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A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils [PDF]
Frontiers in MicrobiologyRoot exudates in a plant’s rhizosphere alters microbial community membership and activity, which can in turn alter a plant’s health and fitness. In this study we characterized bacterial community composition, using 16S rRNA-gene (DNA) sequencing to ...
Alessandra Ceretto +4 more
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Variable Region Sequences Influence 16S rRNA Performance
Microbiology Spectrum, 2023 16S rRNA gene sequences are commonly analyzed for taxonomic and phylogenetic studies because they contain variable regions that can help distinguish different genera. However, intra-genus distinction using variable region homology is often impossible due
Nikhil Bose, Sean D. Moore
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Bacterial genotyping by 16S rRNA mass cataloging [PDF]
BMC Bioinformatics, 2006 Background It has recently been demonstrated that organism identifications can be recovered from mass spectra using various methods including base-specific fragmentation of nucleic acids.
Fox George E +3 more
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Identification of Vibrio anguillarum in fish by using partial 16S rRNA sequences and a specific 16S rRNA oligonucleotide probe [PDF]
Applied and Environmental Microbiology, 1989 16S rRNA from seven different Vibrio anguillarum strains was partially sequenced and compared. From this sequence information we could design a 25-base-long oligonucleotide and use it as a specific probe for identification of V. anguillarum. This was determined by RNA-DNA colony hybridization and slot-blot hybridization.
Ann-Sofi Rehnstam +3 more
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PLoS ONE, 2013 16S ribosomal RNA currently represents the most important target of study in bacterial ecology. Its use for the description of bacterial diversity is, however, limited by the presence of variable copy numbers in bacterial genomes and sequence variation ...
Tomáš Větrovský, Petr Baldrian
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Classic Spotlight: 16S rRNA Redefines Microbiology [PDF]
Journal of Bacteriology, 2016 Igor B. Zhulin
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Frontiers in Microbiology, 2023 The Lactobacillaceae are lactic acid bacteria harnessed to deliver important outcomes across numerous industries, and their unambiguous, species-level identification from mixed community environments is an important endeavor.
Sandra A. Olivier +9 more
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Phylogenetic Clustering of Soil Microbial Communities by 16S rRNA but Not 16S rRNA Genes [PDF]
Applied and Environmental Microbiology, 2012 ABSTRACT We evaluated phylogenetic clustering of bacterial and archaeal communities from redox-dynamic subtropical forest soils that were defined by 16S rRNA and rRNA gene sequences. We observed significant clustering for the RNA-based communities but not the DNA-based communities, as well as increasing clustering over time of the highly ...
Kristen M, DeAngelis, Mary K, Firestone
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OTU analysis using metagenomic shotgun sequencing data. [PDF]
PLoS ONE, 2012 Because of technological limitations, the primer and amplification biases in targeted sequencing of 16S rRNA genes have veiled the true microbial diversity underlying environmental samples. However, the protocol of metagenomic shotgun sequencing provides
Xiaolin Hao, Ting Chen
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Frontiers in Marine Science, 2023 The activities of bacterioplankton sustain open ocean biogeochemical and ecological processes, however, little is known about the activity of specific bacterioplankton, especially related to their biogeography across oceanic scales.
Ro Allen +5 more
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