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Top competitors on query "why is 16s rrna suitable as a marker to be used for genotypic identification of bacteria"
Mycobacterium tuberculosis Pathogenesis and Molecular Determinants of Virulence
http://cmr.asm.org/content/16/3/463.full Competition: low
The most frequently used antibiotic resistance cassettes in mycobacteria are those conferring resistance to kanamycin, hygromycin, and streptomycin (47). Sigma R is then able to transcribe several genes such as its own structural gene sigR and the trx operon, encoding thioredoxin and thioredoxin reductase, which can reduce proteins that were oxidized by diamide treatment
http://www.hyphen.info/rdf/hero/16_ra2_author.php Competition: low
2000 University of Reading Food Microbial Sciences Lawson P APapademas PWacher C Robinson R K Effect on the cholesterol content of fresh lamb of supplementing the feed of Awassi ewes and lambs with Lactobacillus acidophilus. 2000 University of Wales Institute, Cardiff Food Research and Consultancy Unit Harrison W APeters A CKanekanian A Fielding L M The effect of electron beam irradiation combined with acetic acid on the survival and recovery of Escherichia coli and Lactobacillus curvatus 1997 University of Wales Institute, Cardiff Food Research and Consultancy Unit Cook P EGrandison A S Fielding L M Evaluation of two methods for monitoring surface cleanliness - ATP bioluminescence and hygiene swabbing
http://www.selfcarejournal.com/view.article.php?id=10088 Competition: low
The group concluded that the faecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability (Figure 2). aureus MN8 is greater than for the pathogen and the surface, indicating that the staphylococci are more likely to adhere to the lactobacilli than to remain on the surface
Bacteria - Bacteria Guide - Bacteria Types,Bacteria Research
http://www.microbexpert.com/bacteria.html Competition: low
In the process of killing the bacteria for which they are prescribed, they also kill off all the friendly lactobacteria in your intestines, severely impairing digestion and assimilation of nutrients at a time when your body needs them most. Physiology: Chlamydia are unusual bacteria - unusual enough that they were originally classified as...Read more Septic Bacteria : Bacteria In Septic Systems: There are many different types of bacteria that occur naturally in a septic system
Gut Microbiota in Health and Disease
http://physrev.physiology.org/content/90/3/859.long Competition: low
Quantitative real-time PCR (qPCR) revealed that children who developed allergies were less frequently colonized with Lactobacillus spp., Bifidobacterium spp., and Clostridium difficile at 2 mo of age and that children belonging to larger households consistently generated more diverse microbiota profiles (276). Alternatively, certain microbial species can have direct cytotoxic effects on cells at the intestinal mucosa or cause toxicity through a bystander effect (in which host tissue can be damaged by host cells activated by certain microbial species)
polymerase chain reaction: Definition from Answers.com
http://www.answers.com/topic/polymerase-chain-reaction Competition: low
If even a trace of DNA from a disease carrier contaminates any of the PCR reagents, then assays performed on samples from non-disease carriers are likely to produce the diagnostic PCR amplification product. Each three-step cycle (separating the two strands of the DNA double helix, marking the ends of the segment to be copied, and catalyzing the formation of bonds), which takes only minutes to complete, doubles the number of DNA strands present in the reaction medium
Bovine Rumen - MicrobeWiki
http://microbewiki.kenyon.edu/index.php/Bovine_Rumen Competition: low
Protozoans also help facilitate methanogenesis by taking up oxygen which creates a more anaerobic environment which allows the anerobic bacteria and archae to carry out methanogenesis (28). Then, abomasum, also called "true stomach," is very similar to human stomach, as it is responsible for producing acids and enzymes to break down proteins, and it sends the chyme to small intestine (2)
454 Sequencing - GS Junior - Around the Globe
http://www.gsjunior.com/proof/ Competition: low
Compared to Sanger sequencing, we can now analyze a large number of amplicons in several samples and see the results in individual reads, not just consensus sequences. Currently, we are successfully developing and validating resequencing assays for single genes or gene panels, which can readily be used as plug-in applications
http://commonfund.nih.gov/highlights/index.aspx Competition: low
The chromatin state maps reveal that cells of different developmental stages, or exposed to different environmental conditions, can be distinguished by characteristic differences in chromatin state maps. They then determined the structure and properties of the molecules and showed that the molecules bind to a region of the enzyme different from that bound by the natural activator of PKM2
http://www.indiegogo.com/projects/american-gut-what-s-in-your-gut--7 Competition: low
Now, American Gut gives you an opportunity to participate and to compare the microbes in your gut to those in the guts of thousands of other people in the US and elsewhere. If you are a Type 2 diabetic, you can also get on a list to be considered for a FREE kit - click here.Dogs welcomeWe started looking at the dog gut microbiota in 2008 to start understanding the role of genetics in influencing microbial communities, and to look at microbe transfer within families
Polymerase chain reaction
http://schools-wikipedia.org/wp/p/Polymerase_chain_reaction.htm Competition: low
Nested PCR is often more successful in specifically amplifying long DNA fragments than conventional PCR, but it requires more detailed knowledge of the target sequences. This method permits PCR targeting smaller primer binding regions, and is particularly useful to amplify unknown, but conserved, DNA sequences, such as the 16S (or eukaryotic 18S) rRNA gene
JournalTOCs for Zotero
http://www.journaltocs.hw.ac.uk/api/jass/zotero.php?rft.issn=1590-4261&maximumRecords=100&query_issn=Submit+Query Competition: low
This study has shown that oleaginous red yeasts could have great potential for converting crude glycerol to valuable lipids and carotenoids in respect of efficient bioresources utilization. The activity of purified laccase was increased by more than four-fold by Cu 2+ , Mn 2+ and Mg 2+ , while it was completely inhibited by Fe 2+ and Fe 3+
JournalTOCs for Zotero
http://www.journaltocs.hw.ac.uk/api/jass/zotero.php?rft.issn=1432-0991&maximumRecords=100&query_issn=Submit+Query Competition: low
Results indicated that Bt isolates could be utilized for bioinsecticide production, aiming to reduce the use of chemical insecticide which could be useful to use in integrated pest management to control agriculturally important pests for sustainable crop production. On the basis of the chemotaxonomic and phenotypic characteristics and the phylogenetic evidence, strain JL2009 T represents a novel genus and species in the family Hyphomonadaceae , for which the name Euryhalocaulis caribicus gen
http://www.nap.edu/openbook.php?record_id=11902&page=47 Competition: low
Genomic char- acteristics that covaried with the environment were evident and suggested depth-specific functional and evolutionary themes in microbial communities and genomes (DeLong et al. We know little about how our microbial component has evolved or about the forces that are shaping it as our biosphere, our lifestyles, and our technologies change
Metagenomics - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Metagenomics Competition: low
However, early metagenomic studies revealed that there are probably large groups of microorganisms in many environments that cannot be cultured and thus cannot be sequenced. As viruses lack a shared universal phylogenetic marker (as 16S RNA for bacteria and archaea, and 18S RNA for eukarya), the only way to access the genetic diversity of the viral community from an environmental sample is through metagenomics
http://www.chemweb.com/journals/journals?type=issue&jid=SV11274&iid=0002400009 Competition: low
HPLC analysis of the extract showed that it contained saponins and some phenolic compounds such as chlorogenic, caffeic, vanillic, and salicylic acids, and scopoletin, which have been identified as antifungal agents on phytopathogenic fungi. The studies on optimization of agitation time, adsorbent dosage, and pH showed that the FeCl3 treated biomass had the maximum capacity to adsorb As(III) and live biomass was found to be minimum compared to all pretreated
http://www.chemweb.com/journals/journals?type=issue&jid=SV11274&iid=0002800003 Competition: low
High-speed counter-current chromatography (HSCCC) was applied for preparative separation of helvolic acid from the crude extract of the endophytic fungus Pichia guilliermondii Ppf9, associated with the medicinal plant Paris polyphylla var. In every case, multiple bands were amplified, indicating that these markers can be successfully used in different species belonging to the Colletotrichum genus
Pseudomonas - Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Pseudomonas Competition: low
A few decades after the proposal of the new genus Pseudomonas by Migula in 1894, the accumulation of species names assigned to the genus reached alarming proportions. In fact, this approximated reduction may be even more dramatic if one considers the present list contains many new names, i.e., relatively few names of the original list survived in the process
American Gut
http://humanfoodproject.com/americangut/ Competition: low
One RNA subunit, called the 16S rRNA, is especially effective as a barcode for understanding which microbes (specifically, bacteria and archaea) are found in a given sample. You will get a list of the dominant microbes in your gut, and several visualizations showing how they compare to the population at large (charts showing the dominant kinds of microbes along with what they are most associated with, and an overall view of the kinds of possible microbial configurations and how they compare to other people, including the Human Microbiome Project)
http://www.indiegogo.com/projects/american-gut Competition: low
One RNA subunit, called the 16S rRNA, is especially effective as a barcode for understanding which microbes (specifically, bacteria and archaea) are found in a given sample. Additionally, all American Gut samples will be entered into a database so you will be able to look up your sample by a unique identifier known only to you and to the Institutional Review Board-approved staff and see how it compares to others as additional samples accumulate.Open source learning and citizen science - it just has to beData from American Gut will be open source and be included as part of the Earth Microbiome Project (EMP), which is a massively collaborative international study aimed at systematically characterizing microbial life on earth
http://jcm.asm.org/content/42/8/3711.full Competition: low
thuringiensis from Thuringiensis A subgroup (Table 2), in spite of a great difference between representatives of these two subgroups in phenetic (46) relationship that includes differences both in genotype and in phenotype. We did not include in Table 2 the 108 inconsistencies found in the six 16S rRNA sequences mentioned above, which had been deposited in GenBank by Ash et al
Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC523561/ Competition: low
They can have a greater impact on the assignment of relationships of the deeper (more distantly related) branches (36).The 16S rRNA gene sequence is about 1,550 bp long and is composed of both variable and conserved regions. The advantage of some of the possible nomenclatures is that they allow an immediately apparent relationship with better-known species to be understood without having to do a literature search with each clinical microbiology patient's report.MAJOR IMPROVEMENTS IN CLINICAL MICROBIOLOGY PRACTICE BY IDENTIFYING BACTERIA BY SEQUENCE INSTEAD OF PHENOTYPE16S rRNA Gene Sequences Can Better Identify Poorly Described, Rarely Isolated, or Phenotypically Aberrant StrainsBecause 16S rRNA gene sequence analysis can discriminate far more finely among strains of bacteria than is possible with phenotypic methods, it can allow a more precise identification of poorly described, rarely isolated, or phenotypically aberrant strains
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
http://jcm.asm.org/content/45/9/2761 Competition: low
In such instances 16S rRNA gene sequence data cannot provide a definitive answer since it cannot distinguish between recently diverged species (13, 16). We support Drancourt's guidelines for including full 16S rRNA gene sequences whenever possible, and in particular, for groups such as Campylobacter species that absolutely require it for accurate species identifications
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045242/ Competition: low
Some of these problems are related to bacterial nomenclature and taxonomy while others are related to different issues cited below.TABLE 2.Selected examples of bacterial genera and species with identification problems using 16S rRNA gene sequencingA further problem regarding the resolution of 16S rRNA gene sequencing concerns sequence identity or very high similarity scores. In such instances 16S rRNA gene sequence data cannot provide a definitive answer since it cannot distinguish between recently diverged species (13, 16)
Mycobacterium tuberculosis Pathogenesis and Molecular Determinants of Virulence
The most frequently used antibiotic resistance cassettes in mycobacteria are those conferring resistance to kanamycin, hygromycin, and streptomycin (47). Sigma R is then able to transcribe several genes such as its own structural gene sigR and the trx operon, encoding thioredoxin and thioredoxin reductase, which can reduce proteins that were oxidized by diamide treatment
2000 University of Reading Food Microbial Sciences Lawson P APapademas PWacher C Robinson R K Effect on the cholesterol content of fresh lamb of supplementing the feed of Awassi ewes and lambs with Lactobacillus acidophilus. 2000 University of Wales Institute, Cardiff Food Research and Consultancy Unit Harrison W APeters A CKanekanian A Fielding L M The effect of electron beam irradiation combined with acetic acid on the survival and recovery of Escherichia coli and Lactobacillus curvatus 1997 University of Wales Institute, Cardiff Food Research and Consultancy Unit Cook P EGrandison A S Fielding L M Evaluation of two methods for monitoring surface cleanliness - ATP bioluminescence and hygiene swabbing
The group concluded that the faecal microbiota of the elderly shows temporal stability over limited time in the majority of subjects but is characterized by unusual phylum proportions and extreme variability (Figure 2). aureus MN8 is greater than for the pathogen and the surface, indicating that the staphylococci are more likely to adhere to the lactobacilli than to remain on the surface
Bacteria - Bacteria Guide - Bacteria Types,Bacteria Research
In the process of killing the bacteria for which they are prescribed, they also kill off all the friendly lactobacteria in your intestines, severely impairing digestion and assimilation of nutrients at a time when your body needs them most. Physiology: Chlamydia are unusual bacteria - unusual enough that they were originally classified as...Read more Septic Bacteria : Bacteria In Septic Systems: There are many different types of bacteria that occur naturally in a septic system
Gut Microbiota in Health and Disease
Quantitative real-time PCR (qPCR) revealed that children who developed allergies were less frequently colonized with Lactobacillus spp., Bifidobacterium spp., and Clostridium difficile at 2 mo of age and that children belonging to larger households consistently generated more diverse microbiota profiles (276). Alternatively, certain microbial species can have direct cytotoxic effects on cells at the intestinal mucosa or cause toxicity through a bystander effect (in which host tissue can be damaged by host cells activated by certain microbial species)
polymerase chain reaction: Definition from Answers.com
If even a trace of DNA from a disease carrier contaminates any of the PCR reagents, then assays performed on samples from non-disease carriers are likely to produce the diagnostic PCR amplification product. Each three-step cycle (separating the two strands of the DNA double helix, marking the ends of the segment to be copied, and catalyzing the formation of bonds), which takes only minutes to complete, doubles the number of DNA strands present in the reaction medium
Bovine Rumen - MicrobeWiki
Protozoans also help facilitate methanogenesis by taking up oxygen which creates a more anaerobic environment which allows the anerobic bacteria and archae to carry out methanogenesis (28). Then, abomasum, also called "true stomach," is very similar to human stomach, as it is responsible for producing acids and enzymes to break down proteins, and it sends the chyme to small intestine (2)
454 Sequencing - GS Junior - Around the Globe
Compared to Sanger sequencing, we can now analyze a large number of amplicons in several samples and see the results in individual reads, not just consensus sequences. Currently, we are successfully developing and validating resequencing assays for single genes or gene panels, which can readily be used as plug-in applications
The chromatin state maps reveal that cells of different developmental stages, or exposed to different environmental conditions, can be distinguished by characteristic differences in chromatin state maps. They then determined the structure and properties of the molecules and showed that the molecules bind to a region of the enzyme different from that bound by the natural activator of PKM2
Now, American Gut gives you an opportunity to participate and to compare the microbes in your gut to those in the guts of thousands of other people in the US and elsewhere. If you are a Type 2 diabetic, you can also get on a list to be considered for a FREE kit - click here.Dogs welcomeWe started looking at the dog gut microbiota in 2008 to start understanding the role of genetics in influencing microbial communities, and to look at microbe transfer within families
Polymerase chain reaction
Nested PCR is often more successful in specifically amplifying long DNA fragments than conventional PCR, but it requires more detailed knowledge of the target sequences. This method permits PCR targeting smaller primer binding regions, and is particularly useful to amplify unknown, but conserved, DNA sequences, such as the 16S (or eukaryotic 18S) rRNA gene
JournalTOCs for Zotero
This study has shown that oleaginous red yeasts could have great potential for converting crude glycerol to valuable lipids and carotenoids in respect of efficient bioresources utilization. The activity of purified laccase was increased by more than four-fold by Cu 2+ , Mn 2+ and Mg 2+ , while it was completely inhibited by Fe 2+ and Fe 3+
JournalTOCs for Zotero
Results indicated that Bt isolates could be utilized for bioinsecticide production, aiming to reduce the use of chemical insecticide which could be useful to use in integrated pest management to control agriculturally important pests for sustainable crop production. On the basis of the chemotaxonomic and phenotypic characteristics and the phylogenetic evidence, strain JL2009 T represents a novel genus and species in the family Hyphomonadaceae , for which the name Euryhalocaulis caribicus gen
Genomic char- acteristics that covaried with the environment were evident and suggested depth-specific functional and evolutionary themes in microbial communities and genomes (DeLong et al. We know little about how our microbial component has evolved or about the forces that are shaping it as our biosphere, our lifestyles, and our technologies change
Metagenomics - Wikipedia, the free encyclopedia
However, early metagenomic studies revealed that there are probably large groups of microorganisms in many environments that cannot be cultured and thus cannot be sequenced. As viruses lack a shared universal phylogenetic marker (as 16S RNA for bacteria and archaea, and 18S RNA for eukarya), the only way to access the genetic diversity of the viral community from an environmental sample is through metagenomics
HPLC analysis of the extract showed that it contained saponins and some phenolic compounds such as chlorogenic, caffeic, vanillic, and salicylic acids, and scopoletin, which have been identified as antifungal agents on phytopathogenic fungi. The studies on optimization of agitation time, adsorbent dosage, and pH showed that the FeCl3 treated biomass had the maximum capacity to adsorb As(III) and live biomass was found to be minimum compared to all pretreated
High-speed counter-current chromatography (HSCCC) was applied for preparative separation of helvolic acid from the crude extract of the endophytic fungus Pichia guilliermondii Ppf9, associated with the medicinal plant Paris polyphylla var. In every case, multiple bands were amplified, indicating that these markers can be successfully used in different species belonging to the Colletotrichum genus
Pseudomonas - Wikipedia, the free encyclopedia
A few decades after the proposal of the new genus Pseudomonas by Migula in 1894, the accumulation of species names assigned to the genus reached alarming proportions. In fact, this approximated reduction may be even more dramatic if one considers the present list contains many new names, i.e., relatively few names of the original list survived in the process
American Gut
One RNA subunit, called the 16S rRNA, is especially effective as a barcode for understanding which microbes (specifically, bacteria and archaea) are found in a given sample. You will get a list of the dominant microbes in your gut, and several visualizations showing how they compare to the population at large (charts showing the dominant kinds of microbes along with what they are most associated with, and an overall view of the kinds of possible microbial configurations and how they compare to other people, including the Human Microbiome Project)
One RNA subunit, called the 16S rRNA, is especially effective as a barcode for understanding which microbes (specifically, bacteria and archaea) are found in a given sample. Additionally, all American Gut samples will be entered into a database so you will be able to look up your sample by a unique identifier known only to you and to the Institutional Review Board-approved staff and see how it compares to others as additional samples accumulate.Open source learning and citizen science - it just has to beData from American Gut will be open source and be included as part of the Earth Microbiome Project (EMP), which is a massively collaborative international study aimed at systematically characterizing microbial life on earth
thuringiensis from Thuringiensis A subgroup (Table 2), in spite of a great difference between representatives of these two subgroups in phenetic (46) relationship that includes differences both in genotype and in phenotype. We did not include in Table 2 the 108 inconsistencies found in the six 16S rRNA sequences mentioned above, which had been deposited in GenBank by Ash et al
Impact of 16S rRNA Gene Sequence Analysis for Identification of Bacteria on Clinical Microbiology and Infectious Diseases
They can have a greater impact on the assignment of relationships of the deeper (more distantly related) branches (36).The 16S rRNA gene sequence is about 1,550 bp long and is composed of both variable and conserved regions. The advantage of some of the possible nomenclatures is that they allow an immediately apparent relationship with better-known species to be understood without having to do a literature search with each clinical microbiology patient's report.MAJOR IMPROVEMENTS IN CLINICAL MICROBIOLOGY PRACTICE BY IDENTIFYING BACTERIA BY SEQUENCE INSTEAD OF PHENOTYPE16S rRNA Gene Sequences Can Better Identify Poorly Described, Rarely Isolated, or Phenotypically Aberrant StrainsBecause 16S rRNA gene sequence analysis can discriminate far more finely among strains of bacteria than is possible with phenotypic methods, it can allow a more precise identification of poorly described, rarely isolated, or phenotypically aberrant strains
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
In such instances 16S rRNA gene sequence data cannot provide a definitive answer since it cannot distinguish between recently diverged species (13, 16). We support Drancourt's guidelines for including full 16S rRNA gene sequences whenever possible, and in particular, for groups such as Campylobacter species that absolutely require it for accurate species identifications
16S rRNA Gene Sequencing for Bacterial Identification in the Diagnostic Laboratory: Pluses, Perils, and Pitfalls
Some of these problems are related to bacterial nomenclature and taxonomy while others are related to different issues cited below.TABLE 2.Selected examples of bacterial genera and species with identification problems using 16S rRNA gene sequencingA further problem regarding the resolution of 16S rRNA gene sequencing concerns sequence identity or very high similarity scores. In such instances 16S rRNA gene sequence data cannot provide a definitive answer since it cannot distinguish between recently diverged species (13, 16)
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