16s ribosomal rna gene sequencing. Medical search. Frequent questions

In a subset of 10 representative patients, bacterial DNA was extracted from ascites and whole blood, followed by 16S rRNA gene amplicon sequencing. (frontiersin.org)
The authors used the now-familiar molecular techniques of microbial ecology (16S ribosomal RNA (rRNA) gene amplicon sequencing) to characterise bacterial communities in sputum and bronchoalveolar lavage fluid collected from a large and well-matched cohort of patients with non-cystic fibrosis bronchiectasis. (ersjournals.com)
Using 16S ribosomal RNA gene amplicon sequencing and metagenomics, we resolved the microbial community composition on the North and South Shelves of Iceland, analyzed its evolution from 2011 to 2018, identified frequently occurring taxa, and predicted their potential metabolism. (matis.is)
To test this hypothesis, the phylogenetic composition of faecal microbiomes was investigated by a 16S rRNA gene amplicon sequence-based approach for Bacteria and Archaea . (springer.com)
The gut microbiota composition of seventeen healthy male college students was analysed before and after nine weeks of high-intensity interval cycling training by 16S rRNA amplicon sequencing. (biomedcentral.com)

The three mock communities, featuring as many as 87 microbial strains spanning 29 bacterial and archaeal phyla, were created by researchers at Oakridge National Laboratory led by Mircea Podar and are likely some of the most complex communities that could be sequenced, according to senior author Mathieu Almeida, a research fellow at INRAE. (genomeweb.com)
In the present study, we characterized forty isolates of indigenous black gram bradyrhizobia from Myanmar based on the sequence analysis of the bacterial 16S rRNA gene. (scirp.org)
One type of RNA, the 16S ribosomal RNA (rRNA), is encoded by a gene whose sequence is highly conserved between bacterial taxa. (technologynetworks.com)
It is an acronym for Quantitative Insights Into Microbial Ecology, and has been used to analyze and interpret nucleic acid sequence data from fungal, viral, bacterial, and archaeal communities. (nau.edu)
The A and B clones of Borrelia burgdorferi sensu stric- maintenance of these clonal complexes in natural bacterial to, distinguished by outer surface protein C ( ospC ) gene populations ( 3 , 4 ). (cdc.gov)
To resolve phylogenetic relationships among ries of bacterial clonal complexes by using concatenated isolates, we sequenced 68 isolates from Europe and North sequences of housekeeping genes when within-loci and America at 1 chromosomal locus (16S-23S ribosomal RNA between-loci recombinations are infrequent ( 5 ). (cdc.gov)
16S rRNA and ITS regions of extracted bacterial and fungal genomic DNA were amplified and sequenced using Sanger sequencing. (cdc.gov)
Objective: To detect the presence and transmission of S. mutans carrier of the spaP gene in samples of bacterial plaque in mother/child pairs from municipal child education centers, and the possible association with dental caries. (bvsalud.org)
Some of the enzymes which generate aromatic radicals that break down most prominent bacterial strains found were isolated and tax- the complex linkages present in lignin to compounds of lower onomically identified using 16S ribosomal RNA (rRNA) se- molecular weight. (lu.se)
16S sequencing is performed to determine which bacterial species are present in a clinical sample or isolate. (folkhalsomyndigheten.se)
The method uses an internal control sequence (spike) which is amplified and sequenced simultaneously with the sample to facilitate the assessment of the bacterial content and to detect amplification-inhibiting factors in the sample that may lead to a negative result. (folkhalsomyndigheten.se)
For contact tracing or inquiries related to antibiotic resistance, whole genome sequencing (WGS) of bacterial isolates is offered. (folkhalsomyndigheten.se)

The laboratory procedure is based on amplifying and sequencing four variable regions of the 16S rRNA gene with two amplicons. (folkhalsomyndigheten.se)

Using QIIME to analyze 16S rRNA gene sequences from microbial communities. (nau.edu)

A phylogenetic analysis of 19 sibling taxa in the Vertigo gouldii group was conducted on 73 individuals sampled across North America using DNA sequence data of the mitochondrial genes cytochrome oxidase subunit 1 (CO1) and 16S ribosomal RNA (16S), and the internal transcribed spacer-2 of the nuclear ribosomal RNA (ITS-2) gene. (researchgate.net)
The most commonly used molecular approach for exploring microbial diversity is based on the PCR amplification and sequencing of genes encoding small subunit ribosomal RNA (16S rRNA) directly from environmental sources [ 16 ]. (biomedcentral.com)
In contrast to metagenomic detection of unknown pathogens which sequences all available genetic material, 16S sequencing specifically targets the small ribosomal subunit. (folkhalsomyndigheten.se)

colistin-resistance gene mcr-1 in clinical isolates and stool bioMérieux). (cdc.gov)
The sequence analysis confirmed that all isolates were categorized and identified as the genus Bradyrhizobium and they were conspecific with B . elkanii , B . sp. (scirp.org)
We performed AST and whole genome sequencing (WGS) for 593 C. difficile isolates collected between 2012-2017 through the Centers for Disease Control and Prevention's Emerging Infections Program. (cdc.gov)
WGS was performed on all isolates to detect the presence of genes or mutations previously associated with resistance. (cdc.gov)
RT027 isolates also showed higher MICs to clindamycin and moxifloxacin and were more likely to harbor associated resistance genes or mutations. (cdc.gov)
To characterize the pathotype, 1,019 isolates collected through this project underwent antimicrobial susceptibility testing and whole-genome sequencing. (cdc.gov)
While only 7 (0.1%) isolates harbored carbapenemase genes, 66 (6.5%) had acquired non-carbapenemase -lactamase genes, and these were more likely to have OprD dysfunction and be resistant to all carbapenems tested. (cdc.gov)
The increased carbapenem resistance in isolates with acquired non-carbapenemase -lactamase genes suggests that horizontally transmitted mechanisms aside from carbapenemases themselves may be important drivers of the spread of carbapenem resistance in P. aeruginosa. (cdc.gov)
The genetic homogeneity of ospC -A isolates was confi rmed agent, Borrelia burgdorferi , a spirochete that parasitizes by sequences at 6 additional chromosomal housekeeping vertebrates, is transmitted by hard-bodied ticks through- loci ( gap, alr, glpA, xylB, ackA, and tgt ). (cdc.gov)
Only 16S rRNA sequencing was able to determine the subspecies of P. multocida and to determine the genetic relatedness of the 2 isolates. (medscape.com)
ribosomal RNA identification of the isolates showed high score similarity with Pseudomonas spp. (lu.se)

The authors further note that results from their genome sequencing analysis of DIEPV viruses from the D. longicaudata wasp venom gland, along with comparative genomic and other analyses, suggest that the symbiotic poxvirus "retains the exogenous viral genome of its poxvirus ancestor and the majority of conserved poxvirus core genes. (genomeweb.com)
Researchers from the University of Maryland School of Medicine's (UMSOM) Institute for Genome Sciences (IGS) have created VIRGO (human vaginal non-redundant gene catalog): the first genomic catalog of the vaginal microbiome. (technologynetworks.com)
Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected through CDC's Emerging Infections Program, United States, 2016-2018. (cdc.gov)
Sequenced genomes were classified using the seven-gene multilocus sequence typing (MLST) scheme and a core genome (cg)MLST scheme was used to determine phylogeny. (cdc.gov)
By sequencing the entire genome, a comprehensive understanding of the genetic composition is obtained. (folkhalsomyndigheten.se)
Whole genome sequencing can also provide insights into the specific genes or mutations that may be linked to antibiotic resistance. (folkhalsomyndigheten.se)
It is a platform and database for the automated analysis of whole genome sequencing data. (folkhalsomyndigheten.se)

Bacteria 16S ribosomal RNA gene, partial sequence. (nih.gov)
uncultured bacterium nitrogenase reductase (nifH) gene, partial cds. (nih.gov)
Pseudomonadota nitrogenase reductase (nifH) gene, partial cds. (nih.gov)
Sequence accession no. 16S rRNA gene: AF009477, 16S ribosomal RNA gene, partial sequence: NR_036918. (dsmz.de)
The present work examines the phylogenetic relationships of two populations of this land snail from Egypt and Saudi Arabia using mitochondrial markers (partial 16S rDNA and COI gene sequencing) in addition to traditional methods of shell's shape analysis. (researchgate.net)

In their proof-of-principle application of MANTA, the authors used the platform to explore potential ties between gut microbiome features by 16S ribosomal RNA gene sequencing on fecal samples, body composition, blood test results, and self-reported lifestyle features such as activity levels and dietary patterns in 20 seemingly healthy male volunteers between the ages of 21 and 41 years old from Japan. (genomeweb.com)
The researchers extracted DNA from the samples and sequenced a portion of the 16S ribosomal RNA gene, widely used in microbiome studies to help identify and compare bacteria. (news-medical.net)

Methods: The individual taxonomic microbiota composition of fecal samples from 90 NAFLD patients and 21 healthy controls was analyzed using 16S rRNA gene sequencing. (uni-frankfurt.de)

They determined the DNA sequences of the genes that coded for the mitochondrial 12S and 16S ribosomal RNA, and compared them with the aid of a computer. (newscientist.com)

Design and test primers for this sequence using Primer-BLAST. (beds.ac.uk)

Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. (wikipedia.org)
Archaea were first classified separately from bacteria in 1977 by Carl Woese and George E. Fox, based on their ribosomal RNA (rRNA) genes. (wikipedia.org)
Only few archaeal sequences were detected, primarily Methanomassiliicoccales representing potential methanogenic Archaea . (springer.com)

Baseline gut microbial composition (16S rRNA sequencing) and metabolic capacity (PICRUSt) were determined. (medscape.com)

The Illumina MiSeq sequencing of 16S rRNA gene amplicons revealed that genus Flavobacterium was the predominant group that preferentially accumulated in Allium rhizospheres. (nature.com)
The procedure's high sequence depth allows for these amplicons to be analysed separetely so different bacteria from the same sample can be identified. (folkhalsomyndigheten.se)

In 1965, Emile Zuckerkandl and Linus Pauling instead proposed using the sequences of the genes in different prokaryotes to work out how they are related to each other. (wikipedia.org)
EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. (microbiologyresearch.org)

CMY-2 transferable plasmid from a colistin-resistant KPC carbapenemase- vealed insertion of a 101,257-bp fragment carrying both producing Klebsiella pneumoniae strain of sequence type 512. (cdc.gov)

The 16S rRNA gene is highly conserved with certain variable regions. (folkhalsomyndigheten.se)

NEW YORK - Researchers from France's National Research Institute for Agriculture, Food, and Environment (INRAE) have published data on the performance of both short- and long-read sequencing platforms in analyzing highly complex metagenomic samples. (genomeweb.com)
When we started, we were aware of the strong requirements for long-read sequencing, requesting long DNA fragments and high DNA purity, and expected low performance for quantitative metagenomic analysis compared to conventional short-read methods in such complex mock samples," Almeida said. (genomeweb.com)
Furthermore, we were surprised by the DNBSEQ-T7 performance, providing ultra-deep sequencing in a single run with similar low error rate compared to the other technologies, making it at the time of our study one of the cheapest technologies for metagenomic sequencing. (genomeweb.com)
Access to data from complex metagenomic sequencing studies aren't often provided, "because these data are produced for the purpose of hypothesis testing," said first author Victoria Meslier, also of INRAE. (genomeweb.com)
Metagenomic sequencing is offered in cases where infection is suspected but other methods have failed to identify a pathogen. (folkhalsomyndigheten.se)
Metagenomic sequencing engables a thorough mapping of the genetic material in the clinical sample, providing a broader understanding of the microbiological profile. (folkhalsomyndigheten.se)
The result of of metagenomic sequencing is the outcome of a collaborative effort between bioinformaticians and clinical microbiologists, where the clinical interpretation confirms and complements the technical analysis. (folkhalsomyndigheten.se)

Designed for Cepheid's GeneXpert Systems, the Xpert MTB/RIF test detects Mycobacterium tuberculosis complex (MTB-complex) DNA in approximately 2 hours, as well as rifampin-resistance associated mutations of the rpoB gene. (aacc.org)
The lack of vanA/B genes or mutations consistently associated with elevated vancomycin MICs suggests there are multifactorial mechanisms of resistance. (cdc.gov)

Sequence variations between different bacteria provide a unique identity, and the analysis of these sequence enables taxonomic placement. (folkhalsomyndigheten.se)

Here we obtained a well-resolved polymorphism type of intergenic spacer (IGS) sequence phylogeny of B. burgdorferi sensu stricto clonal complexes (corresponding to the ospC- A and -B groups) is associated by using multilocus sequence typing at housekeeping loci with hematogenous dissemination in patients with early as well as loci under adaptive evolution. (cdc.gov)

All bacteria carry certain basic housekeeping genes necessary for life, notably the 16S ribosomal RNA gene. (wustl.edu)
All bacteria carry ribosomes that consist of proteins and RNAs. (technologynetworks.com)

The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities. (nau.edu)

resistance genes to the chromosome. (cdc.gov)

Prediction of taxonomy for marker gene sequences such as 16S ribosomal RNA (rRNA) is a fundamental task in microbiology. (peerj.com)
The relationship between identity and taxonomy was quantified as the probability that a rank is the lowest shared by a pair of sequences with a given pair-wise identity. (peerj.com)
With the V4 region, 95% identity was found to be a twilight zone where taxonomy is highly ambiguous because the probabilities that the lowest shared rank between pairs of sequences is genus, family, order or class are approximately equal. (peerj.com)
A fundamental step in such studies is to predict the taxonomy of sequences found in the reads. (peerj.com)

Cluster of ortholog genes (COG) functional annotation and Kyoto encyclopedia of genes and genomes (KEGG) were used to detect enrichment pathways among the three groups. (frontiersin.org)

Find regions of similarity between this sequence and other sequences using BLAST. (beds.ac.uk)

results of 16S ribosomal RNA gene sequencing. (wikipedia.org)
To check their results, the researchers obtained from a database the DNA sequences of the myoglobin of 10 whales and dolphins. (newscientist.com)
The aim of this study was to prove the reproducibility of published results and to provide a detailed overview of all findings in our NAFLD cohort using next generation sequencing methods. (uni-frankfurt.de)

Such analysis will require the development of computational tools to identify the viruses by their genetic sequences, classify them into family groups, identify potential genes within viral sequences, and propose functions of the genes. (wustl.edu)
In epidemiological contact tracing, this technology enables the mapping of infection spread and identification of sources of infection through the comparison of genetic sequences. (folkhalsomyndigheten.se)

Multilocus sequence typing (MLST) is the use of DNA dorferi ( 9 , 10 ). (cdc.gov)

All nucleic acid in the clinical sample is sequenced and the resulting data is analysed by experienced bioinformaticians. (folkhalsomyndigheten.se)

lamina propria and mesenteric lymph node tissues were analyzed by RNA sequencing and flow cytometry. (nih.gov)

The tool works with standard single letter nucleotide or protein codes including ambiguities and can match Prosite patterns in protein sequences. (beds.ac.uk)

Classification is difficult because most have not been isolated in a laboratory and have been detected only by their gene sequences in environmental samples. (wikipedia.org)

Scientists use this universal gene to screen mixed communities of unidentified bacteria by pulling out all the 16S ribosomal RNA genes and using the sequences to classify the bacteria into families. (wustl.edu)

Bontron S, Poirel L, Nordmann P. Real-time PCR for detection resistant strains harboring the mcr- 1 gene might have been of plasmid-mediated polymyxin resistance ( mcr-1 ) from cultured isolated in the hospital but not identified because this resis- bacteria and stools. (cdc.gov)

Most researchers largely use 16S rRNA gene sequencing. (technologynetworks.com)

Most experimentally observed sequences are diverged from reference sequences of authoritatively named organisms, creating a challenge for prediction methods. (peerj.com)

When the accuracy of genus predictions was averaged over a representative range of identities with the reference database (100%, 99%, 97%, 95% and 90%), all tested methods had ≤50% accuracy on the currently-popular V4 region of 16S rRNA. (peerj.com)

This is a nice comparison of the long- and short-read platforms, and shows overall comparability between methods," said Chris Mason, a sequencing expert at Weill Cornell Medicine who was not involved in the study. (genomeweb.com)
In these papers, accuracy is defined as the fraction of sequences that are correctly classified at each rank (see Acc RDP in Methods). (peerj.com)

2007. Biphenyl-utilizing bacteria and their functional genes in a pine root zone contaminated with polychlorinated biphenyls (PCBs). (nih.gov)

enrichment culture DGGE gel band B6 16S ribosomal RNA gene, p. (beds.ac.uk)

DCs incubated with the FFAR2 agonist no longer had gene expression patterns associated with activation or IL27 production. (nih.gov)
Finds sub-sequences or patterns in the sequence and highlights the matching regions. (beds.ac.uk)
Finds sub-sequence or patterns in the sequence and highlights the matching region. (beds.ac.uk)

Mason said that he would like to see data from the latest sequencing platforms. (genomeweb.com)
The mtDNA sequence data suggest that some previous members of the traditional V. gouldii group may be more closely related to V. modesta. (researchgate.net)
The basis of the GENSAM project is the joint national management of clinical microbial sequencing data. (folkhalsomyndigheten.se)

They found that the DNA sequence of the sperm whale and pygmy sperm whale were more closely related to the baleen whales than to other toothed whales and dolphins. (newscientist.com)

I assessed the accuracy of several algorithms using cross-validation by identity, a new benchmark strategy which explicitly models the variation in distances between query sequences and the closest entry in a reference database. (peerj.com)

c) By contrast, in chronic mycobacterial infections, biomass remains modest, diversity remains unchanged and the pathogen is a minor constituent of the lung community close to the limit of detection for current sequencing technologies. (ersjournals.com)

Its overall accuracy is 93.6% when compared to the accuracy of 16S Ribosomal RNA gene sequencing, the gold standard for identifying anaerobic bacteria, Enterobacteriaceae, Gram-positive aerobes, fastidious Gram-negative bacteria, Gram-negative non-Enterobacteriaceae, and yeast. (aacc.org)

There were 336 sequence types (STs) among the 1,019 sequenced genomes, and the genomes varied by an average of 84.7% of the cgMLST alleles used. (cdc.gov)
Bacteroides, Ruminococcaceae, Faecalibacterium prausnitzii) and three Kyoto Encyclopedia of Genes and Genomes orthologues, of which two relate to carbohydrate metabolism. (medscape.com)

Anatomy3

Organisms9

Diseases2

Chemicals and Drugs25

Analytical, Diagnostic and Therapeutic Techniques and Equipment7

Phenomena and Processes19

Information Science3

Health Care2

Amplicon5

Bacterial12

Regions of the 16S rRNA gene1

RRNA gene sequences1

Subunit3

Isolates11

Genome7

Partial5

Microbiome2

Fecal samples1

Mitochondrial1

Primers1

Archaea3

Metabolic1

Amplicons2

Prokaryotes2

Strain1

Highly conserved1

Metagenomic7

Mutations2

Taxonomic1

Phylogeny1

Bacteria carry2

Analyze1

Resistance genes1

Taxonomy4

Detect1

Similarity1

Results3

Genetic2

Multilocus1

Nucleic acid1

Tissues1

Nucleotide1

Samples1

Scientists1

Plasmid1

Researchers1

Organisms1

Genus1

Methods2

Functional1

Enrichment1

Patterns3

Data3

Baleen1

Database1

Pathogen1

Accuracy1

Genomes2