Results 11 to 20 of about 183,216 (261)

Deep learning for predicting 16S rRNA gene copy number

Scientific Reports, 2022
Culture-independent 16S rRNA gene metabarcoding is a commonly used method for microbiome profiling. To achieve more quantitative cell fraction estimates, it is important to account for the 16S rRNA gene copy number (hereafter 16S GCN) of different ...
Jiazheng Miao, Tianlai Chen, Mustafa Misir, Yajuan Lin   +3 more
doaj   +3 more sources

Comparison of 16S rRNA gene amplicon and whole-genome shotgun metagenomic sequencing for subgingival oral microbiome profiling [PDF]

Journal of Oral Microbiology
Background Periodontitis is a chronic inflammatory disease driven by a dysbiotic subgingival microbiome. While 16S rRNA gene amplicon sequencing is widely used, whole-genome shotgun (WGS) metagenomics is increasingly applied for higher taxonomic and ...
Jung Hwa Park, Jin Chung, Hyo-Jung Lee, Hee Sam Na   +3 more
doaj   +2 more sources

Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing

mSphere, 2021
In 16S rRNA gene sequencing, certain bacterial genera were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings.
Isabel Abellan-Schneyder, Monica S. Matchado, Sandra Reitmeier, Alina Sommer, Zeno Sewald, Jan Baumbach, Markus List, Klaus Neuhaus   +7 more
doaj   +3 more sources

A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils

Frontiers in Microbiology
Root 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, Alessandra Ceretto, Cynthia Weinig, Cynthia Weinig, Cynthia Weinig   +4 more
doaj   +3 more sources

Mycoplasma gallisepticum16S rRNA genes [PDF]

FEMS Microbiology Letters, 1995
The genome of Mycoplasma gallisepticum A5969 contains a truncated pseudogene for 16S rRNA in addition to a single unsplit rRNA-operon and a second discontinuous set of rRNA genes. Other M. gallisepticum strains tested do not possess the truncated gene.
A, Skamrov, M, Goldman, J, Klasova, R, Beabealashvilli   +3 more
openaire   +3 more sources

Long-read MinION™ sequencing of 16S and 16S-ITS-23S rRNA genes provides species-level resolution of Lactobacillaceae in mixed communities

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, Sandra A. Olivier, Michelle K. Bull, Michelle K. Bull, Mikael Lenz Strube, Robert Murphy, Tom Ross, John P. Bowman, Belinda Chapman, Belinda Chapman   +9 more
doaj   +1 more source

Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens

Microbiology Spectrum, 2022
16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S
Pruke Eamsakulrat, Pitak Santanirand, Angsana Phuphuakrat   +2 more
doaj   +1 more source

A renaissance for the pioneering 16S rRNA gene [PDF]

Current Opinion in Microbiology, 2008
Culture-independent molecular surveys using the 16S rRNA gene have become a mainstay for characterizing microbial community structure over the past quarter century. More recently this approach has been overshadowed by metagenomics, which provides a global overview of a community's functional potential rather than just an inventory of its inhabitants ...
Tringe, SG, Hugenholtz, P
openaire   +5 more sources

Linking 16S rRNA Gene Classification to amoA Gene Taxonomy Reveals Environmental Distribution of Ammonia-Oxidizing Archaeal Clades in Peatland Soils

mSystems, 2021
A highly resolved taxonomy for ammonia-oxidizing archaea (AOA) based on the alpha subunit of ammonia monooxygenase (amoA) was recently established, which uncovered novel environmental patterns of AOA, challenging previous generalizations.
Haitao Wang, Alexandre Bagnoud, Rafael I. Ponce-Toledo, Melina Kerou, Micha Weil, Christa Schleper, Tim Urich   +6 more
doaj   +1 more source

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
openaire   +2 more sources