Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing. [PDF]
PLoS ONE, 2019 The ribosome small subunit is expressed in all living cells. It performs numerous essential functions during translation, including formation of the initiation complex and proofreading of base-pairs between mRNA codons and tRNA anticodons.
Andrew M Smith +4 more
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Updating the 97% identity threshold for 16S ribosomal RNA OTUs [PDF]
Bioinformatics, 2017 AbstractThe 16S ribosomal RNA (rRNA) gene is widely used to survey microbial communities. Sequences are often clustered into Operational Taxonomic Units (OTUs) as proxies for species. The canonical clustering threshold is 97% identity, which was proposed in 1994 when few 16S rRNA sequences were available, motivating a reassessment on current data ...
Robert C. Edgar
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A systematic algorithm using 16S ribosomal RNA for accurate diagnosis of pneumonia pathogens [PDF]
Scientific ReportsOver half of community-acquired pneumonia cases are caused by a few dozen bacterial species, and accurate identification of these pathogens is essential for effective treatment. In this study, we developed a reliable diagnostic method using 16S ribosomal
Ferry Dwi Kurniawan +5 more
doaj +2 more sources
Next-generation Sequencing of 16S Ribosomal RNA Gene Amplicons [PDF]
Journal of Visualized Experiments, 2014 One of the major questions in microbial ecology is "who is there?" This question can be answered using various tools, but one of the long-lasting gold standards is to sequence 16S ribosomal RNA (rRNA) gene amplicons generated by domain-level PCR reactions amplifying from genomic DNA.
Sanschagrin, Sylvie, Yergeau, Étienne
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16S Ribosomal RNA-Based Analysis of Thermophilic Bacteria in Gedongsongo Hot Spring
Microbiology Indonesia, 2010 Denaturing gradient gel electrophoresis was used to identify the bacterial community at the Gedongsongo (WGS-2) hot spring. The bacterial samples were obtained from both culture dependent and independent strategies.
AGUSTINA LULUSTYANINGATI NURUL AMININ1 +3 more
doaj +2 more sources
Gemella bacteraemia characterised by 16S ribosomal RNA gene sequencing [PDF]
Journal of Clinical Pathology, 2003 To define epidemiology, clinical disease, and outcome of gemella bacteraemia by 16S rRNA gene sequencing. To examine the usefulness of the Vitek, API, and ATB systems in identifying two gemella species.All alpha haemolytic streptococci other than Streptococcus pneumoniae isolated from blood cultures during a six year period were identified by ...
Patrick C. Y. Woo
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Considerations and best practices in animal science 16S ribosomal RNA gene sequencing microbiome studies. [PDF]
J Anim Sci, 2022 Microbiome studies in animal science using 16S rRNA gene sequencing have become increasingly common in recent years as sequencing costs continue to fall and bioinformatic tools become more powerful and user-friendly. The combination of molecular biology,
Weinroth MD +16 more
europepmc +2 more sources
Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA. [PDF]
Proc Natl Acad Sci U S A, 2021 Significance Ribosomes are complexes between ribosomal RNA (rRNA) and a number of proteins. Because ribosome assembly begins with rRNA folding, we simulated the molecular details of Mg2+-driven folding of the central domain of the bacterial rRNA.
Hori N, Denesyuk NA, Thirumalai D.
europepmc +2 more sources
Diagnostic Value of 16S Ribosomal RNA Gene Polymerase Chain Reaction/Sanger Sequencing in Clinical Practice. [PDF]
Clin Infect Dis, 2021 BACKGROUND Accurate microbiologic diagnosis is important for appropriate management of infectious diseases. Sequencing-based molecular diagnostics are increasingly used for precision diagnosis of infections.
Fida M +8 more
europepmc +2 more sources
30S Ribosomal proteins associated with the 3′‐terminus of 16S RNA [PDF]
FEBS Letters, 1975 A.P. Czernilofsky +2 more
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