16S RRNA Gene
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Most cited papers in 16S RRNA Gene
The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants. In lichen symbiotic Nostoc, the P6b stem-loop of trnL intron... more
The group I intron interrupting the tRNALeu UAA gene (trnL) is present in most cyanobacterial genomes as well as in the plastids of many eukaryotic algae and all green plants. In lichen symbiotic Nostoc, the P6b stem-loop of trnL intron always involves one of two different repeat motifs, either Class I or Class II, both with unresolved evolutionary histories. Here we attempt to resolve the complex evolution of the two different trnL P6b region types. Our analysis indicates that the Class II repeat motif most likely appeared first and that independent
and unidirectional shifts to the Class I motif have since taken place repeatedly. In addition, we compare our results with those obtained with other genetic markers and find strong evidence of recombination in the 16S rRNA gene, a marker widely used in phylogenetic studies on Bacteria. The congruence of the different genetic markers is successfully evaluated with the recently published software Saguaro, which has not previously been utilized in comparable studies.
and unidirectional shifts to the Class I motif have since taken place repeatedly. In addition, we compare our results with those obtained with other genetic markers and find strong evidence of recombination in the 16S rRNA gene, a marker widely used in phylogenetic studies on Bacteria. The congruence of the different genetic markers is successfully evaluated with the recently published software Saguaro, which has not previously been utilized in comparable studies.
- by Ulla Kaasalainen and +1
- •
- Cyanobacteria, trnL, 16S RRNA Gene
Background Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal... more
Background
Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which “universal” archaeal 16S rRNA gene primers are impacted by the presence of intron sequences.
Results
Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes.
Conclusions
The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different “universal” 16S rRNA primers employed in environmental microbial community analysis.
Intron sequences are common in 16S rRNA genes of specific thermophilic lineages of Archaea, specifically the Thermoproteales (phylum Crenarchaeota). Environmental sequencing (16S rRNA gene and metagenome) from geothermal habitats in Yellowstone National Park (YNP) has expanded the available datasets for investigating 16S rRNA gene introns. The objectives of this study were to characterize and curate archaeal 16S rRNA gene introns from high-temperature habitats, evaluate the conservation and distribution of archaeal 16S rRNA introns in geothermal systems, and determine which “universal” archaeal 16S rRNA gene primers are impacted by the presence of intron sequences.
Results
Several new introns were identified and their insertion loci were constrained to thirteen locations across the 16S rRNA gene. Many of these introns encode homing endonucleases, although some introns were short or partial sequences. Pyrobaculum, Thermoproteus, and Caldivirga 16S rRNA genes contained the most abundant and diverse intron sequences. Phylogenetic analysis of introns revealed that sequences within the same locus are distributed biogeographically. The most diverse set of introns were observed in a high-temperature, circumneutral (pH 6) sulfur sediment environment, which also contained the greatest diversity of different Thermoproteales phylotypes.
Conclusions
The widespread presence of introns in the Thermoproteales indicates a high probability of misalignments using different “universal” 16S rRNA primers employed in environmental microbial community analysis.
Aim: This research aimed to identify Staphylococcus species isolated from preputial swabs of healthy Aceh cattle, based on 16S ribosomal RNA gene analysis. Materials and Methods: The bacterium was isolated from preputial swabs of healthy... more
Aim: This research aimed to identify Staphylococcus species isolated from preputial swabs of healthy Aceh cattle, based on 16S ribosomal RNA gene analysis. Materials and Methods: The bacterium was isolated from preputial swabs of healthy Aceh cattle. The total DNA from the isolated bacteria was extracted using the Genomic DNA Mini Kit followed by polymerase chain reaction (PCR) amplification of the 16S rRNA gene. The product of PCR amplification was then sequenced and aligned to the known sequences in the GenBank database by multiple alignments and was also analyzed by bioinformatics software to construct a phylogenetic tree. Results: The results revealed that the bacterial isolate 3A had genetically closed relation to Staphylococcus pasteuri with <97% maximum identity. Data derived from the phylogenetic tree revealed that the bacterial isolate 3A was also related to Staphylococcus warneri, yet, it shows a different evolutionary distance with the ancestors (S. pasteuri). Conclusion: The results of this research suggested that the bacterium 3A, isolated from preputial swabs of healthy Aceh cattle, is a Staphylococcus species.
Background: Yersiniosis is an important foodborne zoonotic disease worldwide. Gastroenteritis and septicemia are the primary forms of yersiniosis. Yersinia enterocolitica is a causative organism, which is frequently isolated from foods... more
Background: Yersiniosis is an important foodborne zoonotic disease worldwide. Gastroenteritis and septicemia are the primary forms of yersiniosis. Yersinia enterocolitica is a causative organism, which is frequently isolated from foods such as milk. This study aimed to evaluate the contamination rate of bovine raw milk with Y. enterocolitica during January-July 2017 and the biotyping of the isolated organisms.
Methods: In total, 100 bovine raw milk samples were collected from Mashhad, Iran. The samples were enriched in peptone sorbitol broth. After alkali treatment, the enriched samples were streaked onto cefsulodin-irgasan-novobiocin agar plates. Suspected colonies of Y. enterocolitica were tested by the amplification of the 16s rRNA gene to confirm the isolates as Y. enterocolitica. The confirmed isolates were biotyped using biochemical tests.
Results: The results showed that 33% of the bovine raw milk samples were contaminated with Y. enterocolitica. Biotype 1A was predominant (26%), while the pathogenic biotypes 1B (6%) and 5 (1%) were also detected.
Conclusion: According to the results, the isolation of pathogenic Y. enterocolitica from bovine raw milk is a public health hazard due to its presence in dairy products.
Methods: In total, 100 bovine raw milk samples were collected from Mashhad, Iran. The samples were enriched in peptone sorbitol broth. After alkali treatment, the enriched samples were streaked onto cefsulodin-irgasan-novobiocin agar plates. Suspected colonies of Y. enterocolitica were tested by the amplification of the 16s rRNA gene to confirm the isolates as Y. enterocolitica. The confirmed isolates were biotyped using biochemical tests.
Results: The results showed that 33% of the bovine raw milk samples were contaminated with Y. enterocolitica. Biotype 1A was predominant (26%), while the pathogenic biotypes 1B (6%) and 5 (1%) were also detected.
Conclusion: According to the results, the isolation of pathogenic Y. enterocolitica from bovine raw milk is a public health hazard due to its presence in dairy products.
The aim of this research work was to explore psychrotrophic microbes from soil sample of NyAlesund, Svalbard, arctic region and to investigate their potential use as an effective tool for industrial application. A novel psychrotrophic... more
The aim of this research work was to explore psychrotrophic microbes from soil sample of NyAlesund, Svalbard, arctic region and to investigate their potential use as an effective tool for industrial application. A novel psychrotrophic bacterial strain showed good growth on minimal medium containing lipid as the only carbon source. Microbiological characterisation of the isolate showed that it was a gram negative rod. The strain was tested for the production of extracellular lipase enzyme. The enzymes were partially purified by 90% saturated ammonium sulfate and dialysis for desalting. The bacterium was identified as Pseudomonas sp ADT3 by 16S rRNA amplification and sequencing which had been deposited in the NCBI GenBank with accession number JX914667. Phylogenetic tree was also constructed with MEGA5 software and showed the highest level of sequence similarity with Pseudomonas sp. HC3-13 strain. The microorganism had a growth optimum at pH 8.0 and temperature 22°C. Optimization of different parameters e.g. temperature, pH, incubation time, cofactors etc. was performed for the extracellular lipase activity. The hydrolytic activity of the enzyme was enhanced 5 times by Pb2+ but strongly inhibited by heavy metals Hg2+ as well as EDTA and β-mercaptoethanol. For the molecular weight estimation of enzyme SDS-PAGE was done which showed an inducible band of approximately 13.9 KDa. Activity staining and mass spectrometry techniques were also performed.
During the last decade, there has been increasing awareness of the massive number of microorganisms, collectively known as the human microbiota, that are associated with humans. This microbiota outnumbers the host cells by approximately a... more
During the last decade, there has been increasing awareness of the massive number of microorganisms, collectively known as the human microbiota, that are associated with humans. This microbiota outnumbers the host cells by approximately a factor of ten and contains a large repertoire of microbial genome-encoded metabolic processes. The diverse human microbiota and its associated metabolic potential can provide the host with novel functions that can influence host health and disease status in ways that still need to be analyzed. The microbiota varies with age, with features that depend on the body site, host lifestyle and health status. The challenge is therefore to identify and characterize these microbial communities and use this information to learn how they function and how they can influence the host in terms of health and well-being. Here we provide an overview of some of the recent studies involving the human microbiota and about how these communities might affect host health and disease. A special emphasis is given to studies related to tuberculosis, a disease that claims over one million lives each year worldwide and still represents a challenge for control in many countries, including Colombia.
Rice is a staple food to almost one-third population of the world. The crop sustainability must therefore be considered to keep pace with the growing world population. Microorganims are one of the key factors affecting crop productivity... more
Rice is a staple food to almost one-third population of the world. The crop sustainability must therefore be considered
to keep pace with the growing world population. Microorganims are one of the key factors affecting crop productivity
and quality. Of particular interest is the plant rhiszosphere microbiome which has gained enormous attention in recent
years due to their role both as pathogen and plant growth promoting agents. Accordingly, the present study is aimed at
identification of bacteria isolated from soil samples collected from rice fields of district Jaffarabad, which belongs to
the major rice growing area of Pakistan. Six strains B9, B15, B34, B40, B52 and B53 were identified as genus Bacillus
whereas isolate B12 as genus Staphylococcus based on morphological and biochemical properties and 16S rRNA gene
sequence analysis. Isolates B9, B40 and B53 showed 99% similarity to Bacillus thuringiensis, Bacillus anthracis and
Bacillus endophyticus respectively. Conflicting results were observed for B15, B34 and B52 for sequence analysis
based on BLAST and SeqMatch alignment. The isolate B12 showed 99% similarity to Staphylococcus aureus. Our
findings indicate that instead of resorting rice bacterial populations through biochemical tests, the validation through
16S rRNA technique provides a more objective view.
to keep pace with the growing world population. Microorganims are one of the key factors affecting crop productivity
and quality. Of particular interest is the plant rhiszosphere microbiome which has gained enormous attention in recent
years due to their role both as pathogen and plant growth promoting agents. Accordingly, the present study is aimed at
identification of bacteria isolated from soil samples collected from rice fields of district Jaffarabad, which belongs to
the major rice growing area of Pakistan. Six strains B9, B15, B34, B40, B52 and B53 were identified as genus Bacillus
whereas isolate B12 as genus Staphylococcus based on morphological and biochemical properties and 16S rRNA gene
sequence analysis. Isolates B9, B40 and B53 showed 99% similarity to Bacillus thuringiensis, Bacillus anthracis and
Bacillus endophyticus respectively. Conflicting results were observed for B15, B34 and B52 for sequence analysis
based on BLAST and SeqMatch alignment. The isolate B12 showed 99% similarity to Staphylococcus aureus. Our
findings indicate that instead of resorting rice bacterial populations through biochemical tests, the validation through
16S rRNA technique provides a more objective view.
- by Attiya Soomro and +4
- •
- Staphylococcus, 16S RRNA Gene, Rice Rhizosphere, Bacilli
Introduction: Khabr national park is one of the invaluable natural sources in our country and its microbial variety has not been investigated. Cyanobacteria are of those organisms that are present in all terrestrial and water ecosystems... more
Introduction: Khabr national park is one of the invaluable natural sources in our country and its microbial variety has not been investigated. Cyanobacteria are of those organisms that are present in all terrestrial and water ecosystems and some minerals are limiting factors in their growth. The goal of this study is to investigate the present cyanobacteria in the soils of the grazed and non-grazed plots in two cold and hot steppes of Khabr Park in the autumn season by means of classic and molecular methods.
Materials and Methods: 32 different regions of Khabr Park were sampled in autumn and were cultured in BG11 medium. Isolation of cyanobacteria was conducted by various sub-cultures. Then the pure colonies were morphologically studied by valid taxonomic keys. Molecular identification of mentioned isolates was performed by amplification and sequencing of 16srRNA gene. The features of mentioned soils were analyzed physically and chemically.
Results: The results showed that for the soil texture of sandy loam, the average electrical conductivity was 99.12 µSiemens/cm and the average acidity of soil was 8.29. The isolates of Cyanobacteria belonged to Chroococcidiopsis, Leptolyngbya, Synechococcus, Nodularia. The results of DNA sequencing were compared to NCBI and its results were subjected to BLAST alignment.
Discussion and conclusion: The present work revealed that the variety and the number of the Cyanobacteria in this desert area are dependent on different parameters such as weather, humidity, source of nutrients, the amount of light absorbed by the surface and the temperature. The results of molecular identification validated the results of morphological tests.
Materials and Methods: 32 different regions of Khabr Park were sampled in autumn and were cultured in BG11 medium. Isolation of cyanobacteria was conducted by various sub-cultures. Then the pure colonies were morphologically studied by valid taxonomic keys. Molecular identification of mentioned isolates was performed by amplification and sequencing of 16srRNA gene. The features of mentioned soils were analyzed physically and chemically.
Results: The results showed that for the soil texture of sandy loam, the average electrical conductivity was 99.12 µSiemens/cm and the average acidity of soil was 8.29. The isolates of Cyanobacteria belonged to Chroococcidiopsis, Leptolyngbya, Synechococcus, Nodularia. The results of DNA sequencing were compared to NCBI and its results were subjected to BLAST alignment.
Discussion and conclusion: The present work revealed that the variety and the number of the Cyanobacteria in this desert area are dependent on different parameters such as weather, humidity, source of nutrients, the amount of light absorbed by the surface and the temperature. The results of molecular identification validated the results of morphological tests.
- by Parisa Mohammadi and +1
- •
- Cyanobacteria, 16S RRNA Gene
The present study has been carried out with focus on Muticaria macrostoma group from the Maltese Islands to characterize and define, from a molecular standpoint, their identity and relationships with topotypical Sicilian Muticaria (i.e.... more
The present study has been carried out with focus on Muticaria macrostoma group from the Maltese Islands to characterize and define, from a molecular standpoint, their identity and relationships with topotypical Sicilian Muticaria (i.e. M. syracusana, M. neuteboomi, M. cyclopica and M. brancatoi). Molecular study included amplification of 16S rDNA (ca. 300 bp) and COI (ca. 700 bp) gene partial sequences which were used for single and combined gene analysis by Bayesian Inference to achieve the phylogenetic reconstructions with the highest posterior probabilities. Obtained results showed that, within M. macrostoma group, the taxa mamotica and os-citans can be elevated to the specific rank, thus bringing to three the Maltese Muticaria species, i.e. M. macrostoma, M. mamotica, and M. oscitans; whereas scalaris may be considered a sub-species, or even a synonim. Present findings confirmed the validity of the Sicilian species M. syracusana, M. neuteboomi, M. cyclopica and M. brancatoi. Furthermore, the populations of the Sicilian and Maltese Muticaria seem to belong to two different levels of differentiation. Finally , we have also examined some Lampedusa populations but the position of this genus still remains to be clarified. In particular, it is confirmed that Lampedusa and Muticaria are different genera, but at present, the relations within the Lampedusa group need further studies to be analysed in details.
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