Choice of 16S Ribosomal RNA Primers Impacts Male Urinary Microbiota Profiling. [PDF]
Front Cell Infect Microbiol, 2022 Accessibility to next-generation sequencing (NGS) technologies has enabled the profiling of microbial communities living in distinct habitats. 16S ribosomal RNA (rRNA) gene sequencing is widely used for microbiota profiling with NGS technologies.
Heidrich V +8 more
europepmc +4 more sources
16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences. [PDF]
Front Bioinform, 2022 Analyzing 16S ribosomal RNA (rRNA) sequences allows researchers to elucidate the prokaryotic composition of an environment. In recent years, third-generation sequencing technology has provided opportunities for researchers to perform full-length sequence
Hsieh YP +4 more
europepmc +4 more sources
Choice of 16S ribosomal RNA primers affects the microbiome analysis in chicken ceca. [PDF]
Sci Rep, 2021 We evaluated the effect of applying different sets of 16S rRNA primers on bacterial composition, diversity, and predicted function in chicken ceca. Cecal contents from Ross 708 birds at 1, 3, and 5 weeks of age were collected for DNA isolation.
Darwish N +3 more
europepmc +3 more sources
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
Location of Ribosomal Protein Binding Sites on 16S Ribosomal RNA [PDF]
Proceedings of the National Academy of Sciences, 1972 The distribution of ribosomal protein binding sites on the 16S ribosomal RNA molecule has been analyzed by limited ribonuclease hydrolysis of RNA-protein complexes, as well as by the interaction of individual proteins with RNA fragments purified from partial enzymatic digests. Of the six 30S subunit proteins known to interact directly with
Robert A. Zimmermann +4 more
openalex +4 more sources
Classification of methanogenic bacteria by 16S ribosomal RNA characterization [PDF]
Proceedings of the National Academy of Sciences, 1977 The 16S ribosomal RNAs from 10 species of methanogenic bacteria have been characterized in terms of the oligonucleotides produced by T 1 RNase digestion. Comparative analysis of these data reveals the methanogens to constitute a distinct phylogenetic group containing two major divisions. These organisms appear to be
Ralph S. Wolfe +4 more
openalex +5 more sources
16S Ribosomal RNA PCR Versus Conventional Diagnostic Culture in the Investigation of Suspected Bacterial Keratitis. [PDF]
Transl Vis Sci Technol, 2020 Purpose The purpose of this study was to compare conventional diagnostic culture (CDC) to 16S ribosomal RNA polymerase chain reaction (PCR) analysis for diagnosing bacterial keratitis. Methods Samples collected from 100 consecutive patients presenting to
Somerville TF +4 more
europepmc +2 more sources
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
semanticscholar +5 more sources