificity of acidobacterial subgroups to soils of different biomes and are a starting point to understand their ecological roles, a topic that needs to be further explored.

scholarly journals Effect of Freezing on PCR Amplification of 16S rRNA Genes from Microbes Associated with Black Band Disease of Corals

2009 ◽  
Vol 75 (8) ◽  
pp. 2581-2584 ◽  
Author(s):  
Raju Sekar ◽  
Longin T. Kaczmarsky ◽  
Laurie L. Richardson
Keyword(s):  
16S Rrna ◽  
Pcr Amplification ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Black Band Disease ◽  
Black Band ◽  
Sulfur Oxidizing ◽  
Polymicrobial Disease ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Molecular analysis of black band disease of corals revealed that samples frozen immediately after collection yielded more proteobacterial 16S rRNA sequences, while unfrozen samples produced more cyanobacterial and sulfur-oxidizing bacterial sequences. These results suggest the need to use multiple approaches for preparation of samples to characterize this complex polymicrobial disease.

MtHc: a motif-based hierarchical method for clustering massive 16S rRNA sequences into OTUs

2015 ◽  
Vol 11 (7) ◽  
pp. 1907-1913 ◽  
Author(s):  
Ze-Gang Wei ◽  
Shao-Wu Zhang
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
High Throughput ◽  
Hierarchical Method ◽  
Rapid Accumulation ◽  
Rrna Sequences ◽  
Recent Sequencing ◽  
16S Rrna Sequences

The recent sequencing revolution driven by high-throughput technologies has led to rapid accumulation of 16S rRNA sequences for microbial communities.

scholarly journals Effect of Temperature and Light on Growth of and Photosynthesis by Synechococcus Isolates Typical of Those Predominating in the Octopus Spring Microbial Mat Community of Yellowstone National Park

2006 ◽  
Vol 72 (1) ◽  
pp. 544-550 ◽  
Author(s):  
Jessica P. Allewalt ◽  
Mary M. Bateson ◽  
Niels Peter Revsbech ◽  
Kimberly Slack ◽  
David M. Ward
Keyword(s):  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Effect Of Temperature ◽  
Ecological Niches ◽  
Genotype Distribution ◽  
Unicellular Cyanobacterium ◽  
Temperature Ranges ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Previous molecular analysis of the Octopus Spring cyanobacterial mat revealed numerous genetically distinct 16S rRNA sequences from predominant Synechococcus populations distantly related to the readily cultivated unicellular cyanobacterium Synechococcus lividus. Patterns in genotype distribution relative to temperature and light conditions suggested that the organisms contributing these 16S rRNA sequences may fill distinct ecological niches. To test this hypothesis, Synechococcus isolates were cultivated using a dilution and filtration approach and then shown to be genetically relevant to natural mat populations by comparisons of similarities of 16S rRNA genes and 16S-23S internal transcribed spacer (ITS) regions. Most isolates were identical or nearly identical at both loci to predominant mat genotypes; others showed 1- to 2-nucleotide differences at the 16S rRNA locus and even greater difference in ITS sequences. Isolates with predominant mat genotypes had distinct temperature ranges and optima for growth that were consistent with their distributions in the mat. Isolates with genotypes not previously detected or known to be predominant in the mat exhibited temperature ranges and optima that were not representative of predominant mat populations and also grew more slowly. Temperature effects on photosynthesis did not reflect temperature relations for growth. However, the isolate with the highest temperature optimum and upper limit was capable of performing photosynthesis at a higher temperature than other isolates. Growth rate and photosynthetic responses provided evidence for light acclimation but evidence of, at best, only subtle light adaptation.

scholarly journals Vaginal Microbiota of Women with Frequent Vulvovaginal Candidiasis

2009 ◽  
Vol 77 (9) ◽  
pp. 4130-4135 ◽  
Author(s):  
Xia Zhou ◽  
Rachel Westman ◽  
Roxana Hickey ◽  
Melanie A. Hansmann ◽  
Colleen Kennedy ◽  
...  
Keyword(s):  
16S Rrna ◽  
Microbial Communities ◽  
Bacterial Communities ◽  
Bacterial Species ◽  
Vulvovaginal Candidiasis ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Novel Bacteria

ABSTRACT Vulvovaginal candidiasis (VVC) is an insidious infection that afflicts a large proportion of women of all ages, and 5 to 8% of affected women experience recurrent VVC (RVVC). The aim of this study was to explore the possible importance of vaginal bacterial communities in reducing the risk of RVVC. The species composition and diversity of microbial communities were evaluated for 42 women with and without frequent VVC based on profiles of terminal restriction fragment polymorphisms of 16S rRNA genes and phylogenetic analysis of cloned 16S rRNA gene sequences from the numerically dominant microbial populations. The data showed that there were no significant differences between the vaginal microbial communities of women in the two groups (likelihood score, 5.948; bootstrap P value, 0.26). Moreover, no novel bacteria were found in the communities of women with frequent VVC. The vaginal communities of most women in both groups (38/42; 90%) were dominated by species of Lactobacillus. The results of this study failed to provide evidence for the existence of altered or unusual vaginal bacterial communities in women who have frequent VVC compared to women who do not have frequent VVC. The findings suggest that commensal vaginal bacterial species may not be able to prevent VVC.

scholarly journals Archaeal Diversity and the Prevalence of Crenarchaeota in Salt Marsh Sediments

2009 ◽  
Vol 75 (12) ◽  
pp. 4211-4215 ◽  
Author(s):  
Katelyn A. Nelson ◽  
Nicole S. Moin ◽  
Anne E. Bernhard
Keyword(s):  
Salt Marsh ◽  
16S Rrna ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Archaeal Diversity ◽  
Group I ◽  
Marsh Sediments ◽  
Salt Marsh Sediments ◽  
Rrna Sequences ◽  
16S Rrna Sequences

ABSTRACT Crenarchaeal 16S rRNA sequences constituted over 70% of the archaeal clones recovered from three salt marsh sites dominated by different grasses. Group I.1a Crenarchaeota dominated at two sites, while group I.3b Crenarchaeota sequences were most abundant at a third site. Abundances of 16S rRNA genes related to “Candidatus Nitrosopumilus maritimus” differed by site and sampling date.

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