Results 1 to 10 of about 158,589 (116)

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were found to be underrepresented or even missing in taxonomic profiles when using unsuitable primer combinations, outdated reference databases, or inadequate pipeline settings.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

MinION™ Nanopore Sequencing of Skin Microbiome 16S and 16S-23S rRNA Gene Amplicons

Frontiers in Cellular and Infection Microbiology, 2022
Human skin microbiome dysbiosis can have clinical consequences. Characterizing taxonomic composition of bacterial communities associated with skin disorders is important for dermatological advancement in both diagnosis and novel treatments.
Miquel Rozas, Miquel Rozas, François Brillet, Chris Callewaert, Bernhard Paetzold   +4 more
doaj   +3 more sources

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

mSystems, 2019
Microbial communities are commonly studied using culture-independent methods, such as 16S rRNA gene sequencing. However, one challenge in accurately characterizing microbial communities is exogenous bacterial DNA contamination, particularly in low ...
Lisa Karstens, Mark Asquith, Sean Davin, Damien Fair, W. Thomas Gregory, Alan J. Wolfe, Jonathan Braun, Shannon McWeeney   +7 more
doaj   +3 more sources

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

Microbial communities in polychlorinated biphenyl (PCB)-contaminated wastewater lagoon sediments: PCB congener, quantitative PCR, and 16S rRNA gene amplicon sequencing datasets

Data in Brief, 2021
The potential for aerobic and anaerobic microbial natural attenuation of PCBs in freshwater sediments is described by PCB congener, quantitative PCR, and 16S rRNA gene amplicon sequencing datasets generated, in duplicate, from 27 sediment samples ...
Timothy E. Mattes, Jessica M. Ewald, Yi Liang, Andres Martinez, Andrew M. Awad, Keri C. Hornbuckle, Jerald L. Schnoor   +6 more
doaj   +1 more source

16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis [PDF]

PeerJ, 2022
Background The full-length 16S rRNA sequencing can better improve the taxonomic and phylogenetic resolution compared to the partial 16S rRNA gene sequencing.
Ke Zhang, Rongnan Lin, Yujun Chang, Qing Zhou, Zhi Zhang   +4 more
doaj   +2 more sources

Performance of Conventional Urine Culture Compared to 16S rRNA Gene Amplicon Sequencing in Children with Suspected Urinary Tract Infection

Microbiology Spectrum, 2021
Because some organisms causing urinary tract infection (UTI) may be difficult to culture, examination of bacterial gene sequences in the urine may provide a more accurate view of bacteria present during a UTI.
Christopher W. Marshall, Marcia Kurs-Lasky, Christi L. McElheny, Sophia Bridwell, Hui Liu, Nader Shaikh   +5 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

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

The profiling of microbiota in vaginal swab samples using 16S rRNA gene sequencing and IS-pro analysis

BMC Microbiology, 2021
Background 16S rRNA gene sequencing is currently the most common way of determining the composition of microbiota. This technique has enabled many new discoveries to be made regarding the relevance of microbiota to the health and disease of the host ...
M. Singer, R. Koedooder, M. P. Bos, L. Poort, S. Schoenmakers, P. H. M. Savelkoul, J. S. E. Laven, J. D. de Jonge, S. A. Morré, A. E. Budding   +9 more
doaj   +1 more source