Phylogenetic Characterization of 16S rRNA Gene Clones from Deep-Groundwater Microorganisms That Pass through 0.2-Micrometer-Pore-Size Filters

ABSTRACT A total of 247 clones of 16S rRNA genes from microorganisms captured by 0.2- and 0.1-μm-pore-size filters from sedimentary and granite rock aquifers were amplified and yielded 37 operational taxonomic units (OTUs). Fifteen OTUs captured by 0.1-μm-pore-size filters were affiliated with the candidate divisions OD1 and OP11, representing novel lineages. On the other hand, OTUs captured by 0.2-μm-pore-size filters were largely affiliated with Betaproteobacteria.

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Molecular community analysis of magnesium-rich bittern brine recovered from a Tunisian solar saltern

Canadian Journal of Microbiology ◽

10.1139/w11-088 ◽

2011 ◽

Vol 57 (12) ◽

pp. 975-981 ◽

Cited By ~ 10

Author(s):

Houda Baati ◽

Raja Jarboui ◽

Néji Gharsallah ◽

Abdelghani Sghir ◽

Emna Ammar

Keyword(s):

16S Rrna ◽

Sequence Similarity ◽

Archaeal Community ◽

Community Analysis ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Solar Saltern ◽

16S Rrna Gene Analysis ◽

Operational Taxonomic Units

The microbial community of a magnesium-rich bittern brine saturated with NaCl (380–400 g/L) from a Tunisian solar saltern was investigated using a molecular approach based on 16S rRNA gene analysis and viability tests. The results revealed the existence of microbial flora. Viability test assessment showed that 46.4% of this flora was viable but not detectable by culturability tests. 16S rRNA genes from 49 bacterial clones and 38 archaeal clones were sequenced and phylogenetically analyzed. Eleven operational taxonomic units (OTUs) determined by the DOTUR program with 97% sequence similarity were generated for Bacteria. These OTUs were affiliated with Bacteroidetes and Gammaproteobacteria. The archaeal community composition exhibited more diversity with 38 clones, resulting in 13 OTUs affiliated with the Euryarchaeota phylum. Diversity measurement showed a more diverse archaeal than bacterial community at the saturated pond.

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Molecular characterization of Mycobacterium intracellulare-related strains based on the sequence analysis of hsp65, internal transcribed spacer and 16S rRNA genes

Journal of Medical Microbiology ◽

10.1099/jmm.0.020727-0 ◽

2010 ◽

Vol 59 (9) ◽

pp. 1037-1043 ◽

Cited By ~ 18

Author(s):

Joo-Hee Park ◽

Tae-Sun Shim ◽

Seung-Ae Lee ◽

Hyungki Lee ◽

In-Kyung Lee ◽

...

Keyword(s):

Sequence Analysis ◽

16S Rrna ◽

Internal Transcribed Spacer ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Mycobacterium Intracellulare ◽

Epidemiological Features ◽

The 16S Rrna Gene

We investigated the molecular epidemiological features of 94 Mycobacterium intracellulare-related strains, isolated from Korean patients, using sequence analysis targeting 3 independent chronometer molecules, hsp65, the internal transcribed spacer 1 region and the 16S rRNA gene. By collective consideration of these three gene-based approaches, the 94 strains were divided into 5 groups (INT1, INT2, INT3, INT4 and INT5). The frequencies of genotype INT1, 2, 3, 4 and 5 in the 94 isolates were 57.4 % (54), 27.7 % (26), 6.4 % (6), 5.3 % (5) and 3.2 % (3), respectively. When correlations between genotypes and clinical parameters (age, sex, radiological type and the presence of a cavity) were analysed in 78 patients with non-tuberculous mycobacteria pulmonary diseases, no relationships were observed with respect to age, sex and radiological type, but genotype and the presence of a cavity tended to be related (P=0.051).

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Genome-Derived Criteria for Assigning Environmental narG and nosZ Sequences to Operational Taxonomic Units of Nitrate Reducers

Applied and Environmental Microbiology ◽

10.1128/aem.00254-09 ◽

2009 ◽

Vol 75 (15) ◽

pp. 5170-5174 ◽

Cited By ~ 49

Author(s):

Katharina Palmer ◽

Harold L. Drake ◽

Marcus A. Horn

Keyword(s):

16S Rrna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

Nitrate Reducers ◽

Multiple Copies ◽

Tree Topologies ◽

Gene Similarity ◽

Very High

ABSTRACT Ninety percent of cultured bacterial nitrate reducers with a 16S rRNA gene similarity of ≥97% had a narG or nosZ similarity of ≥67% or ≥80%, respectively, suggesting that 67% and 80% could be used as standardized, conservative threshold similarity values for narG and nosZ, respectively (i.e., any two sequences that are less similar than the threshold similarity value have a very high probability of belonging to different species), for estimating species-level operational taxonomic units. Genus-level tree topologies of narG and nosZ were generally similar to those of the corresponding 16S rRNA genes. Although some genomes contained multiple copies of narG, recent horizontal gene transfer of narG was not apparent.

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Characterization of Streptomycetes Causing Potato Common Scab in Korea

Plant Disease ◽

10.1094/pdis.2003.87.11.1290 ◽

2003 ◽

Vol 87 (11) ◽

pp. 1290-1296 ◽

Cited By ~ 29

Author(s):

Duck Hwan Park ◽

Yong Man Yu ◽

Jeom Soon Kim ◽

Jun Mo Cho ◽

Jang Hyun Hur ◽

...

Keyword(s):

16S Rrna ◽

16S Rrna Genes ◽

Rrna Genes ◽

Soil Conditions ◽

Rrna Gene ◽

Phenotypic Properties ◽

Minimal Growth ◽

Thaxtomin A ◽

Potato Common Scab

Six representative Korean strains of streptomycetes (S33, S27, S71, S63, S77, and S78) that were pathogenic to potato were characterized based on phenotypic properties, analysis of 16S rRNA genes, production of thaxtomin A, and presence of nec1 and ORFtnp gene homologs. Strains S33 and S27 had typical characteristics of Streptomyces scabies and S. turgidiscabies, respectively, producing thaxtomin A and hybridizing to genes of nec1 and ORFtnp. Strain S71 produced thaxtomin A and had phenotypic and phylogenetic properties similar to those of S. acidiscabies, except having a greater minimum growth pH (4.5), production of a melanoid pigment on tyrosine agar, and failure to hybridize with nec1 and ORFtnp gene probes. In contrast, strains S63, S77, and S78 were phenotypically different from described scab pathogens. Spore colors of strains S63 and S77 were yellow-white or pale orange, respectively, with rectiflexuous chains. Strain S78 had thin and compact spores unlike typical S. acidiscabies (ATCC 49003). Phylogenetic analysis of strains S63, S77, and S78 based on 16S rRNA gene sequences showed low homology to that of described scab pathogens (less than 97.3, 96.0, and 96.3%, respectively). Strain S78 produced thaxtomin A, but did not have homologous sequences to nec1 and ORFtnp genes. Production of thaxtomin A and gene homologs of nec1 and ORFtnp were not detected in strains S63 and S77. All three strains grow at low pH, with minimal growth at pH 3.5 (S77 and S78) or 4.5 (S63). Streptomyces strains S63, S77, and S78 are novel pathogenic streptomycetes adapted to acidic soil conditions in Korea.

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Quantitatively evaluating mistaken clone assignments by RFLP analysis of 16S rRNA genes: a case study

Canadian Journal of Microbiology ◽

10.1139/w08-031 ◽

2008 ◽

Vol 54 (6) ◽

pp. 479-482 ◽

Cited By ~ 1

Author(s):

Han-Bo Zhang ◽

Chan-Wen Xu ◽

Miao-Miao Wang ◽

Tao Li ◽

Zhi-Wei Zhao

Keyword(s):

16S Rrna ◽

Sequence Similarity ◽

Rflp Analysis ◽

Restriction Enzymes ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Taxonomic Rank ◽

Operational Taxonomic Units

We quantitatively evaluated the errors of clone assignment based on the restriction fragment length polymorphism (RFLP) pattern of 16S rRNA genes. Eighty clones were randomly selected from a 16S rRNA gene library and were categorized into 35 operational taxonomic units (OTU) based on their indistinguishable enzyme restriction patterns of 3 tetrameric restriction enzymes RsaI, BsuRI, and HinfI. All of these clones were then sequenced and were reassigned into 36–53 OTUs using the DOTUR program when sequence similarities of 95%–100% were used. The number of the identically assigned clones ranged from 53 to 61 and the percentage varied from 66.3% to 76.3%. The Shannon–Weaver index for the bacterial community observed by RFLP analysis was 2.75, equal to that estimated by DOTUR at a 97% sequence similarity. Compared with clones assigned with the DOTUR program at a 97% sequence similarity, only 61 clones (76.3%) were correctly assigned by RFLP analysis. Six clones (7.5%) were assigned mistakenly at the phylum level, and the positions of 13 clones (16.2%) were phylogenetically different at a lower taxonomic rank.

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Characterization of Burkholderia pseudomallei and Burkholderia pseudomallei-like strains

Epidemiology and Infection ◽

10.1017/s095026889600739x ◽

1997 ◽

Vol 118 (2) ◽

pp. 137-148 ◽

Cited By ~ 91

Author(s):

P. J. BRETT ◽

D. DESHAZER ◽

D. E. WOODS

Keyword(s):

16S Rrna ◽

Dna Sequences ◽

Burkholderia Pseudomallei ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Virulent Strains ◽

Syrian Golden Hamsters ◽

Highly Virulent

Previous reports in the literature suggest that Burkholderia pseudomallei strains can be differentiated on the basis of animal virulence. Twenty environmentally and clinically derived isolates of Burkholderia pseudomallei were examined for the production of exoenzymes, morphological and biochemical phenotypes and virulence for Syrian golden hamsters. The partial sequence of the 16S ribosomal RNA [rRNA] genes from a number of these strains was also determined. Based upon these observations, it is suggested that highly virulent Burkholderia pseudomallei strains are true Burkholderia pseudomallei strains. The DNA sequences of the 16S rRNA genes of the true Burkholderia pseudomallei strains were identical to the published sequences for Burkholderia pseudomallei while differences were revealed between the published sequences and those of the lowly virulent strains. Thus, these latter strains have been designated as Burkholderia pseudomallei-like organisms since they demonstrate significant differences in exoenzyme production, hamster virulence and 16S rRNA gene sequences.

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Impact of Helicobacter Pylori Infection on Duodenal Microbial Community Structure and Microbial Metabolic Pathways

10.21203/rs.3.rs-166718/v2 ◽

2021 ◽

Author(s):

Tadashi Maeda ◽

Hiroaki Zai ◽

Yuto Fukui ◽

Yoshifumi Kato ◽

Eri Kumade ◽

...

Keyword(s):

Helicobacter Pylori ◽

16S Rrna ◽

Metabolic Pathways ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Operational Taxonomic Units ◽

H Pylori ◽

The Impact

Abstract Background The bioactivities of commensal duodenal microbiota greatly influence the biofunction of hosts. We investigated the role of Helicobacter pylori infection in extra-gastroduodenal diseases by determining the impact of H. pylori infection on the duodenal microbiota. We sequenced 16S rRNA genes in samples aspirated from the descending duodenum of 47 (male, 20; female, 27) individuals who were screened for gastric cancer. Samples were analysed using 16S rRNA gene amplicon sequencing, and the LEFSe and Kyoto Encyclopaedia of Genes and Genomes methods were used to determine whether the duodenal microflora and microbial biofunctions were affected using H. pylori infection. Results Thirteen and 34 participants tested positive and negative for H. pylori, respectively. We identified 1,404 bacterial operational taxonomic units from 23 phyla and 253 genera. H. pylori infection increased the relative mean abundance of Proteobacteria and Neisseria and decreased the abundance of the two other phyla (Actinobacteria and TM7) and nine genera (Rothia, TM7-3, Leptotrichia, Lachnospiraceae, Megasphaera, F16, Moryella, Filifactor, and Paludibacter). Microbiota features were significantly influenced in H. pylori-positive participants by 12 taxa mostly classified as Gammaproteobacteria. Microbial functional annotation revealed that H. pylori significantly affected 12 microbial metabolic pathways. Conclusions H. pylori disrupted normal bacterial communities in the duodenum and changed the biofunctions of commensal microbiota primarily by upregulating specific metabolic pathways. Such upregulation may be involved in the onset of diseases associated with H. pylori infection.

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Phylogenetic Characterization of a Polychlorinated-Dioxin- Dechlorinating Microbial Community by Use of Microcosm Studies

Applied and Environmental Microbiology ◽

10.1128/aem.71.8.4325-4334.2005 ◽

2005 ◽

Vol 71 (8) ◽

pp. 4325-4334 ◽

Cited By ~ 98

Author(s):

Naoko Yoshida ◽

Nobutaka Takahashi ◽

Akira Hiraishi

Keyword(s):

16S Rrna ◽

Oxidative Degradation ◽

16S Rrna Genes ◽

Rrna Genes ◽

Aerobic Bacteria ◽

Rrna Gene ◽

Phylogenetic Characterization ◽

Gene Copies ◽

Primer Sets ◽

Microcosm Studies

ABSTRACT Microcosms capable of reductive dechlorination of polychlorinated dibenzo-p-dioxins/dibenzofurans (PCDD/Fs) were constructed in glass bottles by seeding them with a polluted river sediment and incubating them anaerobically with an organic medium. All of the PCDD/F congeners detected were equally reduced without the accumulation of significant amounts of less-chlorinated congeners as the intermediate or end products. Alternatively, large amounts of catechol and salicylic acid were produced in the upper aqueous phase. Thus, the dechlorination of PCDD/Fs and the oxidative degradation of the dechlorinated products seemed to take place simultaneously in the microcosm. Denaturing gel gradient electrophoresis and clone library analyses of PCR-amplified 16S rRNA genes from the microcosm showed that members of the phyla Firmicutes, Proteobacteria, and Bacteroidetes predominated. A significant number of Chloroflexi clones were also detected. Quantitative real-time PCR with specific primer sets showed that the 16S rRNA genes of a putative dechlorinator, “Dehalococcoides,” and its relatives accounted for 0.1% of the total rRNA gene copies of the microcosm. Most of the clones thus obtained formed a cluster distinct from the typical “Dehalococcoides” group. Quinone profiling indicated that ubiquinones accounted for 18 to 25% of the total quinone content, suggesting the coexistence and activity of ubiquinone-containing aerobic bacteria. These results suggest that the apparent complete dechlorination of PCDD/Fs found in the microcosm was due to a combination of the dechlorinating activity of the “Dehalococcoides”-like organisms and the oxidative degradation of the dechlorinated products by aerobic bacteria with aromatic hydrocarbon dioxygenases.

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Composition and variation of the skin microbiota in sympatric species of European newts (Salamandridae)

Amphibia-Reptilia ◽

10.1163/15685381-00002970 ◽

2015 ◽

Vol 36 (1) ◽

pp. 5-12 ◽

Cited By ~ 7

Author(s):

Miguel Vences ◽

Anja B. Dohrmann ◽

Miguel Vences ◽

Anja B. Dohrmann ◽

...

Keyword(s):

16S Rrna ◽

Sympatric Species ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Triturus Cristatus ◽

Operational Taxonomic Units ◽

Lissotriton Vulgaris ◽

Rdna Sequences ◽

High Throughput Dna Sequencing

The mucous skin of amphibians provides a habitat for microorganisms which may interact with their hosts and thereby affect their condition and health. Cultivation-independent analyses of the bacterial communities based on the detection of PCR-amplified bacterial 16S rRNA genes provides a direct approach to characterize their diversity. In the present pilot study we utilized this approach in combination with a high-throughput DNA sequencing technology (454 pyrosequencing), to characterize the bacterial community structure of the skin of three newt species (Lissotriton vulgaris, Ichthyosaura alpestris, Triturus cristatus), collected near Braunschweig, Germany. 16S rDNA sequences were obtained from 19 unique samples. On average, 6113 amplicon sequences were obtained per sample and these could phylogenetically be assigned to a total of 1615 different operational taxonomic units (OTUs). Altogether, most samples were rather similar in their dominant bacterial taxa. Most represented were Betaproteobacteria (46%; mostly Janthinobacterium), Gammaproteobacteria (28%; mostly Pseudomonas), Flavobacteria (phylum Bacteroidetes: 19%, mostly Flavobacterium), and Sphingobacteria (Bacteroidetes: 5%, mostly Pedobacter). We found no significant differences between the three newt species, or between hemi-nested vs. non-nested PCR, but a strong difference among sampling dates (15 and 17 April 2013) which might be explained by the ongoing transition of the newts from their terrestrial to aquatic phase which coincided with this period, or by differences between sexes as these were unevenly sampled on the two dates. 16S rRNA gene sequences retrieved in this study in several cases were identical or very similar to those previously found on the skin of North American salamanders.

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Molecular characterization of Pseudomonas aeruginosa isolates from Sudanese patients: A cross-sectional study

F1000Research ◽

10.12688/f1000research.15316.1 ◽

2018 ◽

Vol 7 ◽

pp. 1135

Author(s):

Reem H. Amoon ◽

Amna H. Abdallha ◽

Ahmed Osman Sharif ◽

Ehssan H. Moglad ◽

Hisham N. Altyb ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Sequence Analysis ◽

16S Rrna ◽

16S Rrna Gene ◽

16S Rrna Genes ◽

Rrna Genes ◽

Rrna Gene ◽

Bacterial Disease ◽

Clinical Specimens

Background:16S rRNA gene sequence analysis is a robust tool for characterization of new pathogens in clinical specimens with suspected bacterial disease. The aim of this study was to characterizePseudomonas aeruginosaisolated from clinical specimens by sequencing the 16S rRNA gene.Methods:Forty bacterial isolates were obtained from different clinical specimens (wound, urine and sputum) using enrichment selective media and biochemical tests to characterize and identify the bacteria asP. aeruginosa.DNA was extracted fromP. aeruginosausing the Chelex method. A universal primer was used to amplify 16S rRNA genes by a conventional PCR technique. The amplified PCR products were sequenced, and the sequences were viewed by Finch TV program version 1.4.0. The identity and similarity of the nucleotide sequence of the isolated strains was detected by comparing them with published sequences using BLASTn. Phylogenetic trees were constructed using Phylogeny.fr software.Results:Sequence analysis by BLASTn displayed high similarity and identity withP. aeruginosafrom China KX461910, Australia JN609194 and with otherP. aeruginosaisolates from the GenBank database.Conclusions:Our observation of isolates from different origin sites, further show the utility of 16s rRNA PCR amplification. This reveals the high specify of the primers and accuracy of the PCR. Thus, 16S rRNA sequencing can be used to identify genetically atypicalP. aeruginosaisolates from different origins.

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