Results 1 to 10 of about 323,905 (300)

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

Differential richness inference for 16S rRNA marker gene surveys [PDF]

Genome Biology, 2022
Background Individual and environmental health outcomes are frequently linked to changes in the diversity of associated microbial communities. Thus, deriving health indicators based on microbiome diversity measures is essential.
M. Senthil Kumar, Eric V. Slud, Christine Hehnly, Lijun Zhang, James Broach, Rafael A. Irizarry, Steven J. Schiff, Joseph N. Paulson   +7 more
doaj   +3 more sources

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

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were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings.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   +4 more sources

metaSPARSim: a 16S rRNA gene sequencing count data simulator [PDF]

BMC Bioinformatics, 2019
Background In the last few years, 16S rRNA gene sequencing (16S rDNA-seq) has seen a surprisingly rapid increase in election rate as a methodology to perform microbial community studies.
Ilaria Patuzzi, Giacomo Baruzzo, Carmen Losasso, Antonia Ricci, Barbara Di Camillo   +4 more
doaj   +3 more sources

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

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   +2 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

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
doaj   +1 more source

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